cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n6k3n
title: Data from: Life-history characteristics of European birds

description: Motivation: Birds are an extremely diverse group in terms of adaptations
 to environmental conditions, which is reflected in their life histories
 and ecological traits. Recently, functional aspects of avian diversity
 have been used frequently in comparative analyses as well as in community
 ecology studies; thus, open access to complete datasets of traits will be
 valuable. We focused on European bird species and compiled information
 about crucial ecological traits. This dataset is thus useful for research
 investigating large-scale patterns in European avifauna and can be used in
 various analyses in evolutionary ecology, macroecology or conservation
 biology. Main types of variables contained: We chose several types of
 avian traits, such as morphological (e.g., weight, wing, bill or tarsus
 length), reproductive (e.g., clutch size, egg mass, incubation period or
 type of young) and behavioural traits (type of nest, mating system or type
 of parental care), dietary (e.g., folivore, granivore, insectivore or
 carnivore) and habitat preferences (e.g., deciduous/coniferous forest,
 reed or grassland). Spatial location and grain: Europe; all breeding bird
 species (n = 499). Major taxa and level of measurement: In total, we
 created a dataset for 499 bird species breeding in Europe and 34 key
 life-history traits represented in 85 variables. As a primary source of
 information we used the comprehensive handbook The birds of the Western
 Palearctic. The traits provide information about species-specific mean
 values. We did not record values for different geographical subspecies
 (i.e., the trait value always represents the average for the whole
 breeding area of a particular species). Software format: The data file is
 in ASCII text, tab delimited, not compressed.
description: Life-history
 characteristics of European birdsWe created a dataset for
 499 bird species breeding in Europe and 34 key life-history traits
 represented in 85 variables. As a primary source of information we used
 the comprehensive handbook the Birds of the Western Palearctic. The traits
 inform about species specific mean values. We did not record values for
 different geographical subspecies, i.e. the trait value always represents
 average for the whole breeding area of particular
 species.
DOI: 10.5061/dryad.8bk20
title: Data from: Contemporary ecotypic divergence during a recent range expansion was facilitated by adaptive introgression

description: Although rapid phenotypic evolution during range expansion associated with
 colonization of contrasting habitats has been documented in several taxa,
 the evolutionary mechanisms that underlie such phenotypic divergence have
 less often been investigated. A strong candidate for rapid ecotype
 formation within an invaded range is the three-spine stickleback in the
 Lake Geneva region of central Europe. Since its introduction only about
 140 years ago, it has undergone a significant expansion of its range and
 its niche, now forming phenotypically differentiated parapatric ecotypes
 that occupy either the pelagic zone of the large lake or small inlet
 streams, respectively. By comparing museum collections from different
 times with contemporary population samples, we here reconstruct the
 evolution of parapatric phenotypic divergence through time. Using genetic
 data from modern samples, we infer the underlying invasion history. We
 find that parapatric habitat-dependent phenotypic divergence between the
 lake and stream was already present in the first half of the twentieth
 century, but the magnitude of differentiation increased through time,
 particularly in antipredator defence traits. This suggests that divergent
 selection between the habitats occurred and was stable through much of the
 time since colonization. Recently, increased phenotypic differentiation in
 antipredator defence traits likely results from habitat-dependent
 selection on alleles that arrived through introgression from a distantly
 related lineage from outside the Lake Geneva region. This illustrates how
 hybridization can quickly promote phenotypic divergence in a system where
 adaptation from standing genetic variation was constrained.
description: Lucek_et_al_JEB-2014-00477.R1_DryadMicrosatellite data for contemporary and linear morphology for historical and contemporary stickleback populations from the Lake Geneva region and Switzerland.
DOI: 10.5061/dryad.gh18c
title: Data from: Asplenium pifongiae (Aspleniaceae: Polypodiales), a new species from Taiwan

description: We describe and illustrate a new species, Asplenium pifongia., currently
 known only from Taiwan. Although superficially similar to A. monanthe.,
 this species is a sexual diploid and has little perforation on its spore
 surfaces. Phylogenetic analyses demonstrate that A. pifongia. is not
 closely related to A. monanthe., and is instead sister to the A. normal.
 complex. Asplenium pifongia. differs from A. normal. in having sori mostly
 only on, and parallel to, the basiscopic side of pinnae, a common feature
 in A. monanthes.
description: Asplenium_trnLF_rps4_trnS_trnGR_rbcLThe nexus file used to generate the phylogeny tree.Asplenium_trnLFtrps4trnStrnGRrbcL_datafile_forsubmission.nexus
DOI: 10.5061/dryad.mb37t1q
title: Data from: Limited hatchery introgression into wild brook trout (Salvelinus fontinalis) populations despite reoccurring stocking

description: Due to increased anthropogenic pressures on many fish populations,
 supplementing wild populations with captive-raised individuals has become
 an increasingly common management practice. Stocking programs can be
 controversial due to uncertainty about the long-term fitness effects of
 genetic introgression on wild populations. In particular, introgression
 between hatchery and wild individuals can cause declines in wild
 population fitness, resiliency, and adaptive potential, and contribute to
 local population extirpation. However, low survival and fitness of
 captive-raised individuals can minimize the long-term genetic consequences
 of stocking in wild populations, and to date the prevalence of
 introgression in actively stocked ecosystems has not been rigorously
 evaluated. We quantified the extent of introgression in 30 populations of
 wild brook trout (Salvelinus fontinalis) in a Pennsylvania watershed, and
 examined the correlation between introgression and 11 environmental
 covariates. Genetic assignment tests were used to determine the origin
 (wild vs. captive-raised) for 1742 wild-caught and 300 hatchery brook
 trout. To avoid assignment biases, individuals were assigned to two
 simulated populations that represented the average allele frequencies in
 wild and hatchery groups. Fish with intermediate probabilities of wild
 ancestry were classified as introgressed, with threshold values determined
 through simulation. Even with reoccurring stocking at most sites, over 93%
 of wild-caught individuals probabilistically assigned to wild origin, and
 only 6% of wild-caught fish assigned to introgressed. Models examining
 environmental drivers of introgression explained less than 3% of the
 among-population variability, and all estimated effects were highly
 uncertain. This was not surprising given overall low introgression
 observed in this study. Our results suggest that introgression of
 hatchery-derived genotypes can occur at low rates, even in actively
 stocked ecosystems and across a range of habitats. However, a cautious
 approach to stocking may still be warranted, as the potential effects of
 stocking on wild population fitness and the mechanisms limiting
 introgression are not known.
description: White_et_al_Brook_Trout_IntrogressionMicrosatellite genotypes for wild and hatchery fish used to quantify the proportion of introgressed individuals at 30 streams in a Pennsylvania watershed. Also contains environmental covariate data for site- and watershed-level predictors used to model introgression as a function of habitat covariates.
DOI: 10.5061/dryad.q586c
title: Data from: Disassembly of a tadpole community by a multi-host fungal pathogen with limited evidence of recovery

description: Emerging infectious diseases can cause host community disassembly, but the
 mechanisms driving the order of species declines and extirpations
 following a disease outbreak are unclear. We documented the community
 disassembly of a Neotropical tadpole community during a chytridiomycosis
 outbreak, triggered by the generalist fungal pathogen, Batrachochytrium
 dendrobatidis (Bd). Within the first 11 months of Bd arrival, tadpole
 density and occupancy rapidly declined. Rarity, in terms of tadpole
 occupancy and adult relative abundance, did not predict the odds of
 tadpole species occupancy declines. But species losses were taxonomically
 selective, with glassfrogs (Family: Centrolenidae) disappearing the
 fastest and tree frogs (Family: Hylidae) and dart-poison frogs (Family:
 Dendrobatidae) remaining the longest. We detected biotic homogenization of
 tadpole communities, with post-decline communities resembling one another
 more strongly than pre-decline communities. The entire tadpole community
 was extirpated within 22 months following Bd arrival, and we found limited
 signs of recovery within 10 years post-outbreak. Because of imperfect
 species detection inherent to sampling species rich tropical communities
 and the difficulty of devising a single study design protocol to sample
 physically complex tropical habitats, we used simulations to provide
 recommendations for future surveys to adequately sample diverse
 Neotropical communities. Our unique dataset on tadpole community
 composition before and after Bd arrival is a valuable baseline for
 assessing amphibian recovery. Our results are of direct relevance to
 conservation managers and community ecologists interested in understanding
 the timing, magnitude, and consequences of disease outbreaks as emerging
 infectious diseases spread globally.
description: Tadpole_occTadpole detection/nondetection data for 8 species in 3 microhabitats during the wet and dry season, encompassing a period before and after chytrid arrival.
DOI: 10.5061/dryad.r15h104
title: Data from: Wettability of juvenile plumage as a major cause of mortality threatens endangered Barau’s Petrel

description: Seabirds spend most of their life at sea and have to possess a waterproof
 plumage to be able to sit on water for extended periods. We tracked
 juvenile Barau’s petrels for the first time, when they leave their birth
 colony and found that half of the transmitters stopped soon after they
 first landed on the water off Réunion Island. We suspected from
 observation at sea that birds may have problems with the waterproofness of
 their plumage. Therefore during the next season we set up a simple
 protocol to assess waterproofness of the plumage of the birds just before
 they fledge. This protocol is based on the calculation of a wettability
 index expressed as the mass of water logged in the plumage after
 simulating the bird sitting on the sea surface. We found that at least one
 third of chicks ready to fledge gained more than 4 g of water in 20 sec,
 indicating that plumage was not waterproof. Within a sample of birds
 having fledged and before reaching the sea surface, a similar proportion
 of birds had their plumage not waterproof. For the birds tracked, only
 those with an index indicating a waterproof plumage successfully dispersed
 after their first touch on the sea surface. We provide evidence of a
 possible major cause of mortality of juvenile seabirds that has not been
 described previously in wild seabirds, but could exist in other species.
 This issue may be a major cause of threat to the endangered Barau’s
 petrel.
description: all location juvenile
 Barau's petrels weimerskirch
DOI: 10.5061/dryad.0sd41
title: Data from: Female song is widespread and ancestral in songbirds

description: Bird song has historically been considered an almost exclusively male
 trait, an observation fundamental to the formulation of Darwin’s theory of
 sexual selection. Like other male ornaments, song is used by male
 songbirds to attract females and compete with rivals. Thus, bird song has
 become a textbook example of the power of sexual selection to lead to
 extreme neurological and behavioural sex differences. Here we present an
 extensive survey and ancestral state reconstruction of female song across
 songbirds showing that female song is present in 71% of surveyed species
 including 32 families, and that females sang in the common ancestor of
 modern songbirds. Our results reverse classical assumptions about the
 evolution of song and sex differences in birds. The challenge now is to
 identify whether sexual selection alone or broader processes, such as
 social or natural selection, best explain the evolution of elaborate
 traits in both sexes.
description: Female Song Data - Odom
 Et al. 2014Female song scored for
 1,141 oscine passerine species (all oscine passerine species except those
 within Passerida). The README.rtf file contains information on columns and
 scoring of female song.FemaleSongData_OdomEtal2014_ForDryad.xls
DOI: 10.5061/dryad.3pf61
title: Data from: Pace of life, predators and parasites: predator-induced life history evolution in Trinidadian guppies predicts decrease in parasite tolerance

description: A common evolutionary response to predation pressure is increased
 investment in reproduction, ultimately resulting in a fast life history.
 Theory and comparative studies suggest that short-lived organisms invest
 less in defence against parasites than those that are longer lived (the
 pace of life hypothesis). Combining these tenets of evolutionary theory
 leads to the specific, untested prediction that within species,
 populations experiencing higher predation pressure invest less in defence
 against parasites. The Trinidadian guppy, Poecilia reticulata, presents an
 excellent opportunity to test this prediction: guppy populations in lower
 courses of rivers experience higher predation pressure, and as a
 consequence have evolved faster life histories, than those in upper
 courses. Data from a large-scale field survey showed that fish infected
 with Gyrodactylus parasites were of a lower body condition (quantified
 using the scaled mass index) than uninfected fish, but only in lower
 course populations. Although the evidence we present is correlational, it
 suggests that upper course guppies sustain lower fitness costs of
 infection, i.e. are more tolerant, than lower course guppies. The data are
 therefore consistent with the pace of life hypothesis of parasite defence
 allocation, and suggest that life-history traits mediate the indirect
 effect of predators on the parasites of their prey.
description: Data for Pace of life,
 predators and parasites: Stephenson et al. Biology
 LettersThese data are from
 guppies, Poecilia reticulata, from several sample sites across Trinidad.
 For each fish, we recorded the sex, weight, condition (using the scaled
 mass index), and the presence and number of Gyrodactylus spp. parasites
 infecting the fish. We provide the drainage, river, course and site, as
 well as the nested terms where appropriate, where each fish was
 collected.StephensonetalData.xlsx
DOI: 10.5061/dryad.p49q0
title: Data from: Introduced Scotch broom (Cytisus scoparius) invades the genome of native populations in vulnerable heathland habitats

description: Cytisus scoparius is a global invasive species that affects local flora
 and fauna at the intercontinental level. Its natural distribution spans
 across Europe, but seeds have also been moved among countries, mixing
 plants of native and non-native genetic origins. Hybridization between the
 introduced and native gene pool is likely to threaten both the native gene
 pool and the local flora. In this study, we address the potential threat
 of invasive C. scoparius to local gene pools in vulnerable heathlands. We
 used nuclear single nucleotide polymorphic (SNP) and simple sequence
 repeat (SSR) markers together with plastid SSR and indel markers to
 investigate the level and direction of gene flow between invasive and
 native heathland C. scoparius. Analyses of population structures confirmed
 the presence of two gene pools: one native and the other invasive. The
 nuclear genome of the native types was highly introgressed with the
 invasive genome, and we observed advanced-generation hybrids, suggesting
 that hybridization has been occurring for several generations. There is
 asymmetrical gene flow from the invasive to the native gene pool, which
 can be attributed to higher fecundity in the invasive individuals,
 measured by the number of flowers and seed pods. Strong spatial genetic
 structure in plastid markers and weaker structure in nuclear markers
 suggest that seeds spread over relatively short distances and that gene
 flow over longer distances is mainly facilitated by pollen dispersal. We
 further show that the growth habits of heathland plants become more
 vigorous with increased introgression from the invaders. Implications of
 the findings are discussed in relation to future management of invading C.
 scoparius.
description: SNP
 dataThe file contains SNP
 data for 249 Cytisus scoparius individuals. Sequences from which the SNPs
 are extracted are included.SSR
 dataThe file contains
 nuclear and plastid SSR data for 249 individuals of Cytisus
 scopariusPlastid sequence
 dataThe file contains
 plastid sequences representing native and invasive Cytisus scoparius
 haplotypes.Phenotype and fecundity
 dataThe file contains
 phenotype data for 249 individuals and fecundity data for 100 individuals
 of Cytisus scoparius.Geographical
 coordinatesTHe file contains
 georeferences for 249 individuals of Cytisus scoparius
DOI: 10.5061/dryad.15qf2
title: Data from: Population structure and connectivity of the mountainous star coral, Orbicella faveolata, throughout the wider Caribbean region

description: As coral reefs continue to decline worldwide, it becomes ever more
 necessary to understand the connectivity between coral populations to
 develop efficient management strategies facilitating survival and
 adaptation of coral reefs in the future. Orbicella faveolata is one of the
 most important reef-building corals in the Caribbean and has recently
 experienced severe population reductions. Here, we utilize a panel of nine
 microsatellite loci to evaluate the genetic structure of O. faveolata and
 to infer connectivity across ten sites spanning the wider Caribbean
 region. Populations are generally well-mixed throughout the basin (FST =
 0.038), although notable patterns of substructure arise at local and
 regional scales. Eastern and western populations appear segregated with a
 genetic break around the Mona Passage in the north, as has been shown
 previously in other species; however, we find evidence for significant
 connectivity between Curaçao and Mexico, suggesting that the southern
 margin of this barrier is permeable to dispersal. Our results also
 identify a strong genetic break within the Mesoamerican Barrier Reef
 System associated with complex oceanographic patterns that promote larval
 retention in southern Belize. Additionally, the diverse genetic signature
 at Flower Garden Banks suggests its possible function as a downstream
 genetic sink. The findings reported here are relevant to the ongoing
 conservation efforts for this important and threatened species, and
 contribute to the growing understanding of large-scale coral reef
 connectivity throughout the wider Caribbean.
description: Microsatellite genotype
 dataGenotype information for
 each sample is displayed on a single line. Labels for diploid loci are
 organized as column headers along the top. Dataset includes 369
 individuals collected from 10 geographic locations. This file is formatted
 for input in GenAlEx v.6.502OfavCarib_allSites.xlsxSTRUCTURE individual output fileSTRUCTURE output file with inferred population assignment probabilities for individual samples (K=5). Burn-in period of 300,000 followed by 1,000,000 MCMC repetitions.K5.indfile.txtSTRUCTURE population output fileSTRUCTURE output file with mean assignment probabilities for each of ten populations, pre-defined by sampling location (K=5). Burn-in period of 300,000 followed by 1,000,000 MCMC repetitions.K5.popfile.txt
DOI: 10.5061/dryad.gb6g6
title: Data from: The genomic bases of morphological divergence and reproductive isolation driven by ecological speciation in Senecio (Asteraceae)

description: Ecological speciation, driven by adaptation to contrasting environments,
 provides an attractive opportunity to study the formation of distinct
 species, and the role of selection and genomic divergence in this process.
 Here, we focus on a particularly clear-cut case of ecological speciation
 to reveal the genomic bases of reproductive isolation and morphological
 differences between closely related Senecio species, whose recent
 divergence within the last ~200,000 years was likely driven by the uplift
 of Mt. Etna (Sicily). These species form a hybrid zone, yet remain
 morphologically and ecologically distinct, despite active gene exchange.
 Here, we report a high-density genetic map of the Senecio genome and map
 hybrid breakdown to one large and several small quantitative trait loci
 (QTL). Loci under diversifying selection cluster in three 5 cM regions
 which are characterized by a significant increase in relative (F(ST)), but
 not absolute (d(XY)), interspecific differentiation. They also correspond
 to some of the regions of greatest marker density, possibly corresponding
 to 'cold-spots' of recombination, such as centromeres or
 chromosomal inversions. Morphological QTL for leaf and floral traits
 overlap these clusters. We also detected three genomic regions with
 significant transmission ratio distortion (TRD), possibly indicating
 accumulation of intrinsic genetic incompatibilities between these recently
 diverged species. One of the TRD regions overlapped with a cluster of high
 species differentiation, and another overlaps the large QTL for hybrid
 breakdown, indicating that divergence of these species may have occurred
 due to a complex interplay of ecological divergence and accumulation of
 intrinsic genetic incompatibilities.
description: F2 genotypes for linkage
 mappingRaw genotypes for 966
 markers (obtained from RNA-seq data) for 64 F2 individuals from a cross
 between Senecio aethnensis and S. chrysanthemifoliusRawGenotypesForDryad.xlsx
DOI: 10.5061/dryad.1n199
title: Data from: Directional postcopulatory sexual selection is associated with female sperm storage in Trinidadian guppies

description: Female sperm storage (FSS) is taxonomically widespread and often
 associated with intense sperm competition, yet its consequences on
 postcopulatory sexual selection (PCSS) are poorly known. Theory predicts
 that FSS will reduce the strength of PCSS, because sperm characteristics
 favored before and after FSS may be traded-off, and opportunities for
 nondirectional PCSS should increase. We explored these questions in the
 guppy (Poecilia reticulata), by allowing females to mate multiply and by
 comparing the paternity pattern in two successive broods. Contrary to
 predictions, the variance in male fertilization success increased after
 FSS, driven by a change in male paternity share across broods. This change
 was positively associated with sperm velocity (measured before FSS) but
 not with the duration of FSS, indirectly suggesting that faster sperm were
 better in entering female storage organs, rather than in persisting within
 them. Other male traits, such as male size and orange color,
 heterozygosity, and relatedness to the female, did not influence paternity
 after FSS. These results indicate that processes associated with FSS tend
 to reinforce the strength of PCSS in guppies, rather than weaken it.
 Further work is necessary to test whether this pattern changes in case of
 more prolonged FSS.
description: dataset MS female sperm
 storageraw
 data