cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1rn8pk0pz
title: Data from: The laboratory domestication of zebrafish: from diverse populations to inbred substrains

description: We know from human genetic studies that practically all aspects of biology
 are strongly influenced by the genetic background, as reflected in the
 advent of ‘personalized medicine’. Yet, with few exceptions, this is not
 taken into account when using laboratory populations as animal model
 systems for research in these fields. Laboratory strains of zebrafish
 (Danio rerio) are widely used for research in vertebrate developmental
 biology, behaviour and physiology, for modelling diseases, and for testing
 pharmaceutic compounds in vivo. However, all of these strains are derived
 from artificial bottleneck events and therefore are likely to represent
 only a fraction of the genetic diversity present within the species. Here
 we use Restriction site-Associated DNA sequencing (RAD-seq) to genetically
 characterize wild populations of zebrafish from India, Nepal and
 Bangladesh, and to compare them to previously published data on four
 common laboratory strains. We measured nucleotide diversity,
 heterozygosity and allele frequency spectra, and find that wild zebrafish
 are much more diverse than laboratory strains. Further, in wild zebrafish
 there is a clear signal of GC-biased gene conversion that is missing in
 laboratory strains. We also find that zebrafish populations in Nepal and
 Bangladesh are most distinct from all other strains studied, making them
 an attractive subject for future studies of zebrafish population genetics
 and molecular ecology. Finally, isolates of the same strains kept in
 different laboratories show a pattern of ongoing differentiation into
 genetically distinct substrains. Together, our findings broaden the basis
 for future genetic, physiological, pharmaceutic and evolutionary studies
 in Danio rerio.
description: All data used for producing this dataset originates from
 RAD-sequencing of wild and laboratory zebrafish genomic DNA digested
 with <i>SbfI</i>. Sequences were mapped to GRCz11 using
 <i>BWA-MEM</i> (version 0.7.17-r1188).
 <i>Samtools</i> (version 1.9) was used to filter out unmapped
 reads and non-primary alignments. Variant calling itself was performed
 with <i>Stacks (</i>version 2.4).Variants were annotated using
 <em>Ensembl Variant Effect Predictor</em>.
description: The allele in the "reference" column of the .vcf was
 determined in the associated study itself and does not always correspond
 to the reference genome. Populations:
 CHT - Wild fish from Chittagong,
 Bangladesh KHA - Wild fish from Khair Khola,
 Nepal UT - Wild fish from Uttarbhag, India
 CB - Wild derived fish from Cooch Behar, India
 AB, EKW, Nadia, TU, WIK - laboratory strains
 Files in the dataset: 
 wildlabdanio.vcf.gz - polymorphic sites identified in data from
 wild and laboratory zebrafish
 wildlabdanio.sumstats.tsv - output file from the
 <em>populations </em>module of Stacks v2.4
 wildlabdanio.vep.tsv - functional annotation of variants in the
 .vcf wildlabdanio.vep_summary.html - summary of the
 functional annotation
DOI: 10.5061/dryad.dv41ns1ts
title: Beyond the landscape: resistance modelling infers physical and behavioural gene flow barriers to a mobile carnivore across a metropolitan area

description: Urbanization affects key aspects of wildlife ecology. Dispersal in urban
 wildlife species may be impacted by geographical barriers but also by a
 species’ inherent behavioural variability. There are no functional
 connectivity analyses using continuous individual-based sampling across an
 urban-rural continuum that would allow a thorough assessment of the
 relative importance of physical and behavioural dispersal barriers. We
 used 16 microsatellite loci to genotype 374 red foxes (Vulpes vulpes) from
 the city of Berlin and surrounding rural regions in Brandenburg in order
 to study genetic structure and dispersal behaviour of a mobile carnivore
 across the urban-rural landscape. We assessed functional connectivity by
 applying an individual-based landscape genetic optimization procedure.
 Three commonly used genetic distance measures yielded different model
 selection results, with only the results of an eigenvector-based
 multivariate analysis reasonably explaining genetic differentiation
 patterns. Genetic clustering methods and landscape resistance modelling
 supported the presence of an urban population with reduced dispersal
 across the city border. Artificial structures (railways, motorways) served
 as main dispersal corridors within the cityscape, yet urban foxes avoided
 densely built-up areas. We show that despite their ubiquitous presence in
 urban areas, their mobility and behavioural plasticity, foxes were
 affected in their dispersal by anthropogenic presence. Distinguishing
 between man-made structures and  human activity, rather than
 between natural versus artificial structures, is thus essential to
 understand urban fox dispersal and  to predict how behaviour can
 shape population genetic structure beyond physical barriers.
DOI: 10.5061/dryad.2bvq83bkx
title: Diversification in evolutionary arenas – assessment and synthesis

description: Understanding how and why rates of evolutionary diversification vary is a
 central issue in evolutionary biology, ecology and biogeography. The
 concept of adaptive radiation has attracted much interest, but is
 metaphorical and verbal in nature, making it difficult to quantitatively
 compare different evolutionary lineages or geographic regions. In
 addition, the causes of evolutionary stasis are relatively neglected. Here
 we review the central concepts in the evolutionary diversification
 literature and bring these together by proposing a general framework for
 studying rates of diversification and quantifying their underlying
 dynamics, which can be applied across clades and regions and across
 spatial and temporal scales. Our framework describes the
 diversification rate (d) as a function of the abiotic environment (a), the
 biotic environment (b) and clade-specific phenotypes or traits (c); thus d
 ~ a, b, c. We refer to the four components (a–d) and their interactions
 collectively as the ‘Evolutionary Arena’. We outline analytical approaches
 to this conceptual model that may open up new avenues for research, and
 present a case study on conifers, for which we parameterise the general
 model. We also discuss three conceptual examples based on existing
 literature: the Lupinusradiation in the Andes in the context of
 emerging ecological opportunity and fluctuating connectivity due to
 climatic oscillations; oceanic island radiations in the context of
 archipelago isolation and island formation and erosion; and biotically
 driven radiations of the Mediterranean orchid genus Ophrys. The
 results of the conifer case study are consistent with the long-standing
 scenario that large niches, lack of competition, and high rates of niche
 evolution differentially promote diversification. The conceptual examples
 illustrate how using the synthetic Evolutionary Arena framework results in
 highlighting gaps in current knowledge, and thus help to identify and
 structure future directions for research on evolutionary
 radiations. In this way, the Evolutionary Arena framework
 promotes a more general understanding of variation in evolutionary rates
 by making quantitative results comparable between case studies, thereby
 allowing new syntheses of evolutionary and ecological processes to emerge.
DOI: 10.5061/dryad.k3j9kd53w
title: Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity

description: Hybridisation has the potential to generate or homogenize biodiversity and
 is a particularly common phenomenon in plants, with an estimated 25% of
 plant species undergoing inter-specific gene flow. However, hybridisation
 in Amazonia’s megadiverse tree flora was assumed to be extremely rare
 despite extensive sympatry between closely related species, and its role
 in diversification remains enigmatic because it has not yet been examined
 empirically. Using members of a dominant Amazonian tree family (Brownea,
 Fabaceae) as a model to address this knowledge gap, our study recovered
 extensive evidence of hybridisation among multiple lineages across
 phylogenetic scales. More specifically, using targeted sequence capture
 our results uncovered several historical introgression events between
 Brownea lineages and indicated that gene tree incongruence in Brownea is
 best explained by reticulation, rather than solely by incomplete lineage
 sorting. Furthermore, investigation of recent hybridisation using ~19,000
 ddRAD loci recovered a high degree of shared variation between two Brownea
 species that co-occur in the Ecuadorian Amazon. Our analyses also showed
 that these sympatric lineages exhibit homogeneous rates of introgression
 among loci relative to the genome-wide average, implying a lack of
 selection against hybrid genotypes and persistent hybridisation. Our
 results demonstrate that gene flow between multiple Amazonian tree species
 has occurred across temporal scales, and contrasts with the prevailing
 view of hybridisation’s rarity in Amazonia. Overall, our results provide
 novel evidence that reticulate evolution influenced diversification in
 part of the Amazonian tree flora, which is the most diverse on Earth.
DOI: 10.5061/dryad.w0vt4b8mk
title: Data from: Hybridization patterns between two marine snails, Littorina fabalis and L. obtusata

description: Characterizing the patterns of hybridization between closely related
 species is crucial to understand the role of gene flow in speciation. In
 particular, systems comprising multiple contacts between sister species
 offer an outstanding opportunity to investigate how reproductive isolation
 varies with environmental conditions, demography and geographic contexts
 of divergence. The flat periwinkles, Littorina obtusata and L. fabalis
 (Gastropoda), are two intertidal sister species with marked ecological
 differences compatible with late stages of speciation. Although
 hybridization between the two was previously suggested, its extent across
 the Atlantic shores of Europe remained largely unknown. Here, we combined
 genetic (microsatellites and mtDNA) and morphological data (shell and male
 genital morphology) from multiple populations of flat periwinkles in
 north-western Iberia to assess the extent of current and past
 hybridization between L. obtusata and L. fabalis under two contrasting
 geographic settings of divergence (sympatry and allopatry). Hybridization
 signatures based on both mtDNA and microsatellites were stronger in
 sympatric sites, although evidence for recent extensive admixture was
 found in a single location. Misidentification of individuals into species
 based on shell morphology was higher in sympatric than in allopatric
 sites. However, despite hybridization, species distinctiveness based on
 this phenotypic trait together with male genital morphology remained
 relatively high. The observed variation in the extent of hybridization
 among locations provides a rare opportunity for future studies on the
 consequences of different levels of gene flow for reinforcement, thus
 informing about the mechanisms underlying the completion of speciation.
DOI: 10.5061/dryad.h44j0zpft
title: Fruit syndromes in Viburnum: correlated evolution of color, nutritional content, and morphology in bird-dispersed fleshy fruits

description: Premise A key question in plant dispersal via animal vectors is where and
 why fruit colors vary between species and how color relates to other fruit
 traits. To better understand the factors shaping the evolution of fruit
 color diversity, we tested for the existence of syndromes of traits
 (color, morphology, and nutrition) in the fruits of Viburnum. We
 placed these results in a larger phylogenetic context and reconstructed
 ancestral states to assess how Viburnum fruit traits
 have evolved across the clade. Results We find that
 blue Viburnum fruits are not very juicy, have high lipid
 content, and large, round endocarps surrounded by a small quantity of
 pulp. Red fruits display the opposite suite of traits: they are very juicy
 with low lipid content and smaller, flatter endocarps. The
 ancestral Viburnum fruit may have gone through a
 sequence of color changes before maturation (green to yellow to red to
 black), though our reconstructions are equivocal. In one major clade
 of Viburnum (Nectarotinus), fruits mature synchronously
 with reduced intermediate color stages. Most transitions between fruit
 colors occurred in this synchronously fruiting clade. Conclusions It is
 widely accepted that fruit trait diversity has primarily been driven by
 the differing perceptual abilities of bird versus mammal
 frugivores. Yet within a clade of largely bird-dispersed fruits, we find
 clear correlations between color, morphology, and nutrition. These
 correlations are likely driven by a shift from sequential to synchronous
 development, followed by diversification in color, nutrition, and
 morphology. A deeper understanding of fruit evolution within clades will
 elucidate the degree to which such syndromes structure extant fruit
 diversity.
DOI: 10.5061/dryad.fn2z34tq1
title: Trait-modulated decline of carabid beetle occurrence along elevation gradients across the European Alps

description: Aim: To assess how species traits modulate the responses of carabids to
 elevation gradients, and how consistent these relationships are across
 different Alpine regions. Location: Italian Alps. Taxon: Coleoptera,
 Carabidae (ground beetles) Methods: Carabid communities were sampled using
 pitfall traps along elevation gradients (697-2840 m) in 416 study sites
 comprising a range of habitat types. The probability of carabid occurrence
 was modelled in relation to elevation and its interaction with two key
 traits, body size and wing development, using a mixed-modelling framework.
 The consistency of these associations was then assessed across three
 geographically separated regions. Results: Carabid occurrence declined
 with increasing elevation, although this relationship was modulated by
 both body size and wing development. Smaller species were less likely to
 occur than larger-bodied species at lower elevations. There was a steep
 decline in occurrence of larger species from low to high elevation, but a
 slight increase in smaller species, when considering all regions combined.
 All wing development types declined with elevation, most notably for
 brachypterous (reduced wings) species. However, these patterns also varied
 regionally, especially for wing development, indicating that
 trait-elevation interactions are not geographically consistent. Habitat
 could not explain the differences between regions for body size, but was
 likely an important driver of regional differences in the role of wing
 development on carabid occurrence. Main conclusions: Species traits are
 important in explaining the distribution of carabids along elevation
 gradients in mountains, and they may help to identify the species that are
 the most vulnerable, and the most resilient, to future environmental
 change. Increased probability of occurrence of smaller species at higher
 elevations suggests that they may be particularly vulnerable to
 environmental change in the future. However, the difference in responses
 to elevation between regions has important implications for modelling
 species distributions, as it suggests low model transferability, i.e. a
 trait-based model derived from one region cannot necessarily be used to
 project relative elevational shifts in a wider area.
description: Contents of the data files are listed in Data file
 contents.docx
DOI: 10.5061/dryad.6wwpzgmtk
title: Data from: Gene swamping alters evolution during range expansions in the protist Tetrahymena thermophila

description: At species’ range edges, individuals often face novel environmental
 conditions that may limit range expansion until populations adapt. The
 potential to adapt depends on genetic variation upon which selection can
 act. However, populations at species’ range edges are often genetically
 depauperated. One mechanism to increase genetic variation is to reshuffle
 existing variation through sex. During range expansions, sex can, however,
 act as a double-edged sword. The gene swamping hypothesis predicts that
 for populations expanding along an abiotic gradient, sex can hinder
 adaptation if asymmetric dispersal leads to numerous maladapted dispersers
 from the range core swamping the range edge. In this study, we
 experimentally tested the gene swamping hypothesis by performing
 replicated range expansions in landscapes with or without an abiotic
 pH-gradient, using the ciliate Tetrahymena thermophila, while
 simultaneously manipulating the occurrence of gene flow and sex. We show
 that sex accelerated evolution of local adaptation in the absence of gene
 flow, but hindered it in the presence of gene flow. The effect of sex,
 however, was independent of the pH-gradient, indicating that not only
 abiotic gradients but also the biotic gradient in population density leads
 to gene swamping. Overall, our results show that gene swamping can affect
 adaptation in life-history strategies.
DOI: 10.5061/dryad.sbcc2fr2p
title: Data from: Helping decisions and kin recognition in long-tailed tits: is call similarity used to direct help towards kin?

description: Most cooperative breeders live in discrete family groups, but in a
 minority, breeding populations comprise extended social networks of
 conspecifics that vary in relatedness. Selection for effective kin
 recognition may be expected for individuals in such kin neighbourhoods to
 maximise indirect fitness. Using a long-term social pedigree, molecular
 genetics, field observations and acoustic analyses, we examine how vocal
 similarity affects helping decisions in the long-tailed tit Aegithalos
 caudatus. Long-tailed tits are cooperative breeders in which help is
 typically redirected by males that have failed in their own breeding
 attempts towards the offspring of male relatives living within kin
 neighbourhoods. We identify a positive correlation between call similarity
 and kinship suggesting that vocal cues offer a plausible mechanism for kin
 discrimination. Furthermore, we show that failed breeders choose to help
 males with calls more similar to their own. However, although helpers
 fine-tune their provisioning rates according to how closely related they
 are to recipients, their effort was not correlated with their vocal
 similarity to helped breeders. We conclude that although vocalisations are
 an important part of the recognition system of long-tailed tits,
 discrimination is likely to be based on prior association and may involve
 a combination of vocal and non-vocal cues.
DOI: 10.5061/dryad.cjsxksn29
title: Data from: Why don’t long-finned pilot whales have post-reproductive lifespan? insights from genetic data

description:  In a handful of mammals, females show an extended
 post-reproductive lifespan (PRLS), leading to questions over why they
 spend a substantial portion of their lifespan non-reproductive. 
 Theoretical and empirical studies suggest that PRLS may evolve when (1)
 demographic patterns lead to increasing local relatedness as females age,
 and (2) females come into reproductive competition with their daughters,
 as these conditions lead to high relative benefits of helping kin versus
 reproducing in later life. However, evolutionary pathways to PRLS are
 poorly understood and empirical studies are scarce. Here, we use a dataset
 of 1522 individuals comprising 22 pods to investigate patterns of
 reproduction and relatedness in long-finned pilot whales Globicephala
 melas;  a toothed whale without species-wide PRLS. We find a
 similar relatedness structure to whales with PRLS: pods appear composed of
 related matrilines, and relatedness of females to their pod increases with
 age, suggesting that this species could benefit from late-life help.
 However, females with a large number of philopatric adult daughters (but
 not sons) are less likely to reproduce, implying intergenerational
 reproductive competition between females. This suggests that individuals
 may display a plastic cessation of reproduction, switching to investing in
 existing offspring when they come into competition with their daughters.
 To the best of our knowledge, this is the first time such a relationship
 has been described in relation to PRLS, and it raises questions about
 whether this represents a step towards evolving PRLS or is a stable
 alternative strategy to widespread post-reproductive periods.
description: Nichols et al pilot whale female reproduction dataset, and
 relatedness dataset Dataset containing female
 reproductive data: female identity, social group (pod) identity, female
 age (years), number of offspring genetically assigned to the female, the
 number of genetically assigned adult offspring aged 10+, number of
 foetuses (whether or not the focal female was pregnant at time of
 capture), and the number of adult offpring (aged 10+) split into male and
 female offspring. Dataset containing relatedness data:
 The identity, sex and age of individuals 1 and 2, the genetic relatedness
 between individuals 1 and 2, the pod (social group) identity and size that
 the two individuals were found in.
DOI: 10.5061/dryad.sqv9s4n0k
title: Data from: The smallest known Devonian tetrapod shows unexpectedly derived features, Part 1 of 2

description: A new genus and species of Devonian tetrapod,
 Brittagnathus minutus gen. et sp. nov., is described from a single
 complete right lower jaw ramus recovered
 from the Acanthostega mass-death deposit
 in the upper part of the Britta Dal
 Formation (upper Famennian) of Stensiö Bjerg, Gauss Peninsula, East
 Greenland. Visualisation by propagation phase contrast synchrotron
 microtomography (PPC-SRμCT) allows a complete digital dissection
 of the specimen. With a total jaw ramus length of 44.8
 mm, Brittagnathus is by
 far the smallest Devonian tetrapod described to date. It differs from all previously knownDevonian tetrapods in having only a fang pair without a tooth row on the anterior coronoid, and a large posterior process on the posterior coronoid. The presence of an incipient surangular crest and a concave prearticular margin to the adductor fossa together cause the fossa to face somewhat mesially, reminiscent of the condition in Carboniferous tetrapods. A phylogenetic analysis places Brittagnathus crownward to other Devonian tetrapods, adjacent to the Tournaisian genus Pederpes. Together with other recent discoveries, it suggests that diversification of ‘Carboniferous-grade’ tetrapods had already begun before the end of the Devonian and that the group was not greatly affected by the end-Devonian mass extinction.
description: Synchrotron microtomography data set of Devonian tetrapod jaw
 NHMD 116368, holotype and only specimen of Brittagnathus
 minutus. The specimen, NHMD 116368, (field number MGUH
 f.n. 1373) was collected in July 1987 from the<em>
 Acanthostega</em>-yielding horizon on Stensiö Bjerg, Gauss
 Peninsula, East Greenland. It was initially prepared mechanically, which
 revealed the posterior end of the lateral surface and the lower margin and
 prearticular on the medial surface. In September 2016 the specimen was
 imaged using propagation phase contrast synchrotron microtomography
 (PPC-SRmCT) at the European Synchrotron Radiation Facility (ESRF) in
 Grenoble, France. The scan was part of Experiment ES-505 and was made
 courtesy of Valéria Vaskaninova to whom the beamtime had been awarded. The
 voxel size of the scan was 13.49 mm, made with single distance phase
 retrieval and a propagation distance of 5m. The reconstructed volume was
 converted into a stack of 16 bit TIFF images. Because
 each of the 1708 images is a separate file, and Dryad imposes a 1000-file
 limit on data sets, the stack has been split in two: this is Part 1,
 containing the first 973 images. Part 2 is available at doi:10.5061/dryad.vt4b8gtng