cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7t4n0
title: Data from: Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population

description: Despite decades of research assessing the genetic structure of natural
 populations, the biological meaning of low yet significant genetic
 divergence often remains unclear due to a lack of associated phenotypic
 and ecological information. At the same time, structured populations with
 low genetic divergence and overlapping boundaries can potentially provide
 excellent models to study adaptation and reproductive isolation in cases
 where high-resolution genetic markers and relevant phenotypic and life
 history information are available. Here, we combined single nucleotide
 polymorphism (SNP)-based population inference with extensive phenotypic
 and life history data to identify potential biological mechanisms driving
 fine-scale subpopulation differentiation in Atlantic salmon (Salmo salar)
 from the Teno River, a major salmon river in Europe. Two sympatrically
 occurring subpopulations had low but significant genetic differentiation
 (FST = 0.018) and displayed marked differences in the distribution of life
 history strategies, including variation in juvenile growth rate, age at
 maturity and size within age classes. Large, late-maturing individuals
 were virtually absent from one of the two subpopulations, and there were
 significant differences in juvenile growth rates and size at age after
 oceanic migration between individuals in the respective subpopulations.
 Our findings suggest that different evolutionary processes affect each
 subpopulation and that hybridization and subsequent selection may maintain
 low genetic differentiation without hindering adaptive divergence.
description: Aykanat_et_al_Dryad_filesFILES IN THE BUNDLE: mainparams: parameter file for the structure runs. NOTE that k and n are "number of populations" and "number of replicate", respectively and appropriate number should be used instead of these letters when running the software. teno_MS = The GenABEL format main file. The file includes genotype (n= 2874 SNPs), phenotype as well as location information from 662 individuals, which is sufficient to replicate the main results. Structure raw files.zip = Includes raw results from the structure analysis which is sufficient to replicate all structure related results.
DOI: 10.34740/kaggle/dsv/14640673
title: Mahanagar Yatayat Transport Dataset
DOI: 10.5061/dryad.qh631
title: Data from: Hybrid incompatibilities, local adaptation, and the genomic distribution of natural introgression between species

description: Under allopatric speciation, geographic barriers eliminate gene flow
 between eventual species at all loci in the genome simultaneously. There
 is increasing evidence, however, that speciation can be complex, with some
 loci experiencing gene flow during speciation or during bouts of secondary
 contact. In taxa with heteromorphic sex chromosomes— birds, butterflies,
 mammals and Drosophila— the X (or Z) chromosome generally shows reduced
 levels of gene flow compared to autosomes. To investigate why, we develop
 population genetic models of secondary contact and gene flow at a neutral
 locus that is genetically linked to selected loci involved in hybrid
 incompatibilities and/or local adaptation. Using models that assume weak
 migration and strong selection, we compare gene flow at X-linked versus
 autosomal neutral loci as a function of linkage, dominance, selection,
 sex-specific selection, and sex-specific recombination. For most cases,
 gene flow at neutral loci on the X is reduced relative to autosomes, as
 the greater efficacy of hemizygous selection in XY hybrids reduces the
 opportunity for neutral migrant alleles to escape their genetically
 linked, locally disfavored alleles via recombination. There are some
 circumstances, however, involving sex-limited selection and sex-limited
 recombination that allow neutral loci on the X to introgress more readily
 than those on autosomes.
description: MuirheadPresgraves_Fig1_4Simulation results, Figures 1 and 4MuirheadPresgraves_FigA1_LethalSimulation results, Appendix figure A1 (lethal incompatibilities)MuirheadPresgraves_FigA2_AsymmSimulation results, Appendix figure A2 (asymmetric selection coefficients)MuirheadPresgraves_FigA4_MFmigSimulation results, Appendix figure A4 (male vs. female migration)MuirheadPresgraves_FigA5_A6_NrSimulation results, Appendix figures A5, A6 (range of s values when Nr is large, Nr is small)MuirheadPresgraves_FigA7_residSimulation results, Figure A7 (residuals under standard parameter values)MuirheadPresgraves_FigA8_10_popSizeSimulation results, Appendix figures A8, A10 (residuals under various population sizes)MuirheadPresgraves_FigA9_10_migSimulation results, Appendix figures A9, A10 (residuals under different migration levels)
DOI: 10.5281/zenodo.18332981
title: CAMELS USA 421 (Quilty and Jahangir, 2026)

description: A 421-catchment subset of the CAMELS (Catchment Attributes and MEteorology for Large-sample Studies) USA dataset as described in Quilty and Jahangir (2026): https://doi.org/10.1016/j.jhydrol.2026.134986. Sample code to train the different deep learning (DL) models from the paper are also included.

The target and input data have already been pre-processed for entry into the deep learning models. The related GitHub repository (https://github.com/djmq/semicontinuousDL_camelsUSA) provides an example on how to download the data from Zenodo and train the deterministic DL model. 

Future releases of the code will be made available on GitHub.

The MATLAB code has been tested in R2024a but is not guaranteed to work in earlier versions.
DOI: 10.5281/zenodo.18358063
title: CAMELS USA 421 (Quilty and Jahangir, 2026)

description: A 421-catchment subset of the CAMELS (Catchment Attributes and MEteorology for Large-sample Studies) USA dataset as described in Quilty and Jahangir (2026): https://doi.org/10.1016/j.jhydrol.2026.134986. Sample code to train the different deep learning (DL) models from the paper are also included.

The target and input data have already been pre-processed for entry into the deep learning models. The related GitHub repository (https://github.com/djmq/semicontinuousDL_camelsUSA) provides an example on how to download the data from Zenodo and train the deterministic DL model. 

Future releases of the code will be made available on GitHub.

The MATLAB code has been tested in R2024a but is not guaranteed to work in earlier versions.
DOI: 10.5061/dryad.q675s
title: Data from: Linkage mapping reveals strong chiasma interference in sockeye salmon: implications for interpreting genomic data

description: Meiotic recombination is fundamental for generating new genetic variation
 and for securing proper disjunction. Further, recombination plays an
 essential role during the rediploidization process of polyploid-origin
 genomes because crossovers between pairs of homeologous chromosomes retain
 duplicated regions. A better understanding of how recombination affects
 genome evolution is crucial for interpreting genomic data; unfortunately,
 current knowledge mainly originates from a few model species. Salmonid
 fishes provide a valuable system for studying the effects of recombination
 in nonmodel species. Salmonid females generally produce thousands of
 embryos, providing large families for conducting inheritance studies.
 Further, salmonid genomes are currently rediploidizing after a whole
 genome duplication and can serve as models for studying the role of
 homeologous crossovers on genome evolution. Here, we present a detailed
 interrogation of recombination patterns in sockeye salmon (Oncorhynchus
 nerka). First, we use RAD sequencing of haploid and diploid gynogenetic
 families to construct a dense linkage map that includes paralogous loci
 and location of centromeres. We find a nonrandom distribution of paralogs
 that mainly cluster in extended regions distally located on 11 different
 chromosomes, consistent with ongoing homeologous recombination in these
 regions. We also estimate the strength of interference across each
 chromosome; results reveal strong interference and crossovers are mostly
 limited to one per arm. Interference was further shown to continue across
 centromeres, but metacentric chromosomes generally had at least one
 crossover on each arm. We discuss the relevance of these findings for both
 mapping and population genomic studies.
description: Gynogenetic_haploids_genotypesGenotype data for the haploid progenyGynogenetic_diploids_genotypesGenotype data for the diploid progeny
DOI: 10.5061/dryad.19nf6
title: Data from: Mitochondrial capture enriches mito-DNA 100 folds enabling PCR-free mitogenomics biodiversity analysis

description: Biodiversity analyses based on Next Generation Sequencing (NGS) platforms
 have developed by leaps and bounds in recent years. A PCR-free strategy,
 which can alleviate taxonomic bias, was considered as a promising approach
 to delivering reliable species compositions of targeted environments. The
 major impediment of such a method is the lack of appropriate mitochondrial
 DNA enrichment ways. Because mitochondrial genomes (mitogenomes) make up
 only a small proportion of total DNA, PCR-free methods will inevitably
 result in a huge excess of data (&gt; 99%). Furthermore, the massive
 volume of sequence data is highly demanding on computing resources. Here,
 we present a mitogenome enrichment pipeline via a gene capture chip that
 was designed by virtue of the mitogenome sequences of the 1000 Insect
 Transcriptome Evolution project (1KITE, www .1kite . org). A mock sample
 containing 49 species was used to evaluate the efficiency of the
 mitogenome capture method. We demonstrate that the proportion of
 mitochondrial DNA can be increased by ca. 100-fold (from the original
 0.47% to 42.52%). Variation in phylogenetic distances of target taxa to
 the probe set could in principle result in bias in abundance. However, the
 frequencies of input taxa were largely maintained after capture (R2=0.81).
 We suggest that our mitogenome capture approach coupled with PCR-free
 shotgun sequencing could provide ecological researchers an efficient NGS
 method to deliver reliable biodiversity assessment.
description: for_probe_designMitochondrial sequences filtered from 1KTIE project and used for capture array design.clustalw_pdisMitochondrial genes in the mock up samples and its top 5 similarity probes. Then, each cluster were aligned and calculated for P-distance.Mito_capture.final.2X.len65.probeprobes
DOI: 10.5061/dryad.f8rm5
title: Data from: Relative preference and localized food affect predator space use and consumption of incidental prey

description: Abundant, localized foods can concentrate predators and their foraging
 efforts, thus altering both the spatial distribution of predation risk and
 predator preferences for prey that are encountered incidentally. However,
 few investigations have quantified the spatial scale over which localized
 foods affect predator foraging behavior and consumption of incidental
 prey. In spring 2010, we experimentally tested how point-source foods
 altered how generalist predators (white-footed mice, Peromyscus leucopus)
 utilized space and depredated two incidental prey items: almonds (Prunus
 dulcis; highly profitable) and maple seeds (Acer saccharum; less
 profitable). We estimated mouse population densities with trapping webs,
 quantified mouse consumption rates of these incidental prey items, and
 measured local mouse activity with track plates. We predicted that 1)
 mouse activity would be elevated near full feeders, but depressed at
 intermediate distances from the feeder, 2) consumption of both incidental
 prey would be high near feeders providing less-preferred food and, 3)
 consumption of incidental prey would be contingent on predator preference
 for prey relative to feeders providing more-preferred food. Mouse
 densities increased significantly from pre- to post-experiment. Mean mouse
 activity was unexpectedly greatest in control treatments, particularly
 &lt;15 m from the control (empty) feeder. Feeders with highly
 preferred food (sunflower seeds) created localized refuges for incidental
 prey at intermediate distances (15 to 25m) from the feeder. Feeders with
 less-preferred food (corn) generated localized high risk for highly
 preferred almonds &lt;10 m of the feeder. Our findings highlight the
 contingent but predictable effects of locally abundant food on risk
 experienced by incidental prey, which can be positive or negative
 depending on both spatial proximity and relative preference.
description: Schartel and
 Schauber_Raw DataThis zipped data file
 contains all raw data pertaining to this manuscript. Folders containing
 data on small mammal trapping, monitoring of predator space use/activity,
 and predator consumption of incidental prey items are
 included.DRYAD.zipAlmond consumptionThis file contains data on almond consumption by small mammals on 6 plots over the course of 3 experimental periods.Final_Almond_Consumption.xlsxMaple seed consumptionThis file contains data on maple seed consumption by small mammals on 6 plots over the course of 3 experimental periods.Final_MapleSeed_Consumption.xlsxTrack plate activityThis file contains data on small mammal activity, as measured by track plates, on 6 plots over the course of 3 experimental periods.Final_TrackPlate_Activity.xlsxTrapping effortsThis file contains data on trapping efforts on 6 plots for two trapping periods; one pre-experiment, the other post-experiment.Final_Trapping.xlsx
DOI: 10.5061/dryad.v33f0
title: Data from: Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding

description: Captive breeding has the potential to rebuild depressed populations.
 However, associated genetic changes may decrease restoration success and
 negatively affect the adaptive potential of the entire population. Thus,
 approaches that minimize genetic risks should be tested in a comparative
 framework over multiple generations. Genetic diversity in two
 captive-reared lines of a species of conservation interest, Chinook salmon
 (Oncorhynchus tshawytscha), was surveyed across three generations using
 genome-wide approaches. Genetic divergence from the source population was
 minimal in an integrated line, which implemented managed gene flow by
 using only naturally-born adults as captive broodstock, but significant in
 a segregated line, which bred only captive-origin individuals. Estimates
 of effective number of breeders revealed that the rapid divergence
 observed in the latter was largely attributable to genetic drift. Three
 independent tests for signatures of adaptive divergence also identified
 temporal change within the segregated line, possibly indicating
 domestication selection. The results empirically demonstrate that using
 managed gene flow for propagating a captive-reared population reduces
 genetic divergence over the short term compared to one that relies solely
 on captive-origin parents. These findings complement existing studies of
 captive breeding, which typically focus on a single management strategy
 and examine the fitness of one or two generations.
description: Waters_et_al_2015_GenepopThis is the Genepop file for "Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding." The file contains 413 individuals genotyped at 9410 RAD loci. The name of each sample also includes the origin (unmarked is wild or natural origin; hatchery is hatchery origin) and sex (M or F) of the fish.Sequence_SNP_informationThis file contains the baseline sequence and polymorphism information for the 9410 RAD loci analyzed in this study.
DOI: 10.5061/dryad.bk271
title: Data from: Revision of the genus Anasibirites Mojsisovics (Ammonoidea): an iconic and cosmopolitan taxon of the late Smithian (Early Triassic) extinction

description: The family Prionitidae Hyatt represents a major component of ammonoid
 faunas during the Smithian (Early Triassic), and the genus Anasibirites
 Mojsisovics is the most emblematic taxon of this family. Its
 stratigraphical range is restricted to the beginning of the late Smithian
 (Wasatchites distractus Zone). The genus is also characterized by an
 unusual cosmopolitan distribution, thus contrasting with most earlier
 Smithian ammonoid distributions that were typically restricted by
 latitude. Because the late Smithian witnessed an extinction of the nekton
 (e.g. ammonoids, conodonts) whose amplitude is equal to or larger than
 that of the end-Permian crisis, the number of valid species that should be
 included in the genus Anasibirites becomes a highly relevant question when
 addressing this extinction at the highest possible taxonomic resolution.
 Based on a new extensive collection from Timor, the composition of the
 genus Anasibirites is herein revised with respect to its intraspecific and
 ontogenetic variations. Comprehensive morphological and biometric studies
 (c. 950 measured specimens) indicate that, of the c. 60 available species
 names, only two are valid, namely A. kingianus (Waagen) and A. multiformis
 Welter. Continuous ranges of intraspecific variation enable us to
 synonymize A. nevolini Zakharov, 1968 and A. angulosus (Waagen) with A.
 kingianus. The contribution of Anasibirites to species diversity during
 the late Smithian extinction is thus significantly less than previously
 estimated, therefore accentuating the severity of this event.
description: Jattiot et al.
 MeasurementsSpecimen
 measurements
DOI: 10.5061/dryad.s6764
title: Data from: Multiple estimates of effective population size for monitoring a long-lived vertebrate: an application to Yellowstone grizzly bears

description: Effective population size (Ne) is a key parameter for monitoring the
 genetic health of threatened populations because it reflects a
 population's evolutionary potential and risk of extinction due to
 genetic stochasticity. However, its application to wildlife monitoring has
 been limited because it is difficult to measure in natural populations.
 The isolated and well-studied population of grizzly bears (Ursus arctos)
 in the Greater Yellowstone Ecosystem provides a rare opportunity to
 examine the usefulness of different Ne estimators for monitoring. We
 genotyped 729 Yellowstone grizzly bears using 20 microsatellites and
 applied three single-sample estimators to examine contemporary trends in
 generation interval (GI), effective number of breeders (Nb) and Ne during
 1982–2007. We also used multisample methods to estimate variance (NeV) and
 inbreeding Ne (NeI). Single-sample estimates revealed positive
 trajectories, with over a fourfold increase in Ne (≈100 to 450) and near
 doubling of the GI (≈8 to 14) from the 1980s to 2000s. NeV (240–319) and
 NeI (256) were comparable with the harmonic mean single-sample Ne (213)
 over the time period. Reanalysing historical data, we found NeV increased
 from ≈80 in the 1910s–1960s to ≈280 in the contemporary population. The
 estimated ratio of effective to total census size (Ne/Nc) was stable and
 high (0.42–0.66) compared to previous brown bear studies. These results
 support independent demographic evidence for Yellowstone grizzly bear
 population growth since the 1980s. They further demonstrate how genetic
 monitoring of Ne can complement demographic-based monitoring of Nc and
 vital rates, providing a valuable tool for wildlife managers.
description: Kamath et al_Yellowstone
 grizzly bear dataThis data file contains
 genotypes and life history data for Yellowstone grizzly bears (n=729) born
 between 1962 and 2010. Bears were genotyped at 20 microsatellite loci and
 associated life history parameters include sex, birth year, oldest known
 year, and death year.Kamath et al_ME_Grizzly bear
 genotypes.xlsxKamath et al_Yellowstone
 grizzly bear input filesInput files used to
 evaluate grizzly bear recent trends in diversity, generation interval and
 effective population size.Kamath et al_ME_Grizzly bear
 input files.zip
DOI: 10.5061/dryad.972
title: Data from: Gene expression profiles associated with the transition to parasitism in Ancylostoma caninum larvae

description: Ancylostoma caninum is a common canine parasite responsible for anemia and
 death in infected dogs. Gene expression profiling was used to investigate
 molecular differences between two different forms of the third larval
 stage (L3s): infective free-living larvae and in vitro serum-stimulated
 larvae that mimic the initial stages of parasitism of a host. We developed
 an A. caninum cDNA microarray consisting of 4191 EST clones, and used it
 to identify a set of 113 genes that are differentially regulated between
 infective and parasitic larval stages. Real-time RT-PCR was used to
 confirm the expression differences of a subset of the genes. Of the genes
 repressed upon serum stimulation, seven encode members of the
 'Ancylostoma secreted protein' ASP family, while another
 transcript encoding a 24 kDa excretory protein with similarity to ASP was
 up-regulated in serum-stimulated L3s. This suggests that different members
 of a protein family that has important implications for the
 hookworm's parasitic lifestyle are regulated in a complementary
 manner in response to serum stimulation. Comparison of two strains of A.
 caninum from North Carolina and Maryland only identified a single gene,
 one of the members of the ASP family, that was differentially repressed
 upon serum stimulation.
description: Supplementary Table
 1MFAG_Annotation.xlsSupplementary Table 2MFAG_Results.xlsSupplementary Table 3._MFAG_Raw.xlsSupplementary Table 4MFAG_MIAME.doc