cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8v0c3
title: Data from: Combining genetic and demographic information to prioritize conservation efforts for anadromous alewife and blueback herring

description: A major challenge in conservation biology is the need to broadly
 prioritize conservation efforts when demographic data are limited. One
 method to address this challenge is to use population genetic data to
 define groups of populations linked by migration and then use demographic
 information from monitored populations to draw inferences about the status
 of unmonitored populations within those groups. We applied this method to
 anadromous alewife (Alosa pseudoharengus) and blueback herring (Alosa
 aestivalis), species for which long-term demographic data are limited.
 Recent decades have seen dramatic declines in these species, which are an
 important ecological component of coastal ecosystems and once represented
 an important fishery resource. Results show that most populations comprise
 genetically distinguishable units, which are nested geographically within
 genetically distinct clusters or stocks. We identified three distinct
 stocks in alewife and four stocks in blueback herring. Analysis of
 available time series data for spawning adult abundance and body size
 indicate declines across the US ranges of both species, with the most
 severe declines having occurred for populations belonging to the Southern
 New England and the Mid-Atlantic Stocks. While all alewife and blueback
 herring populations deserve conservation attention, those belonging to
 these genetic stocks warrant the highest conservation prioritization.
description: Dryad - Rangewide
 alewife microsatellite dataThis tab-delimited text
 file contains the raw microsatellite data (15 loci) for alewife (A.
 pseudoharengus) used by Palkovacs et al. (2013) 'Combining genetic
 and demographic information to prioritize conservation efforts for
 anadromous alewife and blueback herring' to examine genetic
 population structure, and by Hasselman et al. (2014) 'Human
 disturbance causes the formation of a hybrid swarm between two naturally
 sympatric fish species' to examine rangewide frequency of
 hybridization in river herrings.Dryad - Rangewide
 blueback microsatellite dataThis tab-delimited text
 file contains the raw microsatellite data (15 loci) for blueback herring
 (A. aestivalis) used by Palkovacs et al. (2013) 'Combining genetic
 and demographic information to prioritize conservation efforts for
 anadromous alewife and blueback herring' to examine genetic
 population structure, and by Hasselman et al. (2014) 'Human
 disturbance causes the formation of a hybrid swarm between two naturally
 sympatric fish species' to examine rangewide frequency of
 hybridization in river herrings.
DOI: 10.82294/dvnkagj63
title: COPUS. Territorio: Guainía. Sector: Educación. Año: 2025
title: Dato. Observación estructurada con el protocolo COPUS.

description: Información recopilada durante el año 2025 a partir de observaciones estructuradas realizadas con el protocolo COPUS, dirigidas a educadores artísticos pertenecientes a programas de formación en educación artística y cultural del sector Educación (educación formal) en el departamento de Guainía.
DOI: 10.5061/dryad.n31kq
title: Data from: Conservation genetics and the implication for recovery of the endangered Mitchell’s satyr butterfly, Neonympha mitchellii mitchellii

description: The modern delineation of taxonomic groups is often aided by analyses of
 molecular data, which can also help inform conservation biology. Two
 subspecies of the butterfly Neonympha mitchellii are classified as
 federally endangered in the United States: Neonympha mitchellii
 mitchellii, the Mitchell’s satyr, and Neonympha mitchellii francisi, the
 Saint Francis’s satyr. The recent discovery of additional disjunct
 populations of N. mitchellii in the southeastern US could have important
 implications for both legal protection and management decisions. We
 elucidated the relationships among 48 individuals representing 5 N.
 mitchellii populations using 6 molecular markers (5 nuclear and 1
 mitochondrial) under a variety of analytical frameworks. Phylogenetic
 analysis resulted in moderately supported clades that corresponded with
 the geographic region where samples originated. Clustering analyses
 identified 3 groups, wherein the 2 named subspecies formed separate
 clusters. Coalescent analyses indicated evolutionary divergence between N.
 m. mitchellii and all other populations but weakly supported divergence
 among N. m. francisi and the recently discovered populations. Hence, the 2
 currently accepted subspecies were clearly different from one another, but
 the recently discovered populations could not be completely distinguished
 from N. m. francisi or each other. We propose that N. m. mitchellii and N.
 m. francisi continue to be managed as separate endangered species.
description: AL15_sortSorted nexus file for anonymous locus 15AL21_sortSorted nexus file for anonymous locus 21COI_sortsorted nexus file for cytochrom oxidase IEF1a_sortsorted nexus file for Elongation factor 1aGAPDH_sortSorted nexus file for glyceraldehyde phosphate dehydrogenaseRpS5_sortsorted nexus file for ribsomal protein S5Analysis_codeCode require to run analyses conducted in this paper and reproduce the results.MSB_Sanger_plotsR code needed to create the map, deltaK plot, and IMa2 plot from this paperIM_9File for IMa2 analysis 9MSB_IM_9IM_10File to conduct IMa2 analysis 10MSB_IM_10IM_11File needed to conduct IMa2 analysis 11MSB_IM_11IM_12File to conduct IMa2 analysis 12MSB_IM_12IM_13File to conduct IMa2 analysis 13MSB_IM_13MSB_IM_14File to conduct IMa2 analysis 14MSB_OG2Nexus file needed to run RAxML analysisMSB_PartitionPartition file needed by RAxMLMSB_OG2_partMSB_p9Results from deltaK analysis needed to generate plotMSB_IM_9hPosterior parameter estimates needed to create plots for analysis IM_9MSB_IM_11mPosterior parameter estimates needed to create plots for analysis 11mMSB_IM_14aPosterior parameter estimates needed to create plots for analysis 14aIM_10jPosterior parameter estimates needed to create plots for analysis 10jMSB_IM13dPosterior parameter estimates needed to create plots for analysis 13dMSB_IM_12nPosterior parameter estimates needed to create plots for analysis 12n
DOI: 10.5061/dryad.2d38f
title: Data from: Diet of the insectivorous bat Pipistrellus nathusii during autumn migration and summer residence

description: Migration is widespread among vertebrates. Yet bat migration has received
 little attention and only in the recent decades knowledge of it has been
 gained. Migration can cause significant changes in behaviour and
 physiology, due to increasing energy demands and aerodynamic constraints.
 Dietary shifts, for examples, have been shown to occur in birds before
 onset of migration. For bats it is not known if a change in diet occurs
 during migration, although especially breeding season related dietary
 preference has been documented. It is known that fat-rich diets, and
 subsequent accumulation of high fat deposits, do increase the flight range
 of migratory bats. Some bat species can be regarded as long-distance
 migrants, covering up to 2,000 km on their way between summer and winter
 roosting areas. Pipistrellus nathusii (Vespertilionidae), a European
 long-distant migrant, travels each year along the Baltic Sea from
 north-eastern Europe to hibernate in central and southern Europe. This
 study presents data on the dietary habits of migrating Pipistrellus
 nathusii compared with dietary habits during the breeding season. We
 analysed faecal samples from bats on fall migration caught at the
 Ornithological Field Station in Pape, Latvia and from samples collected in
 North-Latvian summer roosts. We applied both morphological identification
 and molecular methods, as morphological methods also recognize life stages
 of prey and can contribute frequency data. The diets of bats on migration
 and breeding bats were similar, with Diptera and Lepidoptera comprising
 the major prey categories. However certain prey groups could be explained
 by the different hunting habitats used during migration vs. summer
 residence.
description: Sequences of P. nathusii
 dietary samplesFasta file of seuqences
 from ion torrent sequencing of faecal samples from P. nathusii, collected
 in the field.Pips_Data_Clipped.fastaMorphological dietary analysis Pipistrellus nathusiiTxt file with presence/absence data from morphological diet analysis of P. nathusiiSamples-P.nathusii-Migration and Summertxt file with samples used for morphological and molecular analysisjMOTU-output-Pnathtxt-file of jMOTU-data from Ion-Torrent sequencing of dietary sample P.nathusiioutput.sql
DOI: 10.5061/dryad.4h071
title: Data from: Divergent selection on, but no genetic conflict over, female and male timing and rate of reproduction in a human population

description: The sexes often have different phenotypic optima for important
 life-history traits, and because of a largely shared genome this can lead
 to a conflict over trait expression. In mammals, the obligate costs of
 reproduction are higher for females, making reproductive timing and rate
 especially liable to conflict between the sexes. While studies from wild
 vertebrates support such sexual conflict, it remains unexplored in humans.
 We used a pedigreed human population from preindustrial Finland to
 estimate sexual conflict over age at first and last reproduction,
 reproductive lifespan and reproductive rate. We found that the phenotypic
 selection gradients differed between the sexes. We next established
 significant heritabilities in both sexes for all traits. All traits,
 except reproductive rate, showed strongly positive intersexual genetic
 correlations and were strongly genetically correlated with fitness in both
 sexes. Moreover, the genetic correlations with fitness were almost
 identical in men and women. For reproductive rate, the intersexual
 correlation and the correlation with fitness were weaker but again similar
 between the sexes. Thus, in this population, an apparent sexual conflict
 at the phenotypic level did not reflect an underlying genetic conflict
 over the studied reproductive traits. These findings emphasize the need
 for incorporating genetic perspectives into studies of human life-history
 evolution.
description: BolundetalDATAData file and pedigree file used for analyses.
DOI: 10.5061/dryad.1kk2k
title: Data from: Signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) revealed by a genome scan analysis of single nucleotide polymorphisms

description: Understanding the genetic mechanisms of adaptive population divergence is
 one of the most fundamental endeavours in evolutionary biology and is
 becoming increasingly important as it will allow predictions about how
 organisms will respond to global environmental crisis. This is
 particularly important for the honey bee, a species of unquestionable
 ecological and economical importance that has been exposed to increasing
 human-mediated selection pressures. Here, we conducted a single nucleotide
 polymorphism (SNP)-based genome scan in honey bees collected across an
 environmental gradient in Iberia and used four FST-based outlier tests to
 identify genomic regions exhibiting signatures of selection. Additionally,
 we analysed associations between genetic and environmental data for the
 identification of factors that might be correlated or act as selective
 pressures. With these approaches, 4.4% (17 of 383) of outlier loci were
 cross-validated by four FST-based methods, and 8.9% (34 of 383) were
 cross-validated by at least three methods. Of the 34 outliers, 15 were
 found to be strongly associated with one or more environmental variables.
 Further support for selection, provided by functional genomic information,
 was particularly compelling for SNP outliers mapped to different genes
 putatively involved in the same function such as vision, xenobiotic
 detoxification and innate immune response. This study enabled a more
 rigorous consideration of selection as the underlying cause of diversity
 patterns in Iberian honey bees, representing an important first step
 towards the identification of polymorphisms implicated in local adaptation
 and possibly in response to recent human-mediated environmental changes.
description: sampling locations and
 environmental variablesGeographical coordinates
 of sampling locations and environmental data for the 711 Iberian honey bee
 individualsSNP
 genotypes
DOI: 10.17172/nomad/2026.01.27-1
title: NOMAD dataset: Reconciling Models for Infinite-Layer Nickelate Superconductors: Role of the Interstitial-s Band
DOI: 10.5061/dryad.fq48q
title: Data from: The genetic architecture of floral traits in Iris hexagona and Iris fulva

description: The formation of hybrids among closely related species has been observed
 in numerous plant taxa. Selection by pollinators on floral traits can act
 as an early reproductive isolating barrier and may be especially important
 when there is overlap in distribution and flowering time. In this study,
 we use Quantitative Trait Locus (QTL) mapping based on 293 codominant SNP
 markers in an F2 population (n = 328) to assess the size, magnitude, and
 location of the genetic regions controlling floral traits known to be
 important for pollinator attraction in 2 species of Lousiana Irises, Iris
 fulva and Iris hexagona. We also evaluate correlations among F2 traits and
 identify transgression in the hybrid population. Overall, we observe that
 differences in most floral traits between I. fulva and I. hexagona are
 controlled by multiple QTLs and are distributed across several linkage
 groups. We also find evidence of transgression at several QTL, suggesting
 that hybridization can contribute to generating phenotypic variation,
 which may be adaptive in rapidly changing environments.
description: Genetic Architecture
 Data FileSheet one is the
 phenotype data, Sheet 2 is the genotype data, and sheet three includes the
 color data extracted from photographs of Irises.F2_phenotype.xls
DOI: 10.5061/dryad.mn0d5
title: Data from: Genomic selection for recovery of original genetic background from hybrids of endangered and common breeds

description: Critically endangered breeds and populations are often crossed with more
 common breeds or subspecies. This results in genetic admixture that can be
 undesirable when it challenges the genetic integrity of wild and domestic
 populations, causing a loss in special characteristics or unique genetic
 material and ultimately extinction. Here, we present two genomic selection
 strategies, using genome-wide DNA markers, to recover the genomic content
 of the original endangered population from admixtures. Each strategy
 relies on the estimation of the proportion of nonintrogressed genome in
 individuals based on a different method: either genomic prediction or
 identification of breed-specific haplotypes. Then, breeding programs that
 remove introgressed genomic information can be designed. To test these
 strategies, we used empirical 50K SNP array data from two pure sheep
 breeds, Merino (used as target breed), Poll Dorset and an existing admixed
 population of both breeds. Sheep populations with varying degrees of
 introgression and admixture were simulated starting from these real
 genotypes. Both strategies were capable of identifying segment origin, and
 both removed up to the 100% of the Poll Dorset segments. While the
 selection process led to substantial inbreeding, we controlled it by
 imposing a minimum number of individuals contributing to the next
 generation.
description: GenotypesThe file contains the genotypes of 188 pure Merino and 188 pure Poll Dorset. En each row of the file appears the individual Id followed by the genotypes of the 48599 SNP coded as allele content (0,1,2).BreedsThe file contains the codification used in the GBLUP experiment for the pure individuals. The file contains per row the individual Id and the code for breed trait (1=Merino, 0=Poll Dorset)
DOI: 10.5061/dryad.9mg16
title: Data from: Detecting spring after a long winter: coma or slow vigilance in cold, hypoxic turtles?

description: Many freshwater turtle species can spend the winter submerged in
 ice-covered lakes by lowering their metabolism, and it has been proposed
 that such severe metabolic depression render these turtles comatose. This
 raises the question how they can detect the arrival of spring and respond
 in a sensible way to sensory information during hibernation. Using evoked
 potentials from cold or hypoxic turtles exposed to vibration and light we
 show that hibernating turtles maintain neural responsiveness to light
 stimuli during prolonged hypoxia. Furthermore, turtles held under
 hibernation conditions for 14 days increase their activity when exposed to
 light or elevated temperatures, but not when exposed to vibration or
 increased oxygen. It is concluded that hibernating turtles are not
 comatose, but remain vigilant during overwintering in cold hypoxia,
 allowing them to respond to the coming of spring and to adjust their
 behavior to specific sensory inputs.
description: Data from 6 turtles
 exposed to light during anoxia and reoxygenation.zipThe data consists of wav
 files, which contain the recorded data of evoked potential measurements
 performed on anoxic (labeled Anoxi) and reoxygenating (labeled Reox)
 turtles exposed to light stimulation. Each recording was performed after
 one ventilation, during anoxia and reoxygenation.Data from 6 turtles
 exposed to light during temperature changeThe data consists of wav
 files containing recorded data from 6 turtles exposed to light stimulation
 during cooling, from 25 C to 3 C, and during reheating from 5 C to 25
 C.Data from 6 turtles
 exposed to vibration during anoxia and reoxygenationThe data consists of wav
 files containing data recorded from 6 turtles exposed to vibration during
 anoxia (labeld Anoxi) and reoxygenation (labeled Reox). A recording was
 performed after each ventialtion during anoxia and
 reoxygenation.Data from 6 turtles
 exposed to vibrtion during temperature changeData consists of wav
 files containing recorded data from 6 turtles exposed to vibration during
 cooling from 25 C to 3 C, and reheating from 5 C to 25
 C.Movement data for
 hibernating turtlesThe data consists of
 MatLab files containing the differentiated brightness scores from turtle
 movement during hibernation, before and after stimulus (heat, light,
 oxygen and vibration.) Further information is available in the ReadMe
 file.
DOI: 10.5061/dryad.j87v8
title: Data from: Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time

description: Phylogenomic analyses of archaeal genome sequences are providing windows
 into the group's evolutionary past, even though most archaeal taxa
 lack a conventional fossil record. Here, phylogenetic analyses were
 performed using key metabolic genes that define the metabolic niche of
 microorganisms. Such genes are generally considered to have undergone high
 rates of lateral gene transfer. Many gene sequences formed clades that
 were identical, or similar, to the tree constructed using large numbers of
 genes from the stable core of the genome. Surprisingly, such lateral
 transfer events were readily identified and quantifiable, occurring only a
 relatively small number of times in the archaeal domain of life. By
 placing gene acquisition events into a temporal framework, the rates by
 which new metabolic genes were acquired can be quantified. The highest
 lateral transfer rates were among cytochrome oxidase genes that use oxygen
 as a terminal electron acceptor (with a total of 12-14 lateral transfer
 events, or 3.4-4.0 events per billion years, across the entire archaeal
 domain). Genes involved in sulfur or nitrogen metabolism had much lower
 rates, on the order of one lateral transfer event per billion years. This
 suggests that lateral transfer rates of key metabolic proteins are rare
 and not rampant.
description: Blank2012.LowRatesofLGTMesquite file containing phylogenetic tree and character matrix.
DOI: 10.5061/dryad.k9j15
title: Data from: Synaptotagmin 7 functions as a Ca^2+ -sensor for synaptic vesicle replenishment

description: [No abstract entered]
description: Syt7
 ms_eLIFE_Huisheng
DOI: 10.5061/dryad.c413k
title: Data from: The influence sampling design on species tree inference: a new relationship for the New World chickadees (Aves: Poecile)

description: In this study, we explore the long-standing issue of how many loci are
 needed to infer accurate phylogenetic relationships, and whether loci with
 particular attributes (i.e., parsimony informativeness, variability, gene
 tree resolution) outperform others. To do so, we use an empirical dataset
 consisting of the seven species of chickadees (Aves: Paridae), an
 analytically tractable, recently diverged group, and well studied
 ecologically but lacking a nuclear phylogeny. We estimate relationships
 using 40 nuclear loci and mitochondrial DNA using four coalescent-based
 species tree inference methods (BEST, *BEAST, STEM, STELLS). Collectively,
 our analyses contrast with previous studies and support a sister
 relationship between the Black-capped and Carolina Chickadee, two
 superficially similar species that hybridize along a long zone of contact.
 Gene flow is a potential source of conflict between nuclear and
 mitochondrial gene trees, yet, we find a significant, albeit low, signal
 of gene flow. Our results suggest that relatively few loci with high
 information content may be sufficient for estimating an accurate species
 tree, but that substantially more loci are necessary for accurate
 parameter estimation. We provide an empirical reference point for
 researchers designing sampling protocols with the purpose of inferring
 phylogenies and population parameters of closely related taxa.
description: Sequence alignment
 fileNexus
 formatHarrisetal_sequencefile.nexSupplemental materialSupplemental tables, figures, methods, citations, etc.Harrisetal_supplemental.zip
DOI: 10.5061/dryad.th092
title: Data from: Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle

description: The domestication and development of cattle has considerably impacted
 human societies, but the histories of cattle breeds have been poorly
 understood especially for African, Asian, and American breeds. Using
 genotypes from 43,043 autosomal single nucleotide polymorphism markers
 scored in 1,543 animals, we evaluate the population structure of 134
 domesticated bovid breeds. Regardless of the analytical method or sample
 subset, the three major groups of Asian indicine, Eurasian taurine, and
 African taurine were consistently observed. Patterns of geographic
 dispersal resulting from co-migration with humans and exportation are
 recognizable in phylogenetic networks. All analytical methods reveal
 patterns of hybridization which occurred after divergence. Using 19
 breeds, we map the cline of indicine introgression into Africa. We infer
 that African taurine possess a large portion of wild African auroch
 ancestry, causing their divergence from Eurasian taurine. We detect
 exportation patterns in Asia and identify a cline of Eurasian
 taurine/indicine hybridization in Asia. We also identify the influence of
 species other than Bos taurus in the formation of Asian breeds. We detect
 the pronounced influence of Shorthorn cattle in the formation of European
 breeds. Iberian and Italian cattle possess introgression from African
 taurine. American Criollo cattle are shown to be of Iberian, and not
 African, decent. Indicine introgression into American cattle occurred in
 the Americas, and not Europe. We argue that cattle migration, movement and
 trading followed by admixture have been important forces in shaping modern
 bovine genomic variation.
description: Genotypes, SNP
 information, and sample information for 1,543 cattle from 134
 breedsThis file contains the
 genotypes from 43,043 SNP markers scored in 1,543 cattle. Samples were
 genotyped with the Illumina BovineSNP50 BeadChip. Genotypes were called
 using GenomeStudio.WorldWideCattleDryad.zip