chronology of organogenesis and life-history modes. Placental altriciality is inherited from the last common ancestor of amniotes and the precocial lifestyle of many placentals was secondarily acquired. The last common ancestor of marsupials and placentals was intermediate in the altriciality-precocity gradient, but the newborn was anatomically more placental-like. Brain size evolution is related to the length of fetal development, the latter linked to the evolution of viviparity. The mode of ossification (dermal or endochondral) unites bones into integrated evolutionary modules visible through heterochrony and imposes evolutionary constraints. Ossification of the neurocranium occurred considerably earlier than other skull regions during mammalian origins and developmental timing of the skull roof bones and appear to be associated with brain size. We argue that cranial heterochrony in mammals occurred in concert with encephalization within a conserved modular organization.

## Evolutionary pattern of the phosphoproteome in 18 yeast species (53721)

Romain Studer, Judit Villen, Pedro Beltrao.

EMBL-EBI; Department of Genome Sciences, University of Washington.

Posttranslational modifications (PTM) have the ability to fine-tune the regulation of proteins. Phosphorylation, which consists in the addition of a phosphate group to a polar residues (serine, threonine or tyrosine), is one of the most common and studied PTMs. The advance of high-throughput mass spectrometry (MS) technology allows the rapid identification of phosphosites in a single proteome. Recent studies of the human phosphoproteome have identified approximately 200,000 phosphosites. However, only 10% of these sites have a described function. Phosphosite information has been used to investigate the turnover rate of phosphosites by comparing the phosphoproteomes of different organisms, such as human, mouse, claw frog, fly, yeast, plant or bacteria. However, these studies generally focused on only two or three phosphoproteomes at the same time, or using a very small subset of sites. This lack of resolution can impair the significance of the results. Two phosphosites might be conserved between two species, but might also be fast evolving and disappear in other close species. Here we report the phosphoproteomes of 18 yeast species. We identified a rapid turnover of phosphosites, as seen by the increase numbers in recent branches and species only. We also estimated that a shift in binding motif preference occurred in species that predates the whole-genome duplication in yeast. Finally, we observed that old phosphosites are more important than young phosphosites, in term of structural and phenotypic effects.

## Eusociality influence on the effective population size (52985)

Bruno Vieira, Yannick Wurm.

Queen Mary, University of London.
Social insects are the most successful animals on earth, with a combined biomass rivaling that of humans. Most of the research done has focused on their ecology, behavior, and morphology, while we still know relatively little about the effect that social evolution has on the genome evolution. In specific, how social evolution affects the contributions of selection and drift. Indeed, while each social insect colony includes up to hundreds of thousands of individuals, only a small percentage of those individuals (male and female) reproduces. Furthermore, social insects have a longer generation time than solitary insects. These two characteristics should result in a lower effective population size (Ne), which is an important measure of diversity that helps us understand the relative strength of selection and genetic drift. However, due to the difficulty of measuring Ne, a comparison between solitary and social insects has never been tested. Here we use an innovative approach, the Pairwise Sequentially Markov Coalescent (PSMC) method, to obtain the Ne history based on the distance of heterozygous regions in a single diploid genome sequence.
To understand if the evolution of eusociality is associated with a reduction in Ne, we compared several social and solitary insect species.

# Diversity in the genus Begonia (52984)

**Katie Emelianova.**

*Royal Botanic Gardens Edinburgh.*

Begonia is one of the most speciose plant genera, comprising over 1,500 species. The genera's large size and diversification has been attributed to poor dispersal leading to low levels of drift, high endemism and extensive population differentiation. However, indications that the genus underwent a genome duplication early in its history has prompted investigation into the impact of this duplication on Begonia diversity.

The anthocyanin biosynthetic pathway is a preliminary focus of the project, based on the hypothesis that duplication of either regulators or biosynthetic enzymes facilitated the wide variation of anthocyanin pigmentation in Begonia.

Genomic resources developed for the genus include RNA-seq datasets from 6 tissues of two South American species, B. conchifolia and B. plebeja, and a draft genome of B. conchifolia. These resources will be used for expression, selection and copy number analysis in anthocyanin biosynthesis genes. Patterns showing differential duplication and expression and positive selection may support a hypothesis implying genome duplication as a key player in the diversification of Begonia.

Additionally, a bioinformatics pipeline designed for large-scale identification and analysis of gene families will be outlined. Further development of the pipeline will enable genome wide identification of candidate genes involved in diversification of Begonia.

# Improving contact prediction with direct coupling analysis using secondary structural information and amino acid properties (52973)
**Guido Uguzzoni**, Francesco Oteri, Marco Punta, Martin Weigt.

*Laboratoire de Biologie Computationelle et Quantitative; Laboratoire de Biologie Computationelle et Quantitative; Laboratoire de Biologie Computationelle et Quantitative; Laboratoire de Biologie Computationelle et Quantitative.*

Direct coupling analysis (DCA) is a global inference method based on the maximum entropy principle, which aims at predicting residue-residue contacts using the co of residues in multiple-sequence alignments of homologous proteins. DCA permits to disentangle direct and undirect correlation.

Previous works on a restricted number of bacterial PFAM families showed as DCA outperforms Mutual Information in terms of contact prediction, leading to accurate modelling of the 3D structures as well as detection of protein-protein interactions.

In this work, the performance of DCA has been evaluated over the whole PFAM 27 dataset. The behaviour has been characterised taking into account the physico-chemical properties of the residues as well as secondary structure elements of the proteins. The data shed light on different properties of the protein structure underling the correlation signals.

Exploiting this information we are able to improve the true positive rate of contract prediction. Complementing DCA with methods predicting different properties Secondary Structure, Solvent Accessible Surface) is discussed.

Poster session A - POL 300

**Reconstructing past demography from population specific FSTs. (52959)**

**Jerome Goudet**, Bruce Weir.

*Dept Ecology and Evolution, University of Lausanne; Dept of Biostatics, University of Washington.*

Evolutionary biologists have a long standing interest in reconstructing the past demography of species using genetic data. The availability of large data sets and increased computer power have allowed very detailed inferences in several species, particularly in Homo sapiens. One key issue is which summary statistics to use in order to draw these inferences. Here, using simulated data sets as well as phase 3 of the 1000 human genomes project, we show that moment estimators of population specific FSTs are particularly well suited, in particular when used in conjunction with the Site Frequency Spectrum.

Poster session A - POL 300

**A genomic perspective on locally adapted coastal cod populations (52958)**

**Julia M. I. Barth**, Paul R. Berg, Bastiaan Star, Sara Bonanomi, Jakob Hemmer Hansen, Halvor Knutsen, Carl André, Nils Christian Stenseth, Sissel Jentoft.
Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway; Section for Marine Living Resources, Technical University of Denmark, Silkeborg, Denmark; Institute of Marine Research (IMR), Arendal, Norway; Department of Biology and Environmental Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden.

Structured populations represent confined locally adapted interbreeding species units, which have long been assumed to be non-existent in open marine environments due to the lack of geographical barriers. However, this is increasingly disproved and populations with high levels of genetic differentiation important for adaptation to local environments are being documented at fine scales.

Since the 1970's, Atlantic cod (Gadus morhua) populations have been declining in the North Sea, leading to a near extinction of cod in the Norwegian and Swedish fjords. Whether cod in this area represents a large panmictic population where recruitment from offshore areas can substitute for local losses, of whether coastal areas and fjords are home to locally adapted populations is still an open question.

We used a large-scale genomic approach to genotype 500 individuals from 14 different locations at 10.000 single-nucleotide polymorphism (SNP) markers to answer the questions whether locally adapted coastal cod populations exist, which genes are ecologically relevant for adaptation, and to investigate connectivity and past demography of these populations in the light of climate change.

Our results will be highly relevant to provide a management strategy for the protection of locally adapted cod populations and the ecosystems they live in.

# Stability-activity tradeoffs constrain the adaptive evolution of RubisCO (52946)

Romain Studer, Pascal-Antoine Christin, Mark Williams, Christine Orengo.

EMBL-EBI; University of Sheffield; Birkbeck College; University College London.

The importance of the stability effect of mutations in protein evolution has been theorised and established in some single-case studies. When a change of function occurs, some mutations shift the stability outside the neutral range, thus they need other mutations after to compensate this difference. Ribulos-1,5-bisphosphate carboxylase (RubisCO) is the enzyme responsible for fixation of CO2 during photosynthesis. In flowering plants, two forms exist, the C3 and the C4, the latter being faster in terms of catalytic activity. The C4 form emerged by convergent evolution in multiple clades and was the result of a few amino acid substitutions under positive selection. We explored the impact of structural constraints on RubisCO evolution. We reconstructed in silico the ancestral sequences and their associated 3D structures. We were able to follow precisely the evolutionary path, by identifying each mutation on each branch. We found that there are more destabilising mutations at the base of C4 clades, and that these mutations are then followed by other stabilising mutations. These results are consistent with a "stability-activity trade-off" model. These results demonstrated that the evolution of an enzyme can be under strong structural constraints and that adaptive mutations are balanced between stabilising and destabilising effects.
# Demography and local adaptation of Rana temporaria across an environmental gradient (52945)

**Alexandra Jansen van Rensburg**, Josh Van Buskirk.

*University of Zurich.*

Understanding the genomics of local adaptation in natural populations currently suffers from confounding effects of demographic history, exacerbated by small sample sizes and sampling scheme limitations. These problems can be overcome by assessing signatures of adaptation across replicate environmental transects, where potential adaptive loci should be verified in parallel scenarios. Widespread species present an ideal opportunity to study local adaptation as they often occur across a range of environmental conditions, thus replicate transects can be sampled. Here we assess the use of reduced representation libraries to study the genomics of local adaptation in the common frog (Rana temporaria) across its range in Switzerland. Using a large and geographically extensive sampling scheme (1050 samples from 81 populations) across multiple parallel environmental gradients, we can infer fine-scale demographic history, as well as identify genomic regions important for local adaptation. Further, we use a modelling approach to assess the amount of gene flow and selection needed to maintain local adaptation at the range edge, given genomic architecture of the adaptively important trait.

# Geographic variation in resistance of white spruce against spruce budworm (52939)

**Genevieve J. Parent**, Isabelle Giguère, John J. MacKay.

*Centre d'Étude de la Forêt, Département des Sciences du Bois et de la Forêt, Université Laval; Institut de Biologie Intégrative et des Systèmes, Université Laval; Department of Plant Sciences, University of Oxford.*

Variable in selective regimes within a distribution may cause local adaptation. Evidences for local adaptation in perennial species such as trees are sparse, which might be a consequence of variation in selective regimes through their life cycle. In white spruce (Picea glauca), a heritable mechanism of resistance against spruce budworm (Choristoneura fumiferana, SBW), the most damaging forest insect in eastern North America, was discovered for the first time. The PgβGLU-1 enzyme catalyzes the cleavage of acetophenone sugar conjugates to release the aglycons that are toxic for SBW. We investigated if patterns of geographic variations in resistance were present in the population. Levels of Pgβglu-1 transcripts and acetophenones varied widely in natural white spruce population, however putatively resistant trees were less frequent in the southern range of the distribution. Different factors such as temperature and insect feeding pressure are being tested to explain variable frequencies of resistant trees. These abiotic and biotic factors may help to explain the selective regimes exerted on white
spruce population. Furthermore, a genome wide association test is currently underway to identify genetic variants linked to resistance. These results may serve to predict the effects of future outbreaks of SBW in both managed and spruce natural population.

# Genetic diversity of European Pinus sylvestris populations studied with exome sequencing (52917)

**Jaakko Tyrmi**, Juan José Acosta, Zhen Li, Tanja Pyhäjärvi, Outi Savolainen.

*Genetics & Physiology Unit, University of Oulu; Forest Genomics Labs, University of Florida; VIB Department of Plant Systems Biology, Ghent University.*

Pine trees are key species in many ecosystems in Europe and North America also with significant economic value. Pines are also excellent species for studying molecular basis of local adaptation on natural populations because of their large native distribution ranges covering a diversity of environments and high levels of genetic and phenotypic variation. The genetic diversity of Pines have been studied in the past using a small number of candidate genes. The large and complex highly repetitive genomes still prevents whole genome resequencing, but here we have used targeted sequence capture. In several European populations, we have targeted some 10 000 genes. A first study was conducted using exome sequences of the related Pinus taeda to design the probes, a second set using Pinus sylvestris transcriptome derived sequences. We also have tried different options of mapping the captured sequences. Due to the repetitive genome, paralogous sequences need to be dealt with carefully. We examine genome-wide diversity, differentiation of populations, and the extent of genome-wide linkage disequilibrium. We then contrast our candidate locus variation for adaptive traits (cold tolerance, timing of budset) to the genome wide averages and examine them against predictions of selection models.

# Sifting through tangled trees: A particle-filtering method for Bayesian reconstruction of cophylogenies (52890)

**Arman Bilge**, Tim Vaughan, Alexei J Drummond.

*The University of Auckland; Allan Wilson Centre for Molecular Ecology and Evolution.*

Systems of interdependent evolutionary histories, often represented by cophylogenies, are important models for genome evolution (i.e., gene trees versus species trees) and the coevolution between a symbiont and its host organism. A cophylogeny consists of a "host" phylogeny, a "guest" phylogeny, and a reconciliation, the mapping of ancestral guests to their hosts, and is determined by a series of events, including cospeciation, duplication, loss, and host-switching/horizontal transfer. Existing methods for reconstructing cophylogenies generally assume that the host phylogeny is known and that its population dynamics are
deterministic and cannot consider uncertainties in dating and geographic location. We
developed an approach that uses Bayesian Markov chain Monte Carlo to perform joint
inference on the host and guest phylogenies, reconciliation, divergence dates, and event rates.
Because the model complexity makes it impossible to compute analytically the likelihood of a
cophylogeny, we employ a particle filtering method that uses piecewise simulation and
resampling to approximate the likelihood. We implemented the sampler as a plugin for
BEAST, an existing MCMC framework for Bayesian evolutionary analysis, and evaluated its
performance on both simulated and real datasets. Furthermore, the use of simulation makes it
straightforward to extend our code to consider more complex models.

Phylogeography, population structure and phenotypic variation in the wing
dimorphic grasshopper Dichroplus vittatus (Orthoptera: Acrididae). (52863)

Maria Remis.

Depto. Ecologia, Genetica y Evolucion, Facultad Ciencias Exactas y Naturales, Universidad Buenos Aires.

Dichroplus vittatus is a South American grasshopper that in field can display fully-winged (macropterous) or small-winged (brachypterous) morphs. In order to analyse the genetic and phenotypic differentiation, a fragment of 543bp of the mitochondrial COI gene and 5 body size related traits were studied in 7 populations from La Pampa and San Luis Provinces. We demonstrated a variable frequency in the percentage of brachypterous individuals, ranging from 100% to 25%. The MANOVA showed significant differences in body size among populations, between sexes with female-biased size and between wing morphs being the brachypterous morph the larger. Molecular studies detected 10 haplotypes from 5 polymorphic sites. Diversity indices were low, particularly in La Pampa populations with higher frequency of macropterous. The AMOVAs using FST showed significant heterogeneity among provinces, between populations and within populations. Haplotype network indicated a moderate component of geographical variation. Demographic indices and mismatch distribution revealed that one San Luis population fits a recent expansion model. Genetic and phenotypic analysis of populations studied here would indicate a relatively short evolutionary history. Consistent with a trade-off between flight capability and reproduction hypothesis our results suggest that La Pampa Province may be an unstable or less favourable environment for this specie.

Reptilian Transcriptomes v2.0: an extensive resource for Sauropsida genomics
and transcriptomics (52856)

Athanasia C. Tzika, Asier Ullate-Agote, Djordje Grbic, Michel C. Milinkovitch.
Despite the availability of deep-sequencing techniques, genomic and transcriptomic data remain unevenly distributed across phylogenetic groups. For example, reptiles are poorly represented in sequence databases, hindering functional evolutionary and developmental studies in these lineages substantially more diverse than mammals. Here, we present the 'Reptilian Transcriptomes Database 2.0' which provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages. To this end, we sequenced normalized cDNA libraries of the leopard gecko and the corn snake and gathered published reptilian sequence datasets from representatives of the four extant orders of reptiles: Squamata, the tuatara, crocodiles, and turtles. LANE runner 2.0 was implemented to annotate all assemblies within a single integrated pipeline. We show that this approach increases the annotation completeness of the assembled transcriptomes/genomes. We then built large concatenated protein alignments of single-copy genes and inferred phylogenetic trees that support the positions of turtles and the tuatara as sister groups of Archosauria and Squamata, respectively. The 'Reptilian Transcriptomes Database 2.0' resource will be updated to include selected new datasets as they become available, thus making it a reference for differential expression studies, comparative genomics and transcriptomics, linkage mapping, molecular ecology and phylogenomic analyses involving reptiles.

# Morphological adaptation in a marine-freshwater habitat transition of Northern Neotropical Catfishes (52854)

Madlen Stange, Gabriel Aguirre, Walter Salzburger, Marcelo Sánchez.

University of Zürich, Palaeontological Institute; University of Basel, Zoological Institute.

The present study aims to disentangle the patterns of adaptation associated with a marine-freshwater habitat transition in the evolution of siluriform Ariidae (sea catfishes), and how those patterns are related to diversification. Successful habitat transitions require adaptation of populations with subsequent speciation. Such evolutionary habitat transitions are accompanied by morphological changes that in turn should leave signatures of adaptation. Ariidae contain mainly marine species, with some species inhabiting freshwater secondarily. All sister taxa but one inhabit fresh- or brackish water. That makes them the ideal study system to investigate the habitat transition from freshwater to marine and back to freshwater on morphological level. This study aims to assess and compare morphological disparity using 2D geometric morphometrics on opercula between and among freshwater and marine catfish species (Ariidae) and freshwater sister taxa. Opercula have been shown to be suitable structures to examine ecological adaptation as they have been shown to change when changing habitat from marine to freshwater habitat. Observed differences are determined whether they are the result of adaptation to marine or freshwater habitat, and/or phylogenetic signal. Opercula shape change among taxa and patterns of variation are visualised using CVA and PCA, respectively.
# Measuring constraints to cichlid diversification in small lakes (52852)

**Florian N. Moser**, Jacco C. Van Rijssel, Catherine E. Wagner, Ole Seehausen.

*Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; EAWAG Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland.*

Small lakes provide unique opportunities to study speciation in sympatry, as opportunity for geographical isolation within these environments is negligible. Cichlid fishes are famed examples of sympatric speciation due to instances of speciation in small lakes. However, cichlids occur in many other small lakes where they have not diversified. Although comparative studies reveal lake depth as an important predictor of cichlid diversification, and case studies show that natural and sexual selection operating along depth gradients can readily lead to speciation, the underlying microevolutionary processes which promote or constrain speciation along such depth gradients remain unclear. To investigate the constraints to diversification and differentiation, we studied haplochromines of two small lakes that differ greatly in depth, Lake Chala (90m) and Lake Babati (5m). Both lakes host only one known haplochromine species, Astatotilapia sp., which shows higher phenotypic variation in Lake Chala. We quantify phenotypic diversity and divergence in the two cichlid communities, and relate it to variation in fitness landscapes estimated from a fitness proxy, growth rate. We then investigate genetic differentiation using genome-wide SNP data. We discuss the environmental conditions under which phenotypic differentiation can evolve, and the cases in which it is associated with genetic divergence and speciation.

Poster session A - POL 300

# Statistical physics of transcription-factor evolution: speciation with pleiotropic constraint (52846)

Alexander Tulchinsky, Normal Johnson, **Adam Porter**.

*University of Massachusetts - Amherst.*

Speciation can result from gene misregulation in hybrids when transcription factors (TF's) and their cis-regulatory targets differentially coevolve in separate populations. Pleiotropy should constrain the evolution of misregulation because multifunctional TF's should be less likely to diverge. How profound is this constraint?

We used a statistical physics model wherein fractional occupancy of a TF on its cis-regulated target determines gene expression, thus phenotype. TF concentration and free energy of association (-deltaG) determined occupancy. Mutable bit strings represented alleles, and - deltaG depended on their match. Misregulation occurs when a phenotype differs from its environmentally determined optimum. The model can extend to any genetically determined, interacting molecules.

We simulated a pleiotropic regulatory pathway involving a conserved and a positively selected trait, sharing a TF, with two populations evolving in parallel to new optima. Pleiotropy shifted more of the response to the cis-site of the directionally selected trait, and compensatory evolution occurred at the cis-site of the conserved trait. Both traits contributed to misregulation of hybrids.
TF concentration and -deltaG determined much of the evolutionary dynamics of speciation. Pleiotropy inhibited speciation when a mismatched bit changed occupancy too much; misregulation was negligible when a mismatch changed occupancy too little. Between, speciation occurred frequently.

# Genomics of adaptive life history variation in Atlantic salmon (52842)

**Nicola J Barson**, Tutku Aykanat, Kjetil Hindar, Matthew Baranski, Celeste Jacq, Sten Karlsson, Geir Bolstad, Matthew P Kent, Sigbjørn Lien, Craig R Primmer.

*Norwegian University of Life Sciences; University of Turku; Norwegian Institute for Nature Research (NINA); NOFIMA.*

Local adaptation often involves complex quantitative traits. However, when selection for local adaptation occurs with ongoing gene flow, control by a few loci of large effect is expected. This necessity can lead to constraints on the identity of loci and their position in regulatory networks and raises the possibility of a conserved genomic basis of adaptation across taxa.

Atlantic salmon exhibit extreme variation in age and size at maturity. Replicated divergence among populations in these key fitness related traits and ongoing gene flow make salmon an ideal organism in which to study the genomics of local adaptation. We present results of dense SNP genotyping (220k loci) of 1734 individuals from 57 wild populations, covering the coast of Norway, plus a Baltic outgroup. Populations are dominated by either large, late maturing (2-3 sea years), or small, early maturing (1 sea year) salmon. This sampling allowed analysis of genotype-phenotype associations (GWAS) and spatial variation in the genomics of adaptive responses. Our results suggest several major genes contribute to local adaptation, consistent with predictions under migration-selection balance, and a role for "master regulators". Targeted re-sequencing enabled identification of locally adapted candidate gene variants, which will be discussed in a functional context.

# Chronology of fitness traits evolution to climate change over 100 years in the water flea Daphnia magna (52839)

**Maria Cuenca Cambronero**, Hollie Marshall, Hanna Tilley, Luisa Orsini.

*Environmental Genomics Group, School of Biosciences, University of Birmingham.*

The decline of water quality due to climate change and land use determined by the use of pesticides and leading to eutrophication is a recognized threat to ecosystem services and to the economy. However, the causes and effects of climate and land use changes occur over many decades, and are therefore difficult to measure. Critical for gauging the long term consequences of climatic change is the reconstruction of evolutionary dynamics over
extended time axes. Here, we reconstruct the evolution of fitness traits (mortality, fecundity and growth rate) to climatic change in Daphnia magna populations using animals resurrected from sediment biological archives with known history of eutrophication and temperature changes. Experimental evolution trials are used to measure fitness response of populations sampled across 80 years (1960-present) to the forecasted temperature increase for the upcoming century. In addition, we measure the evolution of fitness traits in response to the combined effect of temperature increase with pesticides and food quality changes. This study will identify fitness traits targets of natural selection and the long-term consequences of environmental stress in metazoan populations.

## Evolution of an endosymbiont genome associated with host dependency (52818)

Dré (A.A.) Kampfraath, Ken Kraaijeveld, Jacintha Ellers.

VU university.

Mutualistic relationships often result in the loss of traits that are being compensated for by the partner. Trait loss in endosymbionts is expected to be an ongoing process, but the rate and sequence in which traits are lost during the early stages of the interaction are poorly understood. Wolbachia is one of the most widespread endosymbionts infecting an estimated 40% of all terrestrial arthropod species. Wolbachia is known for manipulating the reproductive system of its hosts, but can also provide the host with benefits including defense against parasites. In some cases, the intimate relation between endosymbiont and host has resulted in host dependency. In the springtail Folsomia candida, eggs cleared from Wolbachia by heat or antibiotics don't hatch, showing that the host has become reliant on its Wolbachia endosymbiont for reproduction. Therefore, we sequenced and assembled the wFol genome. This is the first sequenced Wolbachia genome that is obligatory for its host. By comparing the wFol genome to 12 available Wolbachia genomes we test whether wFol strain (1) has a smaller genome size than other Wolbachia, and (2) has lost some otherwise essential genes that are compensated for by the host.

## Genetic architecture of morphological traits in the Mediterranean mussel *Mytilus galloprovincialis* (52816)

Dorotea Polović, Stuart Dennis, Anamaria Štambuk, Maja Šrut, Víctor Soria-Carrasco, Zachariah Gompert, Vid Baković, Goran Klobučar, Patrik Nosil.

*Department of Biology, Faculty of Science, University of Zagreb; Department of Animal and Plant Sciences, University of Sheffield; Department of Biology, Utah State University.*
The genetic architecture of phenotypic traits, including their heritability, numbers of loci involved, and effect sizes, are not well understood in bivalves. Anthropogenic pollution may create environmental differences that can alter mussel (Mytilus galloprovincialis) morphology through either genotypic or induced environmental effects. To assess the genetic architecture of morphology we measured 17 morphometric traits in over 1400 mussels from two populations inhabiting sites differing in pollution pressure. We used a genotype by sequencing approach to generate genomic data that allowed us to then describe the genetic architecture of these traits in a genome wide association study. Additionally, we estimated the genetic architecture of the same traits as well as proxies for fitness in an additional sample of 15 populations distributed across a pollution gradient using 20 mussels per population. The results thus characterise variation within and among populations in mussel morphology and assess the association between genotype, phenotype and environment.

# A case of rapid postglacial speciation in the songbird genus Junco: genome-wide divergence in SNP data suggests the role of multifarious selection (52810)

Guillermo Friis, Borja Milá.

*National Museum of Natural Sciences (CSIC).*

During early stages of ecological speciation, divergence may be driven by strong selection on a few loci, or alternatively through weaker multifarious selection acting on numerous loci across the genome. Cases of recent and rapid diversification provide the opportunity to examine the relative importance of these types of selection and their effect on genomic landscapes. The rapid postglacial radiation of the genus Junco in North America has given rise to a number of closely related yet phenotypically distinct forms within the last 10,000 years, as documented with mtDNA sequence data. A subset of several thousand high-FST SNPs obtained through Genotyping-by-Sequencing, reveals marked divergence between and even within junco morphs. This pattern is congruent with geographical and phenotypic structure and suggests restricted gene flow even among parapatric sister forms. Divergent SNP loci are spread across the entire genome despite the recent origin of the morphs, suggesting the role of selection acting on numerous loci across the genome from the early stages of the speciation process. This is consistent with preliminary data on the role of sexual selection and ecological niche divergence, suggesting that the diversification of junco forms is driven by a wide range of selective factors.

# Characterizing the architecture of gene expression regulation in the threespine stickleback, Gasterosteus aculeatus. (52801)

Victoria Pritchard, Juha Merilä, Mikko Nikinmaa, Craig Primmer, Heidi Viitaniemi, Erica Leder.
It is increasingly clear that changes in the expression of genes play an important role in local adaptation. Thus, elucidating the genetic architecture of gene expression regulation is an important step to understanding how populations evolve in response to changing environments, and thus how adaptive divergence occurs. Here, we used an expression microarray, in combination with RAD-tag sequencing and a controlled cross, to characterize expression quantitative trait loci (eQTL) underlying variation in gene expression in the threespine stickleback (Gasterosteus aculeatus) - an important model in the study of adaptive radiation. We identified several thousand eQTL, of which >60% were cis acting. Trans acting eQTLs clustered into several putative 'eQTL' hotspots. We further discuss our results with respect to genes exhibiting expression variation between the sexes, and between different thermal treatments.

# Deciphering the molecular basis of a boreal adaptation: the transcriptional landscape of seasonal coat color change in two species of hares (52799)

Mafalda Sousa Ferreira, Paulo Célio Alves, Colin Callahan, L. Scott Mills, Jeffrey M. Good, José Melo-Ferreira.

CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal; Wildlife Biology, College of Forestry and Conservation, University of Montana, Missoula, MT, USA; Division of Biological Sciences, University of Montana, Missoula, MT, USA; Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC USA.

The effects of climate change in biodiversity are both a conservation problem and an opportunity to study the evolution of adaptive traits in response to the new environmental conditions. Seasonal coat color change, a remarkable adaptation of artic and boreal species to their seasonally snow covered environment, is one of such traits. Global warming and the consequent decrease of the number of days with snow on the ground lead to increased periods of mismatch in crypsis, making these species highly conspicuous to predators. How will this phenotype respond to the new environmental conditions is now a pressing question. A crucial step to tackle this is to determine the molecular bases of seasonal coat color change to better understand how environmental cues act to time the production of two color phenotypes. In this work, we track the gene expression changes in the skin in the molting cycle of two distantly related species of hares, the snowshoe hare, Lepus americanus, and the mountain hare, Lepus timidus, using an RNA-sequencing approach. This will provide an unprecedented understanding of the genetic mechanisms underlying seasonal coat color molting and of the possibly independent evolutionary pathways of this phenotype in two distinct species.
# Genomic variation in the virilis group of Drosophila (52796)

**Venera Tyukmaeva**, Konrad Lohse, Ritchie Michael.

*University of St Andrews; University of Edinburgh.*

The Drosophila virilis group species show unique behaviours and adaptations and are an ideal model system to study speciation. The group has a long history of research on the evolution of mating behaviour, chromosome arrangements, adaptations and molecular evolution, however, the species phylogeny has many uncertainties and controversial points. We obtained 18 genome sequences for the species from the group (one fly individual per line, mostly two lines per species from different geographic locations) and adopted the likelihood framework developed by Lohse & Frantz (2014) to co-estimate species divergence times, ancestral population sizes and introgression parameters between closely related species using block-wise alignments sampled from the whole genome. Many species of the group occur both in allopatry and sympatry with their closest relative in North America which makes it possible to explicitly test for the effect of geography on species divergence and historical or on-going gene flow. At the same time the detailed sequence information from closely related species allows a detailed examination of the regions under positive selection between different species and help identifying the key genes involved in speciation.

Poster session A - POL 300

# Evolution of tissue specificity of protein coding genes in vertebrates (52781)

**Nadja Kryuchkova**, Marc Robinson-Rechavi.

*University of Lausanne; Swiss Institute of Bioinformatics.*

One of the major properties of genes is their expression pattern. While there have been recent studies of the correlation of expression between species for a few tissues, little is known about the evolution of tissue-specificity itself. There are several methods to measure this tissue-specificity. In this study we compare available methods and use them to study evolution. More specifically, we inquire:

* Do tissue-specific genes evolve faster?

* Are there major differences between the evolution of tissue-specificity after duplication (paralogs) or without duplication (orthologs)?

* Could previous studies be biased, due to the bias in detecting low expressed genes?

Eight methods for tissue-specificity were analyzed on their robustness for choice and number of tissues and for data normalization. For RNA-seq, the results of most methods, established for ESTs and Microarrays, depend on the data pre-processing. Also tissue-specificity is better detected with RNA-seq than with Microarrays.

We show that new genes and genes with more paralogs tend to have more specific expression. Previous findings, that more broadly expressed genes evolve under stronger purifying selection, could be confirmed.
# Genomic signature of local adaptation in Populus tremula (52780)

**Jing Wang, Pär K. Ingvarsson.**

*Department of Ecology and Environmental Science, Umeå University; Department of Ecology and Environmental Science, Umeå University.*

Identifying the signatures and targets of local adaptation is an increasingly important goal in ecology and evolutionary biology. With the advent of next generation sequencing (NGS) technologies, it has become feasible to perform genomics studies on ecologically and economically important non-model species. Populus tremula, European aspen, is a deciduous forest tree with a geographic distribution ranging throughout Eurasia, and thus, has normally adapted to a wide variety of environmental conditions. Using whole genome re-sequencing data from 85 P. tremula trees collected from twelve sites spanning latitudinal and longitudinal gradients throughout Sweden, we tested for evidence of local adaptation by using three different kinds of methods: (1) searching for elevated population differentiation using FST-based outlier analyses; (2) testing for significant associations between allele frequencies and environmental variables; (3) genome-wide association studies of two ecologically important traits (bud set and bud flush) associated with common garden experiments. In the end, we identified a set of candidate loci that have been subject to local adaptation. Our findings also provide insights into the relative contribution of new mutations and standing genetic variation to the evolution of local adaptation, as well as the genetic architecture of adaptive traits in P. tremula.

# Evolution of convergent floral phenotypes during pollination shifts in Gesneriaceae: transcriptomic evidence (52775)

**Martha Liliana Serrano-Serrano, Anna Marcionetti, Mathieu Perret, Alain Chautems, Nicolas Salamin.**

*University of Lausanne; Conservatoire et Jardin botaniques de la Ville de Genève.*

Morphological changes have impacted the evolution of many groups in the tree of life, among those Angiosperms is an excellent case where evolutionary forces have shaped a great compendium of floral forms. Pollinator variation in the Gesneriaceae family has led to strong convergent floral phenotypes for different functional groups (insects, hummingbirds and bats). Further, Gesneriaceae has a labile pattern of plant-pollinator associations, with multiple changes within a single lineage. These pollinator shifts involve mainly changes in corolla shape and color, as well as, in the timing of anther dehiscence, nectar production, and sexual organ elongation. Here, we present the results from the transcriptomic data of six non-model plant species to investigate the differentiated loci during pollination shifts and their signatures of selection. We also profile the gene expression and regulation differences between the convergent floral phenotypes.
# Local-scale genetics — genetic structure in natural Pinus pinaster populations at short spatial scales (52774)

**Katharina B. Budde**, Myriam Heuertz, Ana Hernández-Serrano, Felix Gugerli, Miguel Verdú, Juli G. Pausas, Santiago C. González-Martínez.

*University of Copenhagen; CIFOR-INIA Forest Research Center, Madrid; INRA BIOGECO, Bordeaux; CIDE-CSIC/UV/GV Centro de Investigaciones sobre Desertificación, Valencia; WSL Swiss Federal Research Institute, Zürich.*

Landscape genetics aims to disentangle which environmental factors shape the genetic structure of species or populations in the light of gene flow. Recent studies have determined environmental factors affecting neutral and adaptive genetic variation in plant species on regional to continental scale. However, selection is expected to be harder to detect over short distance, where extensive gene flow can exceed the migration–selection equilibrium. Here we tested the effect of topography, water availability and biotic indicators on the local genetic structure of maritime pine (Pinus pinaster) at single-nucleotide polymorphisms (SNPs) and adaptive phenotypes in eastern Spain. In one site, a 300 m altitudinal gradient significantly affected maritime pine local genetic structure and tree growth, while no environmental factor seemed strong enough to affect the genetic structure in other sites. Several environmental factors vary along (even short) altitudinal gradients, which could have led to divergent selection between upper and lower parts of slopes. Alternatively, adaptive and/or plastic responses in flowering phenology could have led to assortative mating and shaped the observed genetic structure. We conclude that neutral and adaptive processes at short spatial scales should be considered in landscape genetics studies aiming at understanding genetic structure within natural plant populations.

# Selection pressures and recent adaptation in the genomes of invasive fire ants (52761)

**Eyal Privman**, Amir Cohanim, Yu-Ching Huang, John Wang, DeWayne Shoemaker, Laurent Keller.

*University of Haifa; Academia Sinica; USDA; University of Lausanne.*

Solenopsis fire ants evolved high invasiveness. A sub-clade of Solenopsis species have recently evolved a social polymorphism: a colony can either have one or many reproductive queens. This has been suggested to allow more efficient cooperation and faster population growth, which facilitate invasiveness. Therefore, we hypothesize that this transition was accompanied by positive selection on related adaptive traits. The social form is determined by the "social chromosome", a supergene containing over 600 genes. We set out to identify additional genes that contributed to this evolutionary innovation. We applied a population
genomic approach to infer selection pressures from RAD (Restriction site Associated DNA) sequencing and whole genome sequencing to achieve either high accuracy in allele frequency estimation or high resolution of SNPs, respectively. These data allow for high inference power in different types of tests for positive selection. We identified specific gene families and molecular functions under selection that could be implicated in social evolution. Furthermore, we identified loci with exceptionally high allelic variation, the hallmark of balancing selection. An extreme case is the recently discovered sex determination locus in S. invicta. These analyses provide for the first time a genomic view of selection pressures in an invasive social insect.

# Genomic consequences of hybridization and the loss of meiotic recombination in Root-knot nematodes (52760)

**Laura Salazar-Jaramillo**, Amir Stitzenberg, Dave Lunt, Mark Blaxter.

*University of Edinburgh; University of Hull.*

Root-knot nematodes (genus Meloidogyne) have undergone repeated transitions from sexual to asexual reproduction (besides obligatory sexual, they also exhibit both mitotic and meiotic parthenogenetic species). Transition from sexual reproduction to mitotic parthenogenesis involves the loss of meiotic recombination, which has been shown to result from interspecific hybridization events in some Meloidogyne species. Hybridization is expected to involve large genomic changes such as differences in the copy number of genes and chromosomes, which could result in major changes in biological function. At the same time, hybridization can potentially generate transgressive variation through the mixing of several parental genomes, while the resulting asexual reproduction is expected to limit genomic variation on the long run relative to sexual reproduction. Thus, by comparing the genomes of different root-knot nematode species, we investigate the genomic consequences of hybridization and the loss of meiotic recombination. Whole genome sequencing suggests that at least one of the most damaging asexual root-knot nematode species (M. javanica) is a triploid and shows a surprisingly high level of genomic variation. Such variation could help explain the great expansion of some Meloidogyne species in a wide range of agriculturally important crops.

# You are what you eat – Can selective advantages explain the AT-bias of endosymbiotic genomes? (52757)

**Anne-Kathrin Dietel**, Martin Kaltenpoth, Christian Kost.

*Research Group Experimental Ecology and Evolution, Max-Planck-Institute for Chemical Ecology; Research Group Insect Symbiosis, Max-Planck-Institute for Chemical Ecology.*
Endosymbionts are expected to evolve a reduced metabolic burden they impose on their host. Strikingly, both plasmids and intracellular bacterial symbionts generally exhibit a reduced GC-content relative to the host's chromosome. We hypothesize that competition among cytoplasmic elements for the hosts' nucleotides may explain this observation: Since dATP and dTTP are the most abundant nucleoside triphosphates in a cell, intracellular symbionts with lower GC-contents should be selectively favoured.

Here, we test this hypothesis by experimentally manipulating the GC-content of plasmids and analysing the fitness consequences for the bacterial host. Specifically, we introduced eight 1 kb sequences of eukaryotic DNA that were particularly AT- and GC-rich into two minimal plasmid backbones. Growth experiments with Escherichia coli revealed a significant fitness decrease of cells that harboured GC-rich plasmids as well as a reduced copy number of GC-rich plasmids, thus supporting the above hypothesis. Furthermore, externally supplying GC-nucleotides to plasmid-harbouring cells caused a growth increase of cells containing GC-rich plasmids, while feeding of AT-nucleotides did not cause a similar effect. Our results demonstrate that by altering their base composition, plasmids can reduce the metabolic burden they impose on their bacterial host, which may explain the commonly observed GC-bias of endosymbionts.

Spatial pattern of MHC diversity in barn owl (Tyto alba) (52741)

Arnaud Gaigher, Reto Burri, Walid Gharib, Pierre Taberlet, Alexandre Roulin, Luca Fumagalli.

Department of Ecology and Evolution, University of Lausanne, Biophore, 1015 Lausanne, Switzerland; Laboratory for Conservation Biology, University of Lausanne, Biophore, 1015 Lausanne, Switzerland; Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden; Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, 38041 Grenoble, France.

Major histocompatibility complex (MHC) genes play an essential role in the adaptive immune response and thus constitute a good model to study adaptive genetic variability. The extraordinary diversity exhibited by MHC genes is thought to be maintained by pathogen-driven selection. Because of the major role of MHC in pathogen defense, MHC genotypes can be expected to be locally adapted to pathogens, resulting in a more pronounced genetic structure in these genes compared to neutral expectations. Alternatively, balancing selection at the geographic scale can lead to a weaker genetic structure than compared to the neutral population structure, if for instance prevailing pathogens are the same over the whole study area. To distinguish between these two scenarios, we sequenced MHCIIβ and MHCIIα loci with high-throughput sequencing technology in a large number of barn owls (Tyto alba) sampled throughout Europe (N=400). All samples were also genotyped with 22 neutral microsatellites markers used as a baseline to contrast with MHC diversity and genetic structure. Preliminary results suggest that MHC variation in Europe is a complex process, involving neutral and probably selective forces. Therefore, this study provides interesting perspectives for the understanding of MHC evolutionary ecology.
# Assessing local adaptation in Aleppo pine by comparing molecular and phenotypic variation (52739)

**Ruth Martín-Sanz**, Stephen Cavers, Luis Santos-del-Blanco, Delphine Grivet, José Climent.

Forest Research Centre-INIA; Sustainable Forest Management Research Institute (UVa-INIA); Centre for Ecology and Hydrology-Edinburgh; Department of Ecology and Evolution. University of Lausanne.

The study of the existence of adaptive genetic variation has received substantial attention in short-lived species, but the knowledge in forest trees is still scarce. Mediterranean pines in particular show high adaptive variation demonstrated in different common garden experiments. The fact that some species have a strong geographic structure, deriving from different evolutionary processes makes these species a good model to compare selective and non-selective effects shaping the extant phenotypic variation in key life history traits like threshold size for reproduction, reproductive allocation and fire resilience traits. Our objective was to confirm that the clinal patterns found in such traits are due to selection in Aleppo pine (Pinus halepensis). We measured all traits in a common garden comprising 17 populations covering the species range. Patterns of genetic variation, assessed through quantitative traits and molecular markers (cSSRs and SNPs), were compared by two ways. Firstly by comparing QST and FST estimations and, secondly by extracting molecular variation from the ecotypic variation. Our analyses confirmed that selection has played a significant role in the current population differentiation in key fitness traits as female reproductive intensity and precocity in this species. These findings are relevant for the sustainable management and conservation of the genetic resources of Aleppo pine.

# Dynamics of copy number variation in eight host races of the pea aphid species complex (52694)

**Ludovic Duvaux**, Quentin Geissmann, Karim Gharbi, Jing-Jiang Zhou, Julia Ferrari, Carole M. Smadja, Roger K. Butlin.

University of Sheffield; Imperial College, London; Edinburgh Genomics, University of Edinburgh; Rothamsted Research; University of York; ISEM, Université de Montpellier 2; University of Gothenburg.

Thanks to multiple divergent host races and a genome made of 35,000 genes, the pea aphid Acyrthosiphon pisum is a powerful system for studying the genome dynamics of copy number variation (CNV) and its role in host plant adaptation. Chemosensory multigene families, like gustatory and olfactory receptors (Grs and Ors, respectively), are well known to display large variation in gene content between species and recent studies have highlighted their importance in host race formation and speciation. Here, using targeted re-sequencing allowing a very high depth of sequencing, we contrasted the CNV dynamics of three multigene families with genes randomly sampled from the genome of the pea aphid (for a
total of 381 genes investigated in 104 individuals distributed across eight host races). We
found that CNV was widespread, with higher occurrence in multigene families, especially in
Ors. The probability of complete gene duplication or deletion (CDD) was shown to decrease
with increasing coding sequence length. Genes with CDD variants were more polymorphic
for copy number, especially in the P450 gene family where toxin resistance may be related to
gene dosage. Finally, we found that Grs were over-represented among genes discriminating
host races, as were CDD genes and pseudogenes.

In search for selection signatures and footprints of local adaption in a rock
ptarmigan population in Iceland (52691)

Kristinn P Magnusson, Máney Sveinsdóttir, Kristen Marie Westfall, Zophonías O Jónsson,
Páll Melsted, Ólafur K Nielsen.

Icelandic Institute of Natural History, Akureyri, Iceland; Faculty of Natural Resource Sciences, University of Akureyri, Iceland; Life and Environmental Sciences, University of Iceland; Department of Computer Sciences, University of Iceland ; Icelandic Institute of Natural History, Garðabær, Iceland.

The latest NGS technology and efficient bioinformatics has enabled scientists to characterize
genomes of non-model organisms. We have subjected two ptarmigan species, rock ptarmigan
(Lagopus muta) and willow ptarmigan (Lagopus lagopus) to whole genome sequencing
(WGS).

The study material was obtained from an ongoing longitudinal rock ptarmigan monitoring
project in North-east Iceland. The Icelandic rock ptarmigan population cycles multi-annually,
with peak numbers approximately 10 years apart where the difference in abundance between
low and high numbers is 3–10 fold. The relationships among health, body condition and
related parameters with respect to population cycling of the rock ptarmigan has been studied
in detail.

Understanding the functional role of genetic variation in natural populations is crucial for
applying genomic tools to investigate evolutionary processes and conservation issues, which
are valuable for curbing the accelerating worldwide loss of biodiversity. Here we investigate
the relationships among functional genomic variation, ecological, and physiological
parameters associated with population cycling as part of this long-term study. We will present
reduced genomic representation data generated with the ddRAD method, that has been shown
to be capable of detecting selection signatures and footprints of local adaption.

The evolution of untranslated regions of mRNAs in primates (52680)

Iris Finci, Anamaria Necsulea, Henrik Kaesmann.
University of Lausanne; École Polytechnique Fédérale de Lausanne (EPFL); Swiss Institute of Bioinformatics.

Untranslated regions (UTRs) of protein-coding mRNAs are important in many aspects of post-transcriptional regulation, such as translational control, mRNAs stability and mRNA subcellular localisation. However, functional roles and evolutionary dynamics of UTRs remain poorly understood, mainly due to incomplete UTR annotations in non-model organisms.

We use extensive RNA-sequencing (RNA-seq) data from 8 tissues across 6 primates (human, chimpanzee/bonobo, gorilla, orangutan, macaque and marmoset) to annotate UTRs and assess their functional evolution. We generated refined annotations for each species using RNA-seq data, adding thousands of new exons and extending known exon boundaries. We then classified exonic sequences as UTR or coding based on their evolutionary signatures, open reading frames and similarity to known proteins.

Using this comprehensive UTR dataset, we screened for differential UTR usage across tissues. Interestingly, we observed higher differential exon usage in UTRs compared to internal (coding) exons in primates, identifying many cases of tissue-specific and lineage-specific UTRs. Currently, we are trying to understand the functional relevance of these lineage-specific UTRs by analysing changes in miRNA binding potential and their nonsense-mediated decay susceptibility.

Besides providing novel insights into the functional evolution of UTRs, we believe our annotations and results will create a unique resource for future studies.

## Genome evolution during the radiation of Timema stick insects (52674)

Victor Soria-Carrasco, Moritz Muschick, Stuart R Dennis, Zachariah Gompert, Jeffrey L Feder, Aaron Comeault, Patrik Nosil.

University of Sheffield; Utah State University; University of Notre Dame.

Comparative genomics has grown to become a well-established and active field of research. Fueled by the continuous reduction in the cost of sequencing, the comparison of genomics features of a wide range of diverse organisms has greatly contributed to understand the mechanisms of evolution at the molecular level. However, the genomic changes taking place during the adaptive radiation of a group of closely related organisms from beginning to end are poorly understood. In this study, we have sequenced hundreds of genomes of individuals from multiple populations of several species of Timema, a 30-million-year-old genus of stick insects endemic to California adapted to a range of host plants. This data has allowed us to identify genomic regions of divergence across populations and species and to quantify the degree of genomic parallel evolution at different phylogenetic depths. In addition, using the annotations of the genome of one of the species, T. cristinae, we have tested whether such regions of divergence are preferentially located in coding regions and enriched in certain
functions. Our results contribute to the understanding of the evolution of genomes during
adaptive radiations.

# Exploring the genome of Sparidae: linkage mapping in common pandora, Pagellus erythrinus (52667)

**Tereza Manousaki**, Alexandros Tsakogiannis, John B. Taggart, Christos Palaiokostas, Dimitris Tsaparis, Dimitris Chatziplis, Nikos Papandroulakis, Constantinos C. Mylonas, Costas S. Tsigenopoulos.

*Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research; Department of Biology, University of Crete; Institute of Aquaculture, School of Natural Sciences, University of Stirling; Department of Agricultural Technology, Alexander Technological Educational Institute of Thessaloniki.*

The teleost fishes of the family Sparidae are rising model species in the field of reproductive biology, mainly due to their diverse patterns of sex modes, ranging from hermaphroditism to gonochorism. Their economical importance for the aquaculture industry urges even more to explore the genome evolution of the group, as genomic information (e.g. genetic markers, linkage maps and QTL analyses) is increasingly being used to select for desirable production traits. Common pandora is a recently introduced species in Mediterranean aquaculture. We applied the ddRAD methodology on a full-sib family to identify polymorphic markers widely distributed in the unexplored genome of common pandora. Employing the Illumina technology, we sequenced a large genomic fraction in 99 individuals, which resulted in the discovery of nearly 1000 polymorphic loci. Downstream linkage mapping analysis led to the construction of 24 linkage groups representing the 24 chromosomes of the species. Common pandora linkage map showed a high degree of conserved synteny compared to other teleost genomes, suggesting a rather conserved genome structure. In conclusion, our work exploits the possibilities of RAD sequencing to gain insights regarding genome structure and evolution of the valuable but unexplored Sparidae species.

# Temporal and spatial variation in assortative mating: an example in Blue Tit Mediterranean populations (52661)

**Amélie Fargevieille**, Arnaud Grégoire, Anne Charmantier, Claire Doutrelant.

*Centre d'Ecologie Evolutive et Fonctionnelle, CNRS UMR 5175 Montpellier; Université de Montpellier.*

Assortative mating is a consequence of mate choice, particularly mutual mate choice, in which partners choose each other over the same criteria. Several studies in Blue Tits (Cyanistes caeruleus) suggest the importance of two color patches in female and male
preferences, the blue crown and the yellow breast, but a recent meta-analysis challenges these
results. The aim of our study is to test the existence of a pattern of assortative mating for those
patches. We also cross variables of the color patches to see if preference is based on different
criteria in males and females. The strength of our study lies in our database; which includes
information on feather colorations for these patches and individual life-history traits for more
than 1500 pairs over three populations and ten years. Therefore, additionally to testing for a
potential pattern of assortative mating or mutual mate choice, we test the variation in space
and time for this pattern. Our results confirm that the patterns of color assortative mating in
the blue tit can vary substantially, over years and through populations, shedding a new light
on the processes of sexual selection and evolution of ornaments in a metapopulation context.

GENOME EVOLUTION OF BURKHOLDERIA LEAF NODULE
SYMBIONTS (52659)

Marta Pinto-Carbó, Leo Eberl, Aurélien Carlier.

*Department of Microbiology, Institute of Plant Biology, University of Zurich.*

Bacteria of the genus Burkholderia establish an intimate association with plant species of the Rubiaceae family. This symbiosis is unique among other plant-microbe interactions. The bacteria are housed within the leaves, and the symbiosis is obligate for both partners. Little is known about the molecular nature and genome evolution of the leaf nodule symbionts. We sequenced the genomes of eight leaf nodule symbionts and found that they exhibit features consistent with recently evolved symbionts. They also shared some commonalities with more ancient symbionts such as a reduction in their genome. However the decay in the genome size is heterogeneous among the different leaf nodule symbionts and is not as dramatic as in long-term symbiosis. Strict phylogenetic congruence between partners was not observed, indicating possible events of host switching. We also identified genes possibly acquired through horizontal gene transfer events that could potentially play a role in the establishment of the symbiosis. These genes, conserved only in leaf nodule symbionts, may be involved in the biosynthesis of secondary metabolites. The genomic analysis of leaf nodule symbionts gives, for the first time, new insights in the genome evolution of obligate symbionts in their early stages of the association with plants.

Convergent evolution story of β-lactamase enzyme (52657)

VIVEK KESHRI, Pierre Pontarotti, Jean-Marc Rolain, Didier Raoult.

Aix-Marseille Université, I2M UMR-CNRS 7373, Evolution Biologique et Modélisation;
Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63
CNRS 7278; URMITE CNRS IRD UMR 6236, IHU Méditerranée Infection, Faculté de
Médecine et de Pharmacie.
Extensive and irresponsible use of β-lactam antibiotics has contributed to the widespread dissemination of antibiotic-resistance bacteria. These bacteria have evolved three strategies (alteration of target, reduction of drug permeation in membrane and production of β-lactamase enzyme) to escape the activity of β-lactam antibiotics. The β-lactamase enzymes inactivate β-lactam antibiotics by hydrolyzing the four-membered β-lactam ring. Currently, more than 1300 naturally β-lactamase enzyme have been reported which have classified into four different molecular classes (Class A, B, C and D) and functional group. The aim of this study is to explore the evolutionary history of β-lactamase enzyme followed by investigation the correlation with hydrolyzing properties (function).

MIC is generally regarded as the most basic laboratory measurement of the activity of an antimicrobial agent. Therefore, we have started this study with extraction of MIC value of 1161 β-lactamase enzyme. After collection of MIC's, followed by filtration of unwanted data only 220 enzymes were shortlisted for evolutionary analysis. The phylogenetic analysis were carried out followed by tree were annotated based on hydrolytic properties (MIC) with respect to different β-lactam antibiotic. The detailed phylogenetic analysis of this study reveals the story of functional convergent evolution of β-lactamase enzymes.

# Linkage disequilibrium network analysis (LDna) – an unsupervised approach to study genomic signatures of local adaptation (52655)

Petri Kemppainen, Catherine Walton, Christopher Knight.

Centre for Biodiversity Dynamics, Department of Biology; Computational and Evolutionary Biology, University of Manchester.

Loci similarly affected by selection are expected to be non-randomly associated with each other i.e. in linkage disequilibrium (LD). LD can therefore be highly informative about processes involved in local adaptation. To access such information, we developed LD network analysis (LDna), an unsupervised approach to detect clusters of loci connected by high LD. Each cluster represents a sub-set of loci that bear a distinct evolutionary genetic signal. In data from three-spined sticklebacks we successfully identified LD clusters associated with local adaptation, inversions and geographic structure. Downstream analysis of these loci identified that most differentiation between freshwater and marine ecotypes was found within the Pacific Ocean rather than between the ecotypes from the Pacific and Atlantic Oceans pooled. This represents a more nuanced view of local adaptation in this species compared to previous supervised approaches (where groups between which differences are sought need to be defined a priori).

Our network analytical approach to studying LD enables a novel global view of all evolutionary processes that result in high LD among multiple loci in a data set. It does not require a linkage map or reference genome, so is applicable to any population-genomic dataset, making it especially valuable for non-model species.
# Genome-wide patterns of selection in the nematode *Pristionchus pacificus* (52647)

**Christian Rödelsperger**, Angela McGaughran, Eduardo Moreno, Katy Morgan, Jan Meyer, Dominik Grimm, Karsten Borgwardt, Mark Leaver, Ralf Sommer.

*Max Planck Institute for Developmental Biology, Dept. for Evolutionary Biology; Max Planck Institute for Intelligent Systems; Max Planck Institute of Molecular Cell Biology and Genetics.*

The nematode *Pristionchus pacificus* has been established as a satellite model to Caenorhabditis elegans for comparative studies in developmental biology, ecology, and population genetics. Based on whole-genome sequencing of hundred globally sampled isolates, we have previously identified background selection as a major factor shaping genetic diversity.

In this study, we investigate selective processes that act on top of background selection. To this end, we sequenced genomes of 218 isolates from the island la Reunion, which was previously identified as a hotspot of *P. pacificus* diversity. On this geographically diverse island, we identified several distinct *P. pacificus* populations (defined by location) that group into four evolutionary lineages. Despite the fact, that strains of distinct evolutionary lineages can be successfully crossed in the lab, there is almost no evidence for outcrossing across lineage borders in the wild. Focusing on population comparisons within lineages, we identified numerous genomic loci with almost complete differentiation between populations. These candidate loci for adaptation harbor several genes that were previously described as playing a role in chemosensation and pathogen resistance. In addition, we identified highly polymorphic variants near immune response related genes, that suggest the action of frequency dependent selection.

# Exchange of Genetic Material between Non-Recombining Sequences on a Genomic Scale (52644)

**Claus Vogl.**

*Inst Animal Breeding and Genetics.*

Only the pseudo-autosomal regions of the mammalian sex-chromosomes recombine. But obviously Y-chromosomal genes outside this region also exchange genetic information with the homologous X-chromosomal genes. Similarly, in many allopolyploid species inheritance is disomic, i.e., the homoiologous chromosomes do not recombine. Nevertheless, genetic exchange among homoiologous genes has been observed. Technically, it is difficult to discover such, especially on the genomic scale. The specific molecular and computational methods are presented and discussed. Exchange of genetic materials between non-
recombining regions may thus go undetected and may have a much higher impact on genome evolution than generally believed, which will also be discussed.

# Selectome, a database of positive selection (52640)

Sébastien Moretti, Marc Robinson-Rechavi.

UNIL DEE / SIB Swiss Institute of bioinformatics.

Selectome (http://selectome.unil.ch/) is a database of positive selection, based on a branch-site likelihood test. This model estimates the number of non-synonymous substitutions (dN) and synonymous substitutions (dS) to evaluate the variation in selective pressure (dN/dS ratio) over branches and over sites. Special care is taken to minimize false positives, with a thorough quality control procedure on multiple sequence alignments. The Web interface presents results mapped both onto phylogenetic trees and onto protein alignments. It allows rapid access to results by keyword, gene name, gene ontology term, or taxonomy based queries. Selectome covers most gene trees from vertebrates and Drosophila.

Proux et al 2009 Nucl. Acids Res. 37: D404-D407

Moretti et al 2014 Nucl. Acids Res. 42: D917-D921

# Bgee, a database for the study of gene expression evolution (52639)

Frederic B Bastian, Anne Niknejad, Julien Roux, Marta Rosikiewicz, Sebastien Moretti, Marc Robinson-Rechavi.

University of Lausanne; Swiss Institute of Bioinformatics.

Gene expression patterns (where and when genes are expressed) are a key feature in understanding gene function and evolution. To apply compare results between different model organisms and human, or to study gene expression evolution, a comparative approach must be used, but no tools allow to easily compare gene expression across species.

We have thus developed Bgee (Base for Gene Expression Evolution), a database designed to automatically compare expression patterns between animals. This is achieved by i) the aggregation and curation of expression data from different types and sources, to map them to formal representations of anatomies and developments of different species; Bgee release 13 contains curated and quality controlled data for RNA-seq libraries, Affymetrix chips, EST libraries and in situ hybridizations. ii) The analysis of these data by dedicated statistical tests to define high confidence gene expression patterns. iii) The definition of comparison criteria between anatomies of different species; Bgee curators have designed homology relationships between across all Bilateria, which are integrated into the multi-species anatomical ontology Uberon. Bgee 13 includes 17 species, with a focus on vertebrates, but also D. melanogaster
# An experiment in the wild to test if stickleback males adapt their colour to the ambient light environment (52624)

**Thor Veen**, Chad Brock, Diana Rennison, Dan Bolnick.

*University of Texas at Austin; University of British Columbia.*

Many organism show spatial variation in phenotypic traits correlated with environmental characteristics, some on very small scales. For example colouration of nesting male three-spined stickleback consistently varies with the ambient light along a two-meter depth gradient in multiple populations. An earlier experiment showed that male colour changed predictably after nesting males were transplanted to either deep or shallow enclosures. We set out to test the hypothesis that change in male colour is driven by changes in the ambient light environment. This change is predicted because different colours are required at different depths to maximize contrast (and hence visibility to females). 40 cages were constructed in shallow parts of a freshwater lake in British Columbia and divided into light treatment pairs. Two natural light environments were mimicked by wrapping sheets of light filter around and over each cage, this changed the sunlight to represent the sidewelling irradiance at a depth of 0.5 m and 1.8 m, respectively. To assess the magnitude of the colour adaptation we measured the change of male colouration between the start of the experiment (which depends on natural nesting depth) and the end, and the colour differences between males of the two treatment groups.

# THREE-DIMENSIONAL POST-GLACIAL EXPANSION AND DIVERSIFICATION OF AN EXPLOITED OCEANIC FISH (52603)

**Peter Shum**, Christophe Pampoulie, Ronald Douglas, Rachel Brenchley, Kristján Kristinsson, Stefano Mariani.

*School of Environment & Life Sciences, University of Salford, Salford M5 4WT, UK; Marine Research Institute, Skúlagata 4, 101 Reykjavík, Iceland; Department of Optometry and Visual Science, The City University, London EC1V 7DD, U.K.*

Despite the striking physical and environmental gradients associated with depth variation in the oceans, relatively little is known about their impact on population diversification, adaptation and speciation. The pelagic redfish, Sebastes mentella, exhibits depth-associated patterns of substructure in the central North Atlantic, with a widely distributed shallow-pelagic population inhabiting waters between 250 and 550m depth and a deep-pelagic population dwelling between 550 and 800m.
By sequencing and genotyping S. mentella samples caught between 2006 and 2013, at different depths, across the North Atlantic, we show the existence of two strongly divergent evolutionary lineages, with significantly different distribution patterns and dwelling at different depth layers. We then carried out de novo RNA-seq of retina transcriptome from a subset of “shallow” and “deep” individuals, in order to characterise differential expression and polymorphisms of candidate genes involved in sensory reception in organisms adapted to different depths. Overall, we cast new light on the role of depth in generating biodiversity in the oceans, and consider the practical implications of such findings.

## From positive selection in songbird MHC genes to binding properties of songbird MHC proteins. (52591)

**Helena Westerdahl**, Elna Follin, Michael Rasmusson, Soren Buus, Maria Strandh, Morten Nielsen, Kajsa Paulsson.

*Biology, Lund; Experimental Medical Science, Lund; Experimental Immunology, Denmark; Center for Biological Sequence Analysis, Denmark.*

Hosts cannot predict which pathogens they may encounter in the future but vertebrates have evolved an adaptive immune system that can handle an enormous variety of pathogens. This pathogen recognition is created by random by somatic recombination in B- and T-cell receptors, uniquely so in every individual. Major Histocompatibility Complex (MHC) molecules then enable immunological tolerance so that only ‘non-self’ cells are attacked. MHC genes are highly polymorphic and a classical example of genes subjected to balancing selection. However, to understand the standing genetic variation in host MHC genes the functional aspect, binding properties of MHC molecules, must be considered. Most songbirds have a larger number of MHC genes than other animals: What is the functional relevance of all these gene copies? Does it give songbirds an advantage in handling pathogens? We have taken a functional approach to determine binding properties of songbird MHC molecules and compared them with human MHC molecules. Using two recombinant songbird MHC proteins we were able to generate unique peptide-binding motifs. The preferred peptide length was similar to human MHC molecules though the binding repertoires of songbird MHC molecules were quite different, suggesting that we cannot extrapolate binding repertoires across very distantly related species.

## Ecologically driven divergence between multiple populations of the marine snail Littorina fabalis (52583)

Rui Faria, João Carvalho, Juan Galindo, Graciela Sotelo, **Diana Costa**.

*CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Univ. Porto, Portugal; Depart. de Bioquímica, Xenética e Inmunoloxia, Facultade de Bioloxia,*
Speciation is often a continuous process, with different mechanisms interacting during the buildup of barriers to gene flow. It is well established that ecology can play a critical role in population divergence and ultimately in speciation. Nonetheless, our understanding of how it occurs is still scarce. Characterized by abrupt changes in the environmental conditions over a narrow spatial scale, the marine intertidal is an ideal system to provide valuable insights into ecological speciation. We focus on ecotypes of the flat periwinkle Littorina fabalis from the NE Atlantic to explore to what extent adaptation and genetic divergence are promoted by contrasting wave exposure intensities and other associated factors. We analysed phenotypic differentiation (shell morphology) using geometric-morphometrics, and performed a genomic scan based on AFLPs to estimate divergence between sheltered and exposed populations at different geographic scales (<100 Km and >1000 Km) and to identify putative loci under disruptive selection among ecotypes in a repetitive manner along the species range. Some overlap between outliers was observed at both scales, even among populations from the Iberian Peninsula and Scandinavia. Various hypotheses to explain this pattern will be discussed to shed light on how repeatable (parallel) is divergent evolution in L. fabalis.

# An unexpected oviposition preference of the common bush brown (Bicyclus safitza) may help to explain butterfly-host plant coevolution (52556)

**Ossi Nokelainen**, Brad Ripley, Colin Osborne, Erik van Bergen, Paul Brakefield.

Butterfly oviposition behaviour is a crucial determinant of offspring success. Thus, the decision about choice of substrate on which a female lays an egg will strongly determine the hatching larva's chance of establishment on a food plant. The oviposition decision often follows female scouting in suitable habitat and localisation of a host plant. Individual data on variation in female preference and its consequences for hatchlings, however, remain scarce. We examined oviposition behaviour of the common bush brown (Bicyclus safitza) on ecologically relevant host plants in South Africa. Specifically, we studied whether individual female butterflies preferred species of local grasses with C3 or C4 photosynthetic pathway and that grow in open or shaded habitats. We predicted that C3 grasses would be preferred over C4 grasses due to a generally higher palatability, and shade grasses over open grasses, as the butterfly is typically associated with shaded-habitats. We found a strong interaction between habitat and photosynthetic pathway of the plants. Unexpectedly, females preferred C4 shade grasses, followed by C3 shade over C3 open grasses; they particularly tended to avoid C4 grasses from open habitats. We discuss this pattern of oviposition behaviour in relation to how it relates to co-evolutionary relationships in plant-herbivore interactions.
# Reconstructing metal specificity-evolution in ribonucleotide reductases (52526)

**Daniel Lundin**, Gustav Berggren, Britt-Marie Sjöberg.

*Stockholm University.*

The radical generating subunit (NrdB) of class I ribonucleotide reductases typically harbours a diiron site that is able to initiate a radical on a neighbouring tyrosine residue. In the subclass Ic, the tyrosine is replaced by a phenylalanine and the relevant metal centre is a heterodinuclear iron/manganese centre. Metal specificity in subclass Ic is high, with manganese occupying site 1 and iron occupying site 2 almost exclusively. How the specificity is achieved remains an enigma since the metal-binding site is very similar between diiron and iron/manganese enzymes. Mutagenesis of metal ligands and residues in their vicinity aiming to turn an iron/manganese enzyme to a diiron has not been able to resurrect diiron specificity, suggesting that substitutions in other parts of the protein play a role in selectivity. We have phylogenetically identified a group of diiron NrdBs closely related to the iron/manganese enzymes. This provides us with the opportunity to complement earlier mutagenesis experiments with experiments going in the other direction, trying to convert a diiron enzyme to an iron/manganese one, and to reconstruct ancestral enzymes. Here, we report preliminary data on resurrected proteins as well as a structural analysis of important substitutions.

Poster session A - POL 300

# Carry-over effects of the social environment on future divorce probability in great tits (52520)

Antica Culina, Ben Sheldon, Camilla Hinde, **Reinder Radersma**.

*Oxford University; Wageningen University; Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, UK.*

Suboptimal partnerships can appear when the initial mate choice was constrained by the social environment. To correct for such suboptimal partnerships, individuals of socially monogamous species may adopt secondary mating strategies (infidelity and divorce). In this study we aim to better understand the influence of the social environment in which a pair has formed on later divorce. Using detailed data on social networks of tagged Great tits over four winters we found that males with a higher proportion of female associates, and males whose partner ranked lower amongst these, were more likely to divorce after breeding. We found no evidence that a female's social environment influenced divorce probability. Our study demonstrates that divorce in monogamous species might not only be affected by the social environment to which existing pairs are exposed, but also by the social environment in which pairs have formed (and which is likely to constrain the initial choice). Second, our results indicate that this might be more driven by the male's social environment and preference for a partner. Further exploration of these carry-over effects of the social environment, and how they differ between sexes, may give new valuable insights into processes of mate choice, population dynamics, and sexual selection.
# The consequences of mating system and population dynamics on genome evolution: a comparative study of inbreeding and outcrossing sister species of the spider genus Stegodyphus (52483)

**Virginia Settepani**, Jesper Bechsgaard, Mads F. Schou, Michelle Greve, Lena Grinsted, Trine Bilde.

*Department of Bioscience, Aarhus University; Department of Plant Science, University of Pretoria; School of Life Sciences, University of sussex.*

Regular inbreeding results in reduced effective population size, which reinforces genetic drift and accelerates loss of genetic diversity. These processes act to decrease the efficacy of selection causing a build-up of the genetic load, ultimately impairing the potential of populations to respond to environmental change. Social spiders live in communal nests where they cooperate in prey capture and brood care. Phylogenetic analyses show multiple independent origins of sociality from solitary ancestors, and the transition to permanent group living is associated with a strictly inbreeding mating system. Furthermore, strong metapopulation dynamics of social spiders and frequent extinction events acts to homogenise genetic structure. We performed RAD-sequencing in a comparative population genomic approach to examine the effects of inbreeding and outcrossing mating systems on genetic diversity, population structure, and genome evolution. We included independent sister species pairs of social inbreeding and solitary outcrossing spiders of the genus Stegodyphus that were extensively sampled over a large geographical range. This approach provides extraordinary high power to gain insights into the consequences of mating system and population dynamics on genome evolution in non-model wild species.

# Can fluctuating selection explain levels of variation in natural populations? (52478)

**Sebastian Novak**, Srdjan Sarikas, Nick Barton.

*IST Austria.*

Natural environments are never constant but vary in time and space. Furthermore, from the point of view of a single locus, there is background selection on multiple other loci, possibly for a plethora of traits that are influenced pleiotropically. To what extent can this combination of external and internal factors be described by a scheme of randomly fluctuating selection? What pattern of fluctuations can we expect to be experienced by a single locus? Continuing from there, we can venture forth trying to explain the observed levels of variation in natural populations that could so far not be reproduced convincingly by quantitative trait models of constant selection. Can fluctuating selection models unveil the missing variability?
## Speciation history of Atlantic eels and its genomic footprints (52477)

**Magnus W. Jacobsen**, José Martin Pujolar, Shenglin Liu, Kasper Munch, Louis Bernatchez, M. Thomas P. Gilbert, José Victor Moreno-Mayar, Thomas D. Als, Michael M. Hansen.

*Department of Bioscience, Aarhus University; Bioinformatics Research Centre (BiRC), Aarhus University; Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Laval University; Centre of Geogenetics, Natural History Museum of Denmark, University of Copenhagen; Department of Biomedicine - Human Genetics, Aarhus University.*

Speciation-with-gene flow scenarios are increasingly appreciated. Yet, the specific processes and the resulting genomic footprints of selection are subject to much discussion. To elucidate the genomic mechanisms underlying speciation-with-gene flow, accurate knowledge is needed, not only of the genomic patterns of selection but also the demographic history of the species. Here we present the results of several studies on the European and American eel (Anguilla anguilla and A. rostrata), two panmictic and sympatrically spawning sister-species. Hybrids are known to occur and low but biologically significant gene flow takes place. We employed mitogenome sequencing of 106 individuals in order to test hypotheses about the demographic processes linked to their speciation, including divergence time and the possibility of allopatric periods during the speciation process. Furthermore, RAD sequencing of 60 individuals and alignment of reads to the European eel draft genome was used for analyzing genome-wide linkage disequilibrium, genomic footprints of diversifying selection, divergence time and demographic history. Our results demonstrate that demography has a major effect on genomic footprints. Very high effective population sizes of the two species lead to minimal background genetic differentiation, interrupted by numerous smaller regions of strong differentiation that mark interspecific diversifying selection.

## Landscape genomics of oaks (Quercus spp.): Adaptive genetic variation in candidate genes in respect to present and future climatic conditions (52457)

**Christian Rellstab**, Lorenz Walthert, Christoph Sperisen, Catherine Bodénès, Isabelle Lésur, Andrea R. Pluess, Antoine Kremer, Felix Gugerli.

*WSL Swiss Federal Research Institute, Birmensdorf, Switzerland; INRA Pierroton, Cestas, France; University of Bordeaux, Pessac, France; HelixVenture, Mérignac, France; ETH, Zürich, Switzerland.*

Testing whether and how populations are adapted to their local environment, and predicting their response to future habitat alterations is of key importance in the face of climate change. A powerful approach to investigate such processes is landscape genomics, which identifies genes and environmental factors involved in local adaptation. We investigated whether the three common oak species in Switzerland (Quercus petraea, Q. pubescens, Q. robur) are
adapted to their present and future environmental conditions. In a pooled amplicon
sequencing approach of 95 genes in 71 oak populations, we identified over 3'500 SNPs, many
being private to populations and species. We tested if these SNPs show an association to
abiotic factors related to local topography, climate and soil. We found genes that are
putatively involved in adaptation to the present environment and tested whether these loci
were congruent among all species and defined seed zones. We then used allele frequency
distributions of candidate SNPs along environmental gradients to test the adaptedness of
populations and species for simulated future climatic conditions. Our results help assessing
the classification scheme of the seed zones in an evolutionary perspective, since afforestations
that intend matching future environmental conditions are likely to increase in the future.

Genomic response to rapid convergent evolution in wild crickets (52456)

**Sonia Pascoal**, Timothee Cezard, Xuan Liu, Karim Gharbi, Urmi Trivedi, Sam Haldenby, Marlene Zuk, Michael G. Ritchie, Nathan W. Bailey.

University of St Andrews; University of Edinburgh; University of Liverpool; University of Minnesota.

The initial stages of convergence provide insight into the genomic dynamics of adaptive
evolution in the wild. A rapidly-evolving mutation, flatwing, silences male crickets in Hawaii
by altering their wings, but it persists because of natural selection arising from an
acoustically-orienting parasitoid fly. Despite appearing only a decade ago, silent males now
occur on two islands and have distinct forms on each. Mutants on Kauai have wings that are
almost completely feminized, whereas Oahu flatwings retain a larger portion of the secondary
wing venation typical of normal males. Nevertheless, both are silent and share the same mode
of inheritance, i.e. the phenotype segregates as a sex-linked, sex-limited Mendelian trait in
both populations. I will present results from a combination of complementation crosses and
Bulk Segregant Analysis using RAD-markers to provide evidence that the male-silencing
wing morph has arisen twice, independently, on different islands, but spread under similar
selection. Furthermore, I will illustrate how gene expression profiling using RNA-seq along
with RAD-mapping and QTL analysis elucidates the early genome response to this dramatic
recent wing adaptation and associated effects of its spread. The results provide unprecedented
insights into the adaptive evolution of convergent phenotypes, in real time, in the wild.

The Evolution and Divergence of the Special Homeobox Genes in Pararge
aegeria (52454)

**Luca Livraghi**, Peter W. Holland, Leonardo Dapporto, Roger Vila, Melanie Gibbs, Casper
J. Breuker.
Oxford Brookes University; Zoology Department, Oxford University, South Parks Road, Oxford UK; Institut de Biologia Evolutiva, Pg. Marítim de la Barceloneta 37, Barcelona Spain; Centre for Ecology and Hydrology, Benson Ln, Wallingford UK.

Paralogs arise through gene duplications and their subsequent divergence provides the raw material for functional innovation. Although this has been inferred from studies on interspecific sequence variation in paralogs, not much is known about standing intraspecific paralog variation and associated phenotypic variability. Paralogs in the Hox cluster are rare, but the so called paralogy group 3 (PG3) has undergone independent tandem duplications in several insect clades. Within the ditrysia, a derived clade of the Lepidoptera, duplications in the ancestral PG3 gene zerknüllt (zen) resulted in 4 so-called special homeobox genes (Shx). It has recently been shown that there is significant interspecific variation in these Shx paralogous genes. Sequencing of the Shx genes within my model species, the Speckled Wood butterfly Pararge aegeria, has revealed that although intraspecific variation is lower than interspecific variation, it is very high for a Hox (-derived) gene. To investigate this in more depth, I sequenced the four Shx genes, zen, wingless and the cytochrome oxidase I subunit in 25 populations of P. aegeria spanning from N. Africa to Scandinavia. Preliminary results show the presence of population specific variants, even within the highly conserved homeobox region of one of the Shx paralogs. This suggests possible local adaptation events in response to different selection pressures.

Local adaptation of reproductive traits (52433)

Charlotta Kvarnemo, Erica Leder, Jonathan Havenhand, Kai Lindström, Topi Lehtonen, Ola Svensson.

University of Gothenburg, Sweden; University of Turku, Finland; Åbo Akademi University, Finland.

The distribution of animals is not only determined by which environment adults can tolerate, but in which environment they can reproduce. Based on experiments on the sand goby, Pomatoschistus minutus aimed at understanding local adaptation of reproductive traits, we found that males have difficulties to reproduce outside their native salinity. This is likely to be caused by local adaptation of their gametes, as our study using sperm from males that originate from high vs. low salinity areas, shows that sperm perform poorly in non-native salinity. The two salinities also differ regarding risk of fungus infection of eggs, affecting both paternal care and mate choice behaviours. We also investigated protein and mRNA expression in testes, and found differences in both, when comparing pairs of males of high and low salinity origin. We argue that reproductive traits per se are under divergent selection and that non-random mating and reduced gene flow arise as a bi-product. This is important because local adaptation – and in its extension speciation – can only evolve if the strength of selection overrides the effect of gene flow. Our studies provide new insights into the evolutionary processes and the mechanisms behind geographic distributions of species.
# Adaptive genetic diversity of Apis mellifera populations using whole-genome sequence data (52425)

**Melanie Parejo**, Peter Neumann, Laurent Gauthier, Markus Neuditschko.

Institute of Bee Health, Vetsuisse Faculty, University of Bern; Swiss Bee Research Center, Agroscope.

The original distribution of the honey bee Apis mellifera ranges from Europe, Africa and the Middle East, encompassing a large native range with diverse environmental conditions. There are >29 Apis mellifera subspecies differing in phenotypic traits such as morphology, behavior and resistance to disease and which cluster into four major geographically and genetically different lineages. This evolutionary history offers a great model system to study molecular diversity of local adaptions in geographic range expansions.

The native honey bee of Northern Europe A. m. mellifera is adapted to short foraging seasons and comparatively long winters through, for instance, the ability to form winter clusters. Global trade of this important pollinator for commercial operations in combination with the particular polyandrous mating system pose a risk on the genetic integrity of locally adapted ecotypes through introgression, potentially resulting in the loss of valuable local adaptations shaped by natural selection.

We will present insights into the adaptive genetic diversity of Swiss A. mellifera populations from different lineages by comparing neutral vs. adaptive molecular markers inferred from whole-genome next-generation sequencing data. A special focus will be given on the diversity and conservation of the native European subspecies A. m. mellifera.

# How to estimate selection from evolve and resequence experiments (52418)

**Katarina Bodova**, Srdjan Sarikas, Nick Barton.

IST Austria.

With more data available from evolution experiments on sexual populations in the laboratory, it is now plausible to detect candidates for selected regions in the genome. This, however, brings several challenges. First, it is difficult to distinguish effects of random drift from selection: many candidates may be false positives. Second, various patterns of selection may act, and it is useful to know which properties of selection can be inferred in general. Third, recombination and epistasis influence evolution, and further distort effects of selection. We address the above challenges and provide insight into how to efficiently design an evolutionary experiment.
# Genetic basis of eye and face shape differences in Drosophila mauritiana and Drosophila simulans (52353)

**Michaela Holzem**, Kentaro M. Tanaka, David L. Stern, Maria D. S. Nunes, Alistair P. McGregor.

*University of Konstanz; Oxford Brookes University; Princeton University.*

Differences in head shape between closely related Drosophila subgroups were often described. Still underlying genetic differences in evolution of organ size and shape involved in head development remain unclear. Head shape is mostly maintained by the negative correlated shape and size of compound eyes and face width. The occurrence of heritable variation suggests it might be possible to map underlying genes. We selected extreme backcross individuals of “eye-face trade-off” distribution and performed multiplexed shotgun genotyping. QTL analysis of this data suggested a QTL for shape difference between D. simulans and D. mauritiana at 11.5 Mb on chromosome 3L. To validate the QTL position and narrow down the mapped region we performed independent introgressions of this region from D. mauritiana into D. simulans and further analysed those using geometric morphometrics. We found two regions for face and one for eye shape, this one detected directly at 11.5 Mb. Thus, it was possible to narrow the QTL down and proof that the position at 11.5 Mb is responsible for shape differences between the strains. These regions will be analysed for interesting genes involved in development of eye and face. Overall, this will lead to better understanding of evolutionary and developmental differences in head shape formation.

# Genome-wide genetic variation in populations of Calanus finmarchicus and C. glacialis across their distributional ranges (52351)

Irina Smolina, Marvin Choquet, Martina Kopp, Ann Bucklin, Janne Søreide, **Galice Hoarau**.

*University of Nordland; University of Connecticut; The University Centre in Svalbard.*

Calanus finmarchicus and C. glacialis are the keystone zooplankton species in subarctic and arctic marine food webs respectively. However, as a response to ocean warming, C. finmarchicus is showing a consistent northward shift increasing the competition with C. glacialis that may influence the arctic ecosystems. To understand the ecological and evolutionary potential and functioning of the two species, an ocean-basin-scale analysis of C. finmarchicus and C. glacialis is required. Genome-wide genetic variation was accessed from 10 locations per species encompassing their whole distributional range. Forty females of genetically identified C. finmarchicus and C. glacialis per location were pooled equally and sequenced on Illumina MiSeq platform using restriction site-associated DNA (RAD)-sequencing. SNPs were used to assess genetic differentiation between species populations and possible adaptive polymorphisms across environmental conditions of species distribution. We compared both species in terms of population genetic structure and genetic diversity. The whole transcriptome profiling of both species under thermal stresses was also used to investigate their acclimatory potential to ocean warming.
# Parallel or convergent evolution in human population genomic data revealed by genotype networks (52346)

Ali R. Vahdati, Andreas Wagner.

*University of Zurich.*

A genotype network is a graph whose nodes are genotypes (DNA sequences) with the same broadly defined phenotype. Two nodes are connected if they differ in some minimal way, e.g., in a single nucleotide. Here we analyze human genome variation data from the 1000 genomes project, and construct haploid genotype (haplotype) networks for 12235 protein coding genes. The structure of these networks varies widely among genes, indicating different patterns of variation despite their shared evolutionary history. We focus on those genes whose genotype networks show many cycles, which can indicate homoplasy, i.e., parallel or convergent evolution, on the sequence level. We show that in 47 genes the observed number of cycles is so large that it cannot be explained by either chance homoplasy or recombination. In some of these 47 genes, positive or balancing selection may be responsible for the great abundance of cycles. Genotype networks are representations of genetic variation data that facilitate analyzing unusual patterns of inheritance or variation not easily captured in phylogenetic trees.

# Long-term fitness consequences of a prenatal maternal effect and their impacts on evolutionary dynamics (52328)

Joel Luke Pick, Barbara Tschirren.

*Institute of Evolutionary Biology and Environmental Studies.*

The prenatal environment can have important and long-lasting consequences on offspring morphology, physiology, behaviour, and ultimately fitness. Mothers are in a unique place to alter this environment and so the future phenotype of their offspring, through a process known as maternal effects. Although theoretical work has shown that maternal effects may play an important role in influencing evolutionary dynamics, by affecting how traits respond to selection, there is a lack of empirical work supporting these models. In birds, many of these prenatal maternal effects are mediated through differential allocation of resources into the egg. Despite a considerable amount of data showing investment into the egg has large consequences on early life traits, there is only equivocal evidence of long term effects, and in particular on reproductive performance. Through the use of repeated divergent selection lines for prenatal maternal investment, we investigate how egg size influences both body size and reproductive investment of the offspring. We show that egg size has pronounced effects on
offspring phenotype throughout it's life, most notably on egg size itself. This has important consequences for the strength and predictability with which egg size can respond to selection.

## Evolution of dominance in trait under balancing selection: polymorphic mimicry as a case-study (52323)

**Violaine Llaurens**, Yann Le Poul, Monica Arias, Mathieu Chouteau, Sylvain Billiard, Mathieu Joron.

CNRS - National Museum of Natural History; University of Lille 1.

Spatial heterogeneity promote fixation of locally adaptive alleles but can lead to the persistence of polymorphism within population depending on migration. Such balancing selection might shape the genetic architecture of adaptive trait. Since heterozygotes are frequent in such polymorphic loci, dominance among adaptive alleles can evolve in response to natural selection. Here we used the evolutionary convergence of warning signal in toxic species, i.e. Müllerian mimicry, as an example of local selection. Most species involved in Müllerian mimicry display a single warning signal within population because of selection exerted by predators, fixing the most common signal. However, in the toxic butterfly Heliconius numata, several warning patterns are maintained within localities, and each display high resemblance with distasteful species from different communities. These variations in warning pattern are controlled by a supergene in which each allele encodes for a different mimetic pattern. Heterozygotes might display an intermediate, non-mimetic phenotype, depending on the dominance among alleles. Using experiment in natural populations, we showed a significant selection acting on dominance. We then performed theoretical simulations describing the condition of invasion of dominance modifiers. Finally, we investigated variations of dominance in natural populations to understand the molecular mechanisms shaping dominance in polymorphic adaptive loci.

## Heterozygote deficit through time in a gene (MC1R) encoding melanin-based color morphs involved in predator-prey relationships (52291)

**Valérie Ducret**, Jérôme Goudet, Alexandre Roulin.

*Department of ecology and evolution, university of Lausanne, Lausanne, Switzerland.*

Despite numerous theoretical and empirical studies on geographic phenotypic variation, the relative contribution of selection and gene flow in shaping clines remains largely unknown. In this context, the barn owl (Tyto alba) is a promising study system because its coloration varies clinically with owls being white in southern Europe and darker reddish towards north-eastern Europe, a cline maintained by natural selection. Pheomelanin-based reddish coloration is explained by a mutation of the MC1R gene and its frequency increases from 0.9% in southern
Europe to 60.3% in north-eastern Europe. We studied a Swiss population located in the centre of the pronounced color cline and hence should undergo gene flow from southern and northern owls. Using 10 microsatellite markers we tested for non-random departure from Hardy-Weinberg Equilibrium (HWE) of the MC1R gene during a period of 15 years. We found a deficit of MC1R heterozygotes through time for cohorts but no deviation in neutral genetic markers. In-depth analyses show that temporal variation in assortative mating and transmission ratio distortion are responsible for this deficit. This study highlights the importance of considering populations along phenotypic clines to understand the evolution of phenotypic diversity and its role in reproduction isolation.

# Environment-dependent patterns of phenotypic integration in Aleppo pine.
(52267)

José Climent, Jordi Voltas, Rafael Zas, Ruth Martín-Sanz, Pitter Ferrio, Eduardo Notivol, Luis Sampedro.

Forest Research Centre-INIA; Univ. of Lleida; UMG-CSIC; CITA.

Global Change imposes new challenges to many ecosystems, and among these Mediterranean forests are particularly sensitive due to combined drought, wildfires and biotic stressors. Mediterranean forest populations are expected to harbour high adaptive genetic diversity, but we know too little on their ability to respond to multiple challenges. Precisely, life history theory postulates that adaptive evolution implies optimizing resource investment to growth and maintenance, reproduction and defence to maximize fitness under a given environment. Our objectives were first, to determine the genetic differentiation among populations in key adaptive traits considering their correlations and second, to confirm differences in key trade-offs among a high-stress and a low-stress environment. We measured a wide set of traits in a replicated common garden of Pinus halepensis at two sites. Traits related to growth and maintenance, reproduction, constitutive and induced defences and water and carbon acquisition and storage. While population differentiation was significant for most traits, differences were environment-specific. As expected, key trade-offs were neatly different among the two sites indicating differently plastic strategies of resource usage. These findings may improve our understanding of the real adaptive value of a single trait and how resource shortening can modify it in long-lived woody plants.

# Environment-dependent sexual selection: Bateman's parameters under varying levels of food availability (52265)

Elodie Chapuis, Patrice David, Tim Janicke.

IRD; CNRS.
Sexual selection is considered as a potent evolutionary force that has been shown to vary in strength and direction depending on demographic factors such as density and sex ratio. However, the effect of other environmental factors on the mode of sexual selection remains largely unexplored. Here we tested experimentally how food restriction affects the potential for sexual selection in the male and female sex function of the simultaneously hermaphroditic freshwater snail *Physa acuta*. We manipulated food availability and compared Bateman's metrics of sexual selection between groups of five well-fed and five food-restricted snails. Our results indicate that food-restricted snails had a reduced female reproductive output suggesting that we successfully manipulated the reproductive resources. Importantly, food restriction reduced the male opportunity for sexual selection (in terms of a lowered variance in male mating success) and lead to diminishing returns of mating in both sexes (in terms of non-significant Bateman gradients). Furthermore, we observed significant changes in the relative contribution of different fitness components suggesting stronger post-copulatory selection in the male and stronger fecundity selection in the female sex role under restricted food conditions. This study highlights the need to incorporate ecological factors to better understand how sexual selection operates in the wild.

# Searching for signatures of selection in Iberian honey bee (Apis mellifera iberiensis) using whole genome sequences (52236)

**Dora Sofia Martins Henriques**, Andreas Wallberg, Chavéz-Galarza Julio, Costa F., Rufino José, Webster Mathew, Pinto M.Alice.

Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança; Centro de Biologia Molecular e Ambiental (CBMA), Universidade do Minho; Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Instituto Politécnico de Bragança; Laboratório de Instrumentação e Física Experimental de Partículas, Campus de Gualtar.

The Iberian Peninsula comprises a diverse set of habitats. It was an important glacial refugium during the Pleistocene and has served as a bridge for populations migrating between Africa and Europe, resulting in a complex mix of ancestry and diversity. The Iberian honey bee (A. m. iberiensis) is no exception and has been the subject of numerous incongruent population genetic surveys. Recent mtDNA and SNP analyses indicate a steep northeastern-southwestern cline of African ancestry along the peninsula, which has been explained by selection. Advances in DNA sequencing technology and computational tools provide unprecedented opportunities to study demography, search for signatures of selection across the genome and illuminate its role in shaping genomic diversity. We used Illumina technology to sequence the whole genomes of 86 Iberian honeybees, collected across three longitudinal transects in the Iberian Peninsula and spanning semi-arid climates in the southeastern peninsula to oceanic in the North-West. The dataset was first analyzed for FST-outliers, CLR (composite-likelihood ratio) and EHH (Extended Haplotype Homozygosity) methods were further deployed to evaluate polymorphisms implicated in local adaptation and possibly in the response to human-mediated environmental changes, including known and novel variants in genes related to behavior, vision, xenobiotic detoxification and immune response.
# The evolutionary challenge of climate change : adaptive processes in the Mediterranean red coral (52229)

**Marine Pratlong**, Anne Haguenauer, Olivier Chabrol, Pierre Pontarotti, Didier Aurelle.

Aix Marseille Université, CNRS IMBE UMR 7263, IRD UMR 237 Station Marine d'Endoume;
Aix Marseille Université, CNRS UMR 7373, I2M Équipe Evolution Biologique et Modélisation.

The on-going climate change should have major impacts on the different components of biodiversity, from genes to ecosystems. Mediterranean marine species are already suffering from climate change, as shown by mortality events linked with thermal anomalies. These events hightlighted a diversity of thermotolerance levels in the temperate red coral (Corallium rubrum). The main objective of this work was to understand the origin of these differences and to search for local adaptation of the red coral to thermal conditions. This species is present in very contrasted ecological conditions which correspond to genetically differentiated populations. Moreover, colonies from different regions, depths but also from the same site present thermotolerance differences. These differences might be linked to the individual history through acclimatization or to population level through genetic adaptation. Two complementary approaches were developed to study these mechanisms: i. Transcriptomic (gene expression and polymorphism) basis of thermotolerance differences. ii. Genomic study of local adaptation. We looked for genetic-environment associations through the identification of outlier loci with particular patterns of genetic differentiation using RAD-sequencing (Restriction site Associated DNA sequencing). For this purpose we chose to compare populations from above the thermocline which deal with high thermal variations to population from a more thermal stable zone below the thermocline.

# Harvest induced phenotypic selection in an island moose *Alces alces* population (52227)

**Thomas Kvalnes**, Bernt-Erik Sæther, Hallvard Haanes, Steinar Engen, Erling J. Solberg.

*Centre for Biodiversity Dynamics (CBD)*, Dep. of Biology, NTNU, Trondheim, Norway;
*Norwegian Radiation Protection Authority*, Østerås, Norway; *Centre for Biodiversity Dynamics (CBD)*, Dep. of Mathematical Sciences, NTNU, Trondheim, Norway; *Norwegian Institute for Nature Research (NINA)*, Trondheim, Norway.

Human exploitation has frequently led to evolutionary changes in wild populations. These changes are generally rapid and observable within ecological time scales, often within a few generations. Here we demonstrate selection for later birth dates in males and reduced yearling body mass in females induced by phenotype-based selective harvest in an moose population. We apply a recently developed framework combining population dynamics and quantitative
genetics theory to data from a 20-year study of a wild population, where genetic pedigrees has
been established tracing back to founders. During the study birth date has advanced by 0.75
days per year for both sexes, while no significant changes has occurred in body mass. Both
traits harboured significant additive genetic variance, with heritabilities of 11 % for body
mass and 22 % for birth date, though the evolvability for body mass was only 0.16 %.
Following standard quantitative genetics theory propagating uncertainty in estimates
parameters we predicted a response to selection corresponding to the direction of observed
changes for birth date. While body mass did not respond to selection during the study period
the predicted phenotypic changes will generally not be fully transferred until lifetime
reproduction is achieved.

Detection of locus under selection from temporal samples of partial-selfing
populations (52220)

Arnaud Becheler, Renaud Vitalis, **Miguel Navascués**.

INRA, UMR CBGP Montpellier; IRD, UMR LEGS Gif-sut-Yvette.

In a single isolated populations, allele frequencies will change through time subject to the
processes of selection (acting on specific loci) and genetic drift (acting on the whole genome).
Genetic data collected at different times can be used to make inferences on the effective
population size (i.e. strength of drift) and to detect outlier loci, whose changes in allele
frequencies are unlikely to be only the product of the inferred demography. However, the
presence of self-fertilization may pose a problem for the detection of loci under selection.
Selfing reduces the effective size of populations and the effective recombination among loci
(promoting hitch-hiking). We investigated the effect of the presence of partial selfing
reproduction in the power and false discovery rate for the detection of selected loci. In
addition, we characterized the footprint of selection along the chromosome containing the
selected site.

Genomic changes during adaptation to a common environment in initially
differentiated Drosophila subobscura populations (52205)

**Sofia G. Seabra**, Inês Fragata, Pedro Simões, Gonçalo S. Faria, Marta A. Santos, Miguel Lopes-Cunha, Margarida Matos.

CE3C - Faculdade de Ciências, Universidade de Lisboa.

Real-time evolution studies of laboratory populations of Drosophila subobscura founded from
wild collections in contrasting European latitudes have previously revealed fast convergence
at phenotypic traits. In contrast, though there were also significant temporal changes in
chromosomal inversion frequencies, populations remained differentiated across generations.
We are now performing genome-wide analysis in two foundations derived from the extremes of the European cline, characterizing both the initial genomic differentiation, as well as the temporal changes during laboratory adaptation. We also aim at characterizing genomic content within and outside inversions in order to understand the mechanisms of evolution of inversions. Three different approaches for genome-wide analysis are taken: 1) Genome resequencing of pools of individuals (three replicates from each population) from four different generations; 2) Restriction site associated DNA (RAD) sequencing of individual larvae with known karyotype from two different generations; 3) Genome resequencing of pools of individuals of homokaryotypic lines for two chromosomal inversions in the O chromosome (OST and O3+4) to characterize SNP variation within and outside these inversions. The combination of these approaches will allow us to address the impact of history, chance and selection in genomic variation and evolution, and further the knowledge of the genomic impact of chromosomal inversions.

## Weak conservation of pathways in mouse and human aging tissues (52196)

**Andrea Komljenovic**, Marc Robinson-Rechavi.

*Department of Ecology and Evolution; Swiss Institute of Bioinformatics, Lausanne, Switzerland.*

Despite different experimental designs and different data available to study aging, the mechanisms of aging are still poorly understood. To tackle this, we are interested in evolutionarily conserved marks associated with aging that are different from those eventually specific to long lived species, such as human. We retrieved publicly available aging datasets diverse in species and tissues to analyze the gene expression differences during aging. Using modularization algorithm, we characterized co-modules showing the level of gene expression conservation between mouse and human tissues. Meta-analysis across different tissues in mouse and human shows overall down-regulation of age-related gene expression profiles. Since physiological changes that occur during aging in skeletal muscle and brain are striking, we identified the biological processes using gene set enrichment analysis and found that changes associated with age-related gene expression in skeletal muscle and brain are involved in the mitochondrion pathways and inflammatory response, respectively. However, there is a weak positive correlation between aging effects in the human and mouse brain, and in human and mouse skeletal muscle. The co-module identification showed connection to immune response process in brain tissue between human and mouse. Our study provides a statistical framework for comparative analysis in aging across different species.

## Phenotypic population divergence of the common frog across an elevational gradient in the Swiss Alps (52184)

**Judith C. Bachmann**, Josh Van Buskirk.
Species are distributed across varying environments which leads to variation in fitness and (genetic and phenotypic) divergence between populations, but all species ranges occur within limits. As populations along a species distribution encounter different habitats, natural selection should favor phenotypic traits beneficial in the local environment. Local adaptation is counteracted by gene flow reducing divergence among populations. Species distributions along an elevational gradient encounter environmental changes that happen on a small spatial scale compared to dispersal distances of many species. We study the elevational range of the common frog (Rana temporaria) in the Swiss Alps (200 m - 2775 m a.s.l.). Tadpoles from twelve populations from the elevational distribution were raised until metamorphosis in common conditions manipulating temperature and exposure to predation. Countergradient variation in development time and body mass was found. Populations diverge in larval life-history traits but not as strong as on the latitudinal gradient, suggesting that (potentially) high gene flow reduces phenotypic differentiation between populations. Future work will focus on limits to adaptation at the edge of the elevational distribution by genetic correlations.

# Analysis of mtDNA heteroplasmy in hermaphroditic mussels. First case of doubly uniparental inheritance without dioecy? (52163)

**Aleksandra Przylucka**, Beata Śmietanka, Marek Lubośny, Artur Burzyński.

## IO PAN.

In bivalves having doubly uniparental inheritance (DUI) males are heteroplasmic because they transmit one of their mtDNAs (M-type) to sons. Females have only one mtDNA (F-type), inherited in a regular way. Evolution and mechanism of DUI, despite years of investigations, still remains unclear but it is believed, that it does not occur in hermaphrodites. Furthermore, it has been shown, that sex determination and mitochondrial inheritance are quite closely linked in some bivalves (Unionidae). The very taxonomic distribution of DUI across bivalves remains obscured, largely due to technical difficulties. To overcome these we applied a novel gonadal transcriptome screening approach in hope to easily identify candidate DUI species. The approach was rather successful and here we report, for the first time, a case of a hermaphroditic bivalve with two divergent mitochondrial genomes, indicative of a working DUI. The sequencing of gonadal transcriptomes revealed the presence of two sets of mitochondrial transcripts. Observed high sequence divergence as well as a distinct pattern of amplification from generative tissues tentatively confirm this as a DUI case. We believe that this discovery will require deep revision of our understanding of the relationship between DUI, sex determination and evolution of reproductive strategies, at least in bivalves.

# Mussels from the Chilean Pacific coast: preliminary transcriptomic data (52155)
**Marek Lubośny**, Beata Śmietanka, Aleksandra Przyłucka, Artur Burzyński.

*Institute of oceanology PAN.*

Over the last 20 years, since sequencing of the first bacterial genome in 1995 through the sequencing of the first eukaryote in 1996, and human genome in 2001 till present day, sequencing research and technologies have made a great leap forward. It takes much less time, money and effort to obtain more, longer genomic sequences of higher quality. Organisms with sequenced genomes stand for only a very small percentage of all living beings on Earth. Most of currently available genome sequences (Ensembl database) comes from model organisms. However, much less data is available for marine organisms. In particular, there are only two genomes from phylum mollusca currently available in the database. In contrast to the costly genomic projects, RNA sequencing constitutes a viable alternative of obtaining large amounts of representative sequence data for a reasonable price. Here we present the results of a small transcriptomic survey performed on mussels from Chilean Pacific coast. Total RNA was isolated from generative tissues of several bivalves, subject to library construction and Miseq (Ilumina) sequencing. After assembly, the obtained contigs were analyzed using a set of bioinformatic tools. This gave us a first glimpse at the bivalvian transcriptome, illustrating the productivity of this approach.

**How much can History constrain adaptive evolution? The two sides of a story.
(52153)**

**Inês Fragata**, Pedro Simões, Margarida Bárbaro, Bárbara Kellen, Josiane Santos, Marta A. Santos, Gonçalo S. Faria, Mauro Santos, Margarida Matos.

*CE3C - Faculdade de Ciências, Universidade de Lisboa; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona.*

The ability to adapt to environmental changes is of utmost importance for species survival. Insights on the mechanisms and forces underlying this ability can be obtained from studying species that present a wide geographical distribution. However, few studies have examined how history affects the adaptive dynamics of such species, at several levels of organization. In order to test the impact of historical differentiation during adaptation, we followed the real-time evolutionary dynamics of phenotypic traits and chromosomal inversion frequencies in replicated Drosophila subobscura populations. These populations were derived from the 3 locations along the European latitudinal cline and introduced in a new (laboratorial) common environment. Initially populations were highly differentiated for all traits. However, pervasive phenotypic convergence was achieved after only few generations in the laboratory. A different story was told at the karyotypic level, with selection shaping the evolutionary dynamics of inversion frequencies, but doing so within the constraints imposed by previous history. The signature of history and its impact on the evolutionary dynamics may thus have different outcomes depending on the level of observation. Given that similar phenotypic optima were reached through different genetic routes, this suggests that history plays an important role but does not constrain adaptive evolution.
# MICROGEOGRAPHIC VARIATION IN TROPICAL TREES: SELECTION SHAPES INTRA-POPULATIONAL DIVERGENCE AT HUNDREDS OF LOCI (52143)

Louise Brousseau, Ivan Scotti.

INRA - URFM; CNR - IBBR; INRA - ECOFOG.

Tree species harbour high levels of within-population genetic diversity, generally explained away based on purely neutral processes. Nevertheless, within-population environmental gradients and mosaics and variable selective pressure suggest that part of the variation may be maintained by Darwinian processes.

To test this hypothesis, we have analysed genome-wide patterns of polymorphism in two adult stands of the tropical tree, Eperua falcata Aubl. (Fabaceae), occupying areas where starkly contrasted habitats can coexist at very short distances. We have assembled a draft containing roughly one fourth of the total genome. After filtering for quality, approximately seventy-thousand SNP loci were retained for further analyses.

One of us (LB) has developed a Bayesian framework to analyse population-specific and locus-specific divergence in nested sampling schemes and we have also applied Nielsen's (2009) G2D test to detect sequences under directional selection.

Approximately 1% of the loci is subject to either stabilising or directional/divergent selection, which is probably an underestimate, because we partitioned our samples based on only one gradient. It is likely that the inclusion of other environmental axes will lead to the detection of further adaptive loci. These results are consistent with a substantial role of Darwinian selection in the shaping of within-population genetic diversity.

# Genome-wide screen for adaptive divergence between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) (52141)

Stefan Dennenmoser, Arne W Nolte, Steven M Vamosi, Sean M Rogers.

Max-Planck Institute for Evolutionary Biology; University of Calgary.

Understanding the genomic basis of adaptive divergence in the presence of gene flow remains a major challenge in evolutionary biology. In prickly sculpin (Cottus asper), high genetic connectivity exists among estuarine habitats of coastal rivers and nearby tributaries, but apparently does not preclude the emergence of genetically differentiated life history ecotypes.

It is unclear whether this is driven by adaptive evolution. We predicted that adaptation to brackish-water and freshwater habitats manifests as increased genetic differentiation at candidate genes underlying salinity tolerance and osmoregulation in teleosts. The high similarity to the genome of the stickleback allowed us to approximate the position of Cottus genomic sequences along the stickleback chromosomes and to explore their gene content.
This permitted sequencing of genomic DNA pools representing two estuarine and two
freshwater habitats in the lower Fraser River system (southwestern British Columbia, Canada)
to explore genetic differentiation across the genome. Among 36 predicted candidate genes,
sodium/potassium ATPase and Na+Cl- co-transporter showed strong signals of differentiation
among habitats, indicating their potential role in local adaptation to different osmotic niches.
Overall, the presence of both parallel and non-parallel signatures of differentiation across
many loci scattered throughout the genome suggests polygenic adaptation that varies among
local populations.

Poster session A - POL 300

How much is adaptive evolution contingent on space and time? A meta-
analysis in Drosophila subobscura (52135)

Pedro Simões, Inês Fragata, Sofia G. Seabra, Gonçalo S. Faria, Marta A. Santos, Margarida Matos.

CE3C-FCUL.

Environmental changes across space and time as well as stochastic events can shape genetic
backgrounds and thus affect evolutionary responses and potential. Here we address
experimentally these effects on the initial performance of populations and their evolutionary
changes in fecundity, physiological traits and inversion polymorphisms during short-term
adaptation to a new environment. We use two sets of two laboratory foundations of
Drosophila subobscura, sampled 3 years apart, from the same contrasting European locations
(Portugal vs. Netherlands). We found initial differentiation between foundations from
different locations, consistent in both years, for most traits. Early differences between years
were found only for age of first reproduction and male starvation resistance. Concerning the
evolutionary rate, starvation resistance showed significant variation across locations and
years. As for chromosomal inversion frequencies, these differed initially across locations but
not years. Differences between locations remained significant after 6/8 generations. Inversion
frequency changes during that period were minor. Altogether, our findings indicate that
spatial rather than temporal variation in source natural populations is more likely to produce
disparate starting points for evolution. Also, it seems that the evolution of traits more loosely
related to fitness (e.g. starvation resistance) is more contingent on location and time of natural
collections.

Poster session A - POL 300

Latitudinal variation in temperature-stress resistance and tolerance in
Arabidopsis lyrata (52133)

Guillaume Wos, Yvonne Willi.

University of Neuchâtel.
Numerous species tend to have distribution boundaries that coincide with thermal isoclines. What limits thermal adaptation? We hypothesized that resistance and tolerance to extreme temperatures cannot be maximized because of genetic trade-offs. We conducted an experiment on eight populations of Arabidopsis lyrata collected along a latitudinal temperature gradient in North America and repeatedly exposed plants to either frost or heat stress. We measured resistance and tolerance to frost and heat using electrolyte leakage and growth data, respectively, and tested whether they (a) co-vary with latitude, (b) are genetically negatively correlated and (c) are costly. Plants from high latitude populations grew to a larger size and were more frost resistant, while those from low latitudes were more heat resistant and heat tolerant. Surprisingly, populations from the north were less frost tolerant, probably because frost tolerance was genetically correlated with small size. We found no indication that trade-offs between resistance and tolerance to the same or different thermal stresses limit adaptation to frost and heat. However, the results suggest that the cost of frost tolerance could be an important constraint to adaptation at the northern distribution boundary.

# The role of sexual selection on a threshold trait in the black scavenger fly Sepsis thoracica (52126)

**Juan Pablo Busso**, Wolf U. Blanckenhorn.

IEU- University of Zürich.

Sexual selection is an important force shaping phenotypic diversity within a species and can ultimately contribute to the evolution of reproductive isolation and sympatric speciation. To analyze the divergent role of sexual selection we focused on Sepsis thoracica (Diptera: Sepsidae), a black scavenger fly that presents a sigmoid relationship between body size and coloration resulting in two condition dependent male morphs: a smaller black and a larger yellow morph. Competitive matings between the two morphs showed that copulation success was greater for larger black males and smaller yellow males. This special type of stabilizing sexual selection should result in a narrower distribution peaking at intermediate male sizes. However, S. thoracica presents a bimodal male size distribution with little overlap between morphs. Since there was no assortative mating within either morph, but there was assortative mating across morphs, this antagonistic selection could not only strengthen the sigmoid relationship between body size and coloration, but also lead to divergence between the morphs. Further experiments varying the strength of sexual selection (different sex ratios) should confirm its role on shaping the particular body size-coloration relationship in this species.

# Effects of temperature dependent survival during early development on adult fitness traits (52119)

**Martin A. Schäfer.**
University of Zurich.

Differential survival during early development may play an important, but neglected, role in shaping allelic variation encoding for traits exposed to natural or sexual selection at later life stages. Using a fine-grained temperature gradient at the upper margin of the thermal tolerance curve, I explored sex-specific selection during development in the dung fly *Scathophaga stercoraria* by comparing the size of non-hatched and hatched pupae. In female pupae and adult flies I further quantified the development of an additional, fourth spermatheca, which is rarely expressed in the field and entails fitness costs at the adult stage. Males had lower temperature-survival thresholds, but survival was not related to body size within both sexes, indicating no physiological costs of growing large in a species with male-biased size dimorphism. In females high temperatures induced the expression of the additional spermatheca as a correlated side effect of fast extrinsic (environmental) and/or intrinsic (genetic) growth. Interestingly, females that survived the pupal stage expressed the naturally rare phenotype more frequently, implying that antagonistic pleiotropy across developmental stages can contribute to the evolutionary diversification of female sperm storage morphology.

Poster session A - POL 300

# Evolution of canalization in gene regulatory networks (52110)

**Estelle Rünneburger.**

*Laboratoire Evolution, Génomes, Comportement, Ecologie.*

The genetic architecture of complex traits involves numerous interacting genes as well as environmental effects. To study the influence of genetic architectures on the evolution of phenotypes and gene networks themselves, we surveyed through in-silico individual-based simulations how quantitative measurements of evolvability and robustness change in time under natural selection. Our main model features gene regulatory networks, in which the evolution of complex phenotypes (gene expression patterns) depends on the evolution of a regulation matrix. We also considered simpler alternative settings, such as the epistatic multilinear model.

It is generally acknowledged that stabilizing selection tends to promote genetic canalization in epistatic architectures. We investigated the influence of various properties of gene networks on this evolution towards low evolvability, focusing on parameters related with the network topology (number of genes, connectivity, ...). Simulation results show that robustness to mutations tends to evolve faster in networks of intermediate complexity, suggesting that evolution of evolvability could be constrained by the size of the underlying gene networks.

Poster session A - POL 300

# Evolution of bow-tie architectures in biology (52101)

**Tamar Friedlander, Avraham E. Mayo, Tsvi Tusty, Uri Alon.**
Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. The maximal compression possible determines the size of the narrowest part of the network - that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved.

# Geographically limited selection at the blood group-related gene B4galnt2 in house mice is associated with gastrointestinal pathogens (52095)

Marie Vallier, Miriam Linnenbrink, Philip Rausch, Guntram Grassl, John Baines.

Max Planck Institute for Evolutionary Biology, Ploen, Germany; Christian-Albrechts-University of Kiel, Germany.

B4galnt2 is a blood group-related glycosyltransferase whose two murine alleles (driving gastrointestinal- and vascular expression) are maintained by balancing selection in house mice and their relatives. The vascular allele induces a defect in coagulation and subsequent bleeding phenotype, suggesting that this fitness cost may be offset by other unknown benefits. Interestingly, despite its overall long-term maintenance, the vascular allele is absent in wild mouse populations from Germany and Northeast France, but recently increased in Southwest France as evidenced by a partial selective sweep. This suggests that geographic-dependent selective forces may be operating. Given other examples of blood group-related glycosyltransferase variation in humans, we hypothesize that resistance to pathogen(s) may mediate selection operating on B4galnt2 over space and time. Indeed, experiments in lab mice show that the presence/absence of B4galnt2 expression in the gastrointestinal tract influences the response to Salmonella infection. By applying metagenomic approaches in a wild mouse population displaying evidence of recent selection (i.e. a partial selective sweep), we found that B4galnt2 genotype correlates with differences in intestinal inflammation and the presence of candidate pathogens that could drive selection at B4galnt2. We thus suggest the limited dispersal of pathogens to be a potentially potent source of variation in selection.
# Opposite forces of selection modify local life history adaptations in insects (52084)

Panu Välimäki, **Netta Keret**, Sami M. Kivelä, Markku Orell, Toomas Tammaru.

*University of Oulu; Stockholm University; University of Tartu.*

Increasing body size is favored by fecundity selection among income breeders. In seasonal environments, larval development time is a key life history trait because individuals have to reach a diapause stage before winter. Theory assumes that large size can be achieved only by a prolonged development time. This may hold true at the phenotypic level, but the evolutionary consequences lies in the genetic level. Genetic correlation of the traits may vary spatially depending on variance in growth rate. We studied quantitative genetics of development time and body size in a laboratory experiment in four latitudinal populations of Chiasmia clathrata (Geometridae). Development time and body size expressed high additive variance at national scale but not at local scale. In univoltines, development time was highly heritable, whereas body size appeared almost a fixed trait, the two being negatively correlated at the genetic level. In bivoltines, opposite pattern emerged but the traits were uncorrelated at the genetic level. This implies that fecundity selection is strong in less time-constrained univoltine populations. In the strongly time-constrained populations short development time is selected for instead. Either compensating (bivoltines) or over-compensating (univoltines) growth rate may break down development time vs. body size trade-off in an adaptive manner.

# Spatial Variation in Natural Selection Determines Patterns of Divergence in an Adaptive Radiation (52057)

**Greg M Walter**, Melanie Wilkinson, David Aquirre, Daniel Ortiz-Barrientos.

*University of Queensland; Massey University.*

A group of organisms that colonise a heterogeneous landscape are exposed to spatial variation in natural selection, facilitating adaptation and diversification possibly leading to adaptive radiation. Divergence during adaptive radiation is potentially driven by adaptation and divergence at a local scale. Although studies of local adaptation are common, particularly in plants, few of them have addressed the role of natural selection in driving population and ecotypic divergence across multiple environments. Here, we use reciprocal transplant experiments of ecotypes and select hybrids to investigate how selection is currently shaping population and ecotype divergence in a widely distributed wildflower. Local populations performed better in their local environment and better than foreign ecotypes. Additionally, populations of the same ecotype exhibited some level of local adaptation themselves. The similarity of the environmental conditions between their native environment and the transplant environment determined the fitness of a population in any given locality. However, despite a strong signature of local adaptation F1 hybrids displayed heterosis while backcrosses and F2's exhibited hybrid breakdown. We provide experimental evidence for
environmentally driven diversification that has resulted in local adaptation on a wide spatial
and historical scale across contrasting environments.

# Looking for Ecologically dependent reproductive barriers and intrinsic genetic incompatibility between ecotypes of Senecio lautus (52055)

Tom Richards, Daniel Ortiz-Barrientos, Katrina McGuigan.

*University of Queensland.*

Ecologically dependent reproductive isolation is a process fundamental to the model of ecological speciation, although evidence of it is relatively limited. A fundamental test is whether barriers to gene flow between divergent wild populations are due to intrinsic genetic incompatibilities or ecologically dependent fitness reductions in hybrids. Senecio lautus is a species complex where these predictions can be tested; there are several ecologically divergent ecotypes however they retain the ability to produce viable crosses when grown in a common environment. In this work, we use a field based reciprocal transplant experiment using parental and hybrid (F1, F2 & Backcross) genotypes from three coastal ecotypes of Senecio lautus to ascertain the relative importance of ecologically-dependent and intrinsic-genetic barriers to gene flow. We find that there is evidence for local adaptation, with reduced fitness seen in some hybrid genotypes and immigrant parentals, and that there is some ecological dependence, as fitness decreases proportionately with the presence of immigrant genes present in the cross. We find some evidence for ecologically dependent isolation, however, support is not as clear as theory would predict, suggesting the existence of other factors.

# Divergent ecology causes within generation polygenic selection and ecotypic differences in American Eel (Anguilla rostrata). (52039)

Louis Bernatchez, Scott Pavey, Jérémy Gaudin, Céline Audet.

*Université Laval; ISMER.*

The two primary ways that species cope with heterogeneous environments is through local adaptation and phenotypic plasticity. American Eel presents a paradox; despite inhabiting drastically different environments, the species is panmictic and long-term local adaptation is impossible. All spawning takes place in the southern Sargasso Sea. Then, the planktonic larvae disperse to rearing locations from Cuba to Greenland and juveniles colonize either freshwater or brackish/saltwater habitats, where they spend 3-25 years before returning to the Sargasso Sea to spawn as a panmictic species. Depending on rearing habitat, individuals exhibit drastically different phenotypes. The hypothesis that phenotypic plasticity alone can account for the differences has been disproven. In this study, we present a genome-wide
association study that demonstrates a genetic basis for the drastic phenotypic differences that is the likely result of within-generation selection. We found that 331 loci out of 42,424 initially considered were most associated with the divergent ecotypes. These 331 loci are within 101 genes that represent vascular and morphological development, calcium ion regulation, growth and transcription factors, and olfactory receptors. Our results demonstrate that divergent natural selection of phenotypes can have a subtle polygenic genomic signal, occur within a single generation, and manifest in divergent ecotypes, despite panmixia.

# The genomic basis of colour dimorphism and cold adaptations in a seabird.
(52036)

**Anna Tigano**, Tone Reiertsen, Kjell Einer Erikstad, Vicki Friesen.

*Queen's University; Norwegian Institute for Nature Research - NINA.*

In the North Atlantic, common guillemots (Uri aalge) are located from arctic to temperate waters and include two morphs: unbridled birds have a completely black or dark brown head, and bridled birds are characterized by a white eye-ring and auricular groove. Mating between the two morphs is random and the dimorphism is based on simple Mendelian inheritance of an autosomal gene, where bridling is recessive. Several lines of evidence suggest that bridled guillemots are more adapted to colder temperatures than are unbridled ones and the frequencies of the two morphs across their range may be the result of fluctuating selection. To designate a trait as 'adaptive' connections between genotype, phenotype and fitness must be made. The correlation between phenotype and fitness has been documented, but genetic characterization of phenotypic variation and genomic signature of selection are needed to close the circle. We are using whole genome resequencing data from bridled and unbridled common guillemots to investigate the genomic basis of bridling and associated cold adaptations. This system allows us not only to characterize the basis of the phenotypic traits of interest, but also to investigate the genomic architecture of adaptation.

# Empirical insights of the effects of pollen flow on the adaptive potential of
*Fagus sylvatica* populations (52030)

**Julie GAUZERE**, Etienne KLEIN, Sylvie ODDOU-MURATORIO.

*CEFE CNRS; BioSP INRA; URFM INRA.*

In temporally variable environments, gene flow is expected to facilitate the adaptive response of populations by spreading pre-adapted genes in the landscape and increasing the genetic variance available for the response to selection. However we still lack empirical evidence of these beneficial effects of gene flow.
Here, we investigate the effects of gene flow on the adaptive potential of three populations of Fagus sylvatica along an altitudinal gradient using direct gene flow estimate based on paternity analyses. We measured eleven ecophysiological traits on 60 maternal families. Genetic data were used to assign the offspring to two categories, “migrant” or “local”, according to the origin of their fathers. We first show that pollen immigration rates were high (56% on average) and that 6 traits genetically diverged along the gradient. Our results overall fail to demonstrate significant effect of pollen flow on trait mean or variation within population. Only for the population at the intermediate altitudinal level, we found that immigrant pollen increase the genetic variances of two traits (timing of budburst and diameter growth). This may be due to a weak power to detect gene flow effect in weakly differentiated populations. A better characterization of the pollen origin may help to reveal the effects of pollen flow on adaptive potential.

# The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates (52025)

Asier Ullate Agote, Michel C. Milinkovitch, Athanasia C. Tzika.

*Laboratory of Artificial & Natural Evolution (LANE); SIB Swiss Institute of Bioinformatics; Institute of Genetics and Genomics of Geneva (iGE3).*

Squamates exhibit a striking variety of phenotypes, with little known on their generative mechanisms. Studies aiming to understand the genetic basis of this diversity in morphology, physiology and ecology will greatly benefit from whole genome sequencing initiatives, as they provide the foundation for comparative analyses and improve our understanding on the evolution, development and diversification of traits. Here, we present the first draft genome of the corn snake Pantherophis guttatus, an oviparous snake that we promote as an appropriate model species for evolutionary developmental studies in squamates. We sequenced 100-bases paired-end reads from multiple individuals of a single family that produced a genome assembly of 1.53 Gb, roughly covering 75% of the expected genome size, and 297,768 scaffolds >1Kb. We were able to retrieve 192 of the 248 CEGMA core genes, indicating that high genome completeness was achieved. Using MAKER2, we annotated 10,917 genes with high confidence. Numerous colour and colour pattern morphs exist in P. guttatus, making it an ideal model to study the genetic determinism, development, and evolution of adaptive colour traits in reptiles. Using our draft genome and a SNP calling approach, we located the interval with the causative mutation for the amelanistic phenotype.

# Genomic footprint of local climate adaptation (52021)

Ann-Marie Oppold, Markus Pfenninger, Simit Patel.
Local adaptation is a common observation in species with a wide distribution range. However, little is known about its underlying genomic basis and therefore the molecular mechanisms driving this adaptation. Especially for ectothermic organisms, as is our non-model organism Chironomus riparius, the ambient temperature is a crucial environmental factor. We analysed C. riparius populations along a climatic gradient across Europe by the integration of genome-scans and common garden experiments.

Common garden experiments at three different temperatures (14, 20, and 26 °C) revealed local climate adaptation in six natural populations. Differences in the population growth rate showed temperature-dependent effects on fitness of the populations. We applied the Pool-Seq method to scan the population genomes and found more than 2.5 million SNPs among six natural populations. Based on FST-analyses more than 2000 highly differentiated SNPs were identified and annotated. We further associated the identified SNPs to environmental variables and found significant correlations. To also account for patterns of polygenic adaptation and not merely focus on outlier loci, we further aimed to perform gene-set enrichment analyses.

Our results give insight in the complexity of the genome-wide distribution of adaptive genetic variation in natural populations.

## An approximate Bayesian estimator of allele age and selection strength (52020)

**Louise ORMOND**, Gregory Ewing, Matthieu Foll, Jeffrey D Jensen.

EPFL; WHO.

Single Nucleotide Polymorphism (SNP) data can be used to infer both the age of a beneficial allele and the strength of selection acting upon it. These estimates can outline variation in selection over time and space, offering important implications regarding the mode and tempo of adaptation. Although new time-sampled methods have been developed, there remains significant scope for improvement in the single time point inference of selection parameters. Here, we first apply forward and backward simulations investigating a range of parameters, including effective population size (Ne), mutation rate (μ), recombination rate (r), the strength of selection (s) and allele age (Ts) to generate summary statistics. We then use an approximate Bayesian (ABC) approach to generate the posterior distribution of s and Ts. Second, we replicate previous results for the Bayesian inference of Ts (Przeworski 2002) and develop an improved single-time point Bayesian estimator for the joint inference of these parameters. We then incorporate demographic scenarios and explore the relative gains in performance from using single- versus multiple-time points. This approach improves on existing methodology through the incorporation of several informative summaries, including data from linked neutral sites, and through the computational efficiency and speed afforded by ABC-based approaches.
# EVOLUTION IN SPATIOTEMPORAL VARIABLE METAPOPULATIONS FACILITATES PERFORMANCE IN NOVEL CHALLENGING CONDITIONS (52006)

**Dries Bonte.**

*Ghent University.*

Human-induced changes of the landscape often lead to the fragmentation or reduction of quality of habitat and forces many organisms to live in a heterogeneous landscape. The landscape structure affects local and metapopulation dynamics which are in turn expected to impact life history evolution.

By means of experimental evolution using the spider mite Tetranychus urticae as a model we demonstrate that spatiotemporal variation in habitat availability affects metapopulation dynamics and that these changes induce evolutionary divergence in life history, physiological endpoints and gene expression. The induced metapopulation-level selection pre-adapts the mites towards an enhanced performance on novel challenging hosts.

Our integrated approach highlights the linkage between spatial structure, local demography and trait evolution. The multivariate responses point towards general adaptations in stress resistance pathways and are suggested to be driven by metapopulation-level variation in competition and patch extinction rates.

# Detecting signals of strain-specific selection in genomic sequences of Staphylococcus aureus (52001)

**Chieh-Hsi Wu, Daniel Wilson.**

*University of Oxford.*

There are myriad examples of bacterial populations rapidly adapting in response to selection pressure imposed by antibiotics, often within individual patients. Selection is therefore pervasive in bacterial evolution. Many species such as the common pathogen Staphylococcus aureus exhibit strong strain structuring – such that the level of diversity among strains is much higher than within – but low geographic structuring, with local sampling capturing global diversity. These observations indicate that strain structuring is maintained by selection, and that patterns of variation cannot be well explained by classical selective sweeps. Strain structure may hinder attempts to discover genomic signatures of selection based on models of selective sweeps. To address this, we extended a recently proposed Bayesian statistical method based on the chromosome painting technique to detect partial selective sweeps. The extension adapts the original method to suit prokaryotic mechanisms of homologous recombination, which differ to those in eukaryotes. Our extension also accommodates recombination rate variation along the genomic sequences. We have applied our method to a
dataset of 100 S. aureus genomes sampled from Oxfordshire, England, to search for strain-
specific adaptation that may explain the long-term coexistence of diverse strains.

Evolutionary analysis linked to epigenetic modifications in the largest
transcription factor family of humans. (51985)

Adamandia KAPOPOULOU, Lisha MATHEW, Didier TRONO, Jeffrey D. JENSEN.

EPFL; SIB.

The KRAB-containing zinc finger (KRAB-ZNF) genes represent the biggest family of
transcription factors in humans, yet for the great majority, their function and specific genomic
target remains unknown. However, it has been shown that a large fraction of these genes arose
from segmental duplications, and that they have expanded in gene and zinc finger number
throughout vertebrate evolution. To determine whether this expansion is linked to selective
pressures acting on different domains, we have manually annotated all KRAB-ZNF genes
present in the human genome and assessed the evolutionary forces acting at the sequence
level as well as on the epigenome. When compared across primates and across tissues,
KRAB-ZNFs demonstrate species-specific expression rather than tissue-specific expression.
Interestingly, those carrying a nonsynonymous SNP in their DNA-contacting amino acids
exhibit significantly reduced expression in all tissues accompanied by repressive histone
marks; these KRAB-ZNF genes also seem to be less strongly constrained than those without
such polymorphism. This work represents the first large-scale effort to characterize selective
effects on KRAB-ZNFs and to correlate those effects with epigenetic modifications and
population genetic data.

The ADiv Project (Analyzing Diversification in the Agaricales, 2013-2017): Analyzing patterns of diversification in the largest group of mushroom-forming basidiomycetous fungi (51981)

János Gergő Szarkándi, Bálint Dima, Sándor Kocsubé, Csilla Szebenyi, Nikolett Rácz, Tamás Papp, Csaba Vágvölgyi, László G Nagy.

*Department of Microbiology, University of Szeged; Fungal Genomics and Evolution Lab, Biological Research Center of the Hungarian Academy of Sciences.*

The ADiv project aims to investigate patterns in the rates of evolution in the Agaricales. The Agaricales is the largest group of mushroom-forming fungi with ca. 14,000 described species. The driving forces underlying taxonomic diversification in these mushrooms are poorly known and are among the most important challenges in mycology.
To address these questions, we will use phylogenetic comparative analyses on a new two-gene dataset (the diversity dataset) for ca. 3,000 species. We selected the nLSU and RPB2
loci, which are known to provide sufficient phylogenetic information for relationships at the infrageneric level. We have already sequenced the nLSU gene in 1,500 species from 2,200 specimens. In addition, a phylogenomic dataset is also being produced from publicly accessible genomes of Agaricales, meaning about 60 to 100 species. These two datasets will be used to examine general patterns of speciation and extinction and to identify shifts in diversification rates. Sampling efforts have been concentrated on regions with poor phylogenetic coverage, e.g. the southern hemisphere (Australia, New Zealand). Currently we are experimenting with different primer sets for the amplification of the RPB2 gene and further sequencing of the LSU gene is in progress.
This study was supported by the grant OTKA NN106394.

# The role of habitat dynamics in driving diversification (51968)

**Thijs Janzen.**

*Max Planck Institute for Evolutionary Biology.*

It is commonly accepted that geographical isolation can play an important role in speciation. Geographic isolation is often assumed to slowly increase over time, for instance through the formation of rivers or mountains. Cyclic changes in connectivity between areas might occur however when water levels fluctuate in a large lake, or when changes in sea level changes the connectivity between islands. These habitat dynamics may act as a driver of allopatric speciation and propel local diversity. Here we present a basic model of this interaction between changes in the environment and speciation. We model fluctuations in water level and compare results of our model with a published phylogeny of cichlid fish from Lake Tanganyika where such cyclic changes have occurred. When confronting our model to the phylogeny of cichlid fish from Lake Tanganyika, we do not find evidence for water level changes and associated allopatric speciation. This suggests that large-scale water level fluctuations have had little impact on the current diversity of cichlids in Lake Tanganyika. However, we argue that the Yule tree model prior used to reconstruct the phylogeny may have biased our results, and therefore advocate the incorporation of more complex tree model priors that take into account habitat dynamics.

# Detecting selection with haplotype-based methods: benchmarking and application to tropical butterflies (51966)

**Angeles de Cara, Annabel Whibley, Marianne Elias, Mathieu Joron, Frederic Austerlitz.**

*Lab d'Ecoanthropologie et Ethnobiologie, Museum National d'Histoire Naturelle, Paris (France); John Innes Centre, Norwich (UK); Museum National d'Histoire Naturelle, Paris (France).*
The vast amount of genome-wide polymorphism data available has led to considerable efforts to develop methods to detect natural selection at the molecular level. Finding regions under selection is one of the first steps towards understanding the processes of adaptation and speciation. Our ability to detect selection depends critically on the data available and on the robustness of the methods to the underlying assumptions. Several commonly used methods look for FST outlier loci. However, these methods sometimes fail to identify loci under weak selection. Conversely, some neutral markers can be inferred to be under selection.

Alternatively, we can use haplotype-based methods to infer selection within populations. These methods rely on the idea that positive selection on a position in the genome will create a region of extended homozygosity. We study here the efficiency of three such methods (iHS, nSL and H12) in simulated data obtained by performing artificial selection on a polygenic trait. We show that these methods work mainly when selection is strong and the traits are only mildly polygenic. Furthermore, we analyse sets of individuals of the tropical butterflies Heliconius and Ithomiini of different species and morphs, to test the power of these methods on known regions under selection and to infer new candidates of selection.

# Genomic insights into the transition from oviparity to viviparity: the case of the reproductively bimodal lizard Zootoca vivipara (51962)

**Luca Cornetti**, Alex Panziera, Andrea Benazzo, Mike W. Bruford, Cristiano Vernesi, Giorgio Bertorelle.

*Department of Biodiversity and Molecular Ecology, Research and Innovation Center, Fondazione Edmund M; Dipartimento di Scienze della Vita e Biotecnologie, University of Ferrara, Ferrara, Italy; Cardiff School of Biosciences, Cardiff University, Wales, UK.*

Squamate reptiles provide a unique model for gaining crucial information about the evolutionary transition from oviparity to viviparity in vertebrates. The lizard Zootoca vivipara is one of the few species with distinct reproductive modalities in different subspecies; in detail Z. v. carniolica (European Alps) and Z. v. louislantzi (Pyrenees) are egg-laying lizards, while Z. v. vivipara (Central Western Europe) is a live-bearing one, with carniolica and vivipara that overlap their distributional ranges in the Alps. This provides an interesting natural setting for studying the evolutionary consequences of the shift from oviparity to viviparity and investigating possible evidence of hybridization between individuals with different reproductive modes.

We used a genomic approach (RAD sequencing), for isolating and analysing about 85 thousand of SNPs that allowed to explore both neutral and adaptive variation. Population genomics analyses indicated that hybridization between egg-laying and live-bearing lizards is unlikely to happen and that oviparous and viviparous populations experienced different demographic dynamics. Additionally, mapping of coding sequences containing polymorphisms with high and significant differences in allele frequencies between oviparous and viviparous populations on Anolis carolinensis genome allowed to highlight genes related to physiological pathways involved in the mode of reproduction.
# Ecological genomics of Betula nana and Fraxinus excelsior in Europe (51961)

**James Borrell**, Elizabeth Sollars, Bernardo Clavijo, Laura Kelly, William Bodles, Steve Lee, Richard Nichols, Sarah Ayling, Richard Buggs.

*Queen Mary University of London; Qiagen, Aarhus; The Genome Analysis Centre, Norwich; Highland Birchwoods, Munlochy; Forest Research, Roslin.*

We present genome-wide polymorphism data for two tree species in Europe, analysed in an ecological and evolutionary contexts. Betula nana is common in boreal environments, and rare in the UK. We present RAD-seq and microsatellite data for 28 populations in the UK and 10 populations in Finland, showing contrasting patterns of genetic structure and allele distribution. Fraxinus excelsior is widespread in Europe and of ecological and economical importance, but threatened by ash dieback and the emerald ash borer. We present a reference genome sequence for F. excelsior and whole genome re-sequence data for 39 populations throughout Europe.

# Recombination hotspots and genomic patterns of horizontal gene transfer in bacteria (51960)

**Sarah Earle**, Martin Maiden, Derrick Crook, Daniel Wilson.

*University of Oxford.*

Bacteria reproduce clonally, but recombination is critical to accelerating adaptive response, both in the core and accessory genome. This research investigates signatures of core genome recombination using ClonalFrameML in the species Mycobacterium tuberculosis, Clostridium difficile, Escherichia coli, Klebsiella pneumoniae, Campylobacter jejuni, Campylobacter coli, and Neisseria meningitidis, which range from genetically monomorphic to highly transformable. One hundred whole genome sequences of each species were analysed, either from mapped or core-genome MLST data, taken to represent species-level diversity. Recombination was estimated both by using a model with a single set of recombination parameters estimated for all branches, and by estimating different parameters per branch. ClonalFrameML estimates the relative probabilities that a nucleotide is changed as the result of recombination relative to point mutation (r/m), which is a direct measure of the relative impact of recombination on evolutionary change, giving a general indication of homologous recombination rates which can be directly compared across the species. We examine the frequency, distribution and local genomic context of recombination in the core genome, discovering various hotspots and coldspots, and find that HGT of very large regions is common to many species, indicating that this is an important process in bacterial evolution.
Inference and misinference under models of Background Selection. (51952)

Gregory Ewing, **Jeffrey Jensen**.

EPFL.

Background selection (BGS), the process where unavoidable deleterious mutations are constantly removed from the population, is widely accepted to have a significant effect on patterns of genetic diversity and the efficiency of selection via linkage. Despite this, it is rarely taken into account in current studies due to the practical difficulties of doing so. This includes availability of adequate simulation software, their performance, tractability of current models and the difficulty of applying theory to real data.

We have developed an efficient coalescent based simulation method, that permits BGS models with arbitrary Distributions of Fitness Effects (DFE) in nonequilibrium populations, to address these issues. Due to the high performance Approximate Bayesian Computation for direct inference from suitable data is practical. We explore estimation of parameters under non trivial demographic models with and without BGS. We find that when BGS is present but not accounted for positively misleading inference are possible. Further we present results of directly inferring the DFE from data.

Poster session A - POL 300

Genomic signatures of adaptation in sticklebacks: convergent or not? (51950)

Philine Feulner.

Eawag.

After the last glaciation, marine three-spined sticklebacks colonized various newly available
freshwater habitats. Comparing populations across a salinity gradient, genome scans have
identified convergent genomic regions showing signatures of adaptation. However, when
comparing sticklebacks from distinct freshwater habitats such as lakes and rivers hardly any
convergent genomic regions have been identified. Here, I will argue that this not due to
different approaches, sampling strategies, or genomic data. Utilizing whole genome
resequencing data from 66 individuals from 11 populations, I will demonstrate that known
candidate regions for the adaptation to freshwater can be readily identified while the same
data and approach does not detect convergent adaptation between lake and river sticklebacks.
I will discuss potential reasons for these differences and provide further evidence utilizing
alternative approaches such as hierarchical models and exploration of polygenic signatures of
local adaptation.

Poster session A - POL 300

The genome of Gonium pectorale reveals early genetic co-option during the evolution of multicellularity (51924)
Erik Hanschen, Bradley Olson.

*University of Arizona; Kansas State University.*

The evolution of multicellularity is a major evolutionary transition which has occurred numerous times throughout all domains of life, yet the evolutionary history of the basis of this transition is unknown. The volvocine green algae, including Chlamydomonas and Gonium, and Volvox, are a common model for evolution of multicellularity. Previous genomics revealed few differences attributed to Volvox morphology and development. Using the undifferentiated multicellular Gonium pectorale, we investigated when the genetic changes associated with the evolution of multicellularity evolved. Expanded or modified pathways shared in Gonium and Volvox include a retinoblastoma cell cycle regulator, cyclinD cell cycle regulators, transcription factors, and predicted gene families. Cell differentiation transcription factors are not expanded, and we demonstrate these genes evolved shortly after the speciation of Gonium. These data suggest that genes important for multicellularity were co-opted early during the evolution of multicellularity. Using multiple lines of evidence, we find the genetic changes associated with multicellularity evolved early during the evolution of multicellularity, which is consistent with other multicellular evolutions, including plants and animals.

# Genomic signatures of contrasting adaptation in cork oak populations across the species' range (51917)

Octávio Paulo, Pina-Martins Francisco, Modesto Inês, Ribeiro Carla, Costa Joana, Miguel Célia, Batista Dora.

CE3C - Centre for Ecology, Evolution and Environmental Changes. Universidade Lisboa. Portugal; Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Portugal; RAIZ - Instituto de Investigação da Floresta e Papel. Herdade de Espirra, 2985-270 Pegões, Portugal; Instituto de Biologia Experimental (IBET), Oeiras, Portugal; Instituto de Investigação Científica Tropical, Oeiras, Portugal.

How natural populations adapt to contrasting environments and which genomics signatures can be detected associated with this process is one of the most challenging question in current evolutionary biology. These questions are particular complex for West-Mediterranean tree species showing both long distance gene flow and evolutionary and demographic histories influenced by Pleistocene glaciation or even older geological events.

Cork Oak populations were sampled and genotyped across the species' range and 21 environmental variables were used. Several types of genetic and genomic data (e.g.: MassArray and GBS) were used to gather a total of approximately 1300 SNPs. The results from traditional molecular markers and NGS based genome scans show the complexity of the evolutionary process and the interplay between structure, adaptation and gene flow.

Furthermore, genomic signatures of positive and balancing selection were unravelled and their potential role in local adaptation through associations with environmental variables was explored under several scenarios and methodologies.

These results reinforce previous work (Modesto et al. 2014) emphasising the role of selection
and gene flow, rather than history and drift as the main driving forces in shaping the pattern of genetic diversity and local adaptation in this species. The implications of contrasting adaptation in the species response to rapid climate change will be discussed.

# Cryptic species within a cardinalfish: evidence for ecological speciation in the coral reef (51900)

**Gabriele Gerlach**, Jelle Atema, Michael Raupach, Michael J. Kingsford.

Carl von Ossietzky University Oldenburg; Boston University; Senckenberg am Meer, German Center of Marine Biodiversity Research; Centre of Excellence for Coral Reef Studies and School of Marine, James Cook University.

Evolutionary theory requires understanding of mechanisms that drive microevolution and maintain population divergence. Isolation of marine populations caused by large-scale geographic barriers cannot alone explain the high speciation rates and biodiversity of coral reef fishes with their larval dispersal that would predict genetic homogeneity. We searched for other isolating mechanisms starting at small spatial scales that drive microevolution despite gene flow.

We show that incipient speciation can be observed on the spatial scale of meters to few kilometers. Genetic analysis of the cardinalfish Ostorhinchus doederleini over ten generations at the Capricorn-Bunker group in the Great Barrier Reef, Australia, revealed five overlapping, phenotypically indistinguishable clades that can be considered different species inhabiting two different ecological niches: coral reef lagoons and coral reef slopes. Sequence data of two mitochondrial gene fragments as well as microsatellite markers indicated almost complete genetic isolation; but hybrids exist.

Our data provide evidence that shortly after hatching larvae imprint on olfactory cues of their natal environment including their own population. Orientation behavior, divergent selection between ecological niches and population recognition contributes to natal recruitment and genetic divergence that can persist despite gene flow.

# Asymmetric gene flow between populations of the marine crab Liocarcinus depurator (51879)

**Francesc Mestres**, Víctor Ojeda, Pere Abelló, Marta Pascual, Teresa García.

Universitat de Barcelona; Universitat de Barcelona; Institut de Ciències del Mar. Barcelona; Universitat de Barcelona; Centro Oceanográfico de Málaga.

In marine species, oceanographic discontinuities may be permanent and asymmetric, allowing mostly unidirectional gene flow. Nonetheless, even so-called permanent fronts can fluctuate, allowing for changes in migrant direction. We analyzed spatial genetic differentiation in the
crab Liocarcinus depurator across the three main oceanographic discontinuities found along the western Mediterranean: Gibraltar Strait, Almeria-Oran Front and Ibiza Channel. A partial fragment of the cytochrome oxidase I gene was sequenced in more than 400 individuals collected in five localities during four different time periods, so that genetic changes could be estimated across space and time. The intensity of interannual differences varied among populations, probably due to local shifts in circulation patterns modifying the asymmetric flow. The discrepancies previously reported on the effect of oceanographic discontinuities over multiple species could result from time-space interactions on the distribution of genetic variation. The present study highlights the importance of temporal replicates to better understand the spatial genetic structure of marine species and implement better management strategies for their conservation.

# Dominance genetic variance for traits under directional selection in Drosophila serrata (51860)

Jacqueline Sztepanacz, Mark W. Blows.

*University of Queensland.*

In contrast to our growing understanding for patterns of additive genetic variance in single and multi-trait combinations, the relative contribution of non-additive genetic variance, particularly dominance variance, to multivariate phenotypes is largely unknown. While mechanisms for the evolution of dominance variance have been, and to some degree remain, subject to debate, the pervasiveness of dominance is widely recognized, and may play a key role in several evolutionary processes. Theoretical and empirical evidence suggests that the contribution of dominance variance to phenotypic variance may increase with the correlation between a trait and fitness; however, direct tests of this hypothesis are few. Using a multigenerational breeding design in an unmanipulated population of Drosophila serrata, we estimated additive and dominance covariance matrices for multivariate wing shape phenotypes, together with a comprehensive measure of fitness, to determine whether there is an association between directional selection and dominance variance. Fitness, a trait unequivocally under directional selection, had no detectable additive genetic variance, but significant dominance genetic variance. For single and multivariate morphological traits, however, no relationship was observed between trait-fitness correlations and dominance variance. These data suggest that for many fitness components a positive association between directional selection and dominance variance may not be expected.

# The genome-wide landscape of population genetic variation in brown rat (Rattus norvegicus) populations. (51839)

Martha Gavan, Alex Douglas, Andy Black, Darren Christie, Sally Poncet, Martin Collins, Stuart Piertney.
University of Aberdeen; University of Aberdeen; Government of South Georgia & South Sandwich Islands; Government of South Georgia & South Sandwich Islands; Government of South Georgia & South Sandwich Islands; University of Aberdeen.

Demographic perturbations such as founder effects can often create small, isolated populations that are at risk of becoming genetically depauperate due to the effects of random genetic drift. However, it has previously been demonstrated that even in small populations, selection can oppose drift to maintain variation at adaptive loci. Understanding the extent to which genetic diversity at immunologically important genes is affected by demographic perturbations is essential for the effective management of genetic resources in natural populations. Here we utilise next-generation sequencing techniques, specifically genotyping-by-sequencing (GBS), to identify genome-wide variation across ten isolated populations stemming from two separate founder events of brown rats (R. norvericus) at the island of South Georgia in the southern Atlantic. GBS target sequences are assembled and mapped to the rat reference genome using a low density linkage map. SNP calls and estimated allele frequencies are used to characterise the patterns of genetic structure across samples, and pinpoint the regions of the genome that are displaying significantly higher sequence diversity than predicted by the genomic background. These "diversity islands" will highlight the genomic regions that are acting in a non-neutral way, and comparison across populations provides insight into the extent to which parallel or convergent responses occur.

# Hidden giant viruses in the public databases. (51837)

Vikas Sharma, Philippe Colson, Pierre Pontarotti, Didier Raoult.

*Evolution Biologique et Modélisation.*

Nucleocytoplasmic large DNA viruses (NCLDVs), or proposed order Megavirales, belong to families of giant viruses that infect a broad range of eukaryotic hosts. Environmental metagenomic studies show that there is a “dark matter”, composed of sequences not linked to any known organism, as determined mainly using ribosomal DNA (rDNA) sequences, which therefore ignore giant viruses. Large scale phylogenetic analysis were performed, where we found few universally conserved genes were able to delineate Megavirales as separate clade which strongly suggest them as distinct biological entity compared to cellular organisms. Among these genes, DNA-dependent RNA polymerase (RNAP) is universally conserved in microbes and as well as in giant viruses. While phylogenetic reconstruction using RNAP gene, we found that three giant virus that have been mis annotated as as Hydra magnipapillata, Marine group II Euryarcheota and Phytophthora parasitica, additionally new viral clades have been detected from environmental database (Sharma et al., 2014)□. Our analysis suggest that RNAP as well as few other genes is a critical marker to detect hidden microbes and dark matter which may replace rDNA to delineate the four branches of life, Archaea, Bacteria, Eukarya and “Megavirales”.
# Variation in the strength and shape of natural selection across three centuries of human civilisation (51832)

**Erik Postma**, Dominique Waldvogel.

*University of Zurich.*

Although natural selection is ubiquitous in plant and non-human animals, the question how selection is acting in human populations remains controversial. Indeed, it has been argued that with the introduction of birth control and dramatic improvements in medical care, selection has become negligible, and human evolution has come to a halt. However, this idea appears to be at odds with reality, with recent studies showing substantial amounts of variation in fitness, and strong selection on a range of human traits. As of yet we know very little about the generality of these findings, as they are based on a few populations and relatively short time periods. Here we will present an analysis of a uniquely detailed, longitudinal and individual-based human dataset, covering a period of three centuries. We will show how the distribution of lifetime reproductive success and its relationship with reproductive timing and lifespan has changed during this period, and how these have been shaped by culture, demography and the environment. Thereby we will provide one of the most complete investigations of variation in selection in our own species, and a fascinating glimpse into life as we know it.

# Reference genome, population genetics and population genomics of wild falcons (51822)

**Xiangjiang Zhan**, Michael Bruford.

*Institute of Zoology, Chinese Academy of Sciences, China; School of Biosciences, Cardiff University, UK.*

Using the next generation sequencing technology, we have sequenced the genome of saker falcons (Zhan et al., 2013). The genome was about 1.2 Gb in length, from which we have annotated 16,204 genes. Falcon genomes were found to have consistent signatures of rapid evolution but less olfactory receptor genes. Compared with its relative species, peregrine falcons, the saker living in the arid environments seems to have evolved a robust gene repertoire to conserve more water and secret more sodium. Then, we used the candidate gene approach referencing the draft genome to study the population genetics of sakers across Eurasia, and we found that exonic SNPs were key to resolving genetic differentiation between the QTP and non-QTP sakers, and were able to infer five SNPs as being subject to directional selection (Zhan et al., 2015). Now we are at the stage of taking our research from candidate genes and the reference genome to a population genomics level.
## Comparative transcriptomics reveals the modular organisation of ant phenotypic traits (51818)

Claire Morandin, Morten Schiøtt, Liselotte Sundström, Jes Søe Pedersen, **Heikki Helanterä**, Alexander S. Mikheyev.

*Centre of Excellence in Biological Interactions, Helsinki University; Centre for Social Evolution, University of Copenhagen; Okinawa Institute of Science and Technology.*

Alternative phenotypes may be the results of genomic novelty or gene network interactions co-opted via natural selection. Reproductive division of labor in eusocial insects represents a major transition in evolution, and is a striking example of the same genetic background giving rise to alternative phenotypes, namely queen and worker castes. The extent to which caste-associated regulatory architecture is preserved across taxa remains unexplored. Applying weighted gene co-expression network analysis to transcriptomic data from 17 ant species, we show that most genes participate in conserved co-expression modules of functionally related transcripts. Furthermore, selection operating on these genes is heavily influenced by the co-expression network properties. Surprisingly, in addition to playing a role in caste differentiation, module expression levels were associated with other important traits, such as the evolution of worker sterility, caste dimorphism, polygyny and even invasiveness. These results provide insights into the complex structure of social insect transcriptional architecture, and identify functionally important units that serve as building blocks of phenotypic innovation. This study gives novel insights into the molecular interactions responsible for outstanding characteristics of eusocial insects, which would not be achieved by analyzing data from a single species.

## Estimating Selection of Skull Shape using Geometric Morphometrics (51796)

Elis Damasceno, Chris Klingenberg.

*University of Manchester.*

Natural selection is the evolutionary theory's centrepiece, and therefore it has drawn the interest of many researchers since its discovery. Although a very sought-after subject, selection gradients are not easily estimated, since it requires a measurement of fitness in addition to the quantitative data throughout several generations. Fitness and cross-generational data are even harder to obtain in wild populations, making such studies quite scarce in the literature. The Soay sheep of St. Kilda is one of the few wild populations in which such data is available, seeing that the population has been closely monitored since 1985. In this study, I used geometric morphometrics to estimate selection on skull shape. I digitized 1,527 Soay sheep skulls, that are stored at the National Museum of Scotland in Edinburgh. Using geometric morphometrics to estimate selection is particularly useful since not only do we get the strength of selection, but we can also visualize exactly how each trait is being selected. Given that skulls are very complex, multi-dimensional structures, it gives an enormous advantage when compared to traditional measurements.
# The evolution of genomes and fitness traits in response to environmental change in the emerging model system Daphnia (51784)

**Luisa Orsini**, Anurag Chaturvedi, Craig Jackson, Nathan Keight, Omid Shams Solari, James Brown, Michael Pfrender, Kelley Thomas, Luc De Meester.

University of Birmingham, UK; University of Leuven, Belgium; Indiana University of Bloomington, USA; University of California Berkeley, USA; Notre Dame University, IN, USA; University of New Hampshire, USA.

Understanding evolutionary adaptive responses of natural populations to environmental stress is challenging, owing in part to the complexity of natural environments. The waterflea Daphnia magna is a keystone species in aquatic ecosystems, a sentinel for water quality, and a model organism for eco-evolutionary genomics. It also creates dormant populations that accumulate in layered sediments of lakes and ponds – which can be resuscitated centuries later – thereby showing clear adaptive responses to environmental changes. Capitalizing on this unique ecological system, we present a complete analysis of genome structural variation and evolution of fitness traits in response to a suite of environmental stressors (parasites, land use, and fish predation) across a complex landscape of shallow ponds. We further validate these findings in time in populations resurrected from sediment cores with known histories for the same stressors. In our analysis of structural variation we link candidate gene networks and CNV genes to fitness traits using statistical tools optimized by the ENCODE consortium, unraveling the genetics of complex traits. We identify the mechanisms of evolution underlying responses to both natural and anthropogenic stressors and assess repeatability of evolutionary adaptive processes in nature.

# Rapid morphological evolution related to male-male combat of invasive green anole in Ogasawara Islands, Japan. (51769)

**Wataru Anzai**, Hiroo Takahashi, Mitsuhiko Toda, Hideki Endo.

*The University of Tokyo; Japan Wildlife Research Center.*

Introduced species have been noted to be model organisms which can be observed rapid evolution. We report that two populations of invasive green anole lizard (Anolis carolinensis) in Chichi-Jima Island and Haha-Jima Island show different morphological traits although it has been only thirty years since invasion of these lizards. By comparison of body size and head size between two populations of islands and sexes, males of Haha-Jima populations showed significant larger body and head considered to be advantageous for territorial combat though females indicated no significant differences between islands. Because of diverse results between sexes, it is considered that these traits are affected by not only ecological factors common to sexes such as pray animals or vegetation but also male-specific factors
such as territorial combat between individuals. Addition, as a result of the comparison of mass
of limb muscles between populations, heavier humeral adductor muscles of lizards in Chichi-
Jima than in Haha-Jima were shown only in males. Our results demonstrate that green anole
have occurred morphological differences between island populations for only fifty years, and
suggest the differences have evolved through sexual selection such as male-male combat.

Investigation of selection patterns across the New Zealand Giant Weta
genome, using comparative transcriptomics (51766)

Victoria Twort, Richard Newcomb, Howard Ross, Thomas Buckley.

*Landcare Research; The Univerisy of Auckland; Allan Wilson Centre; The New Zealand*
*Institute of Plant and Food Research Ltd.*

Giant Weta are among the largest extant insects on earth, and are an iconic part of the New Zealand biota. However, a number of these species are endangered. The Poor Knight Giant Weta (Deinacrida fallai, Orthoptera) is one such species, and is restricted to a small offshore island. Our aim is to construct a comparative genomic dataset that will be used to investigate various aspects of molecular evolution and evolutionary relationships of this endemic New Zealand insect. The D. fallai genome is larger (approximately 8.5 GB) than the only other published Orthoperan genome (Locusta migratoria), with the current draft assembly being generated with SOAPdenovo2. Transcriptome data has been obtained to identify unigenes involved in reproduction, glycolysis and sensory processes in order to study rates and patterns of molecular evolution among species. RNA-seq data has also been generated for a number of Tree and other Giant Weta species, resulting in an average of 190,943 contigs per species, and an average N50 of 875 bp. This current dataset is being combined with Genotyping-By-Sequencing data to investigate various conservation genetics issues, in order to better inform current and future conservation efforts.

Evaluation of adaptive potential of the European eel population suggests a
recovery of its genetic status (51762)

Miguel Baltazar-Soares, Seraina E. Bracamonte, Till Bayer, Frédéric J.J. Chain, Reinhold Hanel, Chris Harrod, Christophe Eizaguirre.

Helmholtz Center for Ocean Research (GEOMAR); Department of Biology, McGill
University, Canada; Thunen-Institute of Fisheries Ecology, Germany; Universidad de
Antofagasta, Chile; School of Biological and Chemical Sciences, Queen Mary University of
London, UK.

The integration of evolutionary theory in conservation programs provides a framework that
has greatly improved our ability to protect endangered species. However, it is only seldom
applied to the management of marine living resources. One of the most staggering examples is that of the European eel, the only critically endangered species in the World whose exploitation is still legal. The recruitment of this species has suffered a sudden collapse in the begging of the 1980s. By 2011, it remained as low as 1% of the values preceding the 1980s period. Surprisingly, conservation measures are limited to the translocation of juveniles and implementation of fishing quotas. Here we present the first study assessing the evolutionary potential of the European eel. We compared the neutral genetic diversity - microsatellites and mtDNA - and the adaptive genetic diversity - the Major Histocompatibility Complex (MHC) – of two distinct generations of eels. The evolution of MHC genes is particularly relevant as the European eel faces a parasitic threat by a recently introduced nematode. Our results show that both the recruitment collapse and the parasite introduction have left signatures of a genetic bottleneck event. However, results also suggested an ongoing recovery positively affecting estimates of genetic diversity - critical for the adaptive potential of the species

Catch me if you can: Adaptation from standing genetic variation to a moving phenotypic optimum (51748)

Sebastian Matuszewski, Joachim Hermisson, Michael Kopp.

University of Vienna; Max F. Perutz Laboratories; Aix Marseille Université.

Natural populations are constantly faced with environmental changes that force them to either adapt or go extinct. Therefore, increasing our understanding of the adaptive process is important for both basic and applied research. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Out of these, two complementary modeling approaches have emerged: While so-called adaptive-walk models consider adaptation from the successive fixation of de-novo mutations only, quantitative genetic models, on the other hand, assume that adaptation proceeds exclusively from pre-existing standing genetic variation. The latter approach, however, has focused on short-term evolution of population means and variances rather than on the statistical properties of adaptive substitutions. Thus, I will here address what has been described as "the most obvious theoretical limitation when describing the adaptive process," and propose an analytical framework for the genetic basis of adaptation from standing genetic variation in terms of the effect-size distribution of individual alleles. This approach addresses one of the central questions in this context: From the multitude of standing genetic variants segregating in a population, which are the ones that ultimately become fixed and contribute to adaptation, and how does their distribution differ from that of de-novo mutations?

Why no stabilizing selection (in damselflies)? (51742)

John Waller.