cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0f839
title: Data from: Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations

description: It has long been known that adaptive evolution can occur through genetic
 mutations in DNA sequence, but it is unclear whether adaptive evolution
 can occur through analogous epigenetic mechanisms, such as through DNA
 methylation. If epigenetic variation contributes directly to evolution,
 species under threat of disease, invasive competition, climate change or
 other stresses would have greater stores of variation from which to draw.
 We looked for evidence of natural selection acting on variably methylated
 DNA sites using population genomic analysis across three climatologically
 distinct populations of valley oaks. We found patterns of genetic and
 epigenetic differentiations that indicate local adaptation is operating on
 large portions of the oak genome. While CHG methyl polymorphisms are not
 playing a significant role and would make poor targets for natural
 selection, our findings suggest that CpG methyl polymorphisms as a whole
 are involved in local adaptation, either directly or through linkage to
 regions under selection.
description: nuc_polys.fstVCF describing non-C/T polymorphismsmeth_polys.CG.fstVCF describing C/T polymorphisms followed by a G nucleotidemeth_polys.CHG.2.fstVCF describing C/T polymorphisms followed by HG nucleotidesvenn.0.1Summaries of polymorphisms with minor allele frequency greater than 0.1 categorized by contig in which they are found, type of polymorphism, minor allele frequency, F_ST, arcsine transformed F_ST, and contig type. Type of polymorphism is SNP for non C/T polymorphisms, CGP for C/T polymorphisms followed by a G, or CHGP for C/T polymorphisms followed by HG. Contig type is 1) contig contains only polymorphisms of type SNP 2) only type CGP 3) only CHGP 4) both SNP and CGP together 5) both CGP and CHGP 6) both SNP and CHGP 7) all three types.batch_1VCF output from Stacks.batch_1.catalog.tagsCatalog file from Stacks outputbatch_1.sumstatsSummary stats output from Stacks
DOI: 10.5061/dryad.ns2jn
title: Data from: Range-wide analysis of genetic structure in a widespread, highly mobile species (Odocoileus hemionus) reveals the importance of historical biogeography

description: Highly mobile species that thrive in a wide range of habitats are expected
 to show little genetic differentiation across their range. A limited but
 growing number of studies have revealed that patterns of broad-scale
 genetic differentiation can and do emerge in vagile, continuously
 distributed species. However, these patterns are complex and often shaped
 by both historical and ecological factors. Comprehensive surveys of
 genetic variation at a broad scale and at high resolution are useful for
 detecting cryptic spatial genetic structure, and for investigating the
 relative roles of historical and ecological processes in structuring
 widespread, highly mobile species. In this study, we analyzed 10
 microsatellite loci from over 1,900 samples collected across the full
 range of mule deer (Odocoileus hemionus), one of the most widely
 distributed and abundant of all large mammal species in North America.
 Through both individual- and population-based analyses we found evidence
 for three main genetic lineages, one corresponding to the ‘mule deer’
 morphological type and two to the ‘black-tailed deer’ type. Historical
 biogeographic events likely are the primary drivers of genetic divergence
 in this species; boundaries of the three lineages correspond well with
 predictions based on Pleistocene glacial cycles and substructure within
 each lineage demonstrates island vicariance. However, across large
 geographic areas, including the entire mule deer lineage, we found that
 genetic variation fit an isolation-by-distance pattern rather than
 discrete clusters. A lack of genetic structure across wide geographic
 areas of the continental west indicates that ecological processes have not
 resulted in restrictions to gene flow sufficient for spatial genetic
 structure to emerge. Our results have important implications for our
 understanding of evolutionary mechanisms of divergence, as well as for
 taxonomy, conservation, and management.
description: Data_Latchetal2014MolEcolDryad_data_submission_2.xls
DOI: 10.5061/dryad.g8t8k
title: Data from: Isolation by distance and isolation by environment contribute to population differentiation in Protea repens (Proteaceae L.), a widespread South African species

description: PREMISE OF THE STUDY: The Cape Floristic Region (CFR) of South Africa is
 renowned for its botanical diversity, but the evolutionary origins of this
 diversity remain controversial. Both neutral and adaptive processes have
 been implicated in driving diversification, but population-level studies
 of plants in the CFR are rare. Here, we investigate the limits to gene
 flow and potential environmental drivers of selection in Protea repens L.
 (Proteaceae L.), a widespread CFR species. METHODS: We sampled 19
 populations across the range of P. repens and used genotyping by
 sequencing to identify 2066 polymorphic loci in 663 individuals. We used a
 Bayesian FST outlier analysis to identify single-nucleotide polymorphisms
 (SNPs) marking genomic regions that may be under selection; we used those
 SNPs to identify potential drivers of selection and excluded them from
 analyses of gene flow and genetic structure. RESULTS: A pattern of
 isolation by distance suggested limited gene flow between nearby
 populations. The populations of P. repens fell naturally into two or three
 groupings, which corresponded to an east-west split. Differences in
 rainfall seasonality contributed to diversification in highly divergent
 loci, as do barriers to gene flow that have been identified in other
 species. CONCLUSIONS: The strong pattern of isolation by distance is in
 contrast to the findings in the only other widespread species in the CFR
 that has been similarly studied, while the effects of rainfall seasonality
 are consistent with well-known patterns. Assessing the generality of these
 results will require investigations of other CFR species.
description: All files for P. repens
 population genomics study.Here we describe the
 various R scripts, input & output data files created for this project.
 Collectively, they support the results and figures presented in our AJB
 paper. Details on each script and associated files follow, first as a
 short list of each R script and data file associated with this project.
 Subsequent sections provide a narrative of the flow of the analysis,
 touching on each R script, and providing detailed metadata on each data
 set as it is first mentioned.P_repens.tar.gz
DOI: 10.5061/dryad.8n776
title: Data from: De novo assembly of the transcriptome of an invasive snail and its multiple ecological applications

description: Studying how invasive species respond to environmental stress at the
 molecular level can help us assess their impact and predict their range
 expansion. Development of markers of genetic polymorphism can help us
 reconstruct their invasive route. However, to conduct such studies
 requires the presence of substantial amount of genomic resources. This
 study aimed to generate and characterize genomic resources using high
 throughput transcriptome sequencing for Pomacea canaliculata, a non-model
 gastropod indigenous to Argentina that has invaded Asia, Hawaii and
 southern United States. De novo assembly of the transcriptome resulted in
 128,436 unigenes with an average length of 419 bp (range: 150 to 8,556
 bp). Many of the unigenes (2,439) contained transposable elements, showing
 the existence of a source of genetic variability in response to stressful
 conditions. A total of 3,196 microsatellites were detected in the
 transcriptome; among 20 of the randomly tested microsatellites, 10 were
 validated to exhibit polymorphism. A total of 15,412 single-nucleotide
 polymorphisms (SNPs) were detected in the ORFs. LC-MS/MS analysis of the
 proteome of juveniles revealed 878 proteins, of which many are
 stress-related. This study has demonstrated the great potential of high
 throughput DNA sequencing for rapid development of genomic resources for a
 non-model organism. Such resources can facilitate various molecular
 ecological studies, such as stress physiology and range expansion.
description: Pomacea_proteinsProtein sequences translated from the assembled unigenesPomacea_unigenesUnigenes assembled from the Illumina raw readsPomacea_SNPSNP information deduced from the unigenesProtein identified by LC-MS/MSA list of 878 proteins identified by LC-MS/MS.Additional File 1 .xlsxIdentified transposable elementsA list of 2,439 predicted transposable elements.Additional File 2.xlsx
DOI: 10.5061/dryad.gc371
title: Data from: Banded mongooses avoid inbreeding when mating with members of the same natal group

description: Inbreeding and inbreeding avoidance are key factors in the evolution of
 animal societies, influencing dispersal and reproductive strategies which
 can affect relatedness structure and helping behaviours. In cooperative
 breeding systems, individuals typically avoid inbreeding through
 reproductive restraint and/or dispersing to breed outside their natal
 group. However, where groups contain multiple potential mates of varying
 relatedness, strategies of kin recognition and mate choice may be
 favoured. Here, we investigate male mate choice and female control of
 paternity in the banded mongoose (Mungos mungo), a cooperatively breeding
 mammal where both sexes are often philopatric and mating between relatives
 is known to occur. We find evidence suggestive of inbreeding depression in
 banded mongooses, indicating a benefit to avoiding breeding with
 relatives. Successfully breeding pairs were less related than expected
 under random mating, which appeared to be driven by both male choice and
 female control of paternity. Male banded mongooses actively guard females
 to gain access to mating opportunities, and this guarding behaviour is
 preferentially directed towards less closely related females. Guard–female
 relatedness did not affect the guard's probability of gaining
 reproductive success. However, where mate-guards are unsuccessful, they
 lose paternity to males that are less related to the females than
 themselves. Together, our results suggest that both sexes of banded
 mongoose use kin discrimination to avoid inbreeding. Although this
 strategy appears to be rare among cooperative breeders, it may be more
 prominent in species where relatedness to potential mates is variable,
 and/or where opportunities for dispersal and mating outside of the group
 are limited.
description: inbreeding
 coefficientsInbreeding coefficients
 calculated from a 9-generation deep pedigree of a wild population of
 banded mongoosesinbreeding
 coefficient.xlsxmate_guardingBehavioural data file. Males ('guard') observed guarding females ('indiv') during morning or afternoon ('time') observation periods. Strength of association: 0 = no association; 1 = strong association; 2 = medium strength association; 3 = weak association. Confidence of observation: 1 = strong; 2 = medium; 3 = weak.pedigreePedigree inferred from MasterBayes and Colony assignments including year individual was born.relatednessPairwise relatedness coefficients calculated from a 9-generation deep pedigree.BMRP_Genotype_data_Dec_2014Raw microsatellite genotype data
DOI: 10.5061/dryad.01j61
title: Data from: Strain differences in the collective behaviour of zebrafish (Danio rerio) in heterogeneous environment

description: Recent studies show differences in individual motion and shoaling tendency
 between strains of the same species. Here, we analyse collective motion
 and response to visual stimuli in two morphologically different strains
 (TL and AB) of zebrafish. For both strains, we observed 10 groups of 5 and
 10 zebrafish swimming freely in a large experimental tank with two
 identical landmarks (cylinders or discs) for 1 h. We tracked the positions
 of the fish by an automated tracking method and compute several metrics at
 the group level. First, the probability of the presence shows that both
 strains avoid free space and are more likely to swim in the vicinity of
 the walls of the tank and the landmarks. Second, the analysis of landmarks
 occupancy shows that AB zebrafish are more present in their vicinity than
 TL ones and that both strains regularly transit from one to the other one
 with no preference on the long duration. Finally, TL zebrafish show a
 higher cohesion than AB zebrafish. Thus, environmental heterogeneity and
 duration of the trials allow to reveal individual and collective
 behavioural variabilities among different strains of zebrafish. These
 results provide a new insight into the need to take into account
 individual variability of zebrafish strains for studying collective
 behaviour.
description: article
 strainsThe name of the
 directory gives the number and the strain of fish used during the
 experiment. Cylinder and disks gives the spots of interest used for the
 experiments. In the files, data are developped as: time step (first
 column) then x position of fish 1 (fish0x) then y position of fish 1
 (fish0y) then x position of fish 2 (fish1x) then y position of fish 2
 (fish1y) then ...
DOI: 10.5061/dryad.353tj334
title: Data from: Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticum

description: Measureable rates of genome evolution are well documented in human
 pathogens but are less well understood in bacterial pathogens in the wild,
 particularly during and after host switches. Mycoplasma gallisepticum (MG)
 is a pathogenic bacterium that has evolved predominantly in poultry and
 recently jumped to wild house finches (Carpodacus mexicanus), a common
 North American songbird. For the first time we characterize the genome and
 measure rates of genome evolution in House Finch isolates of MG, as well
 as in poultry outgroups. Using whole genome sequences of 12 House Finch
 isolates across a 13-year serial sample and an additional four newly
 sequenced poultry strains, we estimate a nucleotide diversity in House
 Finch isolates of only ~2% of ancestral poultry strains and a nucleotide
 substitution rate of 0.8 – 1.2 X 10-5 per site per year both in poultry
 and in House Finches, an exceptionally fast rate rivaling some of the
 highest estimates reported thus far for bacteria. We also found high
 diversity and complete turnover of CRISPR arrays in poultry MG strains
 prior to the switch to the House Finch host, but after the invasion of
 House Finches, there is progressive loss of CRISPR repeat diversity, and
 recruitment of novel CRISPR repeats ceases. Recent (2007) House Finch MG
 strains retain only ~50% of the CRISPR repertoire founding (1994-95)
 strains and have lost the CRISPR-associated genes required for CRISPR
 function. Our results suggest that genome evolution in bacterial pathogens
 of wild birds can be extremely rapid and in this case is accompanied by
 apparent functional loss of CRISPRs.
description: Moderate_2010_Masked_ValAlignment of SNPs at least stringent SNP calling criteria as described in the text.Stringent_Moderate_v2_2010_Masked_ValWorking SNP calling alignment.Stringent_2010_Masked_ValMost stringent SNP alignmentMG_Rate_EstimateOne of many BEAST files formed with the working alignment that can produce the data.
DOI: 10.5061/dryad.bg8h5
title: Data from: Detecting genes for variation in parasite burden and immunological traits in a wild population: testing the candidate gene approach

description: Identifying the genes underlying phenotypic variation in natural
 populations can provide novel insight into the evolutionary process. Here
 we test the candidate gene approach to identifying loci involved in
 variation in gastrointestinal parasite burden, in a wild population of
 Soay sheep. A comprehensive literature review, Gene Ontology databases,
 and comparative genomics resources were used to generate a list of
 candidate genes. In a pilot study these candidates, along with 50 random
 genes, were then sequenced in pools of Soay sheep with low and high
 gastrointestinal nematode burden. Further candidates were identified from
 SNPs that were highly differentiated between high and low resistance sheep
 breeds. A panel of 192 candidate and control SNPs were then typed in 960
 individual Soay sheep to examine whether they individually explained
 variation in parasite burden, as measured as faecal egg count (FEC), as
 well as two immune measures. The cumulative effect of the candidate and
 control SNPs were estimated by fitting genetic relationship matrices
 (GRMs) as random effects in animal models of the three traits. No more
 significant SNPs were identified in the pilot sequencing experiment and
 association study than expected by chance. Furthermore, no significant
 difference was found between the proportions of candidate or control SNPs
 that were found to be significantly associated with parasite burden/immune
 measures. No significant effect of the candidate or control gene GRMs was
 found. There is thus little support for the candidate gene approach to the
 identification of loci explaining variation in parasitological and
 immunological traits in this population.
description: sheeplow_bothpoolstemplate-singlessheephigh_bothpoolstemplate-singlesLocusXDNA_cleaned_dataCleaned SNP dataset.SNPs were genotyped on an Illumina BeadXpress platform using Goldengate Veracode technologyANA_adultsData for associations between SNPs and ANA in adultsANA_lambsData for associations between SNPs and ANA in lambsANA_senesData for associations between SNPs and ANA in senescent individuals.ANA_yearlingsData for associations between SNPs and ANA in yearlingsFEC_adultsData for associations between SNPs and FEC in adultsFEC_lambsData for associations between SNPs and FEC in lambsFEC_senesData for associations between SNPs and FEC in senescent-aged individualsFEC_yearlingsData for associations between SNPs and FEC in yearlingsTCIRC_adultsData for associations between SNPs and TCIRC in adultsTCIRC_lambsData for associations between SNPs and TCIRC in lambsTCIRC_senesData for associations between SNPs and TCIRC in senescent-aged individualsTCIRC_yearlingsData for associations between SNPs and TCIRC in yearlingsDryad statement - Brown Mol EcolGeneral information about the data used in this paper, including Soay Sheep Project contact information.ReadmeDescription of contents of files with names beginning ANA, TCIRC and FEC
DOI: 10.5061/dryad.82jq4
title: Data from: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis

description: The opportunistic pathogens Staphylococcus aureus and Staphylococcus
 epidermidis represent major causes of severe nosocomial infection, and are
 associated with high levels of mortality and morbidity worldwide. These
 species are both common commensals on the human skin and in the nasal
 pharynx, but are genetically distinct, differing at 24% average nucleotide
 divergence in 1,478 core genes. To better understand the genome dynamics
 of these ecologically similar staphylococcal species, we carried out a
 comparative analysis of 324 S. aureus and S. epidermidis genomes,
 including 83 novel S. epidermidis sequences. A reference pan-genome
 approach and whole genome multilocus-sequence typing revealed that around
 half of the genome was shared between the species. Based on a BratNextGen
 analysis, homologous recombination was found to have impacted on 40% of
 the core genes in S. epidermidis, but on only 24% of the core genes in S.
 aureus. Homologous recombination between the species is rare, with a
 maximum of nine gene alleles shared between any two S. epidermidis and S.
 aureus isolates. In contrast, there was considerable interspecies
 admixture of mobile elements, in particular genes associated with the
 SaPIn1 pathogenicity island, metal detoxification, and the
 methicillin-resistance island SCCmec. Our data and analysis provide a
 context for considering the nature of recombinational boundaries between
 S. aureus and S. epidermidis and, the selective forces that influence
 realized recombination between these species.
description: Meric et al. 2015 GBE:
 83 novel Staphylococcus epidermidis genome assembliesZIP archive containing
 contigs for 83 whole genome sequences of S. epidermidis. Metadata is
 attached to the Dryad submission. Contact: Prof Samuel Sheppard
 s.k.sheppard@swansea.ac.ukMeric_2015_GBE_83_Sepi_genomes.zip
DOI: 10.5061/dryad.fk1q6
title: Data from: Feed-forward motor control of ultrafast, ballistic movements

description: To circumvent the limits of muscle, ultrafast movements achieve high power
 through the use of springs and latches. The timescale of these movements
 is too short for control through typical neuromuscular mechanisms, thus
 ultrafast movements are either invariant or are controlled prior to
 movement. We tested whether mantis shrimp (Stomatopoda: Neogonodactylus
 bredini) vary their ultrafast smashing strikes and, if so, how this
 control is achieved prior to movement. We collected high speed images of
 strike mechanics and electromyograms of the extensor and flexor muscles
 that control spring compression and latch release. During spring
 compression, lateral extensor and flexor units were co-activated. The
 strike initiated several milliseconds after the flexor units ceased,
 suggesting that flexor activity prevents spring release and determines the
 timing of strike initiation. We used linear mixed models and Akaike
 Information Criterion to serially evaluate multiple hypotheses for control
 mechanisms. We found that variation in spring compression and strike
 angular velocity were statistically explained by spike activity of the
 extensor muscle. The results show that mantis shrimp can generate
 kinematically variable strikes and that their kinematics can be changed
 through adjustments to motor activity prior to the movement, thus
 supporting an upstream, central nervous system-based control of ultrafast
 movement. Based on these and other findings, we present a shishiodoshi
 model that illustrates alternative models of control in biological
 ballistic systems. The discovery of feed-forward control in mantis shrimp
 sets the stage for the assessment of targets, strategic variation in
 kinematics and the role of learning in ultrafast animals.
description: zip archive of
 Kagaya_Patek_2015JEB_dataset_and_scriptsThe zip archive contains
 one R image file and three R scripts. The R image file contains all R
 objects including data and function objects. The paper's DOI is,
 10.1242/jeb.130518.Kagaya_Patek_2015JEB_dataset_for_dryad.zip