cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.53t4c
title: Data from: High throughput sequencing reveals alterations in the recombination signatures with diminishing spo11 activity

description: Spo11 is the topoisomerase-like enzyme responsible for the induction of
 the meiosis-specific double strand breaks (DSBs), which initiate the
 recombination events responsible for proper chromosome segregation.
 Nineteen PCR-induced alleles of SPO11 were identified and characterized
 genetically and cytologically. Recombination, spore viability and
 synaptonemal complex (SC) formation were decreased to varying extents in
 these mutants. Arrest by ndt80 restored these events in two severe
 hypomorphic mutants, suggesting that ndt80-arrested nuclei are capable of
 extended DSB activity. While crossing-over, spore viability and
 synaptonemal complex (SC) formation defects correlated, the extent of such
 defects was not predictive of the level of heteroallelic gene conversions
 (prototrophs) exhibited by each mutant. High throughput sequencing of
 tetrads from spo11 hypomorphs revealed that gene conversion tracts
 associated with COs are significantly longer and gene conversion tracts
 unassociated with COs are significantly shorter than in wild type. By
 modeling the extent of these tract changes, we could account for the
 discrepancy in genetic measurements of prototrophy and crossover
 association. These findings provide an explanation for the unexpectedly
 low prototroph levels exhibited by spo11 hypomorphs and have important
 implications for genetic studies that assume an unbiased recovery of
 prototrophs, such as measurements of CO homeostasis. Our genetic and
 physical data support previous observations of DSB-limited meioses, in
 which COs are disproportionally maintained over NCOs (CO homeostasis).
description: Analysis of high
 throughput sequencing data from spo11 hypomorphs using
 ReCombine
 PGENETICS_D_12_03065R3_ReCombine_data.zip
DOI: 10.5061/dryad.9sv83
title: Data from: Sound amplification by means of a horn-like roosting structure in Spix's disc-winged bat

description: While sound is a signal modality widely used by many animals, it is very
 susceptible to attenuation, hampering effective long-distance
 communication. A strategy to minimize sound attenuation that has been
 historically used by humans is to use acoustic horns; to date, no other
 animal is known to use a similar structure to increase sound intensity.
 Here, we describe how the use of a roosting structure that resembles an
 acoustic horn (the tapered tubes that form when new leaves of plants such
 as Heliconia or Calathea species start to unfurl) increases sound
 amplification of the incoming and outgoing social calls used by
 Spix's disc-winged bat (Thyroptera tricolor) to locate roosts and
 group members. Our results indicate that incoming calls are significantly
 amplified as a result of sound waves being increasingly compressed as they
 move into the narrow end of the leaf. Outgoing calls were faintly
 amplified, probably as a result of increased sound directionality. Both
 types of call, however, experienced significant sound distortion, which
 might explain the patterns of signal recognition previously observed in
 behavioural experiments. Our study provides the first evidence of the
 potential role that a roost can play in facilitating acoustic
 communication in bats.
description: Horizontal effect Oct 1
 2013Vertical
 effectOutgoing
 responseIncoming
 inquiry
DOI: 10.5061/dryad.nc866
title: Data from: Detection of implausible phylogenetic inferences using posterior predictive assessment of model fit

description: Systematic phylogenetic error caused by the simplifying assumptions made
 in models of molecular evolution may be impossible to avoid entirely when
 attempting to model evolution across massive, diverse datasets. However,
 not all deficiencies of inference models result in unreliable phylogenetic
 estimates. The field of phylogenetics lacks a direct method to identify
 cases where model specification adversely affects inferences. Posterior
 predictive simulation is a flexible and intuitive approach for assessing
 goodness-of-fit of the assumed model and priors in a Bayesian phylogenetic
 analysis. Here, I propose new test statistics for use in posterior
 predictive assessment of model fit. These test statistics compare
 phylogenetic inferences from posterior predictive datasets to inferences
 from the original data. A simulation study demonstrates the utility of
 these new statistics. The new tests reject the plausibility of inferred
 tree lengths or topologies more often when data/model combinations produce
 biased inferences. I also apply this approach to exemplar empirical
 datasets, highlighting the value of the novel assessments.
description: Supplementary
 Information for Detection of Implausible Phylogenetic Inferences Using
 Posterior Predictive Assessment of Model FitSupplementary tables and
 figures.Brown_IBPP_SuppInfo_revised_clean.pdf
DOI: 10.48573/kff5-rp94
title: Schweizer Freiwilligen-Monitor 2025
title: Swiss Volunteering Survey 2025
DOI: 10.5061/dryad.bp3g0
title: Data from: Changes in breeding phenology and population size of birds

description: 1. Although the phenology of numerous organisms has advanced significantly
 in response to recent climate change, the life history and population
 consequences of earlier reproduction remain poorly understood. 2. We
 analyzed extensive data on temporal change in laying date and clutch size
 of birds from Europe and North America to test whether these changes were
 related to recent trends in population size. 3. Across studies, laying
 date advanced significantly while clutch size did not change. However,
 within populations, change in laying date and change in clutch size were
 positively correlated, implying that species that advanced their laying
 date the most were also those that increased their clutch size the most.
 4. Greater advances in laying date were associated with species that had
 multiple broods per season, lived in non-agricultural habitats and were
 herbivorous or predatory. The duration of the breeding season increased
 for multi-brooded species and decreased for single-brooded species. In
 contrast to studies of changes in spring arrival dates (for migratory
 species), the changes we found in laying date and clutch size were not
 related to changes in population size (for resident or migratory species).
 5. This suggests that, across a wide variety of species, mismatches in the
 timing of egg-laying or numbers of offspring have had relatively little
 influence on population size compared with other aspects of phenology and
 life history.
description: LaydateCS_12Mar13.xlsxExcel file with data on changing phenology and population size of birds (N= 196 studies). Variables are explained and sources given in the sheet titled "Variables & Sources"LaydateYr_23Jan13.txtData file for mcmcGLMM in R. Note that slightly different data files were used for different analyses. This file was used for the analyses of laying date change per year in Table 4 of the paper.Tree29Dec12g.nexNexus tree file for mcmcGLMM analyses in R. This tree was used with the data file "LaydateYr_23Jan13.txt" to conduct the analyses shown in Table 4 of the paper. Note that slightly different trees were used for some other analyses. The g in the file name indicates that we used Grafen's method to construct branch lengths. There are 172 studies in the file; multiple studies of the same species were coded as A, B, C, etc. in the phylogenyFig 2 Pop models_16Sep13.xlsExcel worksheets with population models shown in Fig. 2 of the paper. Details of each model are given in the individual worksheets.
DOI: 10.5061/dryad.rs4v1
title: Data from: Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)

description: Recent advances in population genomics have made it possible to detect
 previously unidentified structure, obtain more accurate estimates of
 demographic parameters, and explore adaptive divergence, potentially
 revolutionizing the way genetic data are used to manage wild populations.
 Here, we identified 10 944 single-nucleotide polymorphisms using
 restriction-site-associated DNA (RAD) sequencing to explore population
 structure, demography, and adaptive divergence in five populations of
 Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of
 population structure were similar to those of past studies, but our
 ability to assign individuals back to their region of origin was greatly
 improved (&gt;90% accuracy for all populations). We also calculated
 effective size with and without removing physically linked loci identified
 from a linkage map, a novel method for nonmodel organisms. Estimates of
 effective size were generally above 1000 and were biased downward when
 physically linked loci were not removed. Outlier tests based on genetic
 differentiation identified 733 loci and three genomic regions under
 putative selection. These markers and genomic regions are excellent
 candidates for future research and can be used to create high-resolution
 panels for genetic monitoring and population assignment. This work
 demonstrates the utility of genomic data to inform conservation in highly
 exploited species with shallow population structure.
description: genepop_western_alaska_chinook_RADGenepop formatted file containing genotypes from the 10,944 SNPs and 265 individuals used in this study. SNP names are radtag_snp position i.e. a SNP named 12_46 would be on radtag number 12 and the SNP would be at position 46 in the tag. Population abbreviations are collection year _ individual. For example Koktuli10_0002 would be from the Koktuli River, collected in 2010, and would be individual 2.sequences_for_10944_SNPsFasta file containing the sequences for each allele for each SNP discovered in this study. Sequences are designated by rad tag_allele_SNP position(s). Tags may contain multiple SNPs, for example &gt;84_AT_40-84 would designate the sequence for rad tag 84 which has SNPs at positions 40 and 84. Since we only used one SNP per tag for the study, not all SNPs in this file are found in the genotypes file. To obtain the positions of the SNPs that we did use, please see the locus names in the genepop file.
DOI: 10.5061/dryad.n2645
title: Data from: Sign epistasis limits evolutionary trade-offs at the confluence of single- and multi-carbon metabolism in Methylobacterium extorquens AM1

description: Adaptation of one set of traits is often accompanied by attenuation of
 traits important in other selective environments, leading to fitness
 trade-offs. The mechanisms that either promote or prevent the emergence of
 trade-offs remain largely unknown, and are difficult to discern in most
 systems. Here, we investigate the basis of trade-offs that emerged during
 experimental evolution of Methylobacterium extorquens AM1 to distinct
 growth substrates. After 1500 generations of adaptation to a multi-carbon
 substrate, succinate (S), many lineages had lost the ability to use
 one-carbon compounds such as methanol (M), generating a mixture of M+ and
 M− evolved phenotypes. We show that trade-offs in M− strains consistently
 arise via antagonistic pleiotropy through recurrent selection for
 loss-of-function mutations to ftfL (formate-tetrahydrofolate ligase),
 which improved growth on S while simultaneously eliminating growth on M.
 But if loss of FtfL was beneficial, why were M trade-offs not found in all
 populations? We discovered that eliminating FtfL was not universally
 beneficial on S, as it was neutral or even deleterious in certain evolved
 lineages that remained M+. This suggests that sign epistasis with earlier
 arising mutations prevented the emergence of mutations that drove
 trade-offs through antagonistic pleiotropy, limiting the evolution of
 metabolic specialists in some populations.
description: Data_CombinedData files for the article: Sign epistasis limits evolutionary trade-offs at the confluence of single- and multi-carbon metabolism in Methylobacterium extorquens AM1. Sean Michael Carroll*, Ming-Chun Lee*, Christopher J. Marx *These authors contributed equally to this work Accepted for publication in Evolution. October, 2013
DOI: 10.5061/dryad.qk688
title: Data from: Discriminating plants using the DNA barcode rbcLb: an appraisal based on a large data set

description: The ideal DNA barcode for plants remains to be discovered, and the
 candidate barcode rbcL has been met with considerable skepticism since its
 proposal. In fact, the variability within this gene has never been fully
 explored across all plant groups from algae to flowering plants, and its
 performance as a barcode has not been adequately tested. By analyzing all
 of the rbcL sequences currently available in GenBank, we attempted to
 determine how well a region of rbcL performs as a barcode in species
 discrimination. We found that the rbcLb region was more variable than the
 frequently used rbcLa region. Both universal and plant group-specific
 primers were designed to amplify rbcLb, and the performance of rbcLa and
 rbcLb was tested in several ways. Using BLAST, both regions successfully
 identified all families and nearly all genera; however, the successful
 species identification rates varied significantly among plant groups,
 ranging from 24.58% to 85.50% for rbcLa and from 36.67% to 90.89% for
 rbcLb. Successful species discrimination ranged from 5.19% to 96.33% for
 rbcLa and from 22.09% to 98.43% for rbcLb in species-rich families and
 from 0 to 88.73% for rbcLa and from 2.04% to 100% for rbcLb in
 species-rich genera. Both regions performed better for lower plants than
 for higher plants, though rbcLb performed significantly better than rbcLa
 overall, particularly for angiosperms. Considering the applicability
 across plants, easy and unambiguous alignment, high primer universality,
 high sequence quality, and high species-discrimination power for lower
 plants, we suggest rbcLb as a universal plant barcode.
description: rbcL
 sequencesThe length of rbcL
 sequences more than 1300bp.more than
 1300bp.rar
DOI: 10.5061/dryad.1bh5q
title: Data from: Assessment of coyote-wolf-dog admixture using ancestry-informative diagnostic SNPs

description: The evolutionary importance of hybridization as a source of new adaptive
 genetic variation is rapidly gaining recognition. Hybridization between
 coyotes and wolves may have introduced adaptive alleles into the coyote
 gene pool that facilitated an expansion in their geographic range and
 dietary niche. Furthermore, hybridization between coyotes and domestic
 dogs may facilitate adaptation to human-dominated environments. We
 genotyped 63 ancestry-informative single nucleotide polymorphisms in 427
 canids in order to examine the prevalence, spatial distribution, and
 ecology of admixture in eastern coyotes. Using multivariate methods and
 Bayesian clustering analyses, we estimated the relative contributions of
 western coyotes, western and eastern wolves, and domestic dogs to the
 admixed ancestry of Ohio and eastern coyotes. We found that eastern
 coyotes form an extensive hybrid swarm, with all our samples having
 varying levels of admixture. Ohio coyotes, previously thought to be free
 of admixture, are also highly admixed with wolves and dogs. Coyotes in
 areas of high deer density are genetically more wolf-like, suggesting that
 natural selection for wolf-like traits may result in local adaptation at a
 fine geographic scale. Our results, in light of other previously published
 studies of admixture in Canis, reveal a pattern of sex-biased
 hybridization, presumably generated by male wolves and dogs mating with
 female coyotes. This study is the most comprehensive genetic survey of
 admixture in eastern coyotes and demonstrates that the frequency and scope
 of hybridization can be quantified with relatively few
 ancestry-informative markers.
description: Coyote-Wolf-Dog
 Admixture Data
DOI: 10.5061/dryad.ds304
title: Data from: Fine-scale sampling reveals distinct isolation by distance patterns in chum salmon (Oncorhynchus keta) populations occupying a glacially dynamic environment

description: Populations with spatially restricted gene flow are characterized by
 genetic differentiation that may be positively correlated with the
 geographic distance separating populations, a pattern known as isolation
 by distance (IBD). Here we examined the fine-scale genetic structure of 66
 chum salmon (Oncorhynchus keta) populations spawning in Alaska waterways
 and explored patterns of IBD using 90 nuclear and 3 mitochondrial single
 nucleotide polymorphisms. Estimating population structure of chum salmon
 in Alaska is of increasing concern because of fluctuating census sizes and
 the uncertain effects of harvest on specific populations. We hypothesized
 that IBD would be present because chum salmon spawn in coastal rivers that
 are distributed along a linear array and gene flow is spatially restricted
 due to homing. Evidence of very weak IBD was found throughout the region
 (R2 = 0.06, p &lt; 0.0001) but the strength of the IBD relationship
 varied greatly over different spatial scales and geographic regions.
 Decomposed pairwise regression analyses identified nine outlier
 populations to regional IBD patterns, suggesting that geographic distance
 is not the only factor influencing genetic differentiation in the region.
 Instead, population structure appears to be heavily influenced by glacial
 history of the region and the presence of a glacial refugium on Kodiak
 Island.
description: SNP Genotypes and
 geographic data collected from chum salmon populations in
 AlaskaThis data file contains
 the following data: 1) SNP genotypes for each individual fish, 2)
 geographic and temporal information associated with each collection, 3)
 population genetic indices and citation data for each SNP genotyped, 4)
 waterway distance between each collection site, as calculated by a
 least-cost path analysis in ARC-GIS.Dryad data_July 25
 2013.xlsx
DOI: 10.5061/dryad.mk8p7
title: Data from: Decisive datasets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects

description: Phylogenetic relationships of the primarily wingless insects are still
 considered unresolved. Even the most comprehensive phylogenomic studies
 that addressed this question did not yield congruent results. In order to
 get a grip on these problems, we here analyzed the sources of incongruence
 in these phylogenomic studies using an extended transcriptome dataset.Our
 analyses showed that unevenly distributed missing data can be severely
 misleading by inflating node support despite the absence of phylogenetic
 signal. In consequence, only decisive datasets should be used which
 exclusively comprise data blocks containing all taxa whose relationships
 are addressed. Additionally, we employed Four-cluster Likelihood-Mapping
 (FcLM) to measure the degree of congruence among genes of a dataset, as a
 measure of support alternative to bootstrap. FcLM showed incongruent
 signal among genes, which in our case is correlated with neither
 functional class assignment of these genes, nor with model
 misspecification due to unpartitioned analyses. The herein analyzed
 dataset is the currently largest dataset covering primarily wingless
 insects, but failed to elucidate their interordinal phylogenetic
 relationships. While this is unsatisfying from a phylogenetic perspective,
 we try to show that the analyses of structure and signal within
 phylogenomic data can protect us from biased phylogenetic inferences due
 to analytical artefacts.
description: DellAmpio_et_al_2013:
 Supplementary DataSupplementary File
 Archives of "Decisive Datasets in Phylogenomics: Lessons from Studies
 on the Phylogenetic Relationships of Primarily Wingless
 Insects"DellAmpio_et_al_2013_supplementary_data.tar.gz
DOI: 10.5061/dryad.87rm1
title: Data from: Forest without prey: livestock sustain a common leopard population in Pakistan

description: Human–carnivore conflict is one of the major challenges in the management
 of populations of large carnivores. Concerns include the increasing human
 population; habitat loss as a result of degradation and fragmentation of
 forest; and livestock predation as a result of a lack of natural prey,
 leading to retaliatory killings of wild carnivores. Conflicts may be
 further aggravated by occasional attacks that result in injury and loss of
 human life. The level of consumption of prey species by a predator is a
 benchmark to evaluate the scale of this conflict. We used a newly
 developed DNA-based diet analysis to study the prey profile of common
 leopards Panthera pardus in Ayubia National Park, Pakistan. The results
 suggest that the common leopard is a generalist predator, subsisting
 mainly on domestic animals. Based on the frequency of occurrence of prey
 items in 57 faecal samples, the diet of the leopard is dominated by
 domestic goat Capra hircus (64.9%), followed by domestic dog Canis lupus
 familiaris (17.5%) and cow Bos taurus (12.3%). Domestic animals (goat,
 dog, cow, water buffalo Bubalus bubalis, horse Equus caballus and sheep
 Ovis aries) occurred in 54 (95%) of the 57 samples. We recommend a
 two-step strategy to mitigate this conflict: (1) introducing incentives
 for increased acceptance of leopards among local communities in the
 vicinity of the protected area and (2) increasing the availability of wild
 prey. We hope that the results of this study will contribute to the
 survival of the leopard in Pakistan.
description: Unique sequences
 generated initially by NGS sequencingcontains files with
 unique sequences generated by next generation
 sequencingpp_bk_uniq#_sort.xlspp_uniq#_sort_l60c99_clean_rc_tag#_dryadThe sequences after cleaning the datapp_bk_filtered_dataContains file having data after filtration. The final result file for common leopard diet in Ayubia National Park, Pakistan