cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j7230
title: Data from: Male-biased dispersal causes intersexual differences in the subpopulation structure of the gray-sided vole

description: The genetic structure of gray-sided voles was investigated at a spatial
 scale of 2 km using mtDNA sequences. The control region (674bp) of 162
 voles was sequenced and 18 haplotypes were identified. Within 0.5-ha
 trapping plots (n = 8), the number of haplotypes and gene diversity was
 significantly greater in males than in females. The fixation index among
 plots for females (F GP = 0.241) was 3 times as large as that for males
 (0.075), implying male-biased dispersal. A simulation analysis showed that
 the observed genetic structure in males could be generated by modifying
 the observed haplotype distribution of females by adding the effects of
 local male dispersal. Half of the pairwise F GP (15/28) showed significant
 differentiation in females, whereas almost none (1/28) were significant in
 males. Isolation by distance was observed in females, whereas no clear
 spatial pattern was observed in males. Most pairwise F GP for females were
 not significant in the short- and intermediate-distance classes (≤1.0 km)
 as with those for males, whereas all showed significant differentiation in
 the long-distance class (&gt;1.0 km) for females, but not for males.
 These findings indicate that the extent of subpopulations within which
 individuals interact differs between sexes.
description: Latitude and Longitude
 of 8 trapping plotsPlotLocation.txtSex, captured plot# and mtDNA haplotypes of IndividualsIndividual_data.txtProject file for Arlequin analysesproject file for software Arlequin.ISK2009.txtPairwise geographic distances among 8 plotsInput file for software GenAlEx.PairwiseLn(1+GGD).csvPairwise Fgp values among 8 plots in femalesInput file for software GenAlEx.PairwiseFgpinFemales.csvPairwise Fgp values among 8 plots in malesInput file for software GenAlEx.PairwiseFgpinMales.csvComparison of number of significant Fgp between sexes at 3 distance classesData table for Fisher's exact test in JMP. FGP: Fgp values between plots. GGD: geographic distance between plots (km). GGD class: 1, short -distance class; 2, intermediate-distance class; 3 long-distance class. significantFGP: 0, not significant; 1, significant.Fgp significanceComparisonGGDclass.csvMathematica programs to calculate Fgp and the related statistics and to perform simulation, input data and outputMathematicaProgram_est034.pdf
DOI: 10.15468/dl.7tzha5
title: Occurrence Download

description: A dataset containing 971165 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC-BY-NC 4.0, CC-BY 4.0, CC0 1.0)",
 "Month is December",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves",
 "Year 2025-2026"
 ]
}

 The dataset includes 971165 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001571-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.18j3d
title: Data from: Biogeographic regions of North American mammals based on endemism

description: Since the 19th century, two regions have been recognized for North
 American mammals, which overlap in Mexico. The Nearctic region corresponds
 to the northern areas and the Neotropical region to the southern ones.
 There are no recent regionalizations for these regions under the criterion
 of endemism. We integrate herein two methods to regionalize North America,
 using species distribution models of mammals: Endemicity Analysis (EA) and
 Parsimony Analysis of Endemicity (PAE). EA was used to obtain areas of
 endemism and PAE to hierarchize them. We found 76 consensus areas from 329
 sets, classified in 146 cladograms, and the strict consensus cladogram
 shows a basal polytomy with 14 areas and 16 clades. The final
 regionalization recognizes two regions (Nearctic and Neotropical) and a
 transition zone (Mexican Transition Zone), six subregions (Canadian,
 Alleghanian, Californian-Rocky Mountain, Pacific Central America, Mexican
 Gulf-Central America and Central America), two dominions (Californian and
 Rocky Mountain) and 23 provinces. Our analysis show that North America is
 probably more complex than previously assumed.
description: c0_CalifornianProvinceShape file for Californian Provincec1_IsthmusOfTehuantepec-ChiapasProvinceShapefile for SIGc2_TalamancanCordilleraProvinceShapefile for SIGc4_MexicanTransitionZoneShapefile for SIGc6_AlleghanianSubregionShapefile for SIGc8_ArtemisianProvinceShapefile for SIGc17_TalamancanCordilleraProvinceShapefile for SIGc20_NeotropicalRegionShapefile for SIGc21_OregonianProvinceShapefile for SIGc24_CentralAmericanSubregionShapefile for SIGc25_YucatanPeninsula-Mexican GulfProvinceShapefile for SIGc26_Pacific-CentralAmericaSubregionShapefile for SIGc27_FloridianProvinceShapefile for SIGc28_SierraNevadaProvinceShapefile for SIGc31_Mexican Pacific-CentralMexicoShapefile for SIGc32_Californian-RockyMountainSubregionShapefile for SIGc33_MohavianProvinceShapefile for SIGc37_YucatanPeninsulaProvinceShapefile for SIGc38_TamaulipasProvinceShapefile for SIGc40_SouthesternMexicoProvinceShapefile for SIGc44_GulfOfCaliforniaProvinceShapefile for SIGc45_MexicanPlateauProvinceShapefile for SIGc48_Chiapas-Central AmericaProvinceShapefile for SIGc49_NevadianProvinceShapefile for SIGc53_SierraMadreOccidental-CentralPlateauProvinceShapefile for SIGc54_SierraMadreDelSurShapefile for SIGc56_TransmexicanVolcanicBeltShapefile for SIGc60__Chiapas-CentralAmericaProvinceShapefile for SIGc63_MesoamericanProvinceShapefile for SIGc65_MexicanTransitionZoneShapefile for SIGc70_CentralAmericaProvinceShapefile for SIGc72_NeotropicalRegionShapefile for SIGc74_Pacific-CentralAmericaSubregionShapefile for SIG
DOI: 10.5061/dryad.vh49j
title: Data from: Heterogeneous models place the root of the placental mammal phylogeny

description: Heterogeneity among life traits in mammals has resulted in considerable
 phylogenetic conflict, particularly concerning the position of the
 placental root. Layered upon this are gene- and lineage-specific variation
 in amino acid substitution rates and compositional biases. Life trait
 variations that may impact upon mutational rates are longevity, metabolic
 rate, body size and germ line generation time. Over the past 12 years,
 three main conflicting hypotheses have emerged for the placement of the
 placental root. These hypotheses place: the Atlantogenata (common ancestor
 of Xenarthra plus Afrotheria), the Afrotheria, or the Xenarthra as the
 sister group to all other placental mammals. Model adequacy is critical
 for accurate tree reconstruction and by failing to account for these
 compositional and character exchange heterogeneities across the tree and
 dataset, previous studies have not provided a strongly supported
 hypothesis for the placental root. For the first time, models that
 accommodate both tree and dataset heterogeneity have been applied to
 mammal data. Here we show the impact of accurate model assignment and the
 importance of datasets in accommodating model parameters while maintaining
 the power to reject competing hypotheses. Through these sophisticated
 methods, we demonstrate the importance of model adequacy, dataset power
 and provide strong support for the Atlantogenata over other competing
 hypotheses for the position of the placental root.
description: Phylogenies obtained
 using variety of heterogeneous modelsMorganCC_Phylogenies.xls39TaxonSetAlignment data from 39 species in three formats: nucleotide (39TaxonSet_aa), amino acid (39TaxonSet_day) and dayhoff 6 recoded (39TaxonSet_day).
DOI: 10.7927/d4v6-3b75
title: IPCC AR6 Synthesis Report LR Figure 3.6 (b): Total GHG, CO2 and CH4 emissions and timing of reaching net-zero while keeping warming to 2°C

description: GHG, CO2 and CH4 emissions over time (in GtCO2eq) with historical emissions, projected emissions in line with policies implemented until the end of 2020 (grey), and pathways consistent with temperature goals in colour (blue, purple, and brown, respectively). This figure shows pathways that limit warming to 2°C (&gt;66%) (C3).
DOI: 10.5061/dryad.sg573
title: Data from: Secondary contact and changes in coastal hydrology influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta)

description: Numerous empirical studies have reported lack of migration–drift
 equilibrium in wild populations. Determining the causes of nonequilibrium
 population structure is challenging because different evolutionary
 processes acting at a variety of spatiotemporal scales can produce similar
 patterns. Studies of contemporary populations in northern latitudes
 suggest that nonequilibrium population structure is probably caused by
 recent colonization of the region after the last Pleistocene ice age ended
 ~13 000 years ago. The chum salmon's (Oncorhynchus keta) range was
 fragmented by dramatic environmental changes during the Pleistocene. We
 investigated the population structure of chum salmon on the North Alaska
 Peninsula (NAP) and, using both empirical data and simulations, evaluated
 the effects of colonization timing and founder population heterogeneity on
 patterns of genetic differentiation. We screened 161 single nucleotide
 polymorphisms and found evidence of nonequilibrium population structure
 when the slope of the isolation-by-distance relationship was examined at
 incremental spatial scales. In addition, simulations suggested that this
 pattern closely matched models of recent colonization of the NAP by
 secondary contact. Our results agree with geological and archaeological
 data indicating that the NAP was a dynamic landscape that may have been
 more recently colonized than during the last deglaciation because of
 dramatic changes in coastal hydrology over the last several thousand
 years.
description: SNP genotype data for
 chum salmon from the North Alaska PeninsulaMultilocus genotype data
 for 161 single nucleotide polymorphisms (SNPs) assayed in chum salmon
 (Oncorhynchus oketa) from the North Alaska Peninsula. The data are
 provided in a GenAlEx two column format (Peakall and Smouse 2012) which
 can be easily converted to other file formats or manipulated. SNP
 genotypes are identified by base calls with missing data coded as “0”.
 Keys to population and locus codes are given on separate worksheets.
 Peakall, R. and Smouse P.E. (2012) GenAlEx 6.5: genetic analysis in Excel.
 Population genetic software for teaching and research-an update.
 Bioinformatics 28, 2537-2539.Contact zone data_Dryad
 format.xlsx
DOI: 10.5061/dryad.37b28
title: Data from: Limits to behavioral evolution: the quantitative genetics of a complex trait under directional selection

description: Replicated selection experiments provide a powerful way to study how
 “multiple adaptive solutions” may lead to differences in the
 quantitative-genetic architecture of selected traits and whether this may
 translate into differences in the timing at which evolutionary limits are
 reached. We analyze data from 31 generations (n = 17,988) of selection on
 voluntary wheel running in house mice. The rate of initial response,
 timing of selection limit, and height of the plateau varied significantly
 between sexes and among the four selected lines. Analyses of litter size
 and realized selection differentials seem to rule out counterposing
 natural selection as a cause of the selection limits. Animal-model
 analyses showed that although the additive genetic variance was
 significantly lower in selected than control lines, both before and after
 the limits, the decrease was not sufficient to explain the limits.
 Moreover, directional selection promoted a negative covariance between
 additive and maternal genetic variance over the first 10 generations.
 These results stress the importance of replication in selection studies of
 higher-level traits and highlight the fact that long-term predictions of
 response to selection are not necessarily expected to be linear because of
 the variable effects of selection on additive genetic variance and
 maternal effects.
description: Data on voluntary wheel
 runningData on voluntary wheel
 running from the base population up to generation 31 of the artificial
 selection experiment. See ReadMe.txtCareau_QG_DRYAD_DATA.csvDescriptive statisticsDescriptive statistics (N=number of individuals, mean, variance, sd=standard deviation, range, CV=coefficient of variation) of voluntary wheel running (in revolutions per day) for four control lines (linetype=C) and four selected lines (linetype=HR) as a whole and for the subset of individuals that were selected for reproduction in each generation. These statistics were used to calculate the selection differential (s), the standardized selection differential (s’), the cumulative standardized selection differential (acc s’), the average of the four control lines at each generation (Mean controls), and the selective gain relative to the average of the four control lines at each generation (gain vs. control).Careau_QG_Descriptive_statistics.xlsPedigreePedigree of the population from the base population up to generation 31 of the selection experimentCareau_QG_ped.all.line.txt
DOI: 10.5061/dryad.73p5d
title: Data from: Rapid and robust phylotyping of spa t003, a dominant MRSA clone in Luxembourg and other European countries

description: Background: spa typing is a common genotyping tool for
 methicillin-resistant Staphylococcus aureus (MRSA) in Europe. Given the
 high prevalence of dominant clones, spa-typing is proving to be limited in
 its ability to distinguish outbreak isolates from background isolates. New
 molecular tools need to be employed to improve subtyping of dominant local
 MRSA strains (e.g., spa type t003). Methods: Phylogenetically critical, or
 canonical, SNPs (can-SNPs) were identified as subtyping targets through
 sequence analysis of 40 MRSA whole genomes from Luxembourg. Real-time PCR
 assays were designed around target SNPs and validated using a repository
 of 240 previously sub-typed and epidemiologically characterized Luxembourg
 MRSA isolates, including 153 community and hospital isolates, 69 isolates
 from long term care (LTC) facilities, and 21 prospectively analyzed MRSA
 isolates. Selected isolates were also analyzed by whole genome SNP typing
 (WGST) for comparison to the SNP assays and other subtyping techniques.
 Results: Fourteen real-time PCR assays were developed and validated,
 including two assays to determine presence of spa t003 or t008. The other
 twelve assays successfully provided a high degree of resolution within the
 t003 subtype. WGST analysis of the LTC facility isolates provided greater
 resolution than other subtyping tools, identifying clusters indicative of
 ongoing transmission within LTC facilities. Conclusions: canSNP-based PCR
 assays are useful for local level MRSA phylotyping, especially in the
 presence of one or more dominant clones. The assays designed here can be
 easily adapted for investigating t003 MRSA strains in other regions in
 Western Europe. WGST provides substantially better resolution than other
 typing methods.
description: MRSA_phylogenetic_trees_data_LuxembourgThis data file contains SNP matrices used to build phylogenetic trees. The matrices are provided in both .fasta format (the input that MEGA accepts) and Excel file format. The phylogenetic trees are provided in MEGA tree session format (MEGAsoftware.net).trees_data_dryad.zip
DOI: 10.5061/dryad.1rd2p
title: Data from: Ancient trade routes shaped the genetic structure of horses in eastern Eurasia

description: Animal exchange networks have been shown to play an important role in
 determining gene flow among domestic animal populations. The Silk Road is
 one of the oldest continuous exchange networks in human history, yet its
 effectiveness in facilitating animal exchange across large geographic
 distances and topographically challenging landscapes has never been
 explicitly studied. Horses are known to have been traded along the Silk
 Roads; however, extensive movement of horses in connection with other
 human activities may have obscured the genetic signature of the Silk
 Roads. To investigate the role of the Silk Roads in shaping the genetic
 structure of horses in eastern Eurasia we analysed microsatellite
 genotyping data from 455 village horses sampled from 17 locations. Using
 least-cost path methods, we compared the performance of models containing
 the Silk Roads as corridors for gene flow with models containing single
 landscape features. We also determined whether the recent isolation of
 former Soviet Union countries from the rest of Eurasia has affected the
 genetic structure of our samples. The overall level of genetic
 differentiation was low, consistent with historically high levels of gene
 flow across the study region. The spatial genetic structure was
 characterised by a significant, albeit weak, pattern of isolation by
 distance across the continent with no evidence for the presence of
 distinct genetic clusters. Incorporating landscape features considerably
 improved the fit of the data; however, when we controlled for geographic
 distance, only the correlation between genetic differentiation and the
 Silk Roads remained significant, supporting the effectiveness of this
 ancient trade network in facilitating gene flow across large geographic
 distances in a topographically complex landscape.
description: microsatellite
 genotyping data for 455 horses from 17 locations in eastern
 EurasiaDna was extracted from
 hair root samples collected in the field between 2006 and 2011 and
 amplified using 26 microsatellite markers. PCR products were run on an ABI
 3730 Genetic Analyser (Applied Biosystems) and alleles were called using
 GENEMAPPER software v37 (Applied Biosystems).msat
 data.xlsxlandscape.dataThis folder contains RData objects and R scripts used to carry out the least-cost path analyses described in the ms
DOI: 10.5061/dryad.6g2g2
title: Data from: A spatio-temporal understanding of growth regulation during the salt-stress response in Arabidopsis

description: Plant environmental responses involve dynamic changes in growth and
 signaling, yet little is understood as to how progress through these
 events is regulated. Here, we explored the phenotypic and transcriptional
 events involved in the acclimation of the Arabidopsis thaliana seedling
 root to a rapid change in salinity. Using live-imaging analysis, we show
 that growth is dynamically regulated with a period of quiescence followed
 by recovery then homeostasis. Through the use of a new high-resolution
 spatio-temporal transcriptional map, we identify the key hormone signaling
 pathways that regulate specific transcriptional programs, predict their
 spatial domain of action, and link the activity of these pathways to the
 regulation of specific phases of growth. We use tissue-specific approaches
 to suppress the abscisic acid (ABA) signaling pathway and demonstrate that
 ABA likely acts in select tissue layers to regulate spatially localized
 transcriptional programs and promote growth recovery. Finally, we show
 that salt also regulates many tissue-specific and time point–specific
 transcriptional responses that are expected to modify water transport,
 Casparian strip formation, and protein translation. Together, our data
 reveal a sophisticated assortment of regulatory programs acting together
 to coordinate spatially patterned biological changes involved in the
 immediate and long-term response to a stressful shift in environment.
description: Supplemental Data Sets
 1-8
DOI: 10.5061/dryad.3003f
title: Data from: Identification and mapping of linear antibody epitopes in human serum albumin using high-density peptide arrays

description: We have recently developed a high-density photolithographic, peptide array
 technology with a theoretical upper limit of 2 million different peptides
 per array of 2 cm2. Here, we have used this to perform complete and
 exhaustive analyses of linear B cell epitopes of a medium sized protein
 target using human serum albumin (HSA) as an example. All possible
 overlapping 15-mers from HSA were synthesized and probed with a
 commercially available polyclonal rabbit anti-HSA antibody preparation. To
 allow for identification of even the weakest epitopes and at the same time
 perform a detailed characterization of key residues involved in antibody
 binding, the array also included complete single substitution scans (i.e.
 including each of the 20 common amino acids) at each position of each
 15-mer peptide. As specificity controls, all possible 15-mer peptides from
 bovine serum albumin (BSA) and from rabbit serum albumin (RSA) were
 included as well. The resulting layout contained more than 200.000 peptide
 fields and could be synthesized in a single array on a microscope slide.
 More than 20 linear epitope candidates were identified and characterized
 at high resolution i.e. identifying which amino acids in which positions
 were needed, or not needed, for antibody interaction. As expected,
 moderate cross-reaction with some peptides in BSA was identified whereas
 no cross-reaction was observed with peptides from RSA. We conclude that
 high-density peptide microarrays are a very powerful methodology to
 identify and characterize linear antibody epitopes, and should advance
 detailed description of individual specificities at the single antibody
 level as well as serologic analysis at the proteome-wide level.
description: All data: Binding of
 anti-HSA antibody to Array 1Datafile from peptide
 microarray measuring Human Serum Albumin(HSA) antibody binding to peptides
 from HSA and variations of these peptides.Unranked peptides Array 16220
 Slide 260912_1.txtAll data: Binding of
 anti-HSA antibody to Array 2 (Identical to/Repeat of Array
 1)Datafile from peptide
 microarray measuring Human Serum Albumin(HSA) antibody binding to peptides
 from HSA and variations of these peptides.Unranked peptides Array 16172
 Slide 280312.txt