Spain and the UK. Using capture sequencing, we re-sequenced candidate outlier and control loci in snails from two locations per country. We predicted that, if observed patterns of outlier sharing are genuine, sharing should increase on smaller geographical scales, where genetic variation is more similar and gene flow is higher. If they are caused by spurious outliers, sharing should be low even among geographically close populations, and outliers should often not be confirmable.

We found that the majority of outliers could be confirmed, and outlier sharing increased markedly among geographically close populations. Therefore, low sharing between countries is not solely due to technical reasons but can be explained by separate evolutionary histories and / or less gene flow among geographically distant instances of divergence.

# Drosophila wing shape Integration: A multi-level approach. (52027)

Hugo Benitez, Chris Klingenberg.

*University of Manchester.*

Different levels of biological variation are generated from distinct sources: genetic, developmental and evolutionary variation. These levels of variation interact in morphology, being for instance observed in how correlated or independent are different traits with respect to each other. The following study applies morphometric methods in order to address questions about Drosophila wing shape at three levels of integration: static, developmental and evolutionary. Static integration refers to the level variation among individuals, where all specimens are at the same ontogenetic stage and belong to the same species; developmental integration is produced from the interactions between developmental processes that generate different features, and evolutionary integration is simply the covariation among evolutionary changes considering the phylogenetic structure of the data. We develop this approach in an analysis of wing evolution in 58 species across the genus Drosophila. The present results show that all the 58 Drosophila species exhibit morphological integration. Wing shape showed a noticeable developmental integration both as an overall structure and between developmental compartments. In addition, a clear evolutionary integration of wing shape was found. It is possible to conclude that wing shape shows strong internal covariation, and that the integration process has evolved in the genus.

# The evolution of cuticular hydrocarbon profiles in ants (52700)

Thomas Schmitt, Bonnie Blaimer, Florian Menzel.

*University of Würzburg; Smithonian Institution; University of Mainz.*

Insect cuticles are covered with hydrocarbons (CHC), which serve two main functions: desiccation barrier and information transfer. The CHC profiles of ants carry information on
their species identity, colony, caste, sex, etc. Intraspecific variation is usually restricted to
quantitative changes in hydrocarbon composition, whereas interspecific variation is
characterized by qualitative alterations i.e. variation in substance identities and substance
classes. To date, little is known about the evolutionary causes of interspecific CHC variation.
Moreover, we do not understand the role of phylogenetic or physiological constraints on CHC
evolution. Here, we analysed the CHC profiles of 37 Camponotus and 39 Crematogaster
species from around the world. CHC profiles did not appear to experience strong phylogenetic
constraints. Even sister species could exhibit completely different profiles. However, we
identified several physiological constraints which might be caused by the need to maintain a
semiliquid texture of the epicuticular layer. Climate strongly influenced substance class
composition. We explain this by variance in waterproofing requirements. Interestingly, the
length of the hydrocarbon chains was not affected by climate, but was extended among ants in
interspecific mutualistic associations. We conclude that CHC profiles can evolve quickly, but
experience constraints posed by climatic conditions, interspecific interactions, and their
physico-chemical properties.

Queen signalling in the honeybee (52838)

Thomas Richardson.

University of Lausanne.

In complex animal societies in which there is a reproductive division of labour, the reproductively-active individuals sometimes produce signals that advertise their fertility. In the eusocial insects, mated and reproducing queens produce queen pheromones, which can act to inhibit selfish worker reproduction, and suppress worker rearing of virgin queens.

Although the debate concerning the ultimate explanations for the evolution of queen pheromones – and in particular, whether they should be classed as honest or manipulative signals – has yet to produce a clear consensus, both hypotheses predict that mechanisms that govern the dissemination of the queen signal should preferentially target (i) older workers with functioning ovaries, as these workers have the potential to selfishly lay unfertilized eggs, and (ii) young nurse workers, as it is these workers that control the rearing of virgin queens.

Using a system for simultaneously and automatically tracking the movements of thousands of honeybees, we characterise the ages of the workers targeted by three different pathways for queen pheromone dissemination, (i) direct transmission from queen to workers via physical contacts, (ii) indirect transmission via so-called 'messenger' bees, and (iii) indirect transmission via the wax.

Transcriptomic underpinning of lifespan differentiation between castes in
ants. (52081)
**Eric Lucas**, Oksana Riba-Grognuz, Miguel Corona, Yannick Wurm, Laurent Keller.

*University of Lausanne; USDA; Queen Mary University of London.*

Senescence presents an evolutionary puzzle: why have organisms not evolved to avoid the age-linked degeneration which occurs in most species? The disposable soma theory argues that senescence is governed by a trade-off between longevity and other life-history traits. Ants provide an excellent model for studying the evolution of senescence as they are typically characterised by extreme variation in lifespan between castes, with queens living as much as 15 times longer than workers despite being genetically identical. Furthermore, ant queens are amongst the longest-living insects, with Lasius niger queens living up to 29 years. Using tissue-specific high-throughput RNA sequencing of age-controlled individuals, we tested whether queens and workers of L. niger differ in their expression of genes involved in somatic maintenance. We found that queens over-express these genes relative to workers, but in an age-dependent manner. The difference in lifespan between castes therefore seems to stem from differential investment into maintenance at specific life stages.

Session 1 WED GEN B 35

**Adaptive landscapes of transcription factor binding sites (52693)**

**José Aguilar-Rodríguez**, Joshua L. Payne, Andreas Wagner.

*University of Zurich, Inst. of Evolutionary Biology and Environmental Studies, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; The Santa Fe Institute, Santa Fe, New Mexico, USA.*

The adaptive landscape is a central concept in evolutionary theory. Recent advances in high-throughput technologies have provided us with a first glimpse at the structure and navigability of a few incomplete empirical landscapes. Here, we have studied more than one thousand complete and empirical adaptive landscapes. Each landscape describes the binding specificity of a transcription factor to all possible short DNA sequences. The architecture of such landscapes has important implications for evolution, as a transcription factor's specificity for its cognate binding site determines its influence on gene expression. We find that the adaptive landscapes of transcription factor binding specificities are far less rugged than randomized landscapes and only slightly more than additive landscapes. They contain few peaks that are accessible from throughout the landscape. These peaks do not usually comprise single sites but broad plateaus that can contain dozens to hundreds of sites, indicating the robustness of highly specific binding to mutations. The binding sites found in more accessible peaks are enriched in protein-bound regions of the mouse genome. Our findings suggest that the navigability of transcription factor binding landscapes and the robustness of their peaks may have contributed to the enormous success of transcriptional regulation as a means to achieve novel phenotypes.
# Why shuffle genes? The dynamics of integron evolution in changing environments (52620)

**Jan Engelstädter**, Klaus Harms, Pål Jarle Johnsen.

*University of Queensland; University of Tromsø; University of Copenhagen.*

Integrons are widespread genetic elements in bacteria that function as gene capture and reshuffling devices. They consist of an array of gene cassettes (often encoding antibiotic resistance determinants), and a gene encoding an integrase that can excise and re-insert gene cassettes. In spite of their importance in clinical contexts, little is known about the evolutionary origin and maintenance of integrons.

Here, we present a mathematical model in which bacteria with and without a functional integrase compete with each other. The population is subject to a number of stressors that arise stochastically and to which the different gene cassettes provide resistance. In bacteria carrying a functional integrase, the order of the gene cassettes within the integron is reshuffled, which in turn affects their gene expression patterns.

Our model predicts that for a wide range of realistic parameters, a functional integrase can prevail in the population in spite of substantial fitness costs. Similarly to mutator genes, this advantage comes about through increasing genetic diversity within the population and is strongest when environmental conditions change at intermediate rates. We also show that under some conditions a functional integrase can prevent population extinction and explore how new integrons can emerge through horizontal gene transfer.

Session 1 THU GEN C 4

# Comparing within and between-sex pleiotropy as constraints on the evolution of male and female gene expression (53323)

**Stephen Chenoweth.**

*The University of Queensland.*

Sex-specific selection is widely thought responsible for shaping multiple genomic patterns of sexually dimorphic gene expression. It is well recognised that simultaneous adaptation in males and females can be curtailed whenever alleles controlling regulatory variation have sexually-antagonistic pleiotropic effects. However, pleiotropy between the sexes is but one form pleiotropic constraint, and it may be the case that other forms, such as pleiotropy between genes co-regulated within each sex, contribute greater constraining effects on the evolution of male and female gene expression. In an attempt to address this, I will integrate results across our recent quantitative genetic studies of sex-specific fitness and gene expression, within and among natural populations of the fly, Drosophila serrata.

Session 1 THU GEN C 4
# Sexually antagonistic epigenetic marks (53333)

**William Rice.**

The sexes share the same autosomal genomes yet sexual dimorphism is common due to sex-
specific gene expression. When present, XX and XY karyotypes trigger alternate regulatory
cascades that determine sex-specific gene expression profiles. In mammals, secretion of
testosterone (T) by the testes is the master switch influencing the gene expression pathway
(male vs. female) that will be followed, but many genes have sex-specific expression prior to
T secretion. Environmental factors, like antiandrogens, can disrupt sexual development.
However, sex-specific ontogeny can be canalized by the production of epigenetic marks (epi-
marks) produced during early ontogeny that increase sensitivity of XY embryos to T and
decrease sensitivity of XX embryos. Here I will integrate and synthesize the evidence
indicating that canalizing epi-marks are produced during early ontogeny. I will also describe
the evidence that such epi-marks sometimes carry over across generations and produce
mosaicism in which some traits are discordant with the gonad. Such carry-over epi-marks are
sexually antagonistic because they benefit the individual in which they were formed (via
canalization) but harm opposite-sex offspring when they fail to erase across generations and
produce gonad-trait discordances.

Session 1 THU GEN C 4

# Resource competition and the evolution of sexual dimorphism (51570)

**Stephen De Lisle, Locke Rowe.**

*University of Toronto; University of Toronto.*

Theory suggests the evolution of sexual dimorphism in ecologically relevant traits can evolve
purely through competition between the sexes for a shared resource. Although more
parsimonious hypotheses exist for the evolution of ecological sexual dimorphisms, there are
some underappreciated reasons to expect that resource competition may often play some role
in the evolution of sexual dimorphism. Here, we outline a set of minimal criteria for
empirically demonstrating a role for resource competition in the evolution of dimorphism.
Using a series of experiments, we compare the geometry of fitness surfaces across density and
sex frequency manipulations in a pond-breeding salamander (Notophthalmus viridescens).
We find consistent disruptive selection on multivariate sexual dimorphism in feeding
morphology, that increases in strength with density. Fitness and the strength of divergent
selection are negative-frequency dependent in the manner expected under competition-driven
divergence between the sexes. Taken together, our results constitute evidence of resource
competition between the sexes as a contributor to sexually antagonist selection and the
evolution of sexual dimorphism. We suggest that resource competition may often contribute
to sexual divergence jointly with selection stemming from anisogamy, especially when
ecological opportunity is sex-specific
# Sexual selection drives short- and long-term evolution of the avian Z chromosome (51711)

**Alison Wright**, Peter Harrison, Fabian Zimmer, Stephen Montgomery, Marie Pointer, Judith Mank.

*University College London; University of Oxford.*

Comparisons between sex chromosomes and autosomes are important for understanding the magnitude of sexual conflict acting throughout the genome. We investigated the role of sexual selection in shaping gene expression and coding evolution of the Z chromosome in the Galloanserae, a clade of birds with the full range of sexual selection. Our results reveal that over long-term evolutionary history, the Z chromosome has been convergently and successively masculinized (Wright et al. 2012 Genetics), consistent with theoretical predictions that Z-linked genes should be more often selected for male-benefit alleles due to their unequal inheritance pattern. We next examined the role of mating system in driving masculinization of the Z chromosome over shorter evolutionary timespans, using phylogenetically controlled comparisons among species with high and low levels of sexual selection. Our results, combining coding sequence, polymorphism and gene expression with phenotypic measures of sexual selection, indicate that variance in male reproductive success in promiscuous species reduces the effective population size of the Z chromosome (Wright et al. in review), leading to relaxed purifying selection acting on the coding content. This in turn limits the adaptive role of the Z chromosome in general, and in particular its potential role in encoding sexually selected traits.

# Insights on Sexually Antagonistic Selection in the Human Genome (51817)

Elise Lucotte, Romain Laurent, Evelyne Heyer, Laure Ségurel, **Bruno Toupance**.

*Muséum national d'Histoire Naturelle; Max Planck Institute for Evolutionary Anthropology.*

Sexually antagonistic selection can occur when, within a species, the two sexes have different fitness optima for a trait. If a trait under sexually antagonistic selection is encoded by the same set of genes in the two sexes, an Intralocus Sexual Conflict (IASC) can arise, leading to the evolution of sexual dimorphism. A classical theoretical model predicts that the X chromosome should be a hotspot for the accumulation of loci under IASC, as compared to the autosomes. Although numerous studies have been conducted to test this hypothesis, they provided conflicting results and, so far, no study attempted to map loci under IASC at the genome-wide level in natural populations. Here, we designed a methodological framework to detect loci under IASC using genomic data. Applying this method on a human genome-wide SNP dataset (HapMap, 11 worldwide populations), we show that SNPs exhibiting signatures of ongoing IASC are preferentially located on the X chromosome as compared to autosomes. Moreover, they are enriched in genes involved in the determination of traits known to be sexually dimorphic in humans, including external appearance, metabolism and immune system, supporting an implication of sexually antagonistic selection in the evolution of sexual dimorphism.
# Genetic architecture of aggression and cooperation in the California harvester ant Pogonomyrmex californicus (52324)

**Juergen Gadau**, Jennifer Fewell, Alexander Mikheyev.

*Arizona State University; Okinawa Institute of Science and Technology.*

Aggression is an adaptive behavior that is shown in many different contexts in solitary and social organisms. The regulation of aggression, when, where and how much aggressive behavior is shown, is however an important component that determines whether aggression is adaptive or non-adaptive. Abnormal/non-adaptive aggression in humans is often associated with psychological disorders that are based on an underlying genetic predisposition that can be elicited by a diverse array of environmental factors. Newly mated queens of P.californicus found nests either alone (haplometrosis) or in groups of unrelated yet cooperative individuals. This population differences have a strong genetic basis that manifests itself in significant differences in aggression and conflict escalation during colony founding when queens of the haplometrotic population are paired artificially with queens of their own or the pleometrotic population. We studied the genetic and regulatory mechanisms of aggression and, by corollary, cooperation by comparing the differences in brain gene expression profiles of aggressive and non-aggressive P. californicus foundresses. This allowed shed further light on the evolution of both social phenotypes in P. californicus, and the genetic and regulatory basis of aggression and cooperation.

# Convergent molecular signatures of plastic phenotypes in eusocial evolution (53354)

**Seirian Sumner.**

*School of Biological Sciences, Bristol Life Sciences Building, University of Bristol.*

Convergent phenotypes are apparent across the tree of life, despite contrasting evolutionary histories, ecologies and selection pressures. To what extent does convergence at the phenotypic level reflect convergence at the molecular level? To address this we sequenced and compared the genomes and 23 brain transcriptomes of two eusocial insect species with simple societies, the paper wasp Polistes canadensis and the dinosaur ant Dinoponera quadriceps. Both exhibit simple, behavioural castes with comparable highly plastic phenotypes, but the wasp evolved from a solitary ancestor, representing basal eusociality, whereas the ant evolved via a secondary reversion from a complex eusocial ancestor. We found evidence of shared molecular traits associated with phenotypes that are likely to be hallmarks of simple eusocial castes, irrespective of evolutionary history, and putative molecular signatures of plastic phenotypes. These included little molecular differentiation between castes at the gene, network, regulatory or functional level; molecular specialization
in queens but not workers; a role for both conserved and taxon-restricted genes in phenotypic
differentiation. We also found molecular traits specific to the wasp that are putative signatures
of basal eusocial evolution and included absence of worker-biased transcription, reflecting the
generalist behavioural strategies of subordinate social animals. Ant-specific traits we found
that are likely to be remnants of inherited complex eusociality included equal transcriptional
investment in castes, increased molecular differentiation and role for taxon-specific genes.
Identifying the contrasting, as well as conserved molecular processes that underlie convergent
phenotypes has the potential to unlock the pathways by which evolution repeatedly solves
recurring problems.

Bold individuals live in risky environments: nature, nurture or both? (51807)

Benedikt Holtmann, Shinichi Nakagawa.

University of Otago.

A new hypothesis states that animals choose their habitats according to their personality (phenotypic habitat-selection hypothesis). If sensitivity to predation risk (e.g. shy or bold) exists and if the environment is heterogeneous, this hypothesis predicts that variation in personality would be maintained. Yet, a traditional view is that animals become adjusted to their chosen habitat after settling (habituation hypothesis). This hypothesis predicts that individuals change their levels of responsiveness to predators over time. Here, we test these contrasting hypotheses using a population of dunnocks (Prunella modularis) in a public park where human disturbance risk is heterogeneous over space but constant over time. We found that boldness (i.e., flight-initiation distance) was highly repeatable. Bold birds were found in most disturbed areas while shy birds were found in least disturbed areas. In contrast vigilance was more plastic and birds became less vigilant over time. Although these findings support both hypotheses, clearly, personality plays an important role in habitat selection. We also detected a strong behavioural syndrome between boldness and vigilance, highlighting the importance of examining traits with different degrees of flexibility together. In addition, we investigated associations between boldness and the two candidate genes: DRD4 and SERT (dopamine and serotonin receptor genes).

Direct and indirect genetic effects shape the social phenotype of great tits
(52114)

Reinder Radersma, Joshua A. Firth, Colin J. Garroway, Bernhard Voelkl, Ben C. Sheldon.

*Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford,*
*UK; Département de Sciences Biologiques, Université de Montréal, Canada.*
Many animals regularly engage in interactions with conspecifics. Because those interactions
can have fitness consequences, there is scope for selection on social traits. For selection to
operate traits need to have a heritable component; however, we know little about the genetic
basis of social traits. Here we estimate heritability of social traits derived from six large social
networks of foraging great tits (Parus major) from one pedigreed population in six winters.
Networks consisted of 753-1,166 individuals engaging in 12,740-132,143 flocking events
each winter. We derived three social traits from association indices: gregariousness,
unevenness of relationships and clustering. Because individuals affect each other's social
phenotypes, the heritability of social behaviour is potentially overestimated. To account for
this we introduced indirect genetic and environmental effects in the models. We found within-
individual repeatabilities of 34-46% when we did not account for indirect effects and 27-35%
when accounting for indirect effects. Heritabilities were 13-17% without indirect effects and
12-14% with indirect effects. We show that indirect genetic and environmental effects can
shape the social phenotype. As social selection may act faster and more efficiently than other
forms of selection, this study opens up a new perspective on the evolution of social behaviour.

Session 1 THU MAX 410 24

Baffling: an alternative signalling strategy using self-made tools (52122)

Rittik Deb, Rohini Balakrishnan.

Centre for Ecological Sciences, Indian Institute of Science.

In order to reduce the costs of finding mates animals often use different modes of
communication. From the sexual selection perspective, the general trend has been that males
advertise (signal) and females respond. These signals are also used by males for intra-sexual
competition and by females to choose between males. One of the consequences of inter-male
competition and female choosiness has been the evolution of alternative strategies. Often
these are simple behavioral modifications but occasionally involve extraordinary tools and
complex behavioral patterns. In our study species, a tiny tree cricket, Oecanthus henryi, it was
found that though the dominant strategy was to call from leaf edge to attract females, some
males have evolved an alternative signalling strategy. This strategy encompassed making and
use of a complex tool (a precise acoustic baffle) that enhanced their communication
efficiency. Field observations and controlled experiments revealed that though all males could
make baffles, very few males implemented this strategy in the wild. Following this we
examined who were the males that were adopting this strategy and what were their advantages
(proximate and ultimate). Further ecologically relevant experiments and simulations were
conducted to understand the ecological context and evolution of such an alternative
behavioral strategy.

Session 1 THU MAX 410 24

The influence of age and gene expression on division of labor in a social insect
(52144)
**Philip Kohlmeier**, Foitzik Susanne, Feldmeyer Barbara.

*Johannes Gutenberg University Mainz.*

In complex societies of eusocial insects, workers specialize in certain tasks. Whether an individual acts as a forager or a nurse depends on the colony's needs and is modulated by individual variation in task thresholds. These are influenced by the expression of behavioral genes, which in turn are affected by age, physiology, and environmental factors, among others. For example, old honeybee workers are more likely to forage than younger individuals showing lower titers of vitellogenin but higher expression of octapamine. However, how these factors interact, influence behavioral gene expression, and finally determine behavior, is poorly understood. To disentangle them, we manipulated colony composition in the ant Temnothorax longispinosus to control for worker age and task requirements. Behavioral observations revealed that young workers focus on inside tasks, whereas older individuals take over foraging. However, in manipulated colonies, old workers responded to the young worker removal by increasing their brood care activity, whereas in the reverse case young workers failed to switch to foraging. Whole transcriptomes of designated brood carers and foragers of both ages were then analyzed using RNA-Seq. We here report on the results of behavioral observations and on the genes and functional categories associated with behavioral caste and age.

# How likely is rapid adaptation? Lessons from eco-evolutionary population modelling (53338)

**Katja Schiffers.**

*Biodiversity and Climate Research Centre (BiK-F).*

Recent evidence for rapid adaptive changes in populations exposed to environmental change suggests that projections of species range dynamics based on the premise of ecological niche conservatism may be overly pessimistic. However, eco-evolutionary theory has shown that there exist a number of genetic and demographic constraints that may hamper rapid adaptation and evolutionary rescue. To evaluate the importance of adaptive processes for species' range dynamics, we need to better understand the coupling between ecological and evolutionary processes.

In this talk, I will present two studies based on stochastic simulations of joint allelic and demographic dynamics of spatially-structured populations that examine the prerequisites for evolutionary adaptation. The first study evaluates the equivocal effects of dispersal in heterogeneous habitats on a population's evolutionary potential under changing climate. The second one explores how landscape structure and genetic architecture jointly drive rates of niche evolution. Results of both studies demonstrate the high sensitivity of adaptive processes to genetic, demographic and environmental factors and show that a multitude of prerequisites have to concur to allow populations to rapidly adapt to new environmental conditions.
# Mapping life-cycle phenology of plant genotypes in space and time (53572)

**Liana Burghardt**, C. Jessica E. Metcalf, Amity M. Wilczek, Daniel E. Runcie, Johanna Schmitt, Kathleen Donohue.

*Duke University.*

Predicting how the environment affects the expression of genetic variation remains a perennial challenge to evolutionary ecologists. We have developed a model that predicts environment-dependent timing of plant life-stage transitions and life-cycle expression. Life-cycle expression strongly influences fitness because it determines the environmental conditions to which each differentially tolerant life stage will be exposed. This model, parameterized for A. thaliana, generates predictions of whole life-cycle phenology of different genotypes in complex environments. First, we simulate life cycles in four locations and compared multiple “genotypes” by varying two parameters associated with natural genetic variation in phenology: seed dormancy and floral repression. The model predicts variation in life cycles across locations that qualitatively matched observed natural phenology and suggests that dormancy variation across the range is necessary to maintain an annual life cycle. We also use this framework to predict the reproductive environment A. thaliana is exposed to across the range. Reproductive environments are important because they influence dormancy levels and reproductive rates. We show that a genetic cline in dormancy reduces the breadth of reproductive environments experienced and may contribute to local adaptation in this species. Lastly, we use this framework to explore how changes in temperature and moisture across the European range due to temporal climate change will influence life-cycle expression of these same genotypes.

# The accumulation of mutation load and range dynamics. (51883)

**Roslyn Henry**, Aurélie Coulon, Kamil Bartoń, Justin Travis.

*The University of Aberdeen; Centre d'Ecologie et des Sciences de la Conservation, Paris; Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier.*

Periods of climate change can alter the nature of biological processes within species' ranges, thus the eco-evolutionary dynamics of range formation and expansion are important for understanding and predicting species distributions. Here, we focus on a process that has thus far been overlooked in both contexts; the accumulation of mutation load. For range formation we show that the accumulation of deleterious mutations severely reduces the extent of a range across an environmental gradient, especially when dispersal is limited, growth rate is low and mutations are of intermediate deleterious effect. For range expansion, we demonstrate that the accumulation of mutation load can substantially slow the rate of range expansion however the evolution of dispersal mediates this effect to some extent. Our results illustrate the important role deleterious mutations can play in range dynamics and as such we highlight the incorporation of mutation load as a necessary focus for further work, noting particularly the
potentially opposing effects that mutation load and migration load may have for species'
range dynamics.

Local adaptation versus inbreeding depression in marginal populations of a
Mediterranean alpine plant: are they worthy of conservation in a context of
climate change? (52284)

Javier Morente-López, Alfredo García-Fernández, Carlos Lara-Romero, Maria Luisa Rubio-Teso, Raquel Ruiz, Ainhoa Sánchez, **José María Iriondo**.

Universidad Rey Juan Carlos.

Silene cililata is a chamaephytic cushion plant that grows in alpine cryophylic pastures of the Mediterranean mountains. In the Sistema Central of the Iberian Peninsula, populations occur along an altitudinal gradient from 1900 to 2500 m. Populations that grow at the lower elevations are marginal from the standpoint of the ecological range of the species. However, the higher temperature and lower precipitation regimes that take place in these sites are likely to expand to the rest of the distribution area of the species as a consequence of global warming. In this context, we were interested in contributing to the debate on whether marginal populations are able to locally adapt to the existing limiting environmental conditions or, on the contrary, are genetically impoverished and maladapted. We have implemented an experimental design that involved artificial cross-pollination of mother plants from various marginal populations using pollen from the same population, other marginal populations and central populations. The performance of the resulting seeds was assessed in situ at experimental sowing plots located nearby the marginal populations. This experiment has been complemented with common garden studies implemented in an ex-situ experimental facility to ascertain genetic differences in vegetative, phenological and reproductive traits of the species.

Forecasting the demographic and evolutionary response of perennial Alpine
plants (52404)

Olivier Cotto, Wilfried Thuiller, Frédéric Guillaume.

UNC Chapel Hill; Université de Grenoble 1, CNRS; University of Zurich.

Predicting how climate change will affect species distributions is a major challenge for biologists. Most previous attempts to answer this challenge used projections of the current ecological niche to assess future species distributions. Species niche can change over time due to evolutionary processes and species demography can be deeply affected by selective pressures resulting from climate changes. We used genetically explicit individual based simulations with overlapping generations to investigate the roles of evolution and species
demography for predicting future species distributions. We modeled the life histories and current distributions of four endemic Alpine perennial plant species. We used the latest regional climatic simulations to model the environment up to 2090. We assumed that selection and intraspecific competition occur at the seedling stage. We found that the extinction rate of these species would not change over time. However, the size of local populations would drop accompanied by modifications in age-structure. Old maladapted adults persist and block the recruitment of adapted juveniles. We further found that stopping climate change allow an immediate increase in local population sizes with no extinction debt. Overall we show that, for long-lived species, climate warming would deteriorate the state of local populations without change in extinction rate, possibly until a massive and sudden extinction event.

# Are plastic changes in tree phenology adaptive in the context of climate change? Insights from a mechanistic model. (52492)

Ophélie Ronce, Anne Duputié, Alexis Rutschmann, Isabelle Chuine.

ISEM CNRS.

Concerns are rising about the capacity of species to adapt quickly enough to climate change. In long-lived organisms such as trees, genetic adaptation is slow, and how much phenotypic plasticity can help them cope with climate change remains largely unknown. Here, we assess whether, where and when phenological plasticity is and will be adaptive in three major European tree species. We use a process-based species distribution model, parameterized with extensive ecological data, and manipulate plasticity to suppress phenological variations due to interannual, geographical and trend climate variability, under current and projected climatic conditions. We show that phenological plasticity is not always adaptive and mostly affects fitness at the margins of the species' distribution and climatic niche. Under current climatic conditions, phenological plasticity constrains the northern range limit of oak and beech and the southern range limit of pine. Under future climatic conditions, phenological plasticity becomes strongly adaptive towards the trailing edges of beech and oak, but severely constrains the range and niche of pine. Our results call for caution when interpreting geographical variation in trait means as adaptive, and strongly point towards species distribution models explicitly taking phenotypic plasticity into account when forecasting species distribution under climate change scenarios.

# Functional genomics of marine and freshwater sticklebacks (52566)

Felicity Jones.

Friedrich Miescher Laboratory of the Max Planck Society.
Colonisation of new freshwater habitats has resulted in the repeated adaptive divergence of freshwater sticklebacks from their ancestral marine ecotype. We use these powerful biological replicates of the evolutionary process to identify and functionally dissect the molecular mechanisms underlying adaptive divergence and reproductive isolation. I'll describe how we are using whole genome sequencing and population genomics of stickleback species pairs to identify high-resolution sets of loci underlying parallel adaptive divergence. Many loci fall in non-coding parts of the genome, suggesting non-coding regulatory elements may be particularly important in adaptation. We use a range of methods to functionally dissect the phenotypic effect of these loci. These include transgenic methods to test for divergence in the regulatory potential of marine and freshwater adaptive haplotypes, and powerful new genome editing techniques to knock-out and knock-in adaptive loci. Our ultimate aim is to understand the fitness effects of these loci in natural populations. To do this we study the fitness and survival of naturally occuring recombinant individuals in contact zones between marine and freshwater forms. The ability to identify and functionally dissect adaptive loci in sticklebacks provides powerful insights into the molecular mechanisms underlying adaptation in natural populations.

## The genetic basis for the rapid diversification of male genital morphology among Drosophila species (51763)

Kentaro M. Tanaka, Corinna Hopfen, Matthew R. Herbert, Christian Schlötterer, David L. Stern, John P. Masly, Maria D. S. Nunes, **Alistair P. McGregor**.

Oxford Brookes University; Veterinärmedizinische Universität Wien (Austria); MPI for Biology of Ageing (Cologne, Germany); Janelia Research Campus (VA, USA); University of Oklahoma (OK, USA).

Identifying the genetic and developmental bases of phenotypic evolution is crucial to understanding organismal diversity and the evolutionary forces involved. The morphology of the external genitalia of males of Drosophila simulans clade species has evolved rapidly since their last common ancestor. For example, male D. simulans and D. mauritiana exhibit striking differences in the size, shape and bristle composition of their claspers, posterior lobes and anal plates. To identify the underlying loci we used high-resolution introgression mapping. We detected several small regions on chromosome 3 that contribute to interspecific differences in either the claspers or the posterior lobe and anal plates. While generally these loci affect each trait in the same direction and act additively, we also found evidence for epistasis. We then performed an RNAi screen to investigate if positional candidate genes that are differentially expressed between sexes or species also regulate genital development. We found six genes that are required for development of genital traits consistent with the effects of the introgressed regions in which they are located. We are currently using CRISPR/Cas9 in D. mauritiana and D. simulans to identify which of these candidate genes have contributed to the evolution of genital differences between these two species.
# Functional characterization of an adaptive cis-regulatory polymorphism in Drosophila melanogaster (51637)

**John Parsch**, Amanda Glaser-Schmitt.

*University of Munich (LMU).*

Drosophila melanogaster, which presently has a worldwide distribution, expanded from its ancestral home range in sub-Saharan Africa within the past 15,000 years. This expansion into new habitats is thought to have been accompanied by extensive adaptation. However, the genes involved in this adaptation are almost completely unknown. Transcriptomic studies found that the gene CG9509, which encodes a choline dehydrogenase, consistently shows higher expression in cosmopolitan populations than in sub-Saharan populations. The expression difference is caused by sequence variation in an upstream enhancer that shows population genetic evidence for a selective sweep in cosmopolitan populations. Detailed molecular genetic analyses have revealed three SNPs that contribute to the expression difference. Interestingly, two SNPs with moderate effects on expression are fixed in cosmopolitan populations, while a third SNP, which has a large effect on expression, is at intermediate frequency. Using RNAi knockdown and a null mutant, we show that high expression of CG9509 is associated with diminished larval growth rate, smaller adult body size, and reduced wing load - phenotypic traits that may be advantageous in temperate environments. Our results demonstrate how large-scale transcriptomics can be combined with population genetic, molecular genetic, and phenotypic studies to characterize the functional effects of regulatory changes on gene expression and organismal traits.

# From genome to function: Timing adaptations in the intertidal insect Clunio marinus (52203)

**Tobias S. Kaiser.**

*Max F Perutz Laboratories.*

The marine midge Clunio marinus (Diptera: Chironomidae) lives in the intertidal zone of the European Atlantic coast. Its life cycle is timed to the rhythm of the tides by circadian and circalunar clocks. As the pattern of the tides differs along the coastline, C. marinus populations show a variety of local genetic adaptations in circadian and circalunar timing. Population genetic analysis suggests that timing adaptations evolved within the last 20,000 years. QTL mapping indicates that the timing adaptations are controlled by few major effect loci.

In order to pinpoint the adaptive timing loci, we sequenced, assembled, annotated and genetically mapped a C. marinus reference genome, leading to a full reconstruction of the three chromosomes. Then we re-sequenced pools of 300 individuals from five populations of C. marinus, which differ in circadian and circalunar timing. Genome-wide we detected timing-associated genes based on the correlation of genetic divergence with timing differences. The distribution of genetic variation in the QTLs suggests that timing adaptation
happened from standing genetic variation and involves regulatory changes. Subsequent
molecular analysis substantiated that adaptation in circadian timing relies on modulating
alternative splicing of a metabolic enzyme.

Characterization of the wing colour patterning supergene in a mimetic
butterfly (52256)

Suzanne Saenko, Florence Prunier, Violaine Llaurens.

Museum National d'Histoire Naturelle.

Identification and experimental validation of genes underlying adaptive phenotypic variation
is crucial for our understanding of evolution. Heliconius butterflies are famous for their
extreme diversity in wing colour patterns, associated to aposematism and Müllerian mimicry.
While the majority of Heliconius species are locally monomorphic and vary geographically,
H. numata maintains a high local polymorphism throughout its geographical range, with 7-10
forms coexisting in the Amazon populations, each mimicking different species of Melinaea
butterflies. This dramatic polymorphism is controlled by alleles of a single supergene P,
containing at least 18 genes. Polymorphic inversions at the P locus suppress recombination,
maintaining the favourable genetic combinations that produce mimetic colour patterns.
However, the exact nature of the wing patterning genes within the supergene has not yet been
investigated. Here, we use RNA-sequencing in combination with ‘classical’ approaches such
as qPCR and in situ hybridizations to test the involvement of candidate genes from the P
supergene in wing pattern formation in H. numata. Remarkably, this locus harbors the genes
involved in colour patterning in other species of Lepidoptera and therefore represents a
genomic hotspot of evolutionary change in multiple clades.

Ecological and evolutionary determinants of disease dynamics (51727)

Anna-Liisa Laine

University of Helsinki.

Several key theories have been proposed to explain the diversity of pathogen populations and to predict evolutionary trajectories of disease. Among the key theories are the Red Queen hypothesis, life-history trade-offs, and competition for resources under multiple infection, and while each has been relatively intensively studied also empirically, to date we understand remarkably little about the relevance of these processes for realized epidemiological dynamics under conditions that support spatial and environmental complexity. In this talk I will synthesize what we currently about ecological and coevolutionary processes jointly shaping disease dynamics in the metapopulation of fungal pathogen Podosphaera plantaginis infecting its host across a heterogeneous landscape.
# Side effects of parasitism in microbes (53332)

**Alex Hall.**

*ETH Zürich.*

Parasitism creates selection for resistant hosts, but can also alter the frequencies of other alleles not directly related to the host-parasite interaction. I will describe some experiments with bacteria and their viral parasites showing that parasitism can alter the spread of alleles that determine bacterial drug resistance, mutation rate and growth rate in the abiotic environment. These effects can come about through mechanisms such as genetic hitchhiking or epistasis, and our results show that they depend strongly on ecological factors, which modify the strength of selection for resistance to parasites and their effects on other phenotypic traits.

# Parasite evolution in heterogeneous and spatially structured host populations
(51787)

**Sébastien Lion.**

*CEFE, Montpellier, France.*

Evolutionary epidemiology aims at understanding how host-parasite interactions evolve in response to various ecological factors. However, theoretical studies often assume that the host population is well-mixed, thereby neglecting potential selective pressures caused by genetic and epidemiological spatial structuring. I will present some theoretical and experimental results in order to elucidate the evolutionary impacts of parasite and host dispersal patterns. I will first focus on a population where all hosts have the same quality, and show that the predictions of non-spatial theory are altered by kin competition for susceptible hosts. I will then examine what happens in a heterogeneous population in which a fraction of the hosts are vaccinated. I show that different types of vaccines lead to different evolutionary outcomes, which depend on the interplay between vaccine efficacy, vaccination coverage, and spatial structure. Kin selection is shown to be a key conceptual tool to understand epidemiological feedbacks on parasite traits and to generate predictions for the management of infectious diseases.

# Relative fitness of a generalist parasite on alternative hosts: a cross-infestation experiment of the hen flea among sympatric passerine hosts. (51793)
Anaïs APPELGREN, Karen McCOY, Heinz RICHNER, Blandine DOLIGEZ.

UMR CNRS 5558 - LBBE (LYON, FR); EEL-IEE (BERN, CH); MIVEGEC (MONTELLIER, FR).

Host range is a key element required to understand a parasite's ecology and evolution and can vary greatly depending on the spatial scale considered. Several studies suggest that generalist parasites frequently show local population structure in relation to alternative sympatric hosts (i.e., host races), and are thus less "generalist" than described. Here, we tested this hypothesis for a common nest-based parasite, the hen flea Ceratophyllus gallinae exploiting two abundant host species that share the same breeding habitat, the great tit Parus major and the collared flycatcher Ficedula albicollis. We performed a cross-infestation experiment of fleas between the two host species during a single breeding season and recorded the reproductive success of both hosts and parasites. Hosts were recaptured the following year to assess the long-term impact of cross infestation. Results suggest the presence of local host-specialized parasite populations, with variation in the relative virulence on the two hosts modulated by the host population locality and history.

Session 1 THU POL C 10

## Parasite evolution in a host sexually dimorphic world (51858)

David Duneau, Nicolas Buchon, Brian Lazarro.

Cornell university.

The evolution of the interactions between hosts and their parasites is multifactorial as it depends on the combination of many factors in both the host and the parasite. In a growing number of infectious disease, host sex is one of the key factors that generates strong differences in the outcome of the disease. The mechanisms underlying the effect of the host heterogeneity due to sexual dimorphism remain poorly characterized. We used Drosophila melanogaster, a powerful genetic model organism, to investigate the sexual dimorphism of the response to infection, its underlying mechanisms and its consequences on parasite evolution. We characterized the sexual dimorphism in response to a broad spectrum of parasites covering different types of pathogens. We found that male hosts imposed a stronger selective pressure on bacteria probably because of an adaptive reduction of immune sensitivity of female recognition of infection. We described in depth the immune components involved in the dimorphic response to Providencia rettgeri, a natural pathogenic Gram negative bacteria of D. melanogaster populations. Then, we investigated the consequence of sexual dimorphism on the evolution of bacteria via an experimental evolution approach.

Session 1 THU POL D 9

## A behavioural ecologists' view of bacterial life in the lung (53335)

Ashleigh Griffin.
University of Oxford.

Behavioural ecologists use evolutionary theory to provide adaptive explanations for observations of animals living in their natural environment. Success relies on accurately identifying selection pressures acting upon traits of interest. For this reason, we have made limited progress in understanding the adaptive significance of behavioural traits in microbes. To observe a bacterial cell, we typically isolate it from its natural environment first before bringing it into the lab for examination. This process releases cells from the very selection pressures we wish to understand. Furthermore, the bacteria we are most interested in – human pathogens – live in one of the most inaccessible and irreplicable environments – living human beings. In this talk, I will present evidence that selection to optimise fitness from social interactions can drive long-term phenotypic dynamics in Pseudomonas aeruginosa infecting patients with cystic fibrosis. After ten years of studying P. aeruginosa in precisely controlled experimental evolution studies, we were interested to know if the competitive dynamics of co-operators and cheats in our experiments had any relevance to the real world. But first we had to overcome the challenge of identifying selection pressures inside a human lung.

Session 1 THU POL D 9

## Cooperation, cheating, and collapse in microbial populations (53366)

**Jeff Gore.**

Natural populations can suffer catastrophic collapse in response to small changes in environmental conditions, and recovery can be difficult even after the environment is restored to its original condition. We have used laboratory microbial ecosystems to directly measure theoretically proposed early warning signals of impending population collapse. Our experimental yeast populations are subject to catastrophic collapse because they cooperatively break down the sugar sucrose, meaning that below a critical size the population cannot sustain itself. The cooperative nature of yeast growth on sucrose also makes the population susceptible to "cheater" cells, which do not contribute to the public good and reduce the resilience of the population.

Session 1 THU POL D 9

## Rock-paper-scissors dynamics maintain cooperation and diversity in well-mixed bacterial communities (51679)

**Rolf Kümmerli, Fredrik Inglis, Jay Biernaskie, Andy Gardner.**

University of Zürich; Swiss Federal Institute of Aquatic Science and Technology (EAWAG); University of Oxford; University of St. Andrews.

Cooperation and diversity abound in nature despite the fact that cooperators risk exploitation from cheats and weak competitors risk displacement by superior ones. This is especially true in unstructured, well-mixed environments where cooperators and weak competitors are fully
exposed to exploitative and superior forms. Here, we use theory and experiments with
bacteria to demonstrate a simple mechanism that promotes cooperation and diversity in well-
mixed conditions: coexistence between cooperators and cheaters is stabilized by the presence of
loners who sidestep social interactions. This three-way Rock-Paper-Scissor system occurs in
communities of the bacterium Pseudomonas aeruginosa: cooperators secrete shareable
siderophore molecules to scavenge growth-limiting iron, thereby outcompeting loners who
have an independent yet less efficient iron-uptake system; loners outcompete cheaters who can
only exploit the cooperator's but not the loner's iron uptake system; and cheaters outcompete
cooperators. This circular interaction network maintains cooperation and strain diversity over
time. Thus, our analyses establish a general mechanism for explaining trait, strain and species
diversity, even in natural settings like aquatic habitats, where individual dispersal is high.

Sibling cooperation mitigates effects of low parental care in earwigs: a new perspective on the early evolution of family life (51744)

Jos Kramer, Julia Thesing, Joël Meunier.

Dept. of Evolutionary Biology, Institute of Zoology, University of Mainz.

The evolution of family life requires net fitness benefits for offspring, which are commonly assumed to mainly derive from parental care. However, an additional source of benefits for offspring is often overlooked: cooperative interactions among juvenile siblings. In this study, we examined how sibling cooperation and parental care could jointly contribute to the early evolution of family life. Specifically, we tested in the European earwig Forficula auricularia whether the level of food transferred among siblings (sibling cooperation) (1) depends on the level of maternal food provisioning (parental care), and (2) shapes fitness traits measured in family members. We show that the expression of these two behaviors is negatively correlated, reflecting a compensatory relationship between sibling cooperation and maternal care. Furthermore, the level of sibling food transfer did not influence offspring survival, but was associated with negative effects on the production of the second and terminal clutch by the tending mothers. These findings indicate that sibling cooperation mitigates the detrimental effects on offspring survival that result from being tended by low quality mothers. More generally, they are in line with the hypothesis that sibling cooperation is an ancestral behavior that can be retained to compensate for insufficient levels of parental investment.

Kin Selection and Maternal Effects: the confusion, consequences and case study. (51893)

Caroline Thomson, Jarrod Hadfield.

University of Oxford; University of Edinburgh.
There is abundant evidence in many taxa for positive directional selection on body-size, and yet little evidence for microevolutionary change. In species where variation in body-size is caused by variation in parental care, a proposed explanation is a negative genetic correlation between direct and parental effects; selecting genes that increase body-size causes a correlated reduction in parental care, which reduces body-size in the following generation. However, empirical evidence seems to suggest that this genetic correlation is not sufficiently negative (less than -0.9) to explain evolutionary stasis. Here we show that these arguments implicitly assume that parental care is cost free, and including a cost could allow evolutionary stasis without requiring such extreme genetic architectures. Using a large cross-fostered population of blue tits, we estimate selection on parental care (i.e. the cost) and show that evolutionary stasis would be possible under more reasonable genetic correlations. Thus, we highlight the importance of accounting correctly for the complete selection acting on traits across generations.

## The role of antimicrobials in the evolution of cooperation (51986)

Marie Vasse, Clara Torres-Barceló, Michael E. Hochberg.

Institut des Sciences de l'Evolution-CNRS Université de Montpellier, France; Santa Fe Institute, USA.

Cooperation is a pervasive phenomenon in biological systems and despite considerable study, its establishment and maintenance are incompletely understood. Theoretical and empirical work on social behaviors in single species indicates that cooperation is fostered by positive assortment. However, numerous studies on more complex systems have shown that environmental and social factors may influence the ecological and evolutionary dynamics of cooperation. Using both experimental evolution and theoretical approaches, we studied the impact of antimicrobial compounds on the dynamics of public good cooperation within a bacterial population. Pseudomonas aeruginosa is an opportunistic human pathogen that facultatively produces iron-scavenging molecules called siderophores in response to iron limitation. Siderophore production is costly for the producer and benefits other local individuals carrying the siderophore receptors, and therefore may be subject to evolution as a cooperative trait. Comparing a wild-type and a mutant strain lacking the most important siderophore producing gene, separately or in competition, we showed that the deleterious effects of antimicrobials can shape bacterial populations and affect public good dynamics. Our results highlight the importance of considering environmental factors when studying the evolution of cooperation.

## The role of epistasis in the evolution and epidemiology of multidrug-resistant tuberculosis (53373)

Sebastien Gagneux.
Multidrug-resistant tuberculosis (MDR-TB) is a global public health emergency. Although much is known about the mechanisms of resistance to the different anti-TB drugs, little is known on the evolutionary trajectory of Mycobacterium tuberculosis exposed to prolonged drug pressure and its impact on the spread of MDR-TB. Recent studies by our group and others suggest that this evolutionary trajectory is more complex than previously thought. In particular, epistatic interactions between drug resistance-conferring mutations, compensatory mutations and different strain genetic backgrounds play an important role. For example, we recently identified mutations in rpoA and rpoC of RNA polymerase of M. tuberculosis resistant to rifampicin. These mutations compensate for the fitness cost associated with the resistance-causing mutations in rpoB. Moreover, these compensatory mutations are associated with ongoing transmission of MDR-TB, indicating that compensatory evolution contributes to the success of highly drug-resistant strains of M. tuberculosis in countries with a high burden of MDR-TB. Using an M. smegmatis model, we observed sign epistasis between rpoB mutations causing resistance to rifampicin and mutations in gyrA conferring resistance to fluoroquinolones, indicating that mutations causing resistance to different drugs can compensate for each other's fitness costs. Intriguingly, the particular combinations of rpoB and gyrA mutations exhibiting the highest in vitro fitness were also the more common in clinical strains. Taken together, our findings suggest that epistasis is an important driver of MDR-TB epidemics, and that it should be considered in the development and deployment of new anti-TB drug regimens.

# Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis (51623)

**Rasmus Lykke Marvig**, Lea M. Sommer, Søren Molin, Helle K. Johansen.

*Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark; Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.*

Only little is known about how within-host evolution compares between genotypically different strains of the same pathogenic species. We sequenced the whole genomes of 474 longitudinally collected clinical isolates of Pseudomonas aeruginosa sampled from 34 children and young cystic fibrosis patients. Our analysis of 36 P. aeruginosa lineages identified convergent molecular evolution in 52 genes. This list of genes suggests a role in host-adaptation for remodeling of regulatory networks and central metabolism, acquisition of antibiotic resistance, and loss of extracellular virulence factors. Furthermore, we find an ordered succession of mutations in key regulatory networks. Accordingly, mutations in downstream transcriptional regulators were contingent upon mutations in upstream regulators, suggesting that remodeling of regulatory networks may be important in adaptation. Characterization of genes involved in host-adaptation may help prediction of bacterial evolution in cystic fibrosis patients and design of future intervention strategies.
# Omics of endosymbiosis adaptation during experimental evolution of legume symbionts (52222)

**Camille Clerissi**, Delphine Capela, Marta Marchetti, François Li, Rachel Torchet, Stéphane Cruveiller, Carine Gris, Eduardo PC Rocha, Catherine Masson-Boivin.

INRA, LIPM, UMR 2594/441, 24 chemin de Borde Rouge-Auzeville, 31326, Castanet-Tolosan, France; CEA/FAR, Institut de Génomique, 2 rue Gaston Crémieux, 91057, Evry, France; Microbial Evolutionary Genomics, Institut Pasteur, 28 rue Dr. Roux, 75015, Paris, France; CNRS, UMR3525, 28 rue Dr. Roux, 75015, Paris, France.

Cooperation between legumes and bacteria collectively called rhizobia fixed a fourth of the atmospheric nitrogen each year. Rhizobia are phylogenetically disparate bacteria that have diversified through horizontal transfer of key symbiotic genes converting soil bacteria into legume symbionts. Making the transition to an intracellular lifestyle is a dramatic ecological change. Each plant indeed represents a complex ecosystem to which the bacterium may adapt. How and which re-adjustments allow the shift to endosymbiosis is still poorly unknown. To tackle this issue, we took advantage of the experimental evolution of a pathogenic Ralstonia solanacearum chimera carrying the symbiotic plasmid of the rhizobium Cupriavidus taiwanensis into legume symbionts. Eighteen lineages of chimeric Ralstonia were adapted to nodule tissues for 16 infection cycles. Evolution was very fast, since most lineages acquired and improved the two first major symbiotic steps, nodulation and intracellular infection. To get an integrated view of adaptive changes driving symbiotic adaptation, we performed a combined genomic, transcriptomic and metabolomic analysis of the 18 final clones. The clones exhibit convergent changes that may reflect their capacity to face new endosymbiotic conditions. Our work highlights the potential of coupling experimental evolution with omic approaches to get insight into the emergence of plant endosymbionts.

# Rapid evolution of bacterial pathogens co-infecting an animal host (52348)

**Kayla King**, Michael Brockhurst, Steve Paterson, Greg Hurst.

University of Oxford; University of York; University of Liverpool.

Co-infections, when multiple pathogen species coexist within an individual, are very common in nature. Studies in natural populations have provided compelling evidence that competitive interactions between pathogen species in a given host species strongly alter pathogen fitness and transmission. Thus, we hypothesised that co-infection would alter patterns of pathogen evolution. We tested this by experimentally evolving two opportunistic, bacterial pathogens – *Enterococcus faecalis* and *Staphylococcus aureus* – separately and together within *Caenorhabditis elegans* nematodes in the lab. Using a combination of phenotypic and genomic analyses, we show that the speed and direction of in vivo evolution of pathogen virulence and other infection-related traits were affected by a co-infecting competitor. The evolution of a pathogen, therefore, cannot be understood without knowledge of others infecting the host.
# Phylodynamic analysis of a mycobacterium tuberculosis outbreak (52913)

**Denise Kühnert**, David Stucki, Mireia Coscolla, Lukas Fenner, Tanja Stadler, Sebastian Gagneux.

*Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland; Swiss Tropical & Public Health Institute, Basel, Switzerland; Department of Biosystems Science & Engineering, ETH Zürich, Zürich, Switzerland.*

The fast evolution of pathogenic viruses gave rise to a number of phylodynamic approaches to extract information about the epidemiological characteristics of viral genomes. Here we apply these approaches to the more slowly evolving bacterial genomes of mycobacterium tuberculosis.

Around 1991 the city of Bern, Switzerland, was struck by a small but severe outbreak of tuberculosis. Two initial cases were observed in 1987 and 1988, the majority of patients were sampled between 1991-1998, and up to 2011 patients infected with related strains were observed. Overall 75 infected patients were sampled, and 68 of the resulting bacterial isolates where genetically related and therefore sequenced.

In this study we aim at understanding the epidemiological dynamics of the Bernese tuberculosis outbreak. We analyze the genomes with BEAST2, using a birth-death tree prior that allows to incorporate an exposed phase in which patients are infected but not yet infectious. Piecewise constant changes in the reproduction number allow us to estimate changes in epidemiological dynamics through time.

Our results suggest that the majority of transmissions took place before 1993, supporting previous suggestions that more recently sampled cases may have been latent for years, before being reactivated. We estimate an average latent period of 2-5 years.

# Parallel evolution of a global regulator ameliorates the cost of plasmid carriage (52435)

**Ellie Harrison**, Steve Paterson, Andrew Spiers, Micheal Brockhurst.

*University of York; University of Liverpool; Abertay University.*

Conjugative plasmids present a paradox. Although many carry useful bacterial genes, all plasmids exert a burden on their host. Therefore selection should favour plasmid loss and retention of any useful genes on the bacterial chromosome. Previous studies have shown that evolution can resolve this paradox by ameliorating the cost of plasmid carriage, yet the mechanisms for this are poorly understood. We combine experimental evolution, microarray
analysis and whole genome sequencing to investigate how evolution resolves this plasmid
paradox.

We experimentally evolved replicate populations of Pseudomonas fluorescens carrying the
mercury resistance plasmid pQBR103. Prior to evolution plasmid carriage was associated
with widespread up-regulation of translation-associated genes, suggesting that pQBR103
exerts a translational burden on its host. Following evolution however this was reversed.
Sequencing of evolved clones revealed parallel evolution targeting two bacterial genes: gacA
and gacS, a two-component regulator that positively regulates translation of extracellular
proteins. Knockouts confirmed that loss of gacA/S function ameliorates the cost of plasmid
carriage. As disruption of gacA/S increases post-transcriptional repression of bacterial genes,
these data suggest that the bacteria ameliorate the cost of plasmid carriage by reducing their
own translational workload to accommodate that of the plasmid.

Session 1 THU GEN B 35

A theoretical study of sympatric divergence of whitefish in Scandinavia
(52756)

Xavier Thibert-Plante, Per-Arne Amundsen, Kimmo Kahilainen, Kim Praebel, Kjartan Østbye, Sergey Gavrilets.

Umeå University; The Arctic University of Norway; University of Helsinki; University of Oslo; University of Tennessee, Knoxville.

We have a better understanding of the role of divergent selection and assortative mating in
parapatric speciation event. Unfortunately, the application of those theoretical concepts is not
straightforward in complex empirical systems of contemporary speciation. One of such
complex system is the divergence of whitefish in Scandinavia. There is a large number of
lakes in northern Scandinavia where divergence occurred. In some of those lakes, as much as
three morphotypes have diverged in situ. We use a large scale individual-based numerical
simulation to model the divergence of whitefish in Scandinavia. Our aim is to distinguish the
role of different driving factors (such as habitat preference, divergence in resource
distribution, divergence in mating time and divergence in spawning site) in this divergence.
Speciation and adaptive radiation are the result of a complex intertwined factors. The leading
factor is the divergence in resource types, but reproductive isolation is the result of a much
more complex interaction between habitat preference and assortative mating. It is fairly
instructive to apply theoretical models to empirical systems, as we learn how the different
driving factors interact during speciation.

Session 1 THU GEN B 35

Genomic imprinting and its systematic perturbation in abortive interspecific
tomato seeds (51694)
**Ana Marcela Florez Rueda**, Margot Paris, Anja Schmidt, Alex Widmer, Ueli Grossniklaus, Thomas Städler.

*Institute of Integrative Biology, ETH Zurich, Universitätstrasse 16, CH-8092 Zurich, Switzerland; Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland.*

Hybrid seed failure represents an important postzygotic barrier to interbreeding among species of wild tomatoes (Solanum section Lycopersicon) and other angiosperm groups. We studied this phenomenon in the closely related S. peruvianum and S. chilense; hybrid crosses between these species yield very high proportions of inviable seeds due to endosperm failure and arrested embryo development. Based on seed size differences in reciprocal hybrid crosses and developmental evidence implicating endosperm failure, we hypothesized that (perturbed) genomic imprinting might be involved in this strong postzygotic barrier. Consequently, we surveyed endosperm transcriptomes obtained via laser-microdissecting developing seeds representing both intra- and interspecific pollinations. We implemented a novel approach to estimate parent-of-origin-specific expression using both homozygous and heterozygous nucleotide differences between the two parents and identified hundreds of candidate imprinted genes. Importantly, we uncovered systematic shifts of the ‘normal’ (intraspecific) maternal:paternal transcript proportions in hybrid endosperms; the average maternal proportion of gene expression increases in both directions of the hybrid cross but is strongly negatively correlated with ‘normal’ maternal proportions. This genome-wide shift almost entirely eliminates paternally imprinted gene expression in hybrid endosperms but also affects maternally imprinted genes (which on average shift to lower maternal proportions) and all other genes.

Why are ring species so rare? (52898)

**Ayana B. Martins**, Marcus A. M. de Aguiar.

*Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas; Instituto de Biociências, Universidade de São Paulo.*

Ring species are groups of organisms that dispersed along a ring shaped region in such a way that the two expansion fronts, that meet after many generations, are reproductively isolated despite ongoing gene flow. Here we study the formation of ring species by simulating population expansion around a central geographic barrier. We combine different strategies of parameter space exploration and compare two models with independent sets of assumptions to propose the conditions for ring species formation by speciation by distance. If population expansion takes less than 10000 generations, ring species formation occurs when the time to contact secondary and the time to reproductive isolation are of the same order. We show that both these times depend on landscape, population and individual features. However, in ring shaped scenarios, population structuring leading to the acquisition of reproductive isolation is better explained by landscape configuration than by local mating. The conditions that allow ring species formation appear to be limited, which could by itself explain their rarity. Furthermore, these complexes are most likely to
form for extremely narrow species distributions which are unlikely to persist in nature, and,
therefore, are expected to be rare in nature.

Male barn swallows mimic nestlings to attract females (51938)

Masaru Hasegawa, Emi Arai, Mamoru Watanabe, Masahiko Nakamura.

Sokendai; Tohoku University; University of Tsukuba; Joetsu University of Education.

Courtship behaviors of male birds often resemble the food-begging behavior of their young, at least from a human perspective. However, it is still unclear whether such behavior in males is objectively similar to nestling behavior and, if so, how such similarity is evolved and maintained. The sensory trap hypothesis proposes that this similarity is a consequence of signal evolution, whereby male signals mimic stimuli to which females respond in other contexts (i.e., parental care, in this case). We demonstrated that the enticement calls of male barn swallows structurally resemble the food-begging calls of nestlings, compared with the other three male vocalizations (i.e. songs, alarm calls and contact calls). In addition, we found that females were attracted to the playback of nestlings' food-begging calls during the courtship period, despite nestlings being absent at this time. The response of females to food-begging calls was similar and positively correlated with their response to male enticement calls. To our knowledge, this is the first study to demonstrate the objective similarity as well as a similarity in receiver response towards the two behaviors during courtship, supporting the sensory trap hypothesis. We discuss the evolutionary importance of nestling mimicry in this model species of sexual selection.

How sick are sexy males? Testing Hamilton & Zuk hypothesis with a meta-analytical approach. (52575)

Zofia Prokop, Mateusz Buczek, Agata Plesnar-Bielak, Shinichi Nakagawa, Lukasz Michalczyk.

Jagiellonian University, Krakow, Poland; University of Otago, Dunedin, New Zealand.

Female preferences for specific male phenotypes have been documented in many animal
species, including those where males contribute only gametes to offspring production.
However, selective pressures responsible for the origin and maintenance of such preferences
remain elusive. The Hamilton and Zuk hypothesis proposes that female preferences target
those male traits that reliably signal heritable disease resistance, and hence preferences evolve
by indirect selection – because offspring of choosy females inherit disease resistance alleles
from their fathers. One of the predictions of this hypothesis is a negative correlation between
secondary sexual traits and disease in males. We use meta-analysis to evaluate empirical
evidence for this prediction. Our preliminary results (analysis of ~75% of the final data base)
do not support Hamilton and Zuk hypothesis: the meta-analytic mean for the correlation
between sexual traits and disease measures, calculated across studies and taxa, is not
significantly different from zero (r=-0.14, CI: -0.32 to 0.05). Interestingly, however, we find a
substantial effect of phylogeny on the magnitude of this correlation. In further analyses, we
also test for the effects of several moderators related to biology of host and pathogen taxa, and
to methodology of the study, on the magnitude of the effect.

Worldwide patterns of bird colouration on islands and associated mechanisms
(52146)

Claire Doutrelant, Matthieu Paquet, Julien Renoult, Pierre-André Crochet, Arnaud Grégoire, Rita Covas.

CEFE-CNRS Montpellier, France; ACTE- CNRS Paris, France; CIBIO Porto, Portugal.

Islands are natural simplified replicates around the world that harbour original selective environments and offer unique opportunities to investigate patterns of convergent adaptation, referred as syndromes. Communicative traits are decisive to animal fitness, mediating interactions with the environment. However, whether and how these traits are part of an insularity syndrome is still unclear. We quantitatively analyzed with spectrophotometry and a model of avian vision, the plumage colouration of 232 bird species comprising island endemics from around the world and their close mainland relatives. We found that both plumage brightness and colour conspicuousness (volume in a bird colour space) were reduced on islands in both sexes, and further evidenced a decrease in colourfulness (number of distinct colour patches) in males. We then investigated the ‘species recognition’ and ‘life-history trade-offs’ hypotheses as two of the possible explanations for these changes and found some support for both. Hence, our results reveal convergent colour changes on islands worldwide and confirm that interspecific interactions and trade-offs are two of the important underlying mechanisms affecting the evolution of bird plumage colouration.

The promise of reverse ecology (53311)

Matthew Rockman.

New York University.

Unbiased genome-wide population-genetic analyses hold remarkable promise for revealing
the molecular variants whose frequencies have changed in response to selection within and
among populations and species. These methods have been applied to two classes of question.
One question centers on the roles of selection, linkage, and demography in shaping the
dynamics of genetic variation. A second question centers on discovering specific loci that
have been targets of selection and inferring the causes of selection. Approaches to the second
question are sometimes called reverse ecology, by analogy to reverse genetics, which starts
with mutations and then seeks impacted phenotypes. Reverse ecology promises to provide an
unbiased view of the selective forces operating on populations, but we lack a principled
method for connecting genetic variants discovered in such screens to the ecological factors
that act on them. This gap is especially acute for genetic variants whose known phenotypes
are cell-biological rather than organismal. I will illustrate the challenges with evidence for
ongoing selection on meiotic genes in Caenorhabditis nematodes and the alternative models
of natural selection that can account for the patterns.

Human adaptation to life in the high arctic (53312)

Rasmus Nielsen.

UC Berkeley.

The native people of Greenland, the Inuit, are of special interest to anthropologists and evolutionary biologists because of their extreme adaptations to life in the high arctic. In particular, Inuit traditionally have a diet based primarily on hunting marine mammals, which have a high content of polyunsaturated fatty acids. Inuit provide an opportunity to investigate genetic adaptations to such a diet. We analyze SNP chip data and exome sequencing data from 191 and 18 Inuit, respectively, in order to identify regions targeted by positive selection specifically in Inuit related to metabolic processes. We find extreme selection signals in several loci and using association mapping, we show that alleles associated with positive selection in these loci are strongly associated with multiple phenotypes, including weight. Our study illustrates the use of small understudied populations for understanding the genetic basis of human biological variation.

Genomic basis of the evolution and variation in Drosophila immunity against
parasitoids (52187)

Bregje Wertheim, Laura Salazar-Jaramillo, Sylvia Gerritsma, Kirsten M. Jalvingh.

Groningen Institute for Evolutionary Life Sciences; University of Edinburgh ; Universite de
Lausanne.

To understand the intricate genetic networks that underlie variation in immunity, and to map
how the genome changes during the evolution of immunity, we use the Drosophila-parasitoid
interactions as model system. The ability to survive parasitoid attack varies hugely both
among and within species of the Drosophila genus, from absent to high resistance. Combining
phenotypic assays, comparative genomics, population genomics and experimental evolution
approaches, we identified genome changes associated with gains, losses and increases of
parasitoid resistance. Comparing 11 sequenced Drosophila species, we showed that evolution
of parasitoid resistance coincided with the acquiring of a novel type of differentiated hemocyte (i.e. insect blood cell) and with the duplication of 11 genes that are up-regulated during the immune response after parasitization. To characterize the impact of a selective sweep for parasitoid resistance on the genome, we used experimental evolution followed by genome sequencing. Several narrowly defined genomic regions showed strong signatures of selection and candidate genes were identified that potentially confer increased parasitoid resistance. Comparing 8 natural D. melanogaster populations, we find that physiological and genetic mechanisms underlying phenotypic variation differ substantially among populations. Combined, this emphasizes that short- and long-term evolutionary responses can result in markedly different genome changes.

## A complementary method to genome scans for selection against maladaptive gene flow (52429)

Simon Aeschbacher, Graham Coop.

University of California, Davis.

We quantify the genome-wide signal of selection against maladaptive gene flow, such as in the context of local adaptation or hybridisation. Combining the concept of effective migration rate with the structured coalescent, we predict the aggregate effect of selection against locally deleterious alleles as a function of recombination. Given a linkage map and estimates of between-population diversity, we infer the selection intensity per basepair, the time of onset of selection, and the baseline migration rate. Our method complements genome scans for candidate loci. In particular, it avoids issues of Fst outlier approaches such as their inability to distinguish between global background selection and selection against gene flow. It also borrows strength across multiple sites of weak effect, many of which would be missed by genome scans. Analytical approximations suggest that it is difficult to separate the average selection coefficient from the genomic density of selected sites, but their compound effect can be identified. We test our approach against simulations and apply it to two datasets from the yellow monkeyflower (Mimulus guttatus), one in which we detect the signal of local adaptation to serpentine soils, and another where we show evidence for selection against introgression from the sister species M. nasutus.

## The genomic consequences of local adaptation in deer mice (52614)

Susanne P. Pfeifer, Stefan Laurent, Matthieu Foll, Brant Peterson, Jeffrey D. Jensen, Hopi E. Hoekstra, Rowan D.H. Barrett.

School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland;
School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland;
Although natural selection is the major force driving phenotypic evolution and adaptation to new environments, uncertainty persists concerning the magnitude and causes of genomic changes that occur when populations evolve under novel ecological conditions. Moreover, ecological sources of selection and the genomic basis of adaptive traits are often complex, limiting the predictability of local adaptation. To determine whether natural selection may indeed have predictable effects on specific phenotypes and their underlying mutations, we identified the genetic polymorphisms responsible for adaptive pigmentation traits in wild deer mouse populations (Peromyscus maniculatus) inhabiting the Nebraska Sand Hills, formed 8,000 to 10,000 years ago, and directly estimated the consequences of natural selection on these phenotypes. We conducted a large-scale field-based selection experiment that involved the introduction of 480 wild deer mice (with known genotypes and phenotypes) into replicated field enclosures, representing the two extremes in substrate color found in their natural habitat. These observations were used to estimate the targets and strength of selection acting on pigmentation traits at the phenotypic level. Additionally, we characterized genome-wide changes in allele frequencies in order to estimate how local adaptation can shape broader patterns of evolution at the genotypic level.

# The genetic architecture of recombination rate variation in a wild population.
(52859)

Susan Johnston, Jon Slate, Josephine Pemberton.

University of Edinburgh; University of Sheffield.

Genome scans provide a useful tool for detection of genomic regions underlying both local adaptation between populations (e.g. FST outlier analyses) and fitness-related variation within populations (genome-wide association studies). To date, most studies have focused on detecting the effects of single markers, yet recent work shows that such approaches may fail to capture loci of moderate or small effects on phenotype. Therefore, multi-locus frameworks are more likely to accurately characterise genetic variation segregating within and between populations, especially when the trait has a polygenic architecture. In this study, we used information from a high density SNP chip to calculate individual recombination rate variation in wild Soay sheep. We then investigated the genetic architecture of this moderately heritable trait (h2 ≈ 0.13) using chromosome partitioning and regional heritability mapping. This integration of traditional quantitative genetic approaches and multi-locus information allowed us to identify regions of the genome associated with recombination rate variation, but also allowed us to estimate the proportion of heritable variation caused by additional polygenic effects at unknown loci. We describe additional steps taken to prevent identification of false-positive signals, and show how these statistical approaches allow more accurate investigation of trait evolution both within and between populations.
# Genetic and neural basis for the evolution of schooling behavior in sticklebacks (53318)

**Catherine L. Peichel**, Anna K. Greenwood, Abigail R. Wark, Margaret G. Mills.

Fred Hutchinson Cancer Research Center; Graduate Program in Neurobiology and Behavior, University of Washington; Graduate Program in Molecular and Cellular Biology, University of Washington.

The formation of social groups is prevalent across the animal kingdom, but can vary dramatically among different species, within species, and even across the lifetime of an individual. Schooling behavior in fish provides a particularly dramatic example of social group formation. To study the proximate genetic and neural mechanisms that contribute to the evolution of schooling behavior, we developed the “model school assay” and used it to demonstrate that there are heritable differences in schooling behavior between threespine stickleback (Gasterosteus aculeatus) populations adapted to divergent marine and freshwater benthic habitats. Marine sticklebacks have both a stronger tendency to school and a better ability to maintain a parallel body position when schooling than benthics. Our genetic mapping studies revealed that differences in these two components of schooling behavior are controlled by distinct genetic modules. These studies also revealed that the Ectodysplasin (Eda) gene is tightly linked to body position while schooling. Interestingly, the Eda gene is also tightly linked to variation in the patterning of the sensory hair cells (neuromasts) of the lateral line sensory system, which had been implicated in schooling behavior. To test whether the Eda gene is responsible for variation in both lateral line patterning and schooling behavior, we used transgenic methods to broadly express the marine version of the Eda cDNA in benthic sticklebacks. These transgenic sticklebacks have a marine-like pattern of neuromasts, and the presence of the transgene causes benthic sticklebacks to school in a more parallel orientation. This change in schooling behavior seems to be mediated by the effects of Eda on the lateral line system. Our results thus provide mechanistic insight into how and why fish form schools and yield one of the first genes known to shape vertebrate behavior in an evolutionary context.

# Using live bearing fish as short generation time models in the study of vertebrate brain evolution (52743)

**Niclas Kolm.**

Stockholm University Zoology/Ethology.

Brain morphology variation is ubiquitous in the animal kingdom. Yet the evolutionary processes and mechanisms that have generated this variation remain poorly understood. Till now, the study of the causes and consequences of this variation has mainly used comparative analyses to investigate correlations between brain morphology and behavior, ecology, sexual selection and life histories. Using artificial selection experiments of brain size in the guppy, a
live bearing fish with short generation time, we study multiple hypotheses concerning the
costs and benefits of evolving a larger brain. I will present some of our findings on these
selection lines regarding the genetic architecture of brain size and how several traits,
including behavior, investment into other organs, sexual traits, immune competence and
fitness, are affected by rapid evolution of brain size. Finally, I will present how we use new
artificial selection experiments on the guppy to unravel the evolutionary possibilities and
consequences of rapid evolution of separate brain region sizes and how brain morphology is
affected by artificial selection of social abilities. My aim is thus to show that short generation
time vertebrates such as live bearing fish may form new models for the study of evolutionary
and ecological neurobiology.

Session 1 FRI MAX 410 23

Innate differences in auditory perception and reproductive isolation in an
avian species pair (51804)

David Wheatcroft.

*Uppsala University.*

Vocal learning is a defining characteristic of human intelligence. Researchers have used the song learning process in birds, where over 4000 species learn their vocalizations, to understand the cognitive basis and evolution of vocal learning. The vocal learning process in birds is based on innate auditory preferences that bias young birds to learn the songs of their own species. Divergence across species in the genes underlying song perception may play a key role in the build up of reproductive isolation between species, but their evolutionary origin remains mysterious. Here, I compare innate auditory preferences in two closely related species of songbirds, the collared and pied flycatchers (Ficedula spp.). I demonstrate that juveniles from both species innately recognize their own species' songs. I use immunohistochemistry to investigate the neural and genetic basis of these behaviours, and present behavioral data suggesting that early perceptual differences influence adult song production and preferences. My results imply that genes involved in auditory perception play a driving role in the vocal learning process, which in turn affects sexual isolation between these species.

Session 1 FRI MAX 410 23

From the jungle to the barn: Independent genetic control for increased brain and body size and Mosaic brain evolution in chickens during domestication (52310)

Rie Henriksen, Leif Andersson, Per Jensen, **Dominic Wright**.

Linköping University; Uppsala University; Linköping University; Linköping University.
The evolution of brain size and its relationship with body size and brain substructure composition has proven to be both enduring and perplexing to disentangle. By crossing a domestic breed of chicken with its wild counterpart for multiple generations, we can address this problem by looking at the genes that control intra-specific species variation (and specifically inter-population variation) for overall brain size, body size and brain substructure size independently. We show (i) these traits have entirely separate genetic architectures, with different genes governing these traits. (ii) In contrast to popular belief, domestic chickens have larger, not smaller, brains than their wild counterparts, but as these genes are confounded by LD with the genes for extreme growth in pure domestic populations, this effect is masked by standard allometric measurements. (ii) Different regions control the development of different substructures, and that the cerebellum and cerebral hemisphere is enlarged in domestic birds. (iv) Brooding behaviour (a key behaviours missing from domestic hens) correlates negatively with cerebellum size in this intercross. These results have far-reaching consequences for the use of allometry in brain size study, and highlight how within-species variation can be used to answer general questions regarding the evolution of brain size.

## Evolution of acid-sensing olfactory circuits in Drosophila (52332)

**Lucia Prieto Godino**, Rapahel Rytz, Steeve Cruchet, Liliane Abuin, Benoite Bargeton, Ana Silbering, Vanessa Ruta, Matteo Dal Peraro, Richard Benton.

*Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Rockefeller University, New York, USA; Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.*

Nervous systems evolve to adapt animals' behavior to their ecological niches, but the genetic and cellular changes underlying this process are poorly understood. We have compared the olfactory circuits of the specialist fly species Drosophila sechellia, which feeds and breeds exclusively on the acid-rich fruit of Morinda citrifolia, with its generalist cousins D. melanogaster and D. simulans, which are associated with a wide range of fermenting fruits. We have identified both loss and gain of sensory responses to acids in D. sechellia and link these to single nucleotide differences within a tandem array of olfactory receptor genes, IR75a-IR75b-IR75c. These receptor functional differences are accompanied by multigenic-dependent changes that shape the species-specific neuroanatomical organization of acid-sensing pathways in the periphery, while leaving the organization of second order central neurons largely conserved. Importantly, we show that these peripheral traits can account in part for the distinct behavioral preferences of these species toward environmentally relevant odors, thereby linking chemosensory ecology to adaptive genetic changes influencing nervous system structure and function.

## Communication scenes of weakly-electric fish recorded in natural habitats challenge sensory processing (52598)
**Jan Benda**, Jörg Henninger, Rüdiger Krahe.

*University of Tübingen, Germany; McGill University, Montreal, Canada.*

The importance of using naturalistic stimuli for studying the neurophysiology of sensory information processing has been generally recognized. However, knowledge of species-specific natural stimuli in natural habitats - relevant for the evolution of the neural systems - is largely missing to date. We demonstrate that automated, large scale observations of electro-communication scenes of the neotropical gymnotiform weakly electric fish Apteronotus rostratus in natural habitats provide unexpected and novel insights to both neurophysiological and evolutionary aspects of animal communication. We continuously monitored electric fish behavior and communication interactions during courtship, spawning, and aggression using an array of 60 electrodes over many days. From the data we reconstructed frequencies and amplitudes of electrosensory stimuli received by the fish and compared them to the filter properties of electrosensory receptor neurons. While during male-male interactions the signal frequencies matched the tuning of the electrosensory periphery the signal amplitudes could be dramatically low. Conversely, during male-female interactions the signal amplitudes were much larger, but the frequencies clearly exceeded the receptors' best frequency. Electro-communication is thus used at the limits of electrosensory processing. Our field data provide novel naturalistic stimuli for studying sensory processing and raise interesting questions about the coevolution of sensory and motor systems.

# Nucleotide polymorphism and physiological diversity underlying pigmentation variation in Drosophila melanogaster (52481)

**Aya Takahashi.**

*Department of Biological Sciences, Tokyo Metropolitan University.*

Natural variation in pigmentation intensity in D. melanogaster, which is likely to be under some form of natural selection, is mainly caused by changes in cis-regulated gene expression level of a melanin biosynthesis gene, ebony. We found that knocking down this gene by RNAi changes desiccation resistance, which may be one of the pigmentation-associated physiological traits under selection. We also conducted a fine-scale quantification of the cis-regulated expression levels and sequence analyses of this gene using the sampled alleles from Drosophila Genomic Resource Panel (DGRP). Detailed comparisons between nucleotide and expression polymorphisms showed that there are multiple functional cis-regulatory alleles segregating in the population. Also, a long range LD was detected in the upstream region of this gene, which suggested an existence of complex interactions between nucleotide variants within the region. The detailed analyses on within population variants of this gene revealed a more complex picture compared to the simple model of expression divergence among species by changes in modular enhancers. In addition to the results on ebony, associations detected between various pigmentation traits and other genes in the melanin biosynthesis pathway will also be discussed.
# Do good genes induce a higher metabolic rate? A study in the colour polymorphic barn owl (52555)

**Alexandre Roulin**, Robin Séchaud, Paul Béziers.

*University of Lausanne; University of Lausanne; University of Lausanne.*

Variation in the degree of melanin-based coloration can have a strong underlying genetic basis. Colour morphs often differ in a number of other phenotypic attributes and it is not rare to observe that one morph better performs than other morphs in a large number of situations. This begs the question about how colour variation is evolutionary stable. In the barn owl (Tyto alba), females displaying larger black feather spots better cope with a number of stressful factors raising the question of how variation in spot size persists. We show here that larger-spotted female nestlings consume more oxygen independently of ambient temperature. This suggests that to sustain costly physiological processes that help cope with stressful environmental conditions, larger-spotted females invest more energy and hence have a higher metabolic rate. Large-spotted barn owls may therefore adopt a high cost/high benefit strategy and small-spotted barn owls a low cost/low benefit strategy. Our study may explain why polymorphism in the degree of melanin-based coloration is evolutionary stable. From a proximate point of view, our findings may due to the melanocortin system.

# Tests of the thermal melanism and melanisation desiccation-resistance hypotheses in New Zealand Hemideina maori (Orthoptera: Stenopelmatidae). (51925)

**Keith King**, Brent Sinclair, Jon Waters, Graham Wallis.

*Department of Zoology, University of Otago, Dunedin, New Zealand; Department of Biology, University of Western Ontario, London, ON, Canada; Department of Zoology, University of Otago, Dunedin, New Zealand; Department of Zoology, University of Otago, Dunedin, New Zealand.*

The New Zealand alpine tree weta (Hemideina maori) has melanic and yellow colour morphs. Melanism appears to have evolved repeatedly in this species, occuring sporadically in seven of eight clades mitochondrial DNA clades. The adaptive significance of melanism in H. maori has not been established. There is no evidence that melanism is associated with either increased immune response or incidence of parasitism. We investigated two additional hypotheses; thermal melanism and melanisation-desiccation resistance. Heat gain was measured in weta directly exposed to a heat source (basking simulation) as well as indirectly exposed (microhabitat simulation). In both simulations, thermal melanism was not supported as heat gain was not significantly increased in melanic morphs, compared to yellow. Weight was the significant covariate, with heat gain slower in heavier weta. We used open flow-through respirometry to compare water-loss rates between morphs. Melanic morphs had significantly lower rates of cuticular water loss than yellow morphs, thus supporting the
melanisation-desiccation resistance hypothesis. However, melanic H. maori are typically
found at lower (and presumably less-desiccating) elevations than yellow morphs, suggesting
that desiccation resistance is not the primary adaptive mechanism for melanism in H. maori.

# Effects of MC1R gene on sexual dimorphism in barn owls and the potential conflict between natural and sexual selection on melanin-based colorations (51974)

Luis San José Garcia, Anne-Lyse Ducrest, Valerie Ducret, Paul Béziers, Céline Simon, Kazumasa Wakamatsu, Alexandre Roulin.

*University of Lausanne; Fujita Health University.*

The melanocortin-1 receptor (MC1R) gene has been repeatedly observed to underlie adaptive colour variation in vertebrates. MC1R induces large changes in melanin-based colourations favoured by natural selection as an adaptation to diverse processes such as predator-prey interactions and thermoregulation. However, melanin-based colourations are often sexually dimorphic, suggesting that sexual selection could interact or even conflict with natural selection if MC1R also induces changes in the degree of sexual dimorphism. This hypothesis has not been tested despite evidences support that more sexually dimorphic galliform species accumulate more synonymous mutations at the MC1R. We present results confirming that MC1R colour effects induce correlated changes in sexual dimorphism in the barn owl, Tyto alba. Plumage colour traits in this species vary from white to red and from unspotted to heavily marked with black spots and depend on natural and sexual selection. Although males and females exhibit any phenotype, males are on average whiter and less spotted. MC1R largely explains variation in coloration but, more importantly, certain MC1R alleles allow for larger sexual dimorphism. These findings indicate that MC1R could epistatically act with factors determining sexual dimorphism, supporting that evolution of adaptive colouration through MC1R may interact with sexual selection.

# Could melanin-based plumage colouration be adaptive in environments polluted with trace metals? (52028)

Marion CHATELAIN, Julien GASPARINI, Adrien FRANTZ.

*Institute of Ecology and Environmental Sciences of Paris.*

Anthropogenic activities release significant amounts of trace metals in the biosphere, several of which are known to have deleterious effects on animals. Because of their toxicity, these trace metals may induce selective pressures and select for detoxification mechanisms. Interestingly, metals can bind to both keratin and melanin, resulting in high concentrations of metals in feathers. Metal chelation may consequently constitute one of the main current
biological functions of melanin. We aimed at investigating the adaptive role of melanin by testing 1) the selective pressures that zinc and lead exert on wild birds, 2) the relation between plumage melanin colouration and metal concentrations in both feathers and blood, and 3) the beneficial effect of highly melanic plumages in habitats with high amounts of trace metals. Indeed, we found noxious effects of a low but chronic experimental exposure to lead on feral pigeons' reproductive success and immunity. Positive correlations between both zinc and lead concentrations and plumage melanin colouration suggest that this pigment may allow eliminating circulating metals and may consequently be selected in environments polluted with toxic trace metals. The heterogeneity of metal concentrations in the environmental may participate to the evolutionary maintenance of melanin-based plumage colouration polymorphism.

Session 1 FRI POL A 31

# Larval UV exposure impairs adult immune function through a trade-off with larval investment in cuticular melanin (52344)

Sara Debecker, Ruben Sommaruga, Tim Maes, Robby Stoks.

*Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven;*
*Laboratory of Aquatic Photobiology and Plankton Ecology, Institute of Ecology, University of Innsbr.*

Despite the strong impact of ultraviolet (UV) radiation on invertebrates, it is unknown whether immune function is affected across metamorphosis. More general, the mechanisms on how larval stressors bridge metamorphosis and shape adult fitness remain poorly understood. We studied whether cuticular melanin content is upregulated under UV exposure in the larval stage of the damselfly Coenagrion puella and whether this is traded off across metamorphosis against a key component of the invertebrate immune response, the melanotic encapsulation response, in the adult stage. Larvae exposed to UV increased the melanin content in the exoskeleton and metamorphosed later and at a smaller mass than animals reared without UV. Across metamorphosis, this was associated with a reduced melanotic encapsulation response, thereby constituting the first proof for a UV driven impaired immune response in an invertebrate. Path analysis indicated that the immunosuppressive property of larval UV exposure was not mediated by age and mass at metamorphosis, but instead that the adult immune response was traded off against larval cuticular melanin investment. This melanin-based trade-off across metamorphosis provides a new pathway by which effects of larval stressors are carried over to the adult stage and thereby advances our understanding of the mechanisms of carryover effects of larval stressors across metamorphosis.

Session 1 FRI POL B 17

# Whole genome duplications and recruitment of ecologically relevant genes in alpine Mustards (52011)
Céline Geiser, Amélie Bardil, Terezie Mandáková, Béatrice North, Kevin Leempoel, Martin Lysak, Stéphane Joost, **Christian Parisod**.

*Institute of Biology, University of Neuchâtel, Switzerland; Central European Institute of Technology, Masaryk University, Czech Republic; Laboratory of Geographic Information Systems, École Polytechnique Fédérale de Lausanne, Switzerland.*

Polyploid taxa represent excellent models to address the underpinnings of genome evolution and the building up of new species in heterogeneous environments. Here, I present an overview of recent works in the alpine Biscutella laevigata autopolyploid complex (Brassicaceae). Transcriptomics inferred recurrent whole genome duplication (WGD) events specific to clade of species and that were used to infer processes fostering genome evolution across different timescales:

(i) After a 7-8 million years old WGD event, intense chromosomal repatterning selected for clusters of retained duplicates enriched in functions associated with responses to abiotic stresses. Low coverage genome sequencing unraveled the dynamics of several retrotransposons, supporting interplay between genome reorganization and environmental opportunities in shaping the evolution of paleopolyploids.

(ii) Retrotransposons in autotetraploids having recolonized the Alps after the ice ages showed considerable dynamics going along with ecological radiation following this recent WGD. Ecological genomics involving transplant experiment indeed supported distinct autopolyploid gene pools firmly associated with contrasted habitats despite gene flow. These ecotypes demonstrated adaptive differentiation at loci whose functions match habitat requirements. WGDs thus recurrently fostered genome reorganization and adaptive recruitment of genes responding to environmental factors, indicating that similar proximate and ultimate factors of genome dynamics may consistently act through time.

Session 1 FRI POL B 17

# Application of Associative Transcriptomics to polyploid crops (53307)

**Andrea Harper.**

*University of York.*

Associative Transcriptomics is designed to be rapidly applied to diverse crop species, and has proven particularly useful in polyploid species as, by focussing on transcribed sequences, it reduces the level of complexity that often complicates genetic analyses. Even without access to high quality genomic references, the method enables identification and ordering of both gene sequence and gene expression markers, which can then be associated to traits of interest. By using both types of marker, the method often simplifies the identification of candidate genes, and can uncover valuable information about the causative nature of the underlying variation. In this presentation, the approaches used to adapt the method to the allopolyploids oilseed rape and bread wheat will be discussed.
# Zinc accumulation, transcriptomics and asymmetric adaptation in the allopoly>ploid Arabidopsis kamchatica (51574)

**Timothy Paape**, Masaomi Hatakeyama, Jun Sese, Rie Shimizu-Inatsugi, Kentaro Shimizu.

*University of Zurich; Tokyo Institute of Technology.*

A feature that makes gene duplication through allopoly>ploid hyrbridization interesting compared to that of autopoly>ploidization (autosomal duplication within a single diploid ancestor) is that homeologous copies are not ancestrally identical but have unique evolutionary histories as a result of each diploid progenitor's evolution and their respective adaptations. Uniquely derived ancestral gene copies therefore have the potential to result in the retention of phenotypes that were present in either of the ancestors. Using de novo reference assemblies of both diploid ancestors and a newly developed bioinformatics pipeline to separate homeologous RNAseq reads, we have demonstrated that zinc accumulation in A. kamchatica is largely the result of transcriptional patterns and polymorphism derived from the diploid hyperaccumulating ancestor A. halleri ssp. gemmifera despite hybridization with a non-accumulating A. gyrata ancestor. Moreover, allopoly>ploid hybridization of the diploid parents which each possess highly divergent metal tolerance and hyperaccumulation phenotypes is equivalent to having diverse F1 crosses but without allelic recombination disrupting linkage as the ancestral gene copies evolve as homozygous homeologs. Our findings therefore allow us to explore the dynamic genome evolution of an allopoly>ploid species when asymmetric adaptations can be measured when stress conditions are applied.

# Evolutionary analysis and demographic inference for polyploid genomes using ABC (52703)

**Camille Roux**, John Pannell.

*UNIL; UNIL.*

Polyploidization is a major contributor to diversification of both plants and animals. However, despite its high incidence, the population genetic and evolutionary study of polyploid species has been seriously limited by challenges associated with multiple-copy genomes. Until now, for example, it has been difficult to infer important details histories of polyploid lineages, including the mode of polyploidisation and patterns of gene exchange between genomes and diverging lineages. These challenges stem both from complications arising during data acquisition (e.g., the need to attribute sequences to genome copies) and data analysis. Here, we present the use of approximate Bayesian computation (ABC) for the analysis of sequence data from non-model polyploid species using short-read NGS technologies to expose the recent evolutionary and demographic history of polyploid populations. Our study uses both simulated datasets and real nucleotide sequences from species in the Brassicaceae. We find that ABC is a powerful tool for discriminating between an autopoly>ploid vs. allopoly>ploid origin of a tetraploid species, is robust for detecting signatures of introgression between tetraploid populations and their close diploid relatives, and allows parameter estimation for a range of competing evolutionary and demographic models.
# Molecular basis of ecological diffusion after recurrent allopolyploidization in Dactylorhiza (52831)

**Ovidiu Paun**, Francisco Balao, Maria Lorenzo, Daniel Diehl, Bao-Hai Hao, Emiliano Trucchi, Mikael Hedrén.

*University of Vienna; University of Sevilla; University of Lund.*

Early-generation allopolyploids need to accommodate divergent genomes into one nucleus by adjusting organization and function, thereby influencing the ecological properties and adaptive success of resulting lineages. To identify the drivers of adaptation to distinct environments after iterative genome doubling, we investigate ecologically-divergent, sibling allopolyploids Dactylorhiza majalis and D. traunsteineri (Orchidaceae). By using RADseq we document a genome-wide absence of genetic differentiation between these allopolyploids, despite their phenotypic divergence. In addition, we bring evidence of frequent gene flow between the polyploids in sympatry, which points toward a strong divergent selection required in order to maintain the observed phenotypic divergence. By using the sibling allopolyploids of different ages in their native environmental context we investigate with RNAseq the progression through time of gene expression alterations after allopolyploidization, and their importance to the ecological properties of the polyploids. We observe a general trend of increased overexpression in the younger polyploid, whereas the transcriptome of the older resembles more closely those of the diploid parents. The differential expression between the polyploids is mainly driven by parental dominance in opposite directions and affects genes related to metabolic processes and response to stimulus. We discuss the importance of qualitative versus quantitative expression alterations in allopolyploid genomes, and their role for diversification in general.

# Whole genome duplication events and evolution of the self-incompatibility system are strongly associated within the Brassicaceae (52955)

**Xavier Vekemans**, Laura Henocq, Vincent Castric, Céline Poux.

*CNRS-Université Lille1.*

Recent studies using phylogenetic approaches, mapping of trait evolution, and quantification of species diversification have shown that transitions from outcrossing to selfing and from diploidy to polyploidy are associated with large reductions in species diversification rates. However, the joint evolution of polyploidy and mating system genes has rarely been addressed. We studied the impact of whole genome duplication events on the evolutionary dynamics of the self-incompatibility system in Brassicaceae. A clear signature of strong genetic bottleneck, followed by allelic re-diversification at the S-locus has been detected in three unrelated groups. In all three cases, this bottleneck appears to be associated with an
historical event of polyploidy. Detailed analyses of the S-locus genomic region in two cases have revealed common patterns (deletion of the S-locus in its ancestral position, evolution of a new S-locus at a different position), as well as striking differences (the genes involved in pollen-pistil recognition at the new S-locus are either orthologous or non-orthologous to the SCR and SRK genes of the ancestral Brassicaceae). These results suggest a scenario with temporary loss of self-incompatibility after polyploidization, followed by re-establishment of SI at a different genomic location with rapid allelic re-diversification caused by strong balancing selection.

# The effects of deleterious mutations on patterns of influenza A/H3N2's evolutionary dynamics (53349)

**Katia Koelle.**

*Duke University.*

Recent phylogenetic analyses indicate that RNA virus populations carry a substantial deleterious mutation load. This mutation load has the potential to shape patterns of adaptive evolution via genetic linkage to beneficial mutations. Here, we examine the effect of deleterious mutations on patterns of influenza A subtype H3N2's antigenic evolution in humans. By first analyzing simple mathematical models of influenza that incorporate a mutation load, we show that deleterious mutations act to slow influenza's rate of antigenic evolution, while making it more punctuated in nature. These models further predict three distinct molecular pathways by which antigenic cluster transitions occur, and we find phylogenetic patterns consistent with each of these pathways in influenza viral sequences. Simulations of a more complex phylodynamic model incorporating both antigenic and deleterious mutations further indicate that deleterious mutations act in concert with antigenic mutations to reproduce influenza's spindly hemagglutinin phylogeny, antigenic co-circulation, and high annual attack rates.

# Estimating heritability: old-school parent-offspring versus next-gen phylogenetics (52186)

**Gabriel Leventhal, Sebastian Bonhoeffer.**

*Institute of Integrative Biology, ETH Zurich.*

The heritability of a trait is one of the most used tools to quantify how fast a trait will evolve in a population. As a result, many different methods have been proposed to measure heritability in real populations. With the rise of the availability of genetic data, traditional methods such as parent-offspring regression or sibling analysis have been superseded by phylogeny-based methods to estimate heritability. However, as with all phylodynamic
models, tree-based methods for heritability estimation require an underlying model that describes how the trait evolved along the tree. Using set-point viral load in HIV as an example, I will show that tree-based estimates of heritability are very sensitive to model mis-specification such as the absence of selection. In contrast, estimates from parent-offspring (donor-recipient) regression are more robust to such misspecification. The difficulty of obtaining good parent-offspring pairs must thus be weighed against potentially strongly biased estimates of heritability.

## New routes to phylogeography (51904)

Nicola De Maio, Daniel Wilson.

*nuffield Department of Medicine.*

The inference of migration from pathogen genomic data is important to investigate routes of transmission, within-host infection dynamics, and sources of outbreaks. Statistical investigation is usually performed with discrete trait analysis models (i.e. Mugration) and similar, or with structured coalescent-based methods (e.g. MultiTypeTree). We propose a new method called BaStA (BAyesian STructured coalescent Approximation) based on an efficient approximation to the structured coalescent. We implemented BaStA in BEAST2. Furthermore, we performed a thorough comparison of the three approaches using both simulations and real data. Simulations show that our approach has comparable accuracy to MultiTypeTree, but much broader applicability. In contrast, Mugration showed generally unreliable estimates of both migration rates and ancestral locations. These differences were recapitulated in an analysis of zoonotic transmission events in real-world outbreaks, where Mugration inferred diametrically opposite results from the alternative approaches. Finally, we applied BaStA to an HIV compartmentalization dataset beyond the computational feasibility of MultiTypeTree and other structured coalescent-based methods due to the elevated number of demes.

## Heterogeneity in antibody range and the antigenic drift of influenza A viruses (52307)

Gabriela Gomes.

*Instituto Gulbenkian de Ciencia.*

In this paper we explore the consequences of a heterogeneous immune response in individuals on the evolution of a rapidly mutating virus. We show that several features of the incidence and phylogenetic patterns typical of influenza A may be understood in this framework. In our model, limited diversity and rapid drift of the circulating viral strains result from the interplay
of two interacting subpopulations with different types of immune response, narrow or broad, upon infection. The subpopulation with the narrow immune response acts as a reservoir where consecutive mutations escape immunity and can persist. Strains with a number of accumulated mutations escape immunity in the other subpopulation as well, causing larger epidemic peaks in the whole population, and reducing strain diversity. Overall, our model produces a modulation of epidemic peak heights and patterns of antigenic drift consistent with reported observations, suggesting an underlying mechanism for the evolutionary epidemiology of influenza, in particular, and other infectious diseases, more generally.

Session 1 FRI POL C 12

## Phylodynamic analysis of poliovirus outbreak (52809)

**Lucy Li**, Nicholas C Grassly, Christophe Fraser.

*Imperial College London.*

**Background:** Traditional surveillance of polio via Acute Flaccid Paralysis (AFP) reporting under-estimates the number of poliovirus infections as <1% of infections are symptomatic. Poliovirus genetic sequences collected from positive patient samples can provide an additional information to help quantify the size of the infected population. By concurrently analysing incidence data from AFP surveillance and viral sequence data from molecular surveillance, a more accurate estimate the prevalence of infection could be obtained.

**Method:** We jointly analysed the epidemiological and genealogical data from a poliovirus outbreak in Tajikistan to infer epidemiological parameters and reconstruct the epidemic trajectory. The likelihood of the epidemic trajectory depended on the incidence of reported cases and on the coalescent times of the viral genealogy.

**Results:** We found that the estimate of the infected population size depended on both the case-to-infection ratio and the heterogeneity in transmission. The variance in the number of secondary infections cause by each case was found to be high, suggesting the presence of super spreaders in the population. We also quantified the contribution of the viral genealogy to our estimated parameter values and epidemic trajectory.

Session 1 FRI POL C 12

## Phylodynamic inference for bacterial and viral populations using BEAST 2 (52622)

**Timothy Vaughan**, Gabriel Leventhal, Alexei Drummond, David Welch, Tanja Stadler, Nigel French.
Department of Computer Science, The University of Auckland, New Zealand; Department of
Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zürich);
Institute of Veterinary, Animal and Biomedical Sciences, Massey University, New Zealand.

Since its introduction by Grenfell et al. (Science, 2004), the term "phylodynamics" has been
used to describe a wide variety of relationships between the population and evolutionary
dynamics of rapidly evolving organisms. In this talk I will present our work on two distinct
phylodynamic inference methods which exploit these relationships in order to learn about
population dynamics from sampled genetic sequence data.

Firstly, I will present our progress toward developing and implementing an algorithm for
inferring the population dynamics of rapidly evolving bacterial populations in the presence of
gene conversion. Our algorithm is based on the work of Didelot et al. (Genetics, 2007;
Genetics, 2009). I will briefly introduce the algorithm and demonstrate its application to both
simulated and real bacterial genetic data.

Secondly, I will discuss some results from our recent investigations into the use of the Particle
Marginal Metropolis-Hastings algorithm (Andrieu et al., JRSSB, 2010) to perform exact
phylodynamic inference under stochastic variants of compartmental epidemiological models
such as SIR and SEIR. The method also allows for inference under arbitrary birth-death
models; including models with spatial structure. I will present some encouraging first steps
and discuss our future ambitions for this project.

Epigenetic origin of adaptive phenotypic variants in the blood-fluke
Schistosoma mansoni (52321)

Sara Fneich, André Theron, Céline Cosseau, Jérôme Buard, David Duval,
Nathalie Arancibia, Jérôme Boissier, Guillaume Mitta, Christoph Grunau.

Laboratoire Interactions Hôtes-Pathogènes-Environnements (IHPE) UMR5244
CNRS/University of Perpignan; CNRS, UPR1142, Institute de Génétique Humain (IGH),
Montpellier; INRA, UMR 1198 Biologie du Développement et Reproduction, Jouy en Josas,
France.

Adaptive evolution is impossible without the generation of phenotypic variants. The origin of variation has been a central topic in evolutionary biology. It is now commonly accepted that genetic variation is the only cause of phenotypic variants. The term “mutant” is even often used interchangeable to designate a genetic or a phenotypic variation. However, epigenetic information is emerging as a complementary source of heritable phenotypic variation. It is currently not clear what the relative importance of genetics and epigenetics in generating this variation is. We used a host-parasite system to address this question. The human blood fluke Schistosoma mansoni can adapt rapidly to new intermediate snail hosts. The interaction between parasite and mollusk is characterized by a compatibility polymorphism. The principal molecular marker for compatibility (infection success) is the expression pattern of polymorphic mucins (SmPoMuc). We show here that chromatin structure changes at the SmPoMuc promoters are the principal cause for SmPoMuc transcription polymorphism
leading to phenotypic novelty and increase in infection success i.e. fitness. We establish that epigenetic changes can be the major if not only cause of adaptive phenotypic variants in Schistosoma mansoni, suggesting that epimutations can provide material for adaptive evolution in the absence of genetic variation.

# Facing environmental predictability with different sources of epigenetic variation (52392)

Christelle Leung, Sophie Breton, Bernard Angers.

Université de Montréal.

Epigenetic processes have been proposed as a key mechanism enabling living organisms to cope with environmental challenges and explaining the ecological success of genetically identical organisms. Two contrasting but not mutually exclusive strategies are expected in response to environmental predictability: phenotypic plasticity resulting of epigenetic-environment interactions and diversifying bet-hedging resulting of random epigenetic changes would be respectively selected in stable and unstable environments. Using the asexual fish Chrosomus eos-neogaeus as a biological model, this study aimed to test whether the clonal lineages from distinct environments (lakes vs temporary streams) display different epigenetic variability. Results reveal striking differences in the partition of epigenetic diversity among lineages, suggesting that the clones were selected according to the type of environment. This study provides the first empirical support linking environmental predictability to different sources of epigenetic variation in natural populations.

# Epigenetic contribution to natural heritable variation within apomictic dandelion lineages (52587)

Koen Verhoeven.

Netherlands Institute of Ecology.

Asexual taxa are convenient models to explore the role of epigenetics in adaptation, because heritable epigenetic effects are more easily exposed and arguably also more relevant for adaptation when genetic variation is limited. To gain insight into the epigenetic contribution to heritable variation in asexual plants, we study epigenetic differences that build up between clone members of apomictic dandelion lineages. At the scale of several generations, we exposed clone members to different experimental environments and followed DNA methylation patterns for several subsequent generations, for which we explore a bisulfite sequencing GBS marker approach. At the scale of (micro-)evolutionary divergence, we compared different accessions from a single, geographically widespread apomictic lineage collected from different European countries. Accessions showed heritable differences in
flowering time, which was correlated with genomewide DNA methylation patterns. Flowering time differences between accessions disappeared after experimental in vivo demethylation, demonstrating that accession-specific DNA methylation causally contributes to heritable flowering time differences. Together, these studies shed light on the extent and evolutionary potential of epigenetic variation that builds up in asexuals. But important questions remain to be addressed and I will discuss some of the prospects and challenges for uncovering the adaptive role of epigenetic variation in natural systems.

# Importance of pollution induced epigenetic inheritance for phenotypic diversification in Daphnia pulex (51724)

**Helene Collin, Steve Paterson, Stewart Plaistow.**

*University of Liverpool.*

The transmission of phenotypic novelty from parents to offspring is more than Mendelian inheritance. Although epigenetic inheritance can result in the transmission and persistence across generations of non-genetic effects, empirical evidence that epigenetic inheritance does create such effects is still sparse. Moreover, the underlying molecular mechanisms involved in epigenetic inheritance remain poorly understood. We addressed this shortfall by performing multi-generation experiments in which we exposed three clones from a natural population of water fleas (Daphnia pulex) to sub-lethal doses of a novel freshwater pollutants (herbicide, heavy metal and endocrine disruptor). We then quantified phenotypic changes and epigenetic inheritance patterns (gene expression, micro-RNA expression and DNA methylation) over the next generations among the different clones. Transcriptional profiles generated with microarrays enabled the identification of genes and pathways differentially expressed in three generations of descendants whose ancestors were exposed to pollutants. We then used whole genome bisulphite sequencing and micro-RNAseq to pin down epigenetic modifications across the genome and test the hypothesis that epigenetic inheritance interacts with genetic inheritance to promote phenotypic variation. Overall, we provide an ecologically relevant test of the hypothesis that environmentally induced non-genetic inheritance mediated by epigenetic modifications has important consequences for phenotypic and evolutionary diversification.

# Associations of climate with DNA methylation polymorphisms provide evidence of local response to environment in a California oak, Quercus lobata (51731)

**Victoria Sork, Paul Gugger.**

*University of California Los Angeles.*
Epigenetic variation in natural populations may provide a mechanism to improve population response to environmental conditions. DNA methylation may promote or restrict gene expression that enhances plant performance and local adaptation. Our previous studies of epigenetic differentiation among three populations of Quercus lobata suggests that CpG methylation is either directly a target of natural selection or tightly linked to adaptive genetic variation. If DNA methylation plays a role in local adaptation, some methylation polymorphisms should be strongly associated with climate gradients. Here, we test this hypothesis in populations of Quercus lobata using bud and leaf tissue from 60 adults sampled throughout the species range. We generated reduced-representation bisulfite sequencing libraries (BS-Seq) to identify nucleotide and cytosine methylation polymorphisms (SNPs and SMPs). To identify outliers that are significantly correlated with climate variables, we conducted an environmental association analysis that controls for background demographic history. We found numerous SMPs that were strongly associated with climate. Many of them varied independent of the SNPs and some SNPs also showed significant association with climate. Our findings have important implications for the mechanisms underlying local adaptation to climate, especially in species with long-generation time, and the potential role of epigenetic mutations in adaptive evolution.

A role for methylation in responding to environmental stress in a wild rodent
(52729)

Angela Sims, Joannes van Cann, Esa Koskela, Tapio Mappes, Phill Watts, **Joannes van Cann**.

*University of Jyväskylä; University of Oulu.*

Individuals often require rapid responses to environmental change that can provide effects
that are longer-term than those produced by individual plasticity yet shorter than evolutionary
change. Bank voles (Myodes glareolus) experience population cyclicity which induces
environmental stress, such as increased population density or reduced food availability. By
giving females ecologically-relevant stressors it is possible to reveal the effects of early life
stress upon fitness as well as the underlying epigenetic mechanisms. Pregnant females were
given social stress or food stress (in a 2x2 factorial design) during pregnancy and were
profiled for DNA methylation. Animals were released in field enclosures to ascertain
subsequent differences in offspring fitness when they are introduced to high and low density
environments. Not only do mothers respond to stress during pregnancy by altering the number
and size of offspring, but the stressors also impact the size and number of offspring in the
subsequent generation with support for an epigenetic (DNA methylation) mechanism
associated with these fitness effects. The implication is that the epigenetic response of a
parent to its immediate environment can have lasting fitness effects on offspring and thus may
play a vital evolutionary role in adaptation to a cyclic environment.
# Epigenetic divergence and parallel evolution in Heliosperma pusillum (Caryophylaceae) (52742)

**Emiliano Trucchi**, Ruth Flascher, Maria Lorenzo Romero, Bozo Frajman, Peter Schönswetter, Ovidiu Paun.

*University of Vienna; University of Innsbruck.*

Epigenetic modifications are expected to occur at a faster rate than genetic mutations, and to be a flexible way to respond to stress conditions and to rapidly generate variation that can be visible to natural selection, even in the absence of genetic mutations. We then expect epigenetics to be particularly important in the early phases of adaptation and divergence. The alpine plant Heliosperma pusillum and its recently and recurrently diverged, low-montane sibling H. veselsky constitute a perfect model system to test this hypothesis. They occur in distinct ecological conditions with divergent morphologies (dense trichomes versus glabrous plants), stable and heritable in common garden settings. However, genome-wide data (AFLP, RADseq) fail to group them according to observed phenotypes. Employing a novel approach (bisulfite-converted RAD sequencing – bsRADseq), we screened the DNA methylation patterns across more than 200,000 nucleotide positions in six population pairs of the two ecotypes. Comparing by sequencing the DNA methylation state and context (CpG, CHG, CHH) in 120 individuals, we demonstrate that epigenetic patterns are much more conserved across representatives of the two ecotypes than predictions given the distinct native environments and that several candidate loci for convergent epigenetic modification during parallel adaptation to a similar environment are present.

Session 1 FRI GEN B 35

# The genetic sex determination system predicts adult sex ratio in tetrapods (51723)

**Mark Kirkpatrick**, Ivett Pipoly, Veronika Bókony, Tamás Székely, András Liker.

*University of Texas; University of Pannonia; University of Bath.*

Adult sex ratio (ASR) has critical effects on behaviour, ecology and population dynamics, but the causes of variation in ASR are unclear. Here we study how the type of genetic sex determination influences ASR variation across 354 species from 118 tetrapod families. Taxa with male heterogamy (XY systems) have a more female-biased ASR than taxa with female heterogamy (ZW systems). The effect is strong: the mean proportion of males is 0.48 for XY systems vs. 0.58 for ZW systems, and the type sex determination system explains 22% to 35% of variation between species in ASR. We develop models to understand the genetic factors that may contribute to this pattern, including meiotic drive and sex-linked deleterious mutations. Regardless of their causes, the effects of the genetic sex determination on the adult sex ratio are likely to have profound impacts on social behaviour of diverse tetrapod lineages.

Session 1 FRI GEN B 35
# A quantitative genetic signature of senescence in a short-lived perennial plant (51800)

**Benoit Pujol**, Pascal Marrot, John Pannell.

CNRS - Laboratoire Evolution & Diversité Biologique; CNRS - Centre d'Ecologie Fonctionnelle & Evolutive; University of Lausanne.

Senescence (the physiological decline of organisms with age) poses an apparent paradox because it represents a failure of natural selection to increase the survival and reproductive performance of organisms. The paradox can be resolved if natural selection becomes less effective with age, because the death of post-reproductive individuals should have diminished effects on Darwinian fitness. A substantial body of empirical work is consistent with this prediction for animals. In plants however, conclusions from demographic studies support the hypothesis that plants have avoided the evolution of senescence. Unlike animals, the survival and reproductive success of plants can increase with age. Such phenomenon is often attributed to the fact that reproduction is diffuse and modular across the soma in the plant kingdom. Here, we show that the necessary conditions for senescence to evolve can be found in many plants. We also provide experimental evidence for a quantitative genetic basis of senescence in the short-lived perennial plant Silene latifolia. We found a marked increase with age in the additive genetic variance of traits closely associated with fitness, as expected under the evolutionary theory of senescence. This result thus extends to plants the quantitative genetic support for the evolutionary theory of senescence.

Session 1 FRI GEN B 35

# Bauplan constraints on the evolution of lifespan in Vertebrates (52342)

**Alexander Scheuerlein.**

*Max Planck Institute for Demographic Research.*

Lifespan in vertebrates ranges from months to approximately 300 years. Here I will show using mortality data from 4000+ vertebrate species that average lifespan correlates with the shape of mortality trajectories in mammals, but not in other vertebrates. Specifically, it is the variation in lifespan within a species that is reduced at large body size in mammals. This is not the case in birds, amphibians, reptiles, or fish, where inter-individual variation in lifespan remains high. I will discuss this finding in the light of bauplan constraints that may hinder the evolution of long lifespans in mammals, despite large body size.

Session 1 FRI GEN B 35

# Early-life reproduction is associated with increased mortality risk but enhanced lifetime fitness in humans (51922)

**Virpi Lummaa**, Adam Hayward, Ilona Nenko.
The physiology of reproductive senescence is well-understood, but the drivers of variation in senescence rates are less so. Evolutionary theory predicts that early-life investment in reproduction should be favoured by selection at the cost of reduced survival and faster reproductive senescence. We tested this hypothesis in humans using data collected from preindustrial Finnish church records. Reproductive success of women increased up to age 25 and was relatively stable until a decline from age 41. Women with higher early-life fecundity (producing more children before age 25) subsequently had higher mortality risk, but high early-life fecundity was not associated with accelerated senescence in annual breeding rate. However, women with higher early-life fecundity experienced faster senescence in offspring "quality" (survival to adulthood). Despite these apparent costs, early-life fecundity was under positive selection: individuals with higher early-life fecundity had higher lifetime reproductive success. These results are consistent with evolutionary theory predicting trade-offs between early reproduction and later-life survival, and of interest in the light of recent increases in maternal ages in many societies and the potential consequences for offspring health and fitness.

# Repair or reproduce? Trying to solve an open question - an experimental study on zebra finches (51929)

**Joanna Sudyka**, Giulia Casasole, Joanna Rutkowska, Mariusz Cichoń.

*Institute of Environmental Sciences, Jagiellonian University.*

Somatic deterioration in ageing animals reflected in telomere decay may arise from differential allocation of resources. Telomeres are especially susceptible to the action of reactive oxygen species (ROS) damaging cellular structures. The link between reproduction, telomeres and oxidative stress has been repeatedly explored, but this enquiry remains inconclusive. We employ experimental approach (brood size manipulation) and a challenge with energetically costly burden (low ambient temperature) in zebra finches (Taeniopygia guttata) to evaluate if an array of ageing-related molecular markers: telomere length (qPCR), ROS and antioxidant levels (d-Rom and OXY tests) and DNA damage are influenced by enhanced reproductive effort. Individuals reproducing beyond their chosen rate should lose more telomeric sequences, and negative effect of reproductive effort has indeed been confirmed. Here we aim at revealing underlying mechanisms of this telomere decay. We hypothesize that telomere loss may stem from negative action of free radicals. We confirm that telomere decay in reproducing animals is faster and make this picture complete by showing that oxidative stress and defence are higher among parents experiencing enhanced reproductive effort.

# Reproductive costs in males: does it really matter? (52067)
Reproductive cost is a central concept in life-history theory. Reproduction requires resources that cannot be allocated to other functions resulting in a trade-off between current reproduction and future survival and/or future fecundity. Understanding such trade-offs, shaping life history traits, is crucial for evolutionary studies but also for demographic analyses. While examples of reproductive costs are widespread in the wild in females, there is no study investigating the overall support of direct reproductive costs in males. We screened the literature to gather studies testing the existence of direct costs of reproduction in male mammals and birds. We described the patterns of co-variations between current and future reproduction, and compared the differences between mammals and birds. Then, we examined the influence of paternal care and of the mating system on reproductive costs within birds. Finally, we discussed the possible bias that can mask reproductive costs in males. Because reproductive costs at the individual scale may have demographic consequences at the population scale, and while recent works have pointed out the need to integrate males into population models, we propose to explicitly take into account costs of reproduction in males into population models.

**Slow development as an evolutionary cost of long life (52549)**

**Martin Lind**, Hwei-yen Chen, Sara Meurling, Ana Cristina Guevara Gil, Hanne Carlsson, Martyna Zwoińska, Alexei Maklakov.

*Uppsala University.*

Long life is not for free, but is subjected to trade-offs with other life-history traits, which themselves are often under selection in natural populations. There is a growing appreciation that by focusing on the trade-off between reproduction and lifespan, we overlook the trade-off between development and lifespan. We investigated this trade-off in two independent selection experiments. First, by manipulating extrinsic mortality rate (high/low) and mortality source (random/heat-shock) we showed that high mortality rate under heat-shock leads to the evolution of increased lifespan and fecundity in outcrossing Caenorhabditis remanei nematodes, but at the cost of longer development time. The evolutionary link between development and lifespan was then independently assessed in a separate selection experiment by selecting C. remanei populations for short or long development time. This confirmed our findings above, since selection on slow development resulted in evolution of long lifespan. Because our experimental lines did not differ in body size, our results highlight the key role of development (differentiation of the soma) in the evolution of lifespan. Since development rate is often under strong selection in time-constrained natural populations of many species, reduced somatic maintenance and thus short intrinsic lifespan may be a widespread cost of adaptation to seasonal environments.
# Whole genome meiotic drive in Arthropods (53337)

**Laura Ross.**

*The University of Edinburgh.*

Sexual reproduction tends to be a remarkably “fair” and symmetrical process: a mother and father provide equal shares of their genes to their offspring, and each these has an equal chance of being passed on to future generations. Yet this symmetry has frequently broken down. Among thousands of species of insects and mites mothers monopolize the production of male offspring, by producing sons that eliminate their father's genome from their germline (Paternal genome elimination, PGE). Here I present theoretical and comparative analyses aimed at understanding the phylogenetic distribution and evolutionary dynamics of this unusual reproductive system. In addition I present empirical work on the epigenetic mechanisms by which the paternal genome is eliminated and on its implications for sex determination.

# Origin, evolution and consequences of sex chromosome drive in stalk-eyed flies (53336)

**Gerry Wilkinson, Josephine A. Reinhardt, Kimberly A. Paczolt.**

*Department of Biology, University of Maryland.*

Meiotic drive is a selfish genetic element in which a chromosome is passed preferentially to gametes. When it involves a sex chromosome, biased offspring sex ratios occur and, if unchecked, can quickly cause extinction. Sex chromosome drive can persist either by balancing selection or because it is masked by some form of suppression. Multiple examples of sex chromosome drive have been uncovered in interspecific crosses of Drosophila where a cryptic drive system is exposed due to the absence of appropriate suppressors. Diopsid stalk-eyed flies provide a fascinating group in which to study sex chromosome drive because 1) they possess a neo-X chromosome, 2) populations of multiple species contain drive X chromosomes at frequencies up to 30%, 3) several phenotypic traits, including eyespan, differ among drive and nondrive males, and 4) crosses between populations reveal both cryptic X and Y drive. In this talk I will summarize these findings and then present recent data derived from de novo assembly of testes transcriptomes from 17 different diopsid species, which include both drive and nondrive males from four different species, to reconstruct the evolutionary history of drive and nondrive X chromosomes in the genus Teleopsis and identify genes associated with drive in two independent lineages. I will also describe the extent of divergence between drive and nondrive X chromosomes using pooled genome resequencing data aligned to a reference genome. Finally, I will describe results from an experimental evolution study in which mating has been manipulated each generation either to exclude sexual selection, permit sperm competition without mate choice, or allow mate choice in either the presence or absence of a drive X chromosome. Collectively, these results provide
new insights into a novel sex chromosome drive system in which the genomic landscape of
the sex chromosomes is highly dynamic.

Mating system shifts and transposable element evolution (51670)

J Arvid Ågren, Stephen I Wright.

University of Toronto.

With respect to abundance, transposable elements (TEs) are an unrivalled success story
among selfish genetic elements. TEs make up about half of the human genome and more than
80% of some plant genomes. Replicating faster than the rest of the genome allows TEs to
spread despite their deleterious effects. However, this cannot explain why TEs are so common
in some species, but not in others. Mating system is predicted to play an important role the
evolutionary dynamics of TEs. Shifts to selfing from outcrossing, or from sexual to asexual
reproduction, will affect both the ability of TEs to spread to new lineages and the efficacy of
the selection acting on them. However, whether mating system shifts should lead to a net
accumulation or loss of TEs remains unclear. We discuss results from several whole genome
studies of TE abundances, genome distributions, and population frequencies, of multiple plant
genera to suggest that shifts to selfing or asexuality may initially lead to an increase in TE
copy number but that over longer evolutionary timescales asexual and selfing genomes will
lose TEs. We discuss what this balance between transmission and selection can tell us about
the evolution of selfish genetic elements more broadly.

Spore killer genomics: elucidating causes and consequences of meiotic drive in Neurospora (52515)

Jesper Svedberg, Ruxandra I. Molnar, Thomas M. Hammond, Hanna Johannesson.

Uppsala University; Illinois State University.

Conflict caused by selfish genetic elements is a driving force for evolutionary innovation, and hence, of fundamental importance for all aspects of evolution. Nevertheless, empirical data on the topic is largely lacking. Here, we introduce Neurospora as a novel study system of the evolutionary significance of meiotic drive. In this sexual eukaryote model system, the meiotic drive element Spore killer is found. The Spore killer and its resistance factor have been mapped to an approximately 2 Mbp large region of suppressed recombination on LG3. We have introgressed the Spore killer element, the resistance and sensitive alleles into uniform genetic background, and are screening the phenotypic effects of carrying the element. Furthermore, we have sequenced 90 genomes, representing all known Spore killers as well as sensitive and resistant strains of N. sitophila and N. intermedia using Illumina HiSeq (to 30x coverage). From seven of these we have also gathered MiSeq (100x) and Pac Bio (50x) data
to create high quality, full chromosome assemblies. This data has revealed a complex pattern
of inversions, insertions and deletions that may play an essential role in maintaining the
region of suppressed recombination and in explaining the birth and death of Spore killers over
evolutionary time.

The Molecular Basis of Paris Sex Ratio Meiotic Drive in Drosophila simulans
(52788)

Quentin Helleu, Pierre R. Gérard, Raphaelle Dubruille, David Ogereau, Bastien Saint-Léandre, Benjamin Prud'homme, Benjamin Loppin, Catherine Montchamp-Moreau.

EGCE, CNRS UMR9034, Université Paris-Saclay - Gif sur Yvette; CGφMC, CNRS UMR5534, Université Claude Bernard - Lyon; IBDM, CNRS UMR7288, Aix-Marseille Université.

Sex Ratio segregation distorters are selfish genetic elements that promote their own transmission by subverting the meiotic process to their advantage. The spread of an X-linked distorter in populations results in an excess of females, which triggers a genetic conflict between the X chromosome and the rest of the genome. Such conflicts are important drivers of genome evolution, but little is known about the molecular nature and function of the Sex Ratio selfish elements. I will present our recent work on the Paris Sex Ratio system of Drosophila simulans, in which two distorter elements on the X chromosome co-operate to prevent Y chromosome sister chromatids segregation during meiosis II. We mapped a gene in one of the distorter loci and achieved the functional validation of its involvement in sex-ratio distortion. It is a young and rapidly evolving gene that belongs to a well-known gene family involved in chromatin state regulation. It emerged through duplication about 15-22 Myrs ago and has experienced multiple independant cis-duplications, loss or pseudogenization throughout its evolutionary history. This suggests that this gene could have been involved in multiple genetic conflicts. These findings should help understanding the molecular basis of genetic conflicts and the evolutionary impact of heterochromatin regulation during meiosis.

Genome size variation and song attractiveness in grasshoppers: sexual selection against large genomes? (52928)

Holger Schielzeth, Corinna Streitner, Ulrike Lampe, Alexandra Franzke, Klaus Reinhold.

Bielefeld University.

Genome size evolution is affected by a conflict between selfish-genetic elements and the host genome, such that selfish genetic elements tend to increase genome size to a degree that impairs the fitness of the host. We have studied the impact of genome size on male attractiveness in the bow-winged grasshopper Chorthippus biguttulus. Grasshoppers exhibit
particularly large variation in genome size due to the high prevalence of supernumerary
chromosomes that are considered (mildly) selfish, as evidenced by non-Mendelian inheritance
and fitness costs if present in high numbers. We ranked male grasshoppers by song
characteristics that are known to affect female preferences in this species and scored genome
sizes of attractive and unattractive individuals. We then tested if attractive and unattractive
singers differ in their genomes sizes, which would demonstrate that genome size is reflected
in male courtship songs and that females select songs of males with small genomes. Such
mate preferences would effectively select against further increase in genome size and could
suggest an underappreciated route of how choosy females could gain indirect benefits. The
data can also provide a novel example of how sexual selection can reinforce natural selection
and act as an agent in an intragenomic arms race.

Diversity and the maintenance of sex by parasites (51799)

Ben Ashby, Kayla King.

University of Exeter; University of Oxford.

The Red Queen hypothesis predicts that parasite-mediated selection will maintain sexual
individuals in the face of competition from asexual lineages. The prediction is that sexual
individuals will be difficult targets for coevolving parasites if they give rise to more
genetically diverse offspring than asexuals. However, increasing host genetic diversity is
known to suppress parasite incidence, which could provide a short-term advantage to clonal
populations and lead to the extinction of sex. We test these ideas using a stochastic individual-
based model that fully incorporates ecological dynamics. We find that if parasites are readily
transmissible, then sex is most likely to be maintained when host diversity is high, in
agreement with the Red Queen hypothesis. If transmission rates are lower, however, we find
that sexual populations are most likely to persist for intermediate levels of diversity. Our
findings thus highlight the importance of genetic diversity and its impact on epidemiological
dynamics for the maintenance of sex by parasites.

Geographical parthenogenesis in Hieracium alpinum (Asteraceae): molecular evidence for multiple origin of asexuality and replacement of sexual diploids by asexual triploids (52584)

Patrik Mráz, Matthias Hartmann, Pavel Zdvořák, Delphine Rioux, Philippe Choler, Jindřich Chrtek, Pierre Taberlet.

*Department of Botany, Charles University in Prague, Czech Republic; Laboratoire d'Ecologie Alpine, J. Fourier University, Grenoble, France; Institute of Botany, Academy of Sciences of the Czech Republic, Pruhonice, Czech Republic.*
Many asexual species occupy larger ranges than their sexual relatives, a pattern referred to the term ‘geographical parthenogenesis’. Various hypotheses have been proposed to explain such patterns, nevertheless evidence for any of them is lacking because of limited number of empirical studies. Hieracium alpinum is an arcto-alpine species spreading from the far North (Greenland, Iceland, Fennoscandinavia) to the southerly situated mountains (Alps, Carpathians, Sudetes). While sexual diploids occur solely in the Southern-eastern Carpathians, apomictic autotriploids cover the rest of the range. Using straightforward combination of various approaches, we aim to test the hypotheses putatively underlying the origin, distributional success and adaptive potential of asexual triploids. Molecular data based on AFLPs and three plastid loci show highly congruent patterns and indicate (i) relatively high level of molecular variation within asexuals with, however, a predominance of one widespread genotype; (ii) multiple origin of asexual lineages which did not arise from extant diploids but they are rather remnants of extinct diploid lineages which have been completely replaced by asexuals. This potentially superior fitness / colonization ability of asexuals, when compared, to sexuals is discussed in the light of field data focusing on reproduction / dispersal potential, frequency of apomixis and biotic interactions.

# Interactions between genetic and ecological effects on the evolution of life cycles (52675)

**Marie Rescan**, Thoma Lenormand, Denis Roze.

*Station Biologique de Roscoff, UMI 3614 CNRS/UPMC; CEFE, UMR 5175 CNRS/UM2.*

Sexual reproduction leads to an alternation between a haploid and a diploid phase, whose relative development varies widely across taxa, with vegetative growth occurring in one phase only (haploidy or diploidy) or in both (biphasic cycles). Previous genetic models showed that either diploidy or haploidy can be favored, depending on the dominance of beneficial/deleterious alleles and on effective recombination rates. By contrast, ecological models showed that niche differentiation between phases stabilizes biphasic life cycles.

Here, we explore the interplay between genetic and ecological factors, considering that mutations affect the ecological properties of haploids and diploids, and may have differential effects between phases. We show that selection on a modifier gene affecting the relative length of both phases can be decomposed into a direct selection term favoring the phase with the highest mean fitness (due to ecological differences or to differential effects of mutations), and an indirect selection term favoring the phase in which selection is more efficient. When deleterious alleles occur at many loci and in the presence of ecological differentiation between phases, evolutionary branching often occurs and leads to the stable coexistence of alleles coding for haploidy and diploidy, while temporal variations in niche sizes stabilize biphasic cycles.
# Evidence for inter-individual genetic transfers among the genus Adineta vaga (52791)

**Nicolas Debortoli**, Xiang Li, Cuong Q Tang, Boris Hespeels, Diego Fontaneto, Jean-François Flot, Karine Van Doninck.

*UNamur; Imperial College London; National Research Council; University College London.*

Bdelloid rotifers have survived and diversified into more than 400 morphospecies over the past 40 My asexually. Genomic data suggest that chromosome pairing, and thus conventional meiosis, is impossible within the bdelloid rotifer Adineta vaga. Hence, their persistence and diversification as ancient asexuals is puzzling and suggest that they have developed alternative mechanisms to evolve and diversify. Using a population genetic approach combining nuclear and mitochondrial markers, distinct species delineation methods (GMYC, ABGD and Haplowebs) and genomics, we demonstrate for the first time inter-individual genetic transfers within a bdelloid rotifer lineage.

Our results indicate the existence of 6-7 distinct species in which most individuals reproduce clonally. However, two distinct patterns suggesting inter-individual genetic transfers were observed: (1) seven individuals were assigned to different species depending on the marker considered and (2) three cycles of allele-sharing in a [A||B, B||C, C||A] fashion were reconstructed. This could indicate a form of non-meiotic recombination among bdelloids such as parasexuality during which two whole chromosome sets are merged followed by random chromosome losses to re-establish the original ploidy. Alternatively, desiccation could promote horizontal gene transfers through frequent DNA double-strand breaks and genome repair upon rehydration.

# The Red Queen and the bdelloid rotifers: host-parasite interactions in the long-term absence of sex (51907)

**Christopher Wilson**, Antonios Kriezis, Timothy Penny, Joshua Potter, Timothy Barraclough.

*Imperial College London.*

Bdelloid rotifers are a class of microscopic invertebrates that abandoned males and meiosis millions of years ago. We present a new multi-locus, fossil-calibrated phylogenetic analysis indicating that a specialised clade of fungal parasites, Rotiferophthora, has been evolving and diversifying with bdelloids for at least twenty million years. This longstanding association seemingly challenges the prominent hypothesis that asexuals cannot keep up with coevolving parasites. Ecology offers a possible explanation: when their habitats dry up, bdelloids can persist for months as dormant, desiccated propagules that disperse widely by wind.

Rotiferophthora cannot tolerate extreme drought stress, and is destroyed or left behind, potentially interrupting the coevolutionary process and rescuing asexual hosts. To investigate this hypothesis, we challenged bdelloid clones from three global locations with twenty phylogenetically resolved fungal isolates, sympatric and allopatric. As predicted, Rotiferophthora isolates showed no local adaptation to bdelloid populations, partly because they had rather broad host ranges, as expected if they cannot follow specific hosts through
space and time. We also found some bdelloid clones that detected and destroyed ingested Rotiferophthora spores, demonstrating that although these ancient asexuals frequently 'run' from longstanding enemies, they can also mount an immunological fight, whose basis is an intriguing target for future investigation.

# No evidence for parasites maintaining sex in natural stick insect populations (52405)

Chloé Larose, Tanja Schwander.

UNIL, Department of Ecology & Evolution.

Sex is a conundrum of evolution! Since only females can directly produce offspring, asexual reproduction avoids the cost of producing males inherent to sexual reproduction. Nevertheless, asexuality is rare while obligate sex is widespread. One of the main hypotheses to explain the maintenance of sex is the Red Queen theory. This theory suggests that sex allows organisms to respond more effectively to continual changes in their environment, which is particularly relevant in the case of coevolution with parasites. However, we found no evidence for parasites maintaining sex in natural Timema stick-insect populations. We first identified a fungal parasite that infects a large proportion of individuals in their natural habitat, but found no evidence that sexuals are less infected by the parasite compared to related asexual species. By experimentally infecting individuals, we confirmed that infection induces an immune response, and has negative fitness effects for the host. Infection rates following reciprocal transplantation in the field further indicate local co-evolution between hosts and parasites, but no differences between sexual and asexual hosts. These results suggests that coevolution with this parasite is not selecting for sexual reproduction in Timema.

# Sexually antagonistic effects on development and transcriptomic maturity in Drosophila (52779)

Brian Hollis, Laurent Keller, Tadeusz J Kawecki.

University of Lausanne.

Sexually antagonistic selection exists whenever the evolutionary interests of males and females diverge and is an ultimate explanation for sexual dimorphism. The sexes must share most of the genome, however, so the evolution of sexual dimorphism is likely to be constrained in many ways. Here we will report the results of an experimental evolution study in Drosophila where selection on one sex has been greatly relaxed for over 150 generations by the elimination of all mating competition. This has resulted in parallel evolutionary change in the sexually dimorphic transcriptome of replicate populations. Beyond this, measures of sex-
specific maturation rate, at both the level of gene expression and egg-to-adult developmental timing, show elevated female performance and reduced male performance. Together, these experimental results represent the signature of an evolutionary process by which the genome is being optimized for female function at the expense of males.

# Sex-specific effects of serotonin on behavior and gene expression in a stalk-eyed fly (52813)

**Jaime Grace**, Andrew Bubak, Michael Watt, Kenneth Renner, John Swallow.

*University of Colorado Denver; University of South Dakota.*

Stalk-eyed flies, Teleopsis dalmanni, experience intense sexual selection, both intersexual and intrasexual, as males compete over access to territories and females. Males with longer eyestalks are both more attractive to females and more likely to win aggressive contests with other males. Serotonin (5-HT) plays a critical role in aggressive behavior: males with artificially elevated 5-HT levels are more likely to win competitions with size-matched opponents over a food source. However, the increase in aggression in response to elevated 5-HT may be sexually dimorphic. We first examined whether females treated with 5-HTP (5-hydroxytryptophan, the serotonin precursor that is converted to serotonin in the brain) are more likely to exhibit aggressive behaviors towards other females in size-matched contests. We then performed RNA sequencing on the brains of males and females treated with 5-HTP to determine which genes are differentially expressed relative to controls. Intriguingly, we found that females treated with 5-HTP exhibited fewer aggressive behaviors and were less likely to win aggressive competitions. We also describe candidate genes that may contribute to this dimorphic behavioral response. These studies illuminate the sexually dimorphic role of serotonin in modulating aggression and highlight other genes that may contribute to these sexually dimorphic aggressive behaviors.

# Convergent evolution of female-limited color dimorphism in Drosophila (52828)

**Amir Yassin**, Héloïse Bastide, Justin Lack, Jean David, John Pool.

*University of Wisconsin Madison, USA; Laboratoire EGS, CNRS, France.*

Drosophila melanogaster abdominal pigmentation is a paradigm trait for the study of the genetics of sexual dimorphism. This pattern is highly variable between species, but the genetic basis and evolutionary causes of its liability remain unclear. In D. erecta (melanogaster group) and circa 20 species of the montium group, the dimorphism is restricted only to females, with one female morph resembling monomorphic males. By combining intra- and inter-specific introgression mapping and comparative genomics we showed that female-
limited color dimorphism (FLCD) is associated with the X-linked tan locus in D. erecta, and
with the autosomal transcription factor pdm3 in three species of the montium group.
Population genetics revealed the presence of a partial selective sweep on the dark allele in D.
erecta (where males are dark), and an interspecific introgression of the light allele between
two montium species (where males are light). We hypothesize that male mimicry evolution is
due to female alternative strategies for optimal mating rate, and test this hypothesis using
population cages under different sex-ratio regimes. Given the unique genetic tools available
for these species, we believe that Drosophila FLCD may present a prime model for the study
of the recurrent evolution of sexual dimorphism in action.

Trans-regulation of sexually discordant expression from the Drosophila melanogaster X chromosome (52930)

Michael Stocks, Rebecca Dean, Björn Rogell, Urban Friberg.

University of Sheffield; University College London; Stockholm University; Linköping
University.

The X chromosome constitutes a unique genomic environment because it is present in one
copy in males, but two copies in females. This simple fact has motivated several theoretical
predictions with respect to how standing genetic variation on the X chromosome should differ
from the autosomes. In this study we tested for the amount and the type of genetic variation
on the X chromosome within a population of Drosophila melanogaster, by comparing the
proportion of X linked and autosomal trans-regulatory SNPs with sexually concordant and
discordant effect on gene expression. We find that the X chromosome is depleted for SNPs
with a sexually concordant effect, but hosts comparatively more SNPs with a sexually
discordant effect. Interestingly, this enrichment only concerns SNPs with a larger influence on
expression in females than expression in males. The distribution of these SNPs is shifted
towards regions where dosage compensation is predicted to be less complete. These results
suggest that intrinsic properties of dosage compensation influence either the accumulation of
different types of trans-factors and/or their propensity to accumulate mutations. These results
have general implications for X chromosome evolution, as well as the genetic basis of sex-
specific evolutionary change.

Sexual selection drives evolution and rapid turnover of male-biased genes
(51628)

Peter W. Harrison, Alison E. Wright, Fabian Zimmer, Rebecca Dean, Stephen H. Montgomery, Judith E. Mank.

University College London.
The rapid rates of evolution for sex-biased genes has led to the widespread assumption that they are the genomic manifestation of sexual selection. However, we still lack a clear understanding of the connection between sexual selection and transcriptional dimorphism. To assess the role of sexual selection in shaping evolutionary patterns of sex-biased genes, we assembled transcriptomes from an avian clade representing the full range of sexual selection. Using phylogenetically-controlled comparative methods, we show for the first time that sexual selection drives both rate of turnover in sex-biased expression as well as the degree of transcriptome sexualization. Our data also indicate that the rapid turnover in sex-biased gene expression occurs primarily through male expression evolution, and this is true for both male- and female-biased genes. Finally, our results suggest that the elevated rates of sequence evolution often observed for male-biased genes may not actually be due to adaptive evolution, and therefore sexual selection. Rather, our results implicate relaxed purifying selection as the principal cause of elevated rates of evolution. Taken together, our results provide the first direct links between sexual selection and evolutionary properties of sex-biased genes, highlighting the power of sexual selection in shaping gene expression and genome evolution.

## Evoltution by r- and K-selection in fluctuating environments (51771)

Bernt-Erik Saether, Steinar Engen, Visser Marcel E, Grøtan Vidar.

Centre for Biodiversity Dynamics, NTNU; Centre for Biodiversity Dynamics, NTNU; Netherlands Institute of Ecology; Centre for Biodiversity Dynamics, NTNU.

More than half a century ago r- and K-selection was proposed as a general process for producing evolutionary change, provided that phenotypic fitness depends on population size. Such density dependent selection will favour phenotypes with large growth rates r at small population sizes and phenotypes with high competitive skills when populations are close to the carrying capacity K. Here we present a new stochastic modelling framework that enables us to partition phenotypic selection in fluctuating environments into components due to population growth rate at low densities and strength of density dependence. Using the number of eggs laid in a season in a small song-bird, the great tit, as a phenotype, there is strong evidence for phenotypic variation in the strength of selection, resulting in balancing selection favouring large clutch sizes (r-selection) at small population densities and smaller clutches (K-selection) in years with large populations. Fluctuations in population size thus affect the fitness of individuals that lay different clutch size differently. This provides clear empirical evidence for r- and K-selection as an important selective agent in natural populations, which in turn may contribute to evolutionary rescue of populations affected by environmental perturbations such as climate change.

## Maintenance of polymorphism through small-scale spatial variation in selection (51814)
**Rolanda Lange**, Keyne Monro, Dustin Marshall.

*Monash University.*

How does trait diversity persist even though it is effectively depleted by selection? In theory, polymorphisms can be maintained by spatial and temporal variation in selection. To quantify such variation, we measured selection in a marine bryozoan along a depth gradient of only three meters - a small spatial scale relative to dispersal potential. Using life-time reproductive output in the field as a fitness measure we estimated multivariate selection on five phenotypic traits relating to individual size, colony growth and phenology. We found strong spatial variation in both linear and quadratic selection in several traits. Our results suggest that selection can vary over remarkably small environmental gradients, limiting the ability of dispersive marine species to adapt to any one environment and maintaining trait diversity.

Session 2 MON POL A 28

## Variation in selection in a wild insect population (51888)

**Tom Tregenza**, Rolando Rodríguez-Muñoz, David Fisher, Jon Slate, Ian Skicko, Sophie Kendall, Xingping Liu, Paul Hopwood, Carlos Rodríguez del Valle.

*University of Exeter; University of Sheffield; Jiangxi Agricultural University.*

Quantifying variation in selection in natural populations is essential for understanding its evolutionary importance. There are now a number of long term field studies that have successfully documented patterns of selection in plants and wild vertebrates. Short-lived exothermic animals are likely to experience greater variation in selection across generations than longer lived species. However, despite their abundance, measures of selection across years in wild invertebrates remain scarce. We have remotely monitored an individually tagged population of wild crickets using a network of up to 130 day-night video cameras distributed across individually marked burrows. This allows us to capture detailed information about naturally and sexually selected traits and life-history parameters, and to combine these data with local climatic variables. We have analysed >400,000 hours of video, recording >100,000 behavioural events. Over 9 years of monitoring, annual population size has fluctuated between 51 and 541 adults. There has also been substantial variation among years in sex ratio and traits including adult emergence dates, body size, male wing morphology and lifespan. Our data reveal individual mating patterns, dominance hierarchies, mortality sources and other key events. We combine these data with individual genotyping of the population, to provide insights into variation in selection in a wild insect population.

Session 2 MON POL A 28

## A general condition for adaptive genetic polymorphism in temporally and spatially heterogeneous environments (51891)

Hannes Svardal, **Claus Rüffler**, Joachim Hermisson.
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna; Animal Ecology, Department of Ecology and Genetics, Uppsala University; Mathematics and Biosciences Group, Department of Mathematics, University of Vienna.

Both evolution and ecology have long been concerned with the impact of environmental variability on levels of diversity. We model the evolution of a quantitative trait under selection that fluctuates in both space and time, and derive an analytical condition for when these fluctuations promote genetic diversification through adaptation to different environmental conditions. As ecological scenario we use a generalized island model with soft selection within patches in which we incorporate generation overlap. We allow for arbitrary fluctuations in the environment including spatio-temporal correlations. Using the concepts of invasion fitness and evolutionary branching, we derive a simple and transparent condition for the adaptive evolution and maintenance of genetic diversity. This condition relates the strength of selection within patches to expectations and variances in the environmental conditions across space and time. Our results unify, clarify, and extend a number of previous results on the evolution and maintenance of genetic variation under fluctuating selection. Individual-based simulations show that our results are independent of the details of the genetic architecture and whether reproduction is clonal or sexual. The onset of increased genetic variance is predicted accurately also in small populations in which alleles can go extinct due to environmental stochasticity.

# Spatio-temporal heterogeneity of natural selection in the wild: an experimental approach towards understanding life history adaptation of Arabidopsis thaliana. (52035)

Moises Exposito-Alonso, Adrian Brennan, Carlos Alonso-Blanco, F. Xavier Picó.

Max Plank Institute for Developmental Biology, 72076 Tuebingen, Germany; School of Biological and Biomedical Sciences, University of Durham, DH1 3LN Durham, UK; Spanish National Center for Biotechnology, Spanish National Research Council, 28049 Madrid, Spain; Doñana Biological Station, Spanish National Research Council, 41092 Sevilla, Spain.

The model annual plant Arabidopsis thaliana has become a useful model for evolution and ecology but just a few studies have addressed selection gradients on life history traits. Because A. thaliana shows a duality of life cycle - i.e. winter or spring cycles - we hypothesize enormous adaptive potential via life cycle adjustment in changing environments. We performed common garden experiments with 50 Iberian accessions (with the same genetic background to avoid bias) in two natural settings at different altitudes (350 and 1650 m) and starting at autumn and spring within every year for four years (2010-2014). We recorded germination rate, survivorship, flowering time, number of reproductive individuals, and number of seeds per plant. We detected huge plasticity of life cycle among genotypes, something that allowed good performance under very different conditions. Using integrated fitness, we found significant directional selection for flowering time and germination rate by experiment. Magnitude and sign of selection changed across locations and years. In the light of these results, we confirmed the importance of life cycle adjustment for climatic adaptation.
We also predict that environmental heterogeneity, and hence selection, can maintain phenotypic and genetic diversity in different environments, although at different frequencies.

# Tempo does not infer mode in evolution (52645)

Kjetil Voje.

Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo.

We lack a consensus on evolutionary rates in biology. The claimed dominance of almost no lineage evolution (stasis) in the fossil record does not rest well with the observation of high evolvability of virtually any quantitative trait studied in contemporary populations. This 'paradox of stasis' makes the long-term history of life seem almost decoupled from the evolutionary process we study on shorter time-scales. I analyze the rate of evolution in a large number of fossil time series that fit different modes (e.g. stasis, directional change) using novel statistical tools. I find no relationship between the mode of evolution and rate of change in the fossil record. The fluctuations observed in traits during stasis represent the same distance traveled in phenotype space compared to traits that fit different modes of evolution, including directional change. The result holds for fossil time series on various time scales. The observation of a similar rate of evolution during stasis and directional change in the fossil record has implications on several contemporary debates in evolutionary biology, and may increases our ability to explain macroevolutionary patterns with microevolutionary processes.

# Consequences of multiple-scale variation in selection on microgeographic adaptation (52197)

Philippe Cubry, Sylvie Oddou-Muratorio, Ivan Scotti, François Lefèvre.

INRA URFM "Ecologie des Forêts Méditerranéennes", UR629.

Local adaptation is generally considered at a large geographic scale, due to the common idea that high gene flow at microgeographic scale (i.e. within dispersal neighborhood) should prevent sub-populations to evolve traits conferring them a better fitness in their micro-habitat. However, environmental heterogeneity within populations can be huge, and was shown to result in microgeographic adaptation in some recent empirical studies.

Here we used NEMO simulation framework to simulate patterns of environmental heterogeneity both within (microgeographic scale) and among populations. Considering different strengths of selection, demographic parameters and genetic architectures, we evaluate local adaptation at microgeographic and population scales by using hierarchical Fst and Qst on quantitative loci.
Our results demonstrate that local adaptation at microgeographic scale occurs even under relatively low selection intensities. The decoupling between Qst and Fst appears higher at the microgeographic scale than at higher population scale, likely because the relative contribution of allelic combinations (compared to changes in allele frequencies) to local adaptation is higher at this microgeographic scale due to higher gene flow. This study sheds light on the potential of microgeographic adaptation to maintain local genetic diversity and to contribute to the evolvability of the population.

## Adaptive genome remodeling by massive changes in gene content and gene transfers across gene fungi (52106)

**Antoine Branca**, Jeanne Ropars, Ricardo Rodríguez de la Vega, Manuela López-Villavicencio, Jérôme Gouzy, Erika Sallet, Emilie Dumas, Joëlle Dupont, Tatiana Giraud.

*University Paris-Sud CNRS - ESE; University of Ottawa - CIAR; Museum National d'Histoire Naturelle CNRS - SEB; INRA/CNRS - LIPM.*

Cheesemaking has been an essential innovation for the transformation of milk, a highly perishable food, into a long-term preservable product. Two key Penicillium species have been used for the maturing of cheese: Penicillium roqueforti for blue cheeses and P. camemberti for Brie-type cheeses. These two distantly related molds have been independently selected for growth in a human-made nutrient-rich environment. Here we compared the genomes of ten Penicillium species isolated from various environments, including five newly-sequenced genomes. We show that Penicillium fungi have adapted to the cheese medium through the convergent expansions of multigene families and multiple recent horizontal transfers of crucial metabolic genes. We found in cheese-making Penicillium high numbers of lineage-specific genes family expansions involved in the utilization of the nutrients present in the cheese, such as lactate and phospholipids. Most of these species-specific gene expansions co-occurred in recently horizontally transferred regions, with almost 100% identity between distant species, and flanked by specific transposable elements. Laboratory assays linked the presence of a cheese fungus-specific horizontally-transferred region to both faster growth and greater competitiveness on cheese. Our results have both industrial and food safety implications, and improve our understanding of the genomic processes of adaptation to rapid environmental changes.

## Transcriptome comparisons within a species complex: Half a million years is enough to remove half of the genetic diversity in coding sequences, but not enough for morphological differentiation. Influence of life history (52218)

**Anne CHENUIL**, Nicolas GALTIER, Laurent ABI-RACHED, Alexandra WEBER.
Complexes of closely related species are interesting models especially when species are
sympatric and display contrasted traits. Ophioderma longicauda (Echinodermata) was recently
characterized as such. Although typically reproducing via lecithotrophic larvae, some lineages
brood their offspring. Transcriptomes from few individuals of those species were sequenced.
While whole transcriptome comparisons show that genetic diversity in the brooding species is
about half that of the species with larvae, this difference increases to 3-to-4 fold when
assessed on numerous individuals (with fewer genetic markers). Species delimitation within
the complex was established by discriminant analysis of principal components (DAPC) based
on multilocus genotypes (32 multiallelic loci). Divergence times between species were
obtained using Approximate Bayesian Computation (ABC) and a calibration with a pair of
Ophioderma species separated by the Isthmus of Panama, which closed about 3.5 mya. ABC
also estimated that effective sizes were much lower in the brooder than in ancestral and
broadcasting species. Thus, in only 550000 years (ca 100,000 generations), genetic diversity
drastically decreased in the brooders, probably owing to increased genetic drift. We discuss
whether this evolution would have been as rapid if a species with a large effective size had
emerged from a smaller effective size ancestor.

Evolutionary dynamics of bacterial pan-genomes (52245)

Jane Charlesworth, Daniel Wilson, Derrick Crook.

MMM, University of Oxford.

Bacterial genomes are dynamic landscapes. Gene gain/loss events are common in many
bacteria, such that strains within a species may vary quite a lot in gene content. As a result of
this extreme genome plasticity, bacteria are commonly described as having ‘core’ and
‘accessory’ genomes, where core genes are present in all, or virtually all examined isolates of
a species and accessory genes are variably present and absent. The complete gene repertoire
available to a bacterial species, or ‘pan-genome’, is an important resource for investigating the
genetic basis of phenotypes such as pathogen virulence (for example by looking at the
association of gene gain/loss events with phenotypes of interest) but constructing this set is
computationally very challenging. Using whole genome sequencing data, our work aims to
investigate which functional groups accessory genes represent and the phylogenetic
distribution of gene gain/loss events in population-level datasets from a diverse range of
bacterial species, including Staphylococcus aureus and Escherichia coli. We have developed a
bioinformatics pipeline to rapidly obtain the set of all genes present in thousands of sequenced
bacterial samples and are investigating the consequences of increasingly diverse and
comprehensive sampling on estimates of bacterial pan-genome content and size.
# Avian phylogenomic analyses revealed the macroevolution patterns of bird genomes (52249)

Guojie Zhang.

*Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark; National Genebank, BGI, Shenzhen, China.*

Characterization of genomic biodiversity through comprehensive species sampling has the potential to change our understanding of evolution. To study evolution across a major vertebrate class, dissect the genomics of complex traits, and resolve a centuries-old debate on the avian species tree, we formed a consortium focused on sequencing and analyses 48 bird genomes covered all 30 neognath orders, representing a wide range of avian evolutionary diversity. The phylogenomic analyses with full genome data produced a highly supported avian order phylogeny that resolves many debates on the timing and topology of their radiation. Whole genome comparison for all bird species with other vertebrate species revealed several distinct macroevolution patterns of avian genome. The small genome size of bird was a consequence of massive loss of repeat elements and thousands of functional genes at ancestral stage. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

# Fixation of gene duplications due to beneficial increases in gene expression (52436)

Margarida Cardoso-Moreira, J. Roman Arguello, David Riccardi, Srikanth Gottipati, Lawrence G. Harshman, Jennifer K. Grenier, Andrew G. Clark.

*Department of Molecular Biology and Genetics, Cornell University, USA; Center for Integrative Genomics, University of Lausanne, Switzerland; Translational Medicine and Think Team, Otsuka Pharmaceutical Development and Commercialization, Inc; School of Biological Sciences, University of Nebraska-Lincoln, USA.*

Gene duplications are a crucial source of genetic innovation and serve as major contributors to phenotypic evolution. Despite their evolutionary importance there are critical gaps in our understanding of how gene duplications fix in natural populations. Two outstanding questions remain: 1) Are gene duplications more often fixed by genetic drift or by positive selection?, and 2) If gene duplications are fixed by positive selection, what are the targets of selection? Here we address these two questions using the Drosophila Global Diversity lines, a novel resource of 84 D. melanogaster genomes derived from 5 geographically diverse populations that is well-suited for studies of local adaptation. We detected ~2,200 polymorphic duplications, including ~500 whole-gene duplications. We investigated the potential impact of these duplications by generating gene expression profiles for each line. We found that ~50% of gene duplications lead to significant increases in gene expression, and that these changes in
dosage are usually deleterious. However, the high-frequency gene duplications, for which we
found evidence of positive selection, also had significant increases in gene expression. Our
work suggests that gene duplications can be driven to fixation by positive selection in
Drosophila, probably due to beneficial increases in gene dosage.

Adaptive Evolution of a Clinal Inversion Polymorphism in Drosophila melanogaster (52643)

Martin Kapun, Chloé Schmidt, Jérome Goudet, Paul Schmidt, Thomas Flatt.

*Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland;*
*Department of Biology, University of Pennsylvania, Philadelphia, USA.*

In(3R)Payne, a common cosmopolitan inversion in D. melanogaster, exhibits steep latitudinal clines across multiple continents, but whether this pattern is due to spatially varying selection or demography remains unclear. To address this fundamental question we first estimated inversion frequencies by applying diagnostic marker SNPs to pool-seq data from 10 populations along the North American east coast. By comparing our estimates to published records we find that the inversion cline has remained stable for over thirty years. Consistent with this cline being maintained by selection, QST-FST analysis suggests that In(3R)P evolves non-neutrally. In further support of an adaptive scenario, SNP-wise regression reveals numerous inversion-associated alleles differentiated in parallel between the North American and Australian clines. Second, we sequenced pools of isochromosomal lines of In(3R)P karyotypes from the endpoints of the North American cline and identify major inversion-specific genetic differentiation among karyotypes. Finally, again paralleling observations from Australia, we find that In(3R)P makes a major contribution to the well-known body size cline in North America. Together, these results provide compelling evidence that In(3R)P is maintained by spatially varying selection across multiple continental clines.

Whole genome sequencing reveals an antibiotic resistance determinant driving rapid evolutionary change via several mechanisms in a multi-species outbreak (52688)

Anna Sheppard, Nicole Stoesser, Adam Giess, Robert Sebra, Andrew Kasarskis, Tim Peto, Derrick Crook, Costi Sifri, Amy Mathers.

MMM Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford,
UK; Icahn School of Medicine, Mount Sinai, New York, New York; Public Health England,
Microbiology Services, London, UK; Department of Medicine, University of Virginia Health
System, Charlottesville, Virginia; Office of Hospital Epidemiology, University of Virginia
Health System, Charlottesville, Virginia; Department of Pathology, University of Virginia
Health System, Charlottesville, Virginia.
The presence of the Klebsiella pneumoniae carbapenemase (KPC) gene blaKPC confers resistance to last line antimicrobial therapies, resulting in higher mortality in human infections. Although first described in K. pneumoniae, blaKPC has been acquired by multiple species of gram-negative bacteria and is usually found in association with the mobile transposon Tn4401. Here we describe an outbreak of blaKPC-positive Enterobacteriaceae from patients at a single US hospital prospectively collected over five years. We performed Illumina sequencing of 291 isolates from 189 patients, as well as long-read (Pacific Biosciences) sequencing of a subset to generate closed genomes. Twelve species were identified, with high intra-specific diversity, indicating frequent horizontal transfer of blaKPC within and between species. Two fully sequenced blaKPC plasmids carried by isolates from the index patient were each found in multiple species, demonstrating plasmid transfer as a mechanism for blaKPC spread. A number of unrelated plasmids carrying blaKPC were also identified, indicative of Tn4401 transposition between different plasmids. This work demonstrates that short-term evolution of bacterial pathogens can be driven by inheritance at multiple levels; in addition to vertical inheritance, we found a high frequency of horizontal transmission, facilitated either through promiscuous, highly mobile blaKPC plasmids or Tn4401 transposition.

# The effects of increasing parasite diversity on the evolution of resistance/infectivity and host/parasite growth (51903)

Alex Betts, Craig Maclean, Kayla King

Oxford University

Bacteriophages, the viral parasites of bacteria, have been suggested as an alternative to antibiotics in the face of increasing resistance in harmful bacteria. However, unlike antibiotics, bacteriophages can coevolve to counter new resistant phenotypes. While, most work on bacteria-bacteriophage coevolution has focussed on pairwise combinations of one phage against one bacterial species, phages naturally exist in parasitic communities. Phages vary in their ability to suppress bacterial populations and in the resistant phenotypes they select for in hosts. Phage community diversity may thus have complex ecological and evolutionary consequences in harmful bacterial populations of therapeutic relevance. We investigated the effects of phage community complexity on bacterial population growth and the evolution of resistance and infectivity using Pseudomonas aeruginosa PAO1 and a panel of lytic, dsDNA bacteriophages. Parasite diversity was manipulated by creating different combinations of phage up to a 5 phage cocktail. The bacteria and bacteriophage communities were allowed to coevolve and resistant phenotypes emerged very rapidly. Clones showing resistance to a 5 phage cocktail emerged within 24 hours. Additionally we observed reduced phage titres in more diverse communities, possibly an effect of inter-phage competition. These findings could have potentially important implications for application of bacteriophages as biological control agents.