cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rj15h
title: Data from: Time to get moving: assisted gene flow of forest trees

description: Geographic variation in trees has been investigated since the mid-18th
 century. Similar patterns of clinal variation have been observed along
 latitudinal and elevational gradients in common garden experiments for
 many temperate and boreal species. These studies convinced forest managers
 that a ‘local is best’ seed source policy was usually safest for
 reforestation. In recent decades, experimental design, phenotyping
 methods, climatic data and statistical analyses have improved greatly and
 refined but not radically changed knowledge of clines. The maintenance of
 local adaptation despite high gene flow suggests selection for local
 adaptation to climate is strong. Concerns over maladaptation resulting
 from climate change have motivated many new genecological and population
 genomics studies; however, few jurisdictions have implemented assisted
 gene flow (AGF), the translocation of pre-adapted individuals to
 facilitate adaptation of planted forests to climate change. Here, we
 provide evidence that temperate tree species show clines along climatic
 gradients sufficiently similar for average patterns or climate models to
 guide AGF in the absence of species-specific knowledge. Composite
 provenancing of multiple seed sources can be used to increase diversity
 and buffer against future climate uncertainty. New knowledge will continue
 to refine and improve AGF as climates warm further.
description: Population mean
 phenotypes for 19 conifer species compiled from 23 previous
 studiesThis Excel file contains
 one sheet of metadata, and 23 spreadsheets of phenotypic data. Each
 spreadsheet of data includes results from one study for one species from
 one common garden. Data provided includes unique codes to identify each
 population, the latitude, longitude, elevation, mean annual temperature
 (C), and mean summer precipitation (in units of 100 mm), the number of
 families within population that were tested, and the total number of
 individuals that were tested. Phenotypic traits include height growth in
 varying units (see associated publication), the timing of spring
 phenological events in days relative to a reference date, and the timing
 of fall phenological events relative to a reference
 date.Aitken
 and Bemmels 2016 Dryad dataset.xlsx
DOI: 10.5061/dryad.0st06f0
title: Data from: Ecological niche and phylogeny explain distribution of seed mass in the Central European flora

description: Seed size is a crucial life-history trait determining the amount of
 reserves that are available to establishing seedlings. The most frequently
 observed patterns in seed size distribution are a higher frequency of
 large-seeded species in shaded habitats and a positive correlation of seed
 size with plant size. We analysed to what extent realised niche
 dimensions, as expressed by Ellenberg indicator values and plant
 functional traits such as plant height and life form, explained seed mass
 variation in the Central European flora. By including information on
 phylogenetic relatedness of the species, not only contemporary ecology but
 also the evolutionary history of plant species could be taken into
 account. Seed mass evolution was slow and was best explained by
 selection-inertia models with multiple adaptive peaks as a function of
 either habitat or life form. The highest seed mass optima were observed in
 the deciduous forest and saltwater and seashore habitats, and in
 phanerophytes in case of models with optima as a function of life form.
 The analyses showed that Ellenberg values were more important than habitat
 and life form in explaining seed mass distribution in the Central European
 flora. The often observed relation between shade and large seeds was also
 evident in our study, but we found an equally important relation between
 large seeds and drought and a positive relation between seed mass and
 salinity. Our results indicate that not only plant size and competition
 for light but a complex set of factors influence the ecology of seed size,
 and that a more precise delineation of species' niches improves the
 understanding of seed size evolution.
description: Plant trait data and
 Ellenberg valuesPlant traits Vandelook et al
 Oikos.csvPhylogenetic
 treePhylogeny Vandelook et al
 Oikos.tre
DOI: 10.5061/dryad.f4s16
title: Data from: Genetic and life-history consequences of extreme climate events

description: Climate change is predicted to increase the frequency and intensity of
 extreme climate events. Tests on empirical data of theory-based
 predictions on the consequences of extreme climate events are thus
 necessary to understand the adaptive potential of species and the
 overarching risks associated with all aspects of climate change. We tested
 predictions on the genetic and life-history consequences of extreme
 climate events in two populations of marble trout Salmo marmoratus that
 have experienced severe demographic bottlenecks due to flash floods. We
 combined long-term field and genotyping data with pedigree reconstruction
 in a theory-based framework. Our results show that after flash floods,
 reproduction occurred at a younger age in one population. In both
 populations, we found the highest reproductive variance in the first
 cohort born after the floods due to a combination of fewer parents and
 higher early survival of offspring. A small number of parents allowed for
 demographic recovery after the floods, but the genetic bottleneck further
 reduced genetic diversity in both populations. Our results also elucidate
 some of the mechanisms responsible for a greater prevalence of faster life
 histories after the extreme event.
description: Zak_Lipo_tag_recaptureTag-recapture data for the marble trout populations of Zakojska and Lipovscek (two .csv files). Mark = fish ID; Year = year of sampling; Month = month of sampling; Run = first pass (1) or second pass (2); Sector = stream section in which the fish was sampled; Length = total length of fish (mm); Weight = weight of the fish (g); Age = age of fish - fish emerge in May/June, they are 0+ up to first winter, then 1+ and so on; Cohort: year of birth (format Cyy); Adc: 1 if adipose fin was cut - only for fish with no tag when sampled; Adip = additional tag associated with a piece of the adipose cut.Zak_Lipo_SNP_genotypeGenotype data for the marble trout populations of Zakojska and Lipovscek. LOCATION = name of the stream/population; SAMPLE_ID fish ID, corresponds to Mark in the tag-recapture dataset; SEX = sex of fish - ? and NA mean not available/uncertain; YOB = year of birth of fish. Additional columns are the bi-allelic SNPs (0 means not genotyped).
DOI: 10.5061/dryad.9pn5m
title: Data from: Using semidefinite programming to optimize unequal deployment of genotypes to a clonal seed orchard

description: Tree breeders must often consider the conservation of genetic diversity,
 while at the same time, maximizing response to selection. In the case of
 seed orchards, the buyer of seed wants maximum performance, while
 satisfying a restriction, sometimes legislated, on the diversity deployed
 to the forest. Optimal selection will not completely avoid kinship but
 rather maximize gain while imposing a constraint on average relatedness.
 Here, we present the application of semidefinite programming (SDP) as a
 flexible approach to optimize the deployment of genotypes to a clonal seed
 orchard. We formulate the selection problem as an SDP, where average
 breeding value is to be maximized, while imposing constraints on
 relatedness, as well as maximum and minimum contributions from each
 candidate. An open-source solver, SDPA, was embedded into a tool designed
 to make the optimization of seed orchards by SDP simple and flexible. Case
 studies optimizing seed orchards for Scots pine and loblolly pine
 illustrate how this flexibility can be used to impose additional
 constraints on the scion material available from some candidate genotypes
 and optimize selection even when related candidates have varying degrees
 of coancestry among them. Additional situations where SDP can be employed
 are discussed.
description: Input file for OPSEL run
 for Scots pine case study with unlimited contributionsPedigree and EBV data
 for input into OPSEL, optimizing the selection of Scots pine genotypes
 into a seed orchard with total of 2800 ramets and Status number &lt;= 14.
 Maximum contribution of candidates is set at 2800, i.e.,
 unlimited.sP_unlimited.csvInput file for OPSEL run for Scots pine case study with limited F1 contributionsPedigree and EBV data for input into OPSEL, optimizing the selection of Scots pine genotypes into a seed orchard with total of 2800 ramets and Status number &lt;= 14. Maximum contribution of F1 candidates is set at 50, while maximum contributions for others are set to 2800, i.e., unlimited.sP_limited_F1s.csvInput file for OPSEL run for loblolly pine case study with unlimited contributionsPedigree and EBV data for input into OPSEL, optimizing the selection of clonally replicated loblolly pine genotypes into a seed orchard with total of 2000 ramets and Status number &lt;= 10. Maximum contribution of candidates is set at 2000, i.e., unlimitedlP_unlimited.csv
DOI: 10.5061/dryad.74458
title: Data from: Distribution and population genetic variation of cryptic species of the Alpine mayfly Baetis alpinus (Ephemeroptera: Baetidae) in the Central Alps

description: Background: Many species contain evolutionarily distinct groups that are
 genetically highly differentiated but morphologically difficult to
 distinguish (i.e., cryptic species). The presence of cryptic species poses
 significant challenges for the accurate assessment of biodiversity and, if
 unrecognized, may lead to erroneous inferences in many fields of
 biological research and conservation. Results: We tested for cryptic
 genetic variation within the broadly distributed alpine mayfly Baetis
 alpinus across several major European drainages in the central Alps.
 Bayesian clustering and multivariate analyses of nuclear microsatellite
 loci, combined with phylogenetic analyses of mitochondrial DNA, were used
 to assess population genetic structure and diversity. We identified two
 genetically highly differentiated lineages (A and B) that had no obvious
 differences in regional distribution patterns, and occurred in local
 sympatry. Furthermore, the two lineages differed in relative abundance,
 overall levels of genetic diversity as well as patterns of population
 structure: lineage A was abundant, widely distributed and had a higher
 level of genetic variation, whereas lineage B was less abundant, more
 prevalent in spring-fed tributaries than glacier-fed streams and
 restricted to high elevations. Subsequent morphological analyses revealed
 that traits previously acknowledged as intraspecific variation of B.
 alpinus in fact segregated these two lineages. Conclusions: Taken
 together, our findings indicate that even common and apparently
 ecologically well-studied species may consist of reproductively isolated
 units, with distinct evolutionary histories and likely different ecology
 and evolutionary potential. These findings emphasize the need to
 investigate hidden diversity even in well-known species to allow for
 appropriate assessment of biological diversity and conservation measures.
description: nuclear microsatellite
 genotypes of Baetis alpinus and Baetis melanonyxnuclear data (10
 microsatellites) of Baetis alpinus and Baetis melanonyx populations
 sampled in the central Alps (Switzerland).Nuclear_SSRs_Leys
 et_al_BMCEvolBiol.txt
DOI: 10.5061/dryad.np29h
title: Data from: A linkage disequilibrium perspective on the genetic mosaic of speciation in two hybridizing Mediterranean white oaks

description: We analyzed the genetic mosaic of speciation in two hybridizing
 Mediterranean white oaks from the Iberian Peninsula (Quercus faginea Lamb.
 and Quercus pyrenaica Willd.). The two species show ecological divergence
 in flowering phenology, leaf morphology and composition, and in their
 basic or acidic soil preferences. Ninety expressed sequence tag-simple
 sequence repeats (EST-SSRs) and eight nuclear SSRs were genotyped in 96
 trees from each species. Genotyping was designed in two steps. First, we
 used 69 markers evenly distributed over the 12 linkage groups (LGs) of the
 oak linkage map to confirm the species genetic identity of the sampled
 genotypes, and searched for differentiation outliers. Then, we genotyped
 29 additional markers from the chromosome bins containing the outliers and
 repeated the multilocus scans. We found one or two additional outliers
 within four saturated bins, thus confirming that outliers are organized
 into clusters. Linkage disequilibrium (LD) was extensive; even for loosely
 linked and for independent markers. Consequently, score tests for
 association between two-marker haplotypes and the ‘species trait’ showed a
 broad genomic divergence, although substantial variation across the genome
 and within LGs was also observed. We discuss the influence of several
 confounding effects on neutrality tests and review the evolutionary
 processes leading to extensive LD. Finally, we examine how LD analyses
 within regions that contain outlier clusters and quantitative trait loci
 can help to identify regions of divergence and/or genomic hitchhiking in
 the light of predictions from ecological speciation theory.
description: Dataset-HDY-14-OR0183RGenotypic data for the 192 analyzed trees. Tree names include an abbreviation of their locations, followed by an abbreviation of the species and a numeric identifier (1 to 12). Marker genotypes are described in two adjacent columns.
DOI: 10.5061/dryad.v933m
title: Data from: Cryptic choice of conspecific sperm controlled by the impact of ovarian fluid on sperm swimming behaviour

description: Despite evidence that variation in male-female reproductive compatibility
 exists in many fertilization systems, identifying mechanisms of cryptic
 female choice at the gamete level has been a challenge. Here, under risks
 of genetic incompatibility through hybridization, we show how salmon and
 trout eggs promote fertilization by conspecific sperm. Using in vitro
 fertilization experiments that replicate the gametic micro-environment, we
 find complete inter-fertility between both species. However, if either
 species’ ova were presented with equivalent numbers of both sperm types,
 conspecific sperm gained fertilization precedence. Surprisingly, the
 species’ identity of the eggs did not explain this cryptic female choice,
 which instead was primarily controlled by conspecific ovarian fluid, a
 semi-viscous, protein-rich solution which bathes the eggs and is released
 at spawning. Video-analyses revealed that ovarian fluid doubled sperm
 motile lifespan, and straightened swimming trajectory, behaviours allowing
 chemoattraction up a concentration gradient. To confirm chemoattraction,
 cell migration tests through membranes containing pores that approximated
 to the egg micropyle showed that conspecific ovarian fluid attracted many
 more spermatozoa though the membrane, compared with heterospecific fluid
 or water. These combined findings together identify how cryptic female
 choice can evolve at the gamete level and promote reproductive isolation,
 mediated by a specific chemoattractive influence of ovarian fluid on sperm
 swimming behaviour.
description: SALMON TROUT
 HYBRIDISATIONS SPERM SATURATED FINAL yeates et al 2013 Figure
 1Data
 on fertilization success rates for means in first half of Figure
 1Sperm competition data
 Figure 1 Yeates et al 2013Sperm competition
 success data for second half of Figure 1FERTILIZATION RATE DATA
 YEATES ET AL 2013 FIG 2Data for fertilization
 rate means in Figure 2salmon and trout male OF
 competition success YEATES ET AL 2013 FIG 3Sperm competition
 success data for Figure 3HYBRID EGG DEVELOPMENT
 AND EMBRYO VIABILITY RATE CHECK DATA Yeates et al 2013Embryo development data
 to check hybrid viability does not confound sperm competition success
 resultssperm trait means gage
 et al 2013Sperm trait data for
 Figure 4TRANSWELL_DATA MEANS
 yeates et al 2013Transwell sperm
 migration data raw counts Figure 6
DOI: 10.5061/dryad.v9m50r8
title: Data from: Immigrant song: males and females learn songs post-dispersal in a tropical bird

description: A fundamental hypothesis about vocal learning is that young animals learn
 vocalizations in their natal areas and, following post-natal dispersal,
 they may introduce new types of vocalizations into their breeding areas.
 We tested this hypothesis in a tropical bird, the Rufous-and-white Wren
 (Thryophilus rufalbus), a species in which both sexes produce learned
 songs. We collected blood samples and acoustic recordings from 146 adult
 wrens from three populations in northwestern Costa Rica. We genotyped
 individuals at 10 polymorphic microsatellite loci and identified
 first-generation migrants using partial Bayesian genotype assignment. We
 quantified acoustic variation by comparing fine-scale acoustic structure,
 song sharing, and repertoire novelty between residents and
 first-generation migrants. We found significant population-level
 differences in acoustic structure of songs among the three populations. Of
 the 146 individuals genotyped, 9 individuals were identified as
 first-generation migrants. In contrast to our predictions, however, we
 found that these first-generation migrants did not exhibit differences in
 the acoustic structure of their songs from resident individuals in their
 breeding population, either for males or females. We conclude that song
 learning in first-generation migrants must be behaviourly influenced by
 birds in their breeding populations, following post-natal dispersal. We
 observed population-level acoustic differences among the three study
 sites, which implies sustained divergent selection pressures at each site,
 possibly reflecting acoustic adaptation to different environments or
 social pressure to sing local songs. Understanding and quantifying
 patterns of cultural evolution at multiple scales provides insight into
 how behavioural barriers, such as acoustic signals, contribute to
 population differentiation and even speciation.
description: BEHECO-2017-0505 Dryad
 submission fileIn the data file are
 three sheets: The first sheet contains song data for the analyses of
 individual song-type analyses. Sheet two contains data for the analyses
 repertoire variation. Sheet three contains data for the population-level
 analyses of song variation
DOI: 10.5061/dryad.8979
title: Data from: Domain loss facilitates accelerated evolution and neofunctionalization of duplicate snake venom metalloproteinase toxin genes

description: Gene duplication is a key mechanism for the adaptive evolution and
 neofunctionalization of gene families. Large multi-gene families often
 exhibit complex evolutionary histories as a result of frequent gene
 duplication acting in concordance with positive selection pressures.
 Alterations in the domain structure of genes, causing changes in the
 molecular scaffold of proteins, can also result in a complex evolutionary
 history and has been observed in functionally diverse multi-gene toxin
 families. Here, we investigate the role alterations in domain structure
 have on the tempo of evolution and neofunctionalization of multi-gene
 families using the snake venom metalloproteinases (SVMPs) as a model
 system. Our results reveal that the evolutionary history of viperid
 (Serpentes: Viperidae) SVMPs is repeatedly punctuated by domain loss, with
 the single loss of the cysteine-rich domain, facilitating the formation of
 P-II class SVMPs, occurring prior to the convergent loss of the
 disintegrin domain to form multiple P-I SVMP structures. Notably, the
 majority of phylogenetic branches where domain loss was inferred to have
 occurred exhibited highly significant evidence of positive selection in
 surface-exposed amino acid residues, resulting in the neofunctionalization
 of P-II and P-I SVMP classes. These results provide a valuable insight
 into the mechanisms by which complex gene families evolve and detail how
 the loss of domain structures can catalyse the accelerated evolution of
 novel gene paralogues. The ensuing generation of differing molecular
 scaffolds encoded by the same multi-gene family facilitates gene
 neofunctionalization, whilst presenting an evolutionary advantage through
 the retention of multiple genes capable of encoding functionally distinct
 proteins.
description: PIII_PIISequence alignment (.fas) of translated PIII and PII SVMPs used for tests of adaptive molecular evolution in the manuscriptPII_PISequence alignment (.fas) of translated PII and PI SVMPs used for tests of adaptive molecular evolution in the manuscript
DOI: 10.5061/dryad.r13f5
title: Data from: How to measure maturation: a comparison of probabilistic methods used to test for genotypic variation and plasticity in the decision to mature

description: Maturation is a developmental trait that plays a key role in shaping
 organisms’ life-history. However, progress in understanding how maturation
 phenotypes evolve has been held back by confusion over how best to model
 maturation decisions and a lack of studies comparing genotypic variation
 in maturation. Here, we fitted probabilistic maturation reaction norms
 (PMRNs) to data collected from five clones of Daphnia magna and five of
 Daphnia pulex collected from within and between different populations. We
 directly compared the utility of modeling approaches that assume
 maturation to be a process with an instantaneous rate with those that do
 not by fitting maturation rate and logistic regression models, and
 emphasize similarities and differences between them. Our results
 demonstrate that in Daphnia, PMRNs using a logistic regression approach
 were simpler to use and provided a better fit to the data. The decision to
 mature was plastic across a range of growth trajectories and dependent
 upon both body size and age. However, the age effect was stronger in D.
 magna than D. pulex and varied considerably between clones. Our results
 support the idea that maturation thresholds can evolve but also suggest
 that the notion of a threshold based on a single fixed state is an
 oversimplification that underestimates the adaptability of these important
 traits.
description: Maturation data for D.
 magnaAge (a1, a2) and size
 (s1, s2) intervals of 5 Daphnia magna clones every instar until
 primiparity (eggs). Columns: preova, mature and eggs refer to achieving
 IM-1, IM-2 and IM-3 respectively (see manuscript). Column: trt refers to
 concentration of food (not required for analysis).mat_data_magna.txtMaturation data for D. pulexAge (a1, a2) and size (s1, s2) intervals of 5 Daphnia pulex clones very instar until primiparity (eggs). Columns: preova, mature and eggs refer to achieving IM-1, IM-2 and IM-3 respectively (see manuscript). Column: trt refers to concentration of food (not required for analysis).mat_data_pulex.txt