cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.66jt1
title: Data from: Low levels of hybridization across two contact zones among three species of woodpeckers (Sphyrapicus sapsuckers)

description: Three species of closely related woodpeckers (sapsuckers; Sphyrapicus)
 hybridize where they come into contact, presenting a rare ‘λ‐shape’
 meeting of hybrid zones. Two of the three arms of this hybrid zone are
 located on either side of the Interior Plateau of British Columbia, Canada
 bordering the foothills of the Coast Mountains and the Rocky Mountains.
 The third arm is located in the eastern foothills of the Rocky Mountains.
 The zones of hybridization present high variability of phenotypes and
 alleles in relatively small areas and provide an opportunity to examine
 levels of reproductive isolation between the taxa involved. We examined
 phenotypes (morphometric traits and plumage) and genotypes of 175 live
 birds across the two hybrid zones. We used the Genotyping By Sequencing
 (GBS) method to identify 180 partially diagnostic single nucleotide
 polymorphisms (SNPs) to generate a genetic hybrid index (GHI) for each
 bird. Phenotypically diverged S. ruber and S. nuchalis are genetically
 closely related, while S. nuchalis and S. varius have similar plumage but
 are well separated at the genetic markers studied. The width of both
 hybrid zones is narrower than expected under neutrality, and analyses of
 both genotypes and phenotypes indicate that hybrids are rare in the hybrid
 zone. Rarity of hybrids indicates assortative mating and/or some form of
 fitness reduction in hybrids, which might maintain the species complex
 despite close genetic distance and introgression. These findings further
 support the treatment of the three taxa as distinct species.
description: Summary data - illumina
 RAD GBS sequences of Sphyrapicus SapsuckersSummary of the GBS
 sequences of the 176 individuals of Sphyrapicus Sapsuckers from Western
 Canada.Exported_Genotype_Files_SamHD_JAB_2016.zipIllumina RAD GBS sequence of Sphyrapicus SapsuckersIllumina RAD sequences of 176 Sphyrapicus Sapsuckers from Western Canada.Sapsuckers.zip
DOI: 10.15468/jmj9vq
title: University of Vermont, Pringle Herbarium, Macrofungi

description: The Pringle Herbarium (VT) contains 300,000 specimens, including vascular plants, bryophytes, lichens, algae and fungi. Of these, this portal contains about 2000 fungi specimens, including all of our specimens of macrofungi. Other digitization projects cover type specimens, vascular plant specimens, North American bryophytes and lichens, and macroalgae. These images and data are available through various portals. The herbarium does not maintain its own online database.
DOI: 10.5061/dryad.d9f36
title: Data from: Diversification across a heterogeneous landscape

description: Adaptation to contrasting environments across a heterogeneous landscape
 favors the formation of ecotypes by promoting ecological divergence.
 Patterns of fitness variation in the field can show whether natural
 selection drives local adaptation and ecotype formation. However, to
 demonstrate a link between ecological divergence and speciation, local
 adaptation must have consequences for reproductive isolation. Using
 contrasting ecotypes of an Australian wildflower, Senecio lautus in common
 garden experiments, hybridization experiments, and reciprocal transplants,
 we assessed how the environment shapes patterns of adaptation and the
 consequences of adaptive divergence for reproductive isolation. Local
 adaptation was strong between ecotypes, but weaker between populations of
 the same ecotype. F1 hybrids exhibited heterosis, but crosses involving
 one native parent performed better than those with two foreign parents. In
 a common garden experiment, F2 hybrids exhibited reduced fitness compared
 to parentals and F1 hybrids, suggesting that few genetic incompatibilities
 have accumulated between populations adapted to contrasting environments.
 Our results show how ecological differences across the landscape have
 created complex patterns of local adaptation and reproductive isolation,
 suggesting that divergent natural selection has played a fundamental role
 in the early stages of species diversification.
description: Parental and F1 hybrid
 reciprocal transplant dataParental and F1 hybrids
 (GENO) were transplanted into four environments (ENV). Three populations
 (TypeS) represent each parental ecotype (Type) and six F1 hybrid crosses
 (TypeS) represent the F1 hybrids. Family denotes the full-sibling families
 replicated within each transplant environment (ENV) and environmental
 block (block). GE represents whether seeds germinated. D80 and D100 is the
 presence of seedlings at day 80 and 100, respectively. Surv represents
 survival to truncation, L10 is the ability for plants to reach ten leaves
 and Bud is whether or not they produced a bud and reached maturity.
 Totaldays is the number of days they were alive and CD320 is the censor
 for survival analysis at day 320. D320 is presence at day 320, with NA
 representing plants that did not germinate.PF1_update.csvIntrinsic fitness of hybrids created from the four ecotypesIn the glasshouse we crossed parental, F1, F2 and F3 genotypes (GenoCrossed). Filled is the number of healthy seeds for a cross, unfilled is the number of unhealthy seeds and PropFilled is the proportion of healthy seeds.SB_Seed Set.csv
DOI: 10.5061/dryad.2cv1h
title: Data from: Evolution of wing shape in hornets: why is the wing venation efficient for species identification?

description: Wing venation has long been used for insect identification. Lately, the
 characterization of venation shape using geometric morphometrics has
 further improved the potential of using the wing for insect
 identification. However, external factors inducing variation in wing shape
 could obscure specific differences, preventing accurate discrimination of
 species in heterogeneous samples. Here, we show that interspecific
 difference is the main source of wing shape variation within social wasps.
 We found that a naive clustering of wing shape data from taxonomically and
 geographically heterogeneous samples of workers returned groups congruent
 with species. We also confirmed that individuals can be reliably
 attributed to their genus, species and populations on the basis of their
 wing shape. Our results suggested that the shape variation reflects the
 evolutionary history with a potential influence of other factors such as
 body shape, climate and mimicry selective pressures. However, the high
 dimensionality of wing shape variation may have prevented absolute
 convergences between the different species. Wing venation shape is thus a
 taxonomically relevant marker combining the accuracy of quantitative
 characters with the specificity required for identification criteria. This
 marker may also highlight adaptive processes that could help understand
 the wing's influence on insect flight.
description: Data-specimens-Perrard-etal-2014-JEBTable of data of the specimens measured for the wing shape. This table mention the name of the specimens, identifications, countries where the specimens have been collected and institutions where the specimens are in collection.Wings-coordinates-Perrard-etal-2014-JEBRaw coordinates of the 19 landmarks used to measured the right forewing of the 1025 specimens.Wings-landmark-coordinates-Perrard-etal-2014-JEB.txtScript-R-Perrard-etal-2014-JEBScript R used to perform the analyses in Perrard et al. 2014, Evolution of wing shape in hornets: why is the wing venation efficient for species identification?Mtree-functions-for-R-phylogenetic-signalR functions to compute the phylogenetic signal according to the method described in Klingenberg & Gidaszewski 2010. The functions include an exact computation of the ancestral states minimizing the squared parsimony (according to the algorithm of McArdle & Rodrigo, 1994), a mapping of the phylogenetic tree in a plot of the morphospace and different methods to test that the phylogeny is significantly shorter than a random tree connecting the terminals in the morphospace.
DOI: 10.5061/dryad.4v551
title: Data from: Low spatial genetic differentiation associated with rapid recolonization in the New Zealand fur seal Arctocephalus forsteri

description: Population declines resulting from anthropogenic activities are of major
 consequence for the long-term survival of species because the resulting
 loss of genetic diversity can lead to extinction via the effects of
 inbreeding depression, fixation of deleterious mutations, and loss of
 adaptive potential. Otariid pinnipeds have been exploited commercially to
 near extinction with some species showing higher demographic resilience
 and recolonization potential than others. The New Zealand fur seal (NZFS)
 was heavily impacted by commercial sealing between the late 18th and early
 19th centuries, but has recolonized its former range in southern
 Australia. The species has also recolonized its former range in New
 Zealand, yet little is known about the pattern of recolonization. Here, we
 first used 11 microsatellite markers (n = 383) to investigate the
 contemporary population structure and dispersal patterns in the NZFS
 (Arctocephalus forsteri). Secondly, we model postsealing recolonization
 with 1 additional mtDNA cytochrome b (n = 261) marker. Our data identified
 3 genetic clusters: an Australian, a subantarctic, and a New Zealand one,
 with a weak and probably transient subdivision within the latter cluster.
 Demographic history scenarios supported a recolonization of the New
 Zealand coastline from remote west coast colonies, which is consistent
 with contemporary gene flow and with the species’ high resilience. The
 present data suggest the management of distinct genetic units in the North
 and South of New Zealand along a genetic gradient. Assignment of
 individuals to their colony of origin was limited (32%) with the present
 data indicating the current microsatellite markers are unlikely sufficient
 to assign fisheries bycatch of NZFSs to colonies.
description: NZFS
 ctybMitochondrial Cytochrome
 b sequences for 261 NZ fur seal pupsNZFS_microsatellitesMicrosatellite genotypes for 383 NZ fur seal pupsNZFS genepop_Dussex et al. 2016.txtNZFS_microsat_cytb_DIYABCMicrosatellite and Cytochrome b input data file for DIYABCNZFS colony names locationsNZ fur seal colony names and geographic coordinates
DOI: 10.5061/dryad.r9k57
title: Data from: Weighted quartets phylogenetics

description: Despite impressive technical and theoretical developments, reconstruction
 of phylogenetic trees for enormous quantities of molecular data is still a
 challenging task. A key tool in analyses of large data sets has been the
 construction of separate trees for subsets (e.g., quartets) of sequences,
 and subsequent combination of these subtrees into a single tree for the
 full set (i.e., supertree analysis). Unfortunately, even amalgamating
 quartets into a supertree remains a computationally daunting task.
 Assigning weights to quartets to indicate importance or reliability was
 proposed more than a decade ago, but handling weighted quartets is even
 more challenging and has scarcely been attempted in the past. In this work
 we focus on weighted quartet-based approaches. We propose a scheme to
 assign weights to quartets coming from weighted trees and devise a tree
 similarity measure for weighted trees based on weighted quartets. We also
 extend the quartet MaxCut (QMC algorithm) to handle weighted quartets. We
 evaluate these tools on simulated and real data. Our simulated data
 analysis highlights the additional information that is conveyed when using
 the new weighted tree similarity measure, and shows that extending QMC to
 a weighted setting improves the quality of tree reconstruction. Our
 analyses of a cyanobacterial data set with wQMC reinforce previous results
 achieved with other tools.
description: maxCutPackThe Weighted Quartet Max Cut package.wQMC_testPackA test package for wQMC for generating the data that is given in the paperwQMC packages overviewGuidelines for running wQMC and the simulation tests.wQMCPackagesReadMe.pdf
DOI: 10.5061/dryad.3qn55
title: Data from: Biodiversity gains from efficient use of private sponsorship for flagship species conservation

description: To address the global extinction crisis, both efficient use of existing
 conservation funding and new sources of funding are vital. Private
 sponsorship of charismatic ‘flagship’ species conservation represents an
 important source of new funding, but has been criticized as being
 inefficient. However, the ancillary benefits of privately sponsored
 flagship species conservation via actions benefiting other species have
 not been quantified, nor have the benefits of incorporating such
 sponsorship into objective prioritization protocols. Here, we use a
 comprehensive dataset of conservation actions for the 700 most threatened
 species in New Zealand to examine the potential biodiversity gains from
 national private flagship species sponsorship programmes. We find that
 private funding for flagship species can clearly result in additional
 species and phylogenetic diversity conserved, via conservation actions
 shared with other species. When private flagship species funding is
 incorporated into a prioritization protocol to preferentially sponsor
 shared actions, expected gains can be more than doubled. However, these
 gains are consistently smaller than expected gains in a hypothetical
 scenario where private funding could be optimally allocated among all
 threatened species. We recommend integrating private sponsorship of
 flagship species into objective prioritization protocols to sponsor
 efficient actions that maximize biodiversity gains, or wherever possible,
 encouraging private donations for broader biodiversity goals.
description: NZ PPP database and code
 for DryadData and code for NZ
 prioritization protocol.
DOI: 10.5061/dryad.1813
title: Data from: The making of a rapid plant invader: genetic diversity and differentiation in the native and invaded range of Senecio inaequidens

description: To become invasive, exotic species have to succeed in the consecutive
 phases of introduction, naturalization and invasion. Each of these phases
 leaves traces in genetic structure, which may affect the species'
 success in subsequent phases. We examine this interplay of genetic
 structure and invasion dynamics in the South African Ragwort (Senecio
 inaequidens), one of Europe's fastest plant invaders. We used AFLP
 and microsatellite markers to analyze 19 native African and 32 invasive
 European populations. In combination with historic data, we distinguished
 invasion routes and traced them back to the native source areas. This
 revealed that different introduction sites had markedly different success
 in the three invasion phases. Notably, an observed lag-phase in Northern
 Germany was evidently not terminated by factors increasing the
 invasiveness of the resident population but by invasive spread from
 another introduction centre. The lineage invading Central Europe was
 introduced to sites in which winters are more benign than in the native
 source region. Subsequently, this lineage spread into areas in which
 winter temperatures match the native climate more closely. Genetic
 diversity clearly increases with population age in Europe and less clearly
 decreases with spread rate up to population establishment. This indicates
 that gene flow along well-connected invasion routes counteracted losses of
 genetic diversity during rapid spread. In summary, this study suggests
 that multiple introductions, environmental preadaptation and high gene
 flow along invasion routes contributed to the success of this rapid
 invader. More generally, it demonstrates the benefit of combining genetic,
 historical and climatic data for understanding biological invasions.
description: AFLP_microsatellites_Senecio_inaequidens_CorrAFLP _Microsatellite_data _Senecio inaequidens_Corr.txt
DOI: 10.15468/xznhyk
title: University of Wyoming, Wilhelm G. Solheim Mycological Herbarium

description: Wilhelm G. Solheim Mycological Herbarium (RMS) at the University of Wyoming was formally established in 1979.  It contains 49,000 specimens, mostly of microfungi, that represent the life's work of Dr. Solheim (50 years). Many of the specimens were acquired through exchange. It represents the largest collection of fungi from the Rocky Mountain region. The collection is associated with the Rocky Mountain Herbarium which contains 1.2 million specimens of vascular plants of which 900,000 are databased.
DOI: 10.5061/dryad.384rr593
title: Data from: Genomic signature of natural and anthropogenic stress in wild populations of the waterflea Daphnia magna: validation in space, time and experimental evolution

description: Natural populations are confronted with multiple selection pressures
 resulting in a mosaic of environmental stressors at landscape level.
 Identifying the genetic underpinning of adaptation to these complex
 selection environments and assigning causes of natural selection within
 multidimensional selection regimes in the wild is challenging. The water
 flea Daphnia is a renown ecological model system with its well-documented
 ecology, the possibility to analyze subfossil dormant egg banks, and the
 short generation time allowing an experimental evolution approach.
 Capitalizing on the strengths of this model system, we here link candidate
 genome regions to three selection pressures, known to induce
 micro-evolutionary responses in Daphnia magna: fish predation, parasitism,
 and land-use. Using a genome scan approach in space, time and experimental
 evolution trials, we provide solid evidence of selection at genome level
 under well-characterized environmental gradients in the wild and identify
 candidate genes linked to the three environmental stressors. Our study
 reveals differential selection at genome level in Daphnia populations and
 provides evidence for repeatable patterns of local adaptation in a
 geographic mosaic of environmental stressors fueled by standing genetic
 variation. Extensive, parallel genetic evolution at a genome-wide scale
 implies high evolutionary potential, relevant to understand the dynamics
 of trait changes in natural populations and their impact on community and
 ecosystem responses through eco-evolutionary feedbacks.
description: Orsinietal_sequences_outliers_10kbRegionsList of sequences in fasta format obtained by mapping the outlier regions and 10kb up-and downstream to the genome sequence of Daphnia magna (V2.5-95). These sequence data were produced by The Center for Genomics and Bioinformatics at Indiana University and distributed via wFleaBase in collaboration with the Daphnia Genomics Consortium http://daphnia.cgb.indiana.edu. This project is supported in part by NIH award 5R24GM078274 "Daphnia Functional Genomics Resources" and by the METACyt Initiative of Indiana University, funded in part through a major grant from the Lilly Endowment, Inc. Our work benefits from and contributes to the Daphnia Genomics Consortium.Orsinietal_SNP_genotyping_spaceOrsinietal_SNP_genotyping_parasitecoreOrsinietal_SNP_genotyping_landusecoreOrsinietal_SNP_genotyping_fishcoreOrsinietal_SNP_genotyping_experimentOrsinietal_micros_genotyping_spaceOrsinietal_micros_genotyping_parasitecoreOrsinietal_micros_genotyping_landusecoreOrsinietal_micros_genotyping_fishcoreOrsinietal_micros_genotyping_experiment
DOI: 10.5061/dryad.t7cd6
title: Data from: Historical and anthropogenic factors affecting the population genetic structure of Ontario’s inland lake populations of walleye (Sander vitreus)

description: Populations existing in formerly glaciated areas often display composite
 historical and contemporary patterns of genetic structure. For Canadian
 freshwater fishes, population genetic structure is largely reflective of
 dispersal from glacial refugia and isolation within drainage basins across
 a range of scales. Enhancement of sport fisheries via hatchery stocking
 programs and other means has the potential to alter signatures of natural
 evolutionary processes. Using 11 microsatellite loci genotyped from 2182
 individuals, we analyzed the genetic structure of 46 inland lake walleye
 (Sander vitreus) populations spanning five major drainage basins within
 the province of Ontario, Canada. Population genetic analyses coupled with
 genotype assignment allowed us to; 1) characterize broad and fine scale
 genetic structure among Ontario walleye populations; and 2) determine if
 the observed population divergence is primarily due to natural /
 historical processes or recent anthropogenic events. The partitioning of
 genetic variation revealed higher genetic divergence among lakes than
 among drainage basins or proposed ancestries—indicative of relatively high
 isolation among lakes, study-wide. Walleye genotypes were clustered into
 three major groups, likely reflective of Missourian, Mississippian, and
 Atlantic glacial refugial ancestry. Despite detectable genetic signatures
 indicative of anthropogenic influences, province-wide spatial genetic
 structure remains consistent with the hypothesis of dispersal from
 distinct glacial refugia and subsequent isolation of lakes within primary
 drainage basins. Our results provide a novel example of minimal impacts
 from fishery enhancement to the broad-scale genetic structure of inland
 fish populations.
description: cena_walleye_usatsContains microsatellite data in GenePop format with 3 digit alleles. The allele sizes are binned from raw data generated by Chris Cena.
DOI: 10.5061/dryad.dv0qt
title: Data from: The effect of trait type and strength of selection on heritability and evolvability in an island bird population

description: The heritability (h2) of fitness traits is often low. Although this has
 been attributed to directional selection having eroded genetic variation
 in direct proportion to the strength of selection, heritability does not
 necessarily reflect a trait's additive genetic variance and
 evolutionary potential (“evolvability”). Recent studies suggest that the
 low h2 of fitness traits in wild populations is caused not by a paucity of
 additive genetic variance (VA) but by greater environmental or nonadditive
 genetic variance (VR). We examined the relationship between h2 and
 variance-standardized selection intensities (i or βσ), and between
 evolvability (IA:VA divided by squared phenotypic trait mean) and
 mean-standardized selection gradients (βμ). Using 24 years of data from an
 island population of Savannah sparrows, we show that, across diverse
 traits, h2 declines with the strength of selection, whereas IA and IR (VR
 divided by squared trait mean) are independent of the strength of
 selection. Within trait types (morphological, reproductive, life-history),
 h2, IA, and IR are all independent of the strength of selection. This
 indicates that certain traits have low heritability because of increased
 residual variance due to the age at which they are expressed or the
 multiple factors influencing their expression, rather than their
 association with fitness.
description: Explanation of
 phenotypic traits for Savannah sparrowsWheelwright SAVS Dryad
 7_14.docPhenotypic traits for
 female Savannah sparrowsSAVS All Traits Females
 7_14.xlsxPhenotypic traits for
 male Savannah sparrowsSAVS All Traits Males
 7_14.xlsxSAVS
 pedigree