cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2q1qv
title: Data from: Towards a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris)

description: Endemic gene pools have been severely endangered by human-mediated
 hybridization, which is posing new challenges in the conservation of
 several vertebrate species. The endangered European wildcat is an example
 of this problem, as several natural populations are suffering
 introgression of genes from the domestic cat. The implementation of
 molecular methods for detecting hybridization is crucial for supporting
 appropriate conservation programs on the wildcat. In this study, genetic
 variation at 158 single-nucleotide polymorphisms (SNPs) was analyzed in
 139 domestic cats, 130 putative European wildcats and 5 captive-bred
 hybrids (N=274). These SNPs were variable both in wild (HE=0.107) and
 domestic cats (HE=0.340). Although we did not find any SNP that was
 private in any population, 22 SNPs were monomorphic in wildcats and
 pairwise FCT values revealed marked differences between domestic and
 wildcats, with the most divergent 35 loci providing an average
 FCT&gt;0.74. The power of all the loci to accurately identify
 admixture events and discriminate the different hybrid categories was
 evaluated. Results from simulated and real genotypes show that the 158
 SNPs provide successful estimates of admixture, with 100% hybrid
 individuals (two to three generations in the past) being correctly
 identified in STRUCTURE and over 92% using the NEWHYBRIDS’ algorithm. None
 of the unclassified cats were wrongly allocated to another hybrid class.
 Thirty-five SNPs, showing the highest FCT values, provided the most
 parsimonious panel for robust inferences of parental and first generations
 of admixed ancestries. This approach may be used to further reconstruct
 the evolution of wildcat populations and, hopefully, to develop sound
 conservation guidelines for its legal protection in Europe.
description: SNPs_publication_ATCGfile 1: 'SNPs_publication_ATCG': this file contains the raw SNPs database in GenAlEx format for two sets of samples (sheets 1 and 2): sheet 1: SNPs data for all 274 cat samples used in the analyses (139 domestic cats - FCA; 130 putative European wildcats - FSI; 5 known hybrids FCA x FSI), characterised by 158 loci; sheet 2: SNPs data for 226 cat samples (139 domestic cats - FCA; 82 European wildcats - FSI; 5 known hybrids FCA x FSI), characterised by 158 loci. This sample set was created to exclude possible hybrids from the representatives of European wildcats. These files can be converted to other formats using GenAlEx.SNPs_publication_012File 2: This file contains the same SNPs datasets as in file 1, but in numerical format as required by GenAlEx for data analysis. These files can be converted to other formats using GenAlEx
DOI: 10.5061/dryad.rv08g
title: Data from: The role of pollinators in floral diversification in a clade of generalist flowers

description: Pollinator-mediated evolutionary divergence has seldom been explored in
 generalist clades because it is assumed that pollinators in those clades
 exert weak and conflicting selection. We investigate whether pollinators
 shape floral diversification in a pollination generalist plant genus,
 Erysimum. Species from this genus have flowers that appeal to broad
 assemblages of pollinators. Nevertheless, we recently reported that it is
 possible to sort plant species into pollination niches varying in the
 quantitative composition of pollinators. We test here whether floral
 characters of Erysimum have evolved as a consequence of shifts among
 pollination niches. For this, we quantified the evolutionary lability of
 the floral traits and their phylogenetic association with pollination
 niches. As with pollination niches, Erysimum floral traits show weak
 phylogenetic signal. Moreover, floral shape and color are phylogenetically
 associated with pollination niche. In particular, plants belonging to a
 pollination niche dominated by long-tongued large bees have lilac corollas
 with parallel petals. Further analyses suggest, however, that changes in
 color preceded changes in pollination niche. Pollinators seem to have
 driven the evolution of corolla shape, whereas the association between
 pollination niche and corolla color has probably arisen by lilac-flowered
 Erysimum moving toward certain pollination niches for other adaptive
 reasons.
description: Script.Erysimum.species.traitsR codes and raw dataR codes and data from Evolution #15-0052.zip
DOI: 10.5061/dryad.4t83t
title: Data from: Rates of karyotypic evolution in Estrildid finches differ between island and continental clades

description: Reasons why chromosomal rearrangements spread to fixation and frequently
 distinguish related taxa remain poorly understood. We used cytological
 descriptions of karyotype to identify large pericentric inversions between
 species of Estrildid finches (family Estrildidae) and a time-dated
 phylogeny to assess the genomic, geographic, and phylogenetic context of
 karyotype evolution in this group. Inversions between finch species fixed
 at an average rate of one every 2.26 My. Inversions were twice as likely
 to fix on the sex chromosomes compared to the autosomes. A high repeat
 density on the sex chromosomes may increase mutation rates, but other
 explanations via mutagenic input are not supported, as the number of
 inversions on a chromosome does not correlate with its length or map size.
 Inversions have fixed 3.3× faster in three continental clades than in two
 island chain clades, and fixation rate correlates with both range size and
 the number of sympatric species pairs. These results point to adaptation
 as the dominant mechanism driving fixation and suggest a role for gene
 flow in karyotype divergence. A review shows that the rapid karyotype
 evolution observed in the Estrildid finches appears to be more general
 across birds, and by implication other understudied taxa.
description: Supplemental Tables
 S1-S6Supplemental information
 on: 1) cytological data sources, 2) karyotype data matrix, 3) loci used
 and Genbank references for phylogenetic analyses, 4) range size and
 continentality in five clades of Estrildid finches, 5) pairwise range
 overlap in five clades of Estrildid finches, and 6) summary of karyotype
 variation across all Passerifomes sorted by familyHooper and Price -
 supplement.xlsxSupplemental Figures
 S1-S6Supplemental Figures:
 1-5) geographic distribution and range overlap heat maps for each 5 clades
 of Estrildid finches examined in this study, and 6) maximum clade
 credibility tree for all Estrildid finches with cytological information
 used in this study and outgroup taxa included for time calibration
 purposes.Hooper and Price Supplemental
 Figures.pdf
DOI: 10.15468/dl.37b62y
title: Occurrence Download

description: A dataset containing 485 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "GadmGid is one of (SOM.1_1, SOM.18_1, SOM.16_1, SOM.13_1, SOM.17_1)",
 "OccurrenceStatus is Present",
 "TaxonKey is Arthropoda"
 ]
}

 The dataset includes 485 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001632-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8181
title: Data from: Assessing the complex architecture of polygenic traits in diverged yeast populations

description: Phenotypic variation arising from populations adapting to different niches
 has a complex underlying genetic architecture. A major challenge in modern
 biology is to identify the causative variants driving phenotypic
 variation. Recently the baker’s yeast, Saccharomyces cerevisiae has
 emerged as a powerful model for dissecting complex traits. However, past
 studies using a laboratory strain were unable to reveal the complete
 architecture of polygenic traits. Here, we present a linkage study using
 576 recombinant strains obtained from crosses of isolates representative
 of the major lineages. The meiotic recombinational landscape appears
 largely conserved between populations, however strain-specific hotspots
 were also detected. Quantitative measurements of growth in 23 distinct
 ecologically relevant environments show that our recombinant population
 recapitulates most of the standing phenotypic variation described in the
 species. Linkage analysis detected an average of 6.3 distinct QTLs for
 each condition tested in all crosses, explaining on average 39% of the
 phenotypic variation. The QTLs detected are not constrained to a small
 number of loci and the majority are specific to a single cross combination
 and to a specific environment. Moreover, crosses between strains of
 similar phenotypes generate greater variation in the offspring, suggesting
 the presence of many antagonistic alleles and epistatic interactions. We
 found that subtelomeric regions play a key role in defining individual
 quantitative variation, emphasising the importance of the adaptive nature
 of these regions in natural populations. This set of recombinant strains
 is a powerful tool for investigating the complex architecture of polygenic
 traits.
description: Segregants
 GentoypeThis file contain the
 genotype data of all segregants used in this study. All the yeast
 segregants are available at the National Culture Yeast Collection
 (www.ncyc.co.uk/) Genotype keys are (Genotype,Strain,Cluster):
 WE,DBVPG6765,Wine/European; WA,DBVPG6044,West African; SA,Y12,Sake;
 NA,YPS128,North AmericanTable
 S1.xlsPhenotype
 DataThis file includes the
 growth profile data obtained for the parental strains and all segregants.
 All the yeast segregants are available at the National Culture Yeast
 Collection (www.ncyc.co.uk/)Table
 S3.xls
DOI: 10.5061/dryad.2qf0t
title: Data from: From benchtop to desktop: important considerations when designing amplicon sequencing workflows

description: Amplicon sequencing has been the method of choice in many high-throughput
 DNA sequencing (HTS) applications. To date there has been a heavy focus on
 the means by which to analyse the burgeoning amount of data afforded by
 HTS. In contrast, there has been a distinct lack of attention paid to
 considerations surrounding the importance of sample preparation and the
 fidelity of library generation. No amount of high-end bioinformatics can
 compensate for poorly prepared samples and it is therefore imperative that
 careful attention is given to sample preparation and library generation
 within workflows, especially those involving multiple PCR steps. This
 paper redresses this imbalance by focusing on aspects pertaining to the
 benchtop within typical amplicon workflows: sample screening, the target
 region, and library generation. Empirical data is provided to illustrate
 the scope of the problem. Lastly, the impact of various data analysis
 parameters is also investigated in the context of how the data was
 initially generated. It is hoped this paper may serve to highlight the
 importance of pre-analysis workflows in achieving meaningful, future-proof
 data that can be analysed appropriately. As amplicon sequencing gains
 traction in a variety of diagnostic applications from forensics to
 environmental DNA (eDNA) it is paramount workflows and analytics are both
 fit for purpose.
description: Experiment1Fasta files of amplicon reads from Experiment 1 for both the GS Junior and Ion Torrent. All fasta files are non-dereplicated and have been separated into sample batches based on MID (index) tags and all primers have been removed. No further quality or abundance filtering has been performed on the fasta file.Experiment2Fasta files of amplicon reads from Experiment 2 for both the MiSeq and Ion Torrent. All fasta files are non-dereplicated and have been separated into sample batches based on MID (index) tags and all primers have been removed. No further quality or abundance filtering has been performed on the fasta file.Experiment5Fasta file of amplicon reads from Experiment 5 for the Ion Torrent. The file non-dereplicated and has only been separated based on MID (index) tag. Primers have not been removed and no quality or abundance filtering has been performed on the fasta file.
DOI: 10.5061/dryad.217t3
title: Data from: Equivalence between step selection functions and biased correlated random walks for statistical inference on animal movement

description: Animal movement has a fundamental impact on population and community
 structure and dynamics. Biased correlated random walks (BCRW) and step
 selection functions (SSF) are commonly used to study movements. Because no
 studies have contrasted the parameters and the statistical properties of
 their estimators for models constructed under these two Lagrangian
 approaches, it remains unclear whether or not they allow for similar
 inference. First, we used the Weak Law of Large Numbers to demonstrate
 that the log-likelihood function for estimating the parameters of BCRW
 models can be approximated by the log-likelihood of SSFs. Second, we
 illustrated the link between the two approaches by fitting BCRW with
 maximum likelihood and with SSF to simulated movement data in virtual
 environments and to the trajectory of bison (Bison bison L.) trails in
 natural landscapes. Using simulated and empirical data, we found that the
 parameters of a BCRW estimated directly from maximum likelihood and by
 fitting an SSF were remarkably similar. Movement analysis is increasingly
 used as a tool for understanding the influence of landscape properties on
 animal distribution. In the rapidly developing field of movement ecology,
 management and conservation biologists must decide which method they
 should implement to accurately assess the determinants of animal movement.
 We showed that BCRW and SSF can provide similar insights into the
 environmental features influencing animal movements. Both techniques have
 advantages. BCRW has already been extended to allow for multi-state
 modeling. Unlike BCRW, however, SSF can be estimated using most
 statistical packages, it can simultaneously evaluate habitat selection and
 movement biases, and can easily integrate a large number of movement taxes
 at multiple scales. SSF thus offers a simple, yet effective, statistical
 technique to identify movement taxis.
description: Data for the analysis of
 bison trailsData used for the
 directional analysis of bison trails with respect to directional
 persistence, the target meadow, and the nearest canopy
 gap.Data_Duchesneetal.csv
DOI: 10.5061/dryad.q2k7k
title: Data from: Individual and temporal variation in habitat association of an alien carnivore at its invasion front

description: Gathering information on how invasive species utilize the habitat is
 important, in order to better aim actions to reduce their negative impact.
 We studied habitat use and selection of 55 GPS-marked raccoon dogs (30
 males, 25 females) at their invasion front in Northern Sweden, with
 particular focus on differences between males and females, between
 movement states, and between seasons and times of the day. Daily movement
 pattern was used to classify GPS-locations into dispersing and settled. We
 focused on both anthropogenic and natural landscape characteristics. Since
 we did not have any a priori knowledge about the spatial scale of raccoon
 dog habitat selection, we first assessed how landscape characteristics of
 random points changed with distance from the GPS-location they were paired
 to. Because changes in habitat use became less pronounced at approximately
 5 km for all variables, we focused on habitat use at two spatial scales:
 fine (500 m) and coarse (5 km). Habitat selection was strongest at the
 coarse scale, and reflected the results found for habitat use. Raccoon
 dogs selected agricultural areas and wetlands, lower altitudes, and
 shallow slopes, and avoided forests, open natural areas, and areas close
 to water and roads. There were no differences in habitat selection between
 males and females, or between movement states. This lack of sexual
 segregation increases the probability of encountering potential mates
 during dispersal, and therefore the likelihood for reproduction in new
 areas. The seasonal and diurnal pattern of habitat use may provide
 guidance for where and when to aim management efforts.
description: Habitat characteristics
 of raccoon dog observations at multiple spatial scalesHabitat characteristics
 (habitat type, distance to roads and water, elevation, slope, and length
 of growing season) for raccoon dog GPS-locations (Scale = 0) and paired
 random points located within a given distance (Scale &gt; 0 m). Data is
 aggregated per individual trajectory, season, and light period (day,
 night, twilight). For further details, see the article.Melis_et_al_Raccoon_dog_PLoS_ONE.xlsx
DOI: 10.5283/epub.58125
title: Data archive of "Is Task Switching Avoided to Save Effort or Time? Shorter Intertrial Durations Following Task Switches Increase the Willingness to Switch Tasks"

description: Data archive with coding sheet and raw data for Experiments 1 and 2.
description: Raw data files with description/ Rohdaten mit Beschreibung. Dieses Datenarchiv sind Rohdaten eines Forschungsprojektes, das soeben als Artikel in Motivation Science zur Veröffentlichung angenommen wurde.
DOI: 10.5061/dryad.820
title: Data from: Resolution of a Supertree/Supermatrix Paradox

description: [No abstract entered]
description: Gatesy et al Data
 SetSuperArtio-1.dat
DOI: 10.5061/dryad.rq120
title: Data from: Atlas of Mexican Triatominae (Reduviidae: Hemiptera) and vector transmission of Chagas disease

description: Chagas disease is one of the most important yet neglected parasitic
 diseases in Mexico and is transmitted by Triatominae. Nineteen of the 31
 Mexican triatomine species have been consistently found to invade human
 houses and all have been found to be naturally infected with Trypanosoma
 cruzi. The present paper aims to produce a state-of-knowledge atlas of
 Mexican triatomines and analyse their geographic associations with T.
 cruzi, human demographics and landscape modification. Ecological niche
 models (ENMs) were constructed for the 19 species with more than 10
 records in North America, as well as for T. cruzi. The 2010 Mexican
 national census and the 2007 National Forestry Inventory were used to
 analyse overlap patterns with ENMs. Niche breadth was greatest in species
 from the semiarid Nearctic Region, whereas species richness was associated
 with topographic heterogeneity in the Neotropical Region, particularly
 along the Pacific Coast. Three species, Triatoma longipennis, Triatoma
 mexicana and Triatoma barberi, overlapped with the greatest numbers of
 human communities, but these communities had the lowest rural/urban
 population ratios. Triatomine vectors have urbanised in most regions,
 demonstrating a high tolerance to human-modified habitats and broadened
 historical ranges, exposing more than 88% of the Mexican population and
 leaving few areas in Mexico without the potential for T. cruzi
 transmission.
description: Atlas of Mexican
 TriatominaeATLASTRIATOMINAE.xlsxPopulations ExposedPOPULATIONSEXPOSED.xlsx
DOI: 10.5061/dryad.br4rh
title: Data from: Vocal turn-taking in a nonhuman primate is learned during ontogeny

description: Conversational turn-taking is an integral part of language development, as
 it reflects a confluence of social factors that mitigate communication.
 Humans coordinate the timing of speech based on the behaviour of another
 speaker, a behaviour that is learned during infancy. While adults in
 several primate species engage in vocal turn-taking, the degree to which
 similar learning processes underlie its development in these non-human
 species or are unique to language is not clear. We recorded the natural
 vocal interactions of common marmosets (Callithrix jacchus) occurring with
 both their sibling twins and parents over the first year of life and
 observed at least two parallels with language development. First, marmoset
 turn-taking is a learned vocal behaviour. Second, marmoset parents
 potentially played a direct role in guiding the development of turn-taking
 by providing feedback to their offspring when errors occurred during vocal
 interactions similarly to what has been observed in humans. Though
 species-differences are also evident, these findings suggest that similar
 learning mechanisms may be implemented in the ontogeny of vocal
 turn-taking across our Order, a finding that has important implications
 for our understanding of language evolution.
description: marmoset ontogeny
 dataData structure for
 ontogeny study (Chow, Mitchell, Miller, 2015). Five family groups were
 collected, each with a data structure containing information for the call
 start and end times between pairs in the group. The five group structures
 are save in matlab files, as G_info4, R_info4, M_info4, O_info4, and
 J_info4. Each file has the same format, following as a 6 x 10 cell
 structure. The columns 1-10 corresponds to months, starting from month 3,
 so they are in sequence months 3,4,5,6,7,8,9,10,11,12. The rows correspond
 to different pairs of family members conversing, # - first to second
 speaker. 1 - mother to baby 1, 2 - mother to baby 2, 3 - father to baby 1,
 4 - father to baby 2, 5 - baby 1 to baby 2. An empty cell indicates no
 data was recorded that month. Each cell has the following information for
 conversations: DateNum: [1xN double] % identifier for the N sessions
 recorded that month, Animals: [1x2 double] % animal numbers %**** call
 times for the first speaker Astarts: [1xM double] % times in seconds,
 start of first pulse in a call. Afinish: [1xM double] % times in seconds,
 end of the first pulse. Astarts2: [1xM double] % time in seconds, start of
 the second pulse in call, NaN if no second pulse. Afinish2: [1xM double] %
 time in seconds, end of the second pulse in call, NaN if no second pulse.
 Atypes: [1xM double] % type of call, 1-phee, 2-twitter, 3-trill, 4-other,
 5-unidentified. %**** call times for the second speaker. Bstarts: [1xP
 double] % same format as above for A, but for speaker B, Bfinish: [1xP
 double], Bstarts2: [1xP double], Bfinish2: [1xP double], Btypes: [1x265
 double]Marmoset_Ontogeny_Data.mat