cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.82nt3
title: Data from: Did Late Pleistocene climate change result in parallel genetic structure and demographic bottlenecks in sympatric Central African crocodiles, Mecistops and Osteolaemus?

description: The mid-Holocene has had profound demographic impacts on wildlife on the
 African continent, though there is little known about the impacts on
 species from Central Africa. Understanding the impacts of climate change
 on co-distributed species can enhance our understanding of ecosystem
 dynamics and for formulating restoration objectives. We took a
 multi-genome comparative approach to examine the phylogeographic structure
 of two poorly known Central African crocodile species - Mecistops sp. aff.
 cataphractus and Osteolaemus tetraspis. In addition, we conducted
 coalescent-based demographic reconstructions to test the hypothesis that
 population decline was driven by climate change since the Last Glacial
 Maximum, versus more recent anthropogenic pressures. Using a hierarchical
 Bayesian model to reconstruct demographic history, we show that both
 species had dramatic declines (&gt; 97%) in effective population size
 in the period following the Last Glacial Maximum 1,500 – 18,000 YBP.
 Identification of genetic structuring showed both species have similar
 regional structure corresponding to major geological features (i.e.,
 hydrologic basin), and that small observed differences between them are
 best explained by the differences in their ecology and the likely impact
 that climate change had on their habitat needs. Our results support our
 hypothesis that climatic effects, presumably on forest and wetland
 habitat, had a congruent negative impact on both species.
description: Mecistops
 mtDNAThe file is a
 concatenated alignment of cyt-b (bp 1 - 927) and COI (bp 928 -
 1849).ShirleyandAustin_MolecularEcology2017_comparativecrocs_Mecistops_mtDNA.fasOsteolaemus mtDNAThe file is a concatenated alignment of cyt-b (bp 1 - 621) and COI (bp 622 - 1354).ShirleyandAustin_MolecularEcology2017_comparativecrocs_Osteolaemus_mtDNA.fasMecistops mtDNA Sample LocalitiesGeographic coordinates for each sample used in the mtDNA analysis and for sequences available in the associated fasta file.ShirleyandAustin_MolecularEcology2017_comparativecrocs_Mecistops_mtDNA_geographiccoordinates.xlsxOsteolaemus mtDNA sample localitiesGeographic coordinates for each sample used in the mtDNA analysis and for sequences available in the associated fasta file.ShirleyandAustin_MolecularEcology2017_comparativecrocs_Osteolaemus_mtDNA_geographiccoordinates.xlsxMecistops microsatellite genotypesMicrosatellite genotypes for all individuals used in the analysis. Sample localities are located after the last genotype.ShirleyandAustin_MolecularEcology2017_comparativecrocs_Mecistops_microsats.xlsOsteolaemus microstaellite genotypesMicrosatellite genotypes for all individuals used in the analysis. Sample localities are located after the last genotype.ShirleyandAustin_MolecularEcology2017_comparativecrocs_Osteolaemus_microsats.xlsx
DOI: 10.5061/dryad.fv21h
title: Data from: Genetic identification of Iberian rodent species using both mitochondrial and nuclear loci: application to non-invasive sampling

description: Species identification through non-invasive sampling is increasingly used
 in animal conservation genetics, given that it obviates the need to handle
 free-living individuals. Non-invasive sampling is particularly valuable
 for elusive and small species such as rodents. Although rodents are not
 usually assumed to be the most obvious target for conservation, of the 21
 species or near-species present in Iberia, three are considered endangered
 and declining while several others are poorly studied. Here we develop a
 genetic tool for identifying all rodent species in Iberia by non-invasive
 genetic sampling. To achieve this purpose we selected one mitochondrial
 gene (cytochrome b – cyt-b) and one nuclear gene (interphotoreceptor
 retinoid-binding protein – IRBP), which we first sequenced using tissue
 samples. Both genes allow for the phylogenetic distinction of all species
 except the sibling species Microtus lusitanicus and M. duodecimcostatus.
 Overall, cyt-b showed higher resolution than IRBP, revealing a clear
 barcoding gap. To allow these markers to be applied to non-invasive
 samples, we selected a short highly-diagnostic fragment from each gene,
 which we used to obtain sequences from faeces and bones from owl pellets.
 Amplification success for the cyt-b and IRBP fragment was 85% and 43% in
 faecal and 88% and 64% in owl-pellet DNA extractions, respectively. The
 method allows the unambiguous identification of the great majority of
 Iberian rodent species from non-invasive samples, with application in
 studies of distribution, spatial ecology and population dynamics, and for
 conservation.
description: Cytb LF
 HaplotypesAlignment of Cytb long
 fragment haplotypesCytb SF
 HaplotypesAligment of cytb short
 fragment haplotypesIRBP LF
 HaplotypesAlignment of IRBP long
 fragment haplotypes.IRBP SF
 HaplotypesAlignment of IRBP short
 fragment haplotypesSamples_tableNew sequence data and sequence data retrieved from GenBank for all taxa analysed. Details on sampling locality are given for each specimen analysed. Haplotype names as well as GenBank accession numbers are detailed for each loci per specimen, as well as source of previous published data. Information on were the samples are held in is also displayed.
DOI: 10.5061/dryad.27c8s
title: Data from: Reconstructing the emergence of a lethal infectious disease of wildlife supports a key role for spread through translocations by humans

description: There have been few reconstructions of wildlife disease emergences,
 despite their extensive impact on biodiversity and human health. This is
 in large part attributable to the lack of structured and robust
 spatio-temporal datasets. We overcame logistical problems of obtaining
 suitable information by using data from a citizen science project and
 formulating spatio-temporal models of the spread of a wildlife pathogen
 (genus Ranavirus, infecting amphibians). We evaluated three main
 hypotheses for the rapid increase in disease reports in the UK: that
 outbreaks were being reported more frequently, that climate change had
 altered the interaction between hosts and a previously widespread
 pathogen, and that disease was emerging due to spatial spread of a novel
 pathogen. Our analysis characterized localized spread from nearby ponds,
 consistent with amphibian dispersal, but also revealed a highly
 significant trend for elevated rates of additional outbreaks in localities
 with higher human population density—pointing to human activities in also
 spreading the virus. Phylogenetic analyses of pathogen genomes support the
 inference of at least two independent introductions into the UK. Together
 these results point strongly to humans repeatedly translocating
 ranaviruses into the UK from other countries and between UK ponds, and
 therefore suggest potential control measures.
description: Citizen science reports
 of amphibian mortality events in the UK between 1991 and
 2010This a csv file where
 each record relates to a citizen science report of amphibian mortality in
 the UK between 1991-2010. The fields cover georeference data and data on
 the mortality event (numbers of affected animals and signs of disease
 observed).ReconRVemerg_UK_1991-2010_CitSciRecords_SJP.csvNexus alignment of UK ranaviruses plus viruses which provide global contextThis nexus alignment was used to construct the phylogeny in figure 5 of the attached publication. It is a concatenated alignment of seven partial open reading frames detailed in Price et al. (2014). The resulting phylogeny visualises relationships of UK ranaviruses in a global context.ReconRVemerg_UK_alignment_SJP.nex
DOI: 10.5061/dryad.ct140
title: Data from: Molecular insights into the lichen genus Alectoria (Parmeliaceae) in North America

description: Alectoria is a genus of fruticose lichen characterised by the presence of
 usnic acid and conspicuous raised pseudocyphellae. This genus is
 particularly diverse and abundant in montane, boreal, and Arctic regions
 of North America. Because intermediate forms have been reported for
 several species of Alectoria on the continent, it has been suggested that
 these species were initially delimited based on the extremes of
 morphological gradients. Here, we use the results of molecular
 phylogenetic analyses of two nuclear genes, ITS and Mcm7, with 48
 representatives of 9 taxa to examine the delineation of 5 taxa that have
 been previously shown to be related to, or confused with, A. sarmentosa:
 A. fallacina, A. imshaugii, A. sarmentosa var. sorediosa, A. sarmentosa
 subsp. vexillifera, and A. vancouverensis. Alectoria fallacina was found
 to be well-supported and distantly related to A. sarmentosa. Conversely,
 the other four taxa were recovered as a single monophyletic group with
 little internal structure, which did not support the presently defined
 morphological species. A provisional taxonomic treatment is proposed
 pending more detailed study at the population level. Alectoria sarmentosa
 var. sorediosa is recognized at the species level, which necessitates the
 new combination: A. sorediosa. An updated key to the North American
 species of Alectoria is also provided.
description: original alignment for
 ITSAlecITSNEX3.nexoriginal alignment for MCM7ALECMCM7NEX2.nexoriginal alignment for ITS+MCM7alectoria_ITS_MCM7_combined (1).nexinput dataset for ITS ML analysisAlecITSNEX4.phyinput dataset for MCM7 ML analysisALECMCM7NEX2.phyinput dataset for mtSSU ML analysisAlectoria_mtssu.phyinput dataset for ITS+MCM7 combined ML analysisML_alectoria_ITS_MCM7_combined.phyinput dataset for ITS+MCM7 combined BI analysisBI_Alectoria_COMBINED.nexoutput of results for initial mtSSU analysis with MLRAxML_bipartitions.Alectoria_mtssu_ML.pdfoutput of results for initial MCM7 analysis with MLRAxML_bipartitions.Alectoria_McM7_ML.pdfoutput of results for initial ITS analysis with MLRAxML_bipartitions.Alectoria_ITS_ML.pdfoutput of results for initial ITS+McM7 analysis with M_combinedRAxML_bipartitions.Alectoria_combined_ITS_MCM7_ML.pdf
DOI: 10.5061/dryad.76jr5
title: Data from: Synchrony in small mammal community dynamics across a forested landscape

description: Long-term studies at local scales indicate that fluctuations in abundance
 among trophically similar species are often temporally synchronized.
 Complementary studies on synchrony across larger spatial extents are less
 common, as are studies that investigate the subsequent impacts on
 community dynamics across the landscape. We investigate the impact of
 species population fluctuations on concordance in community dynamics for
 the small mammal fauna of the White Mountain National Forest, USA.
 Hierarchical open population models, which account for imperfect
 detection, were used to model abundance of the most common species at 108
 sites over a three year period. Most species displayed individualistic
 responses of abundance to forest type and physiographic characteristics.
 However, among species, we found marked synchrony in population
 fluctuations across years, regardless of landscape affinities or trophic
 level. Across the region, this population synchrony led to high
 within-year concordance of community composition and aggregate properties
 (e.g., richness and diversity) independent of forest type and low
 among-year similarity in communities, even for years with similar species
 richness. Results suggest that extrinsic factors primarily drive abundance
 fluctuations and subsequently community dynamics, although local community
 assembly may be modified by species dispersal abilities and biotic
 interactions. Concordant community dynamics across space and over time may
 impact the stability of regional food webs and ecosystem functions.
description: Small_Mammal_Daily_CountsDaily count data for 15 small mammal species collected at 108 sampling sites in the White Mountain National Forest. These data were used to model detection corrected abundance.Stephens_et_al_2016_Data_Small_Mammal_Daily_Counts.xlsxDetection_CovariatesDetection covariates (temperature, precipitation, and trap type) used to model abundance for the 15 most common small mammal species.Stephens_et_al_2016_Data_Detection_Covariates.xlsxLandscape_VariablesLandscape covariates (trap type, elevation, percent stream/wetland, percent hardwood forest, percent mixed forest, percent softwood forest, forest age, year) used to model abundance for the 15 most common small mammal species.Stephens_et_al_2016_Data_Landscape_Variables.xlsxDetection_Corrected_Abundance&Landscape_VariablesDetection corrected small mammal abundance data and landscape variables used in community analyses.Stephens_et_al_2016_Data_Detection_Corrected_Abundance&Landscape_Variables.xlsx
DOI: 10.5061/dryad.rp3g3
title: Data from: Differential chromosome conformations as hallmarks of cellular identity revealed by mathematical polymer modeling

description: Inherently dynamic, chromosomes adopt many different conformations in
 response to DNA metabolism. Models of chromosome organization in the yeast
 nucleus obtained from genome-wide chromosome conformation data or
 biophysical simulations provide important insights into the average
 behavior but fail to reveal features from dynamic or transient events that
 are only visible in a fraction of cells at any given moment. We developed
 a method to determine chromosome conformation from relative positions of
 three fluorescently tagged DNA in living cells imaged in 3D. Cell type
 specific chromosome folding properties could be assigned based on
 positional combinations between three loci on yeast chromosome 3. We
 determined that the shorter left arm of chromosome 3 is extended in MATα
 cells, but can be crumpled in MATa cells. Furthermore, we implemented a
 new mathematical model that provides for the first time an estimate of the
 relative physical constraint of three linked loci related to cellular
 identity. Variations in this estimate allowed us to predict functional
 consequences from chromatin structural alterations in asf1 and
 recombination enhancer deletion mutant cells. The computational method is
 applicable to identify and characterize dynamic chromosome conformations
 in any cell type.
description: yil30
 dataHML MAT and HMR
 positions in YIL30yil30-ok-251011.xlsxyil31 dataHML MAT and HMR positionsyil31-ok-281011.xlsxyil30 with deletion of ASFHML MAT and HMR positionsyil30Dasf_200709-reformuler.xlsxyil31 with deletion of ASFHML MAT and HMR positionsyil31Dasf1_200709_reformuler.xlsxdeletion of RE in YIL30HML MAT and HMR positionsyil30DRE-041209.xlsxdeletion of RE in YIL31HML MAT and HMR positionsyil31DRE-041209.xlsxMatlab basic plotbasic_plot.mmatlab colorbarcolor34.mmatlab to compare two strainscomparencor.md1d2th_plotd1d2th_plot2excelroulgent1t2h3kde2dlance2silvia2plotboxplotlance2silviaplotboxplot2plotboxplot3plothistSilvia01sylviaextr2tableplottemp34cusMPI_opti
DOI: 10.5061/dryad.4d789
title: Data from: Characterization of class I- and II-like major histocompatibility complex loci in pedigrees of North Atlantic right whales

description: North Atlantic right whales have one of the lowest levels of genetic
 variation at minisatellite loci, microsatellite loci, and mitochondrial
 control region haplotypes among mammals. Here, adaptive variation at the
 peptide binding region of class I and class II DRB-like genes of the major
 histocompatibility complex was assessed. Amplification of a duplicated
 region in 222 individuals revealed at least 11 class II alleles. Six
 alleles were assigned to the locus Eugl-DRB1 and 5 alleles were assigned
 to the locus Eugl-DRB2 by assessing segregation patterns of alleles from
 81 parent/offspring pedigrees. Pedigree analysis indicated that these
 alleles segregated into 12 distinct haplotypes. Genotyping a smaller
 subset of unrelated individuals (n = 5 and 10, respectively) using
 different primer sets revealed at least 2 class II pseudogenes (with ≥ 4
 alleles) and at least 3 class I loci (with ≥ 6 alleles). Class II
 sequences were significantly different from neutrality at peptide binding
 sites suggesting loci may be under the influence of balancing selection.
 Trans-species sharing of alleles was apparent for class I and class II
 sequences. Characterization of class II loci represents the first step in
 determining the relationship between major histocompatibility complex
 variability and factors affecting health and reproduction in this species.
description: Supplementary Material -
 MHC Class II Nucleotide AlignmentNucleotide sequences of
 North Atlantic right whale DRB-like alleles (Accession Numbers: KF137593-
 KF137605). Alleles are aligned to the cow DRB3, cow DRB2, Human DRB1,
 Human DQB2, beluga DRB and beluga DQB alleles. The positions of the three
 primer sets used in this study are also indicated.Supplementary Material -
 MHC HaplotypesNorth Atlantic right
 whale EuglDRB1-DRB2 haplotypes identified by following transmission
 patterns in four known matrilines and six known
 patrilines.Supplementary Material -
 Right Whale Family GroupsEugl-DRB1 and Eugl-DRB2
 genotypes obtained from the 81 assessed North Atlantic right whale family
 groups used to that were used to infer MHC Class II
 haplotypes.Supplementary Material -
 SSCP ImageExample of SSCP mobility
 patterns of known North Atlantic right whale DRB-like
 alleles.
DOI: 10.5061/dryad.2s8d0f9
title: Data from: Phylogenetic ANOVA: group-clade aggregation, biological challenges, and a refined permutation procedure

description: Phylogenetic regression is frequently utilized in macroevolutionary
 studies, and its statistical properties have been thoroughly investigated.
 By contrast, phylogenetic ANOVA has received relatively less attention,
 and the conditions leading to incorrect statistical and biological
 inferences when comparing multivariate phenotypes among groups remains
 under-explored. Here we propose a refined method of randomizing residuals
 in a permutation procedure (RRPP) for evaluating phenotypic differences
 among groups while conditioning the data on the phylogeny. We show that
 RRPP displays appropriate statistical properties for both phylogenetic
 ANOVA and regression models, and for univariate and multivariate datasets.
 For ANOVA, we find that RRPP exhibits higher statistical power than
 methods utilizing phylogenetic simulation. Additionally, we investigate
 how group dispersion across the phylogeny affects inferences, and reveal
 that highly aggregated groups generate strong and significant correlations
 with the phylogeny, which reduce statistical power and subsequently affect
 biological interpretations. We discuss the broader implications of this
 phylogenetic group aggregation, and its relation to challenges encountered
 with other comparative methods where one or a few transitions in discrete
 traits are observed on the phylogeny. Finally, we recommend that
 phylogenetic comparative studies of continuous trait data utilize RRPP for
 assessing the significance of indicator variables as sources of trait
 variation.
description: RScriptsR scripts and results of simulations evaluating approachSalamander dataSpecies means for Plethodon morphology used in empirical examplemeandata-CinGlutOnly.csvR Script: PlethExampleR script used for empirical examplePlethExample.rsalamander phylogenyMaximum clade credibility tree from set of 1000 posterior trees from: Bonett RM, Blair AL (2017) Data from: Evidence for complex life cycle constraints on salamander body form diversification. Dryad Digital Repository. https://doi.org/10.5061/dryad.pn5kgConsensus of 1000 salamander trees.nex
DOI: 10.5061/dryad.202t3
title: Data from: Surprising flexibility in parental care revealed by experimental changes in offspring demand

description: Parental behaviour often exhibits plasticity to factors expected to affect
 the benefits or costs of care. For example, parent songbirds typically
 increase their provisioning behaviour as nestlings mature. Several
 mechanisms exist that could allow parents to track nestling age and
 provide appropriate care. We performed a short-term experiment on house
 sparrows, Passer domesticus, in which offspring of different ages were
 exchanged to assess the level of flexibility parents exhibit and the
 likely cues they use. We found that a pair's rate of food delivery,
 an individual parent's visit rate to the nest, the duration of a
 foraging trip, and both the time a parent was in the nest and how long
 they perched near the nest after emerging from feeding nestlings changed
 according to the age of the offspring at the time. This shift in parenting
 was evident by the second visit after the swap. The amount of food brought
 per trip did not change with either natural or manipulated age. While
 females spent more time in the nest than males, there were no sex
 differences in the responses to the experiment. Food delivery rate
 increased nestling mass gain during each phase of the experiment,
 suggesting that parental plasticity in delivery was beneficial to
 offspring. However, there was an additional effect of the experiment on
 nestling weight gain, suggesting possible effects of food type brought
 during each phase of the experiment. Parent sparrows appear to use cues of
 offspring age over a time span that differs greatly from the natural time
 course of changes in nestling demand. This extension of plasticity into
 unnatural conditions has implications for understanding individual
 differences in plasticity and how at least some organisms might adjust to
 rapid and unusual environmental change.
description: Pairs_archiveSummary data on each pair of adults involved in the swap experiment.Visitrate_archiveSummary data for each observation session on each individual subject int he swap experimentRawvisits_archiveData on each trip by each subject in the swap experiment