cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nq189
title: Data from: Local and global patterns of admixture and population structure in Iranian native cattle

description: Background: Two separate domestication events gave rise to humped zebu
 cattle in India and humpless taurine cattle in the Fertile Crescent of the
 Near and Middle East. Iran covers the Eastern side of the Fertile Crescent
 and exhibits a variety of native cattle breeds, however, only little is
 known about the admixture patterns of Iranian cattle and their
 contribution to the formation of modern cattle breeds. Results:
 Genome-wide data (700k chip) of eight Iranian cattle breeds (Sarabi N=19,
 Kurdi N=7, Taleshi N=7, Mazandarani N=10, Najdi N=7, Pars N=7, Kermani
 N=9, and Sistani N=9) were collected from across Iran. For a local
 assessment, taurine (Holstein and Jersey) and indicine (Brahman) outgroup
 samples were used. For the global perspective, 134 world-wide cattle
 breeds were included. Between breed variation amongst Iranian cattle
 explained 60% (p&lt;0.001) of the total molecular variation and 82.88%
 (p&lt;0.001) when outgroups were included. Several migration edges
 were observed within the Iranian cattle breeds. The highest indicine
 proportion was found in Sistani. All Iranian breeds with higher indicine
 ancestry were more admixed with a complex migration pattern. Nineteen
 founder populations most accurately explained the admixture of 44 selected
 representative cattle breeds (standard error 0.4617). Low levels of
 African ancestry were identified in Iranian cattle breeds (on average
 7.5%); however, the signal did not persist through all analyses. Admixture
 and migration analyses revealed minimal introgression from Iranian cattle
 into other taurine cattle (Holstein, Hanwoo, Anatolian breeds).
 Conclusion: The eight Iranian cattle breeds feature a discrete genetic
 composition which should be considered in conservation programs aimed at
 preserving unique species and genetic diversity. Despite a complex
 admixture pattern among Iranian cattle breeds, there was no strong
 introgression from other world-wide cattle breeds into Iranian cattle and
 vice versa. Considering Iran’s central location of cattle domestication,
 Iranian cattle might represent a local domestication event that remained
 contained and did not contribute to the formation of modern breeds, or
 genetics of the ancestral population that gave rise to modern cattle is
 too diluted to be linked directly to any current cattle breeds.
description: 8_Iran_Cattle_Breeds_genoThe file contains genotypes of 8 Iranian cattle breeds (75 animals). The file is in a compressed rds format and can be used and modified in R.
DOI: 10.6084/m9.figshare.29864695
title: Utilization of change point detection based on information criterion for monitoring flatness data

description: Flatness, a critical quality metric in engineering, follows a complex normal range distribution that lacks an explicit analytical form. Currently, non parametric change point detection methods are used to monitor flatness data in quality control, but these methods suffer from low accuracy. Our contribution lies in solving the parameter estimation for the normal range distribution and in the numerical calculation of its density function, enabling the application of an information criterion-based change point detection method. This method offers higher accuracy and a lower false positive rate. Case studies are presented to demonstrate the effectiveness of the proposed method in change point detection.
DOI: 10.6084/m9.figshare.29864695.v1
title: Utilization of change point detection based on information criterion for monitoring flatness data

description: Flatness, a critical quality metric in engineering, follows a complex normal range distribution that lacks an explicit analytical form. Currently, non parametric change point detection methods are used to monitor flatness data in quality control, but these methods suffer from low accuracy. Our contribution lies in solving the parameter estimation for the normal range distribution and in the numerical calculation of its density function, enabling the application of an information criterion-based change point detection method. This method offers higher accuracy and a lower false positive rate. Case studies are presented to demonstrate the effectiveness of the proposed method in change point detection.
DOI: 10.6084/m9.figshare.29300583
title: Two Bayesian variable screening procedures

description: In this paper, two Bayesian variable screening procedures (FBRPN and BRPN) are proposed to obtain meaningful protective and risk factors in fast and sequential ways in models with a linear component such as the GLMs to avoid multicollinearity. The two final fitted models from the procedures are compared to find the most efficient model and relatively uncorrelated representative variables of the original predictors. The Bayesian procedures are illustrated in two examples, with comparisons to the stepwise and best subsets regression methods. Simulation studies with no true models are carried out to show how different correlation structures and sample sizes can affect the final fitted models from different procedures, and the Bayesian procedures produce relatively unrelated representative variables, which fit the connotation of “independent variables”‘. Cross-validation comparisons with stepwise, LASSO, LAR, random forest and NNET methods are made based on the generated Efron diabetes data, which contains 64 dummy variables and provides a fair base for comparisons of different methods. The theory and practical issues are discussed, and applications of the procedures in big data analysis are envisioned.
DOI: 10.6084/m9.figshare.29300583.v1
title: Two Bayesian variable screening procedures

description: In this paper, two Bayesian variable screening procedures (FBRPN and BRPN) are proposed to obtain meaningful protective and risk factors in fast and sequential ways in models with a linear component such as the GLMs to avoid multicollinearity. The two final fitted models from the procedures are compared to find the most efficient model and relatively uncorrelated representative variables of the original predictors. The Bayesian procedures are illustrated in two examples, with comparisons to the stepwise and best subsets regression methods. Simulation studies with no true models are carried out to show how different correlation structures and sample sizes can affect the final fitted models from different procedures, and the Bayesian procedures produce relatively unrelated representative variables, which fit the connotation of “independent variables”‘. Cross-validation comparisons with stepwise, LASSO, LAR, random forest and NNET methods are made based on the generated Efron diabetes data, which contains 64 dummy variables and provides a fair base for comparisons of different methods. The theory and practical issues are discussed, and applications of the procedures in big data analysis are envisioned.
DOI: 10.5061/dryad.118vg
title: Data from: Human-mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations

description: While terrestrial megafaunal extinctions have been well characterized
 worldwide, our understanding of declines in marine megafauna remains
 limited. Here, we use ancient DNA analyses of prehistoric
 (&lt;1450–1650 AD) sea lion specimens from New Zealand's isolated
 Chatham Islands to assess the demographic impacts of human settlement.
 These data suggest there was a large population of sea lions, unique to
 the Chatham Islands, at the time of Polynesian settlement. This distinct
 mitochondrial lineage became rapidly extinct within 200 years due to
 overhunting, paralleling the extirpation of a similarly large endemic
 mainland population. Whole mitogenomic analyses confirm substantial
 intraspecific diversity among prehistoric lineages. Demographic models
 suggest that even low harvest rates would likely have driven rapid
 extinction of these lineages. This study indicates that surviving
 Phocarctos populations are remnants of a once diverse and widespread sea
 lion assemblage, highlighting dramatic human impacts on endemic marine
 biodiversity. Our findings also suggest that Phocarctos bycatch in
 commercial fisheries may contribute to the ongoing population decline.
description: BEAST Dloop phylogenetic
 analysis with Birth Death speciation priorChatham_sealions_Dloop_Birth_Death.xmlBEAST Dloop phylogenetic analysis with Yule speciation priorChatham_sealions_Dloop_Yule.xmlIndividual Based Model for anthropogenic mortality estimatesIBM script.rSequence alignment of Chatham Island sea lionsSequence alignment of Chatham Island sea lion mtDNA D-loop including all Chatham Islands individuals (NRO number, location, haplotype - C1 to 9), exemplar haplotype sequences of subantarctic individuals (SA1-3), exemplar haplotype sequences of prehistoric New Zealand individuals (NZ1-14), and outgroups (Australian sea lion, South American sea lion, New Zealand furseal). Please see Suppl. Info. Table S1 for numbers of New Zealand and subantarctic individuals for each haplotype.Chatham Island sealions_final.fasBEAST mitogenome phylogenetic analysis with birth-death speciation priormitogenome_birth_death.xmlBEAST mitogenome phylogenetic analysis with Yule speciation priormitogenome_Yule.xmlChatham Island mitogenome Ion Torrent NGS raw sequencesCHI.sff.raw.fastq.zipPrehistoric mainland New Zealand sea lion mitogenome Ion Torrent NGS raw sequencesDEB.sff.raw.fastq.zipBayeSSC .par filesPinniped whole mitogenome phylogenetic alignmentPinniped_whole_mtDNA.fasta
DOI: 10.15468/dl.7h5qud
title: Occurrence Download

description: A dataset containing 1460 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "Geometry POLYGON((63.68243 2.75126,187.31757 2.75126,187.31757 52.24874,63.68243 52.24874,63.68243 2.75126))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Saundersilarus saundersi",
 "Year 2023-2024"
 ]
}

 The dataset includes 1460 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001465-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.133n7
title: Data from: Rapid divergence and convergence of life-history in experimentally evolved Drosophila melanogaster

description: Laboratory selection experiments are alluring in their simplicity, power,
 and ability to inform us about how evolution works. A longstanding
 challenge facing evolution experiments with metazoans is that significant
 generational turnover takes a long time. In this work, we present data
 from a unique system of experimentally evolved laboratory populations of
 Drosophila melanogaster that have experienced three distinct life-history
 selection regimes. The goal of our study was to determine how quickly
 populations of a certain selection regime diverge phenotypically from
 their ancestors, and how quickly they converge with independently derived
 populations that share a selection regime. Our results indicate that
 phenotypic divergence from an ancestral population occurs rapidly, within
 dozens of generations, regardless of that population's evolutionary
 history. Similarly, populations sharing a selection treatment converge on
 common phenotypes in this same time frame, regardless of selection
 pressures those populations may have experienced in the past. These
 patterns of convergence and divergence emerged much faster than expected,
 suggesting that intermediate evolutionary history has transient effects in
 this system. The results we draw from this system are applicable to other
 experimental evolution projects, and suggest that many relevant questions
 can be sufficiently tested on shorter timescales than previously thought.
description: Burke_Barter_Cabral_DRYADRaw phenotype data analyzed in the manuscript. These are contained as five worksheets within one larger Excel spreadsheet. Please see ReadMe for details.
DOI: 10.5061/dryad.nn5bn
title: Data from: Genetic diversity and genomic signatures of selection among cattle breeds from Siberia, eastern and northern Europe

description: Domestication in the near eastern region had a major impact on the gene
 pool of humpless taurine cattle (Bos taurus). As a result of subsequent
 natural and artificial selection, hundreds of different breeds have
 evolved, displaying a broad range of phenotypic traits. Here, 10 Eurasian
 B. taurus breeds from different biogeographic and production conditions,
 which exhibit different demographic histories and have been under
 artificial selection at various intensities, were investigated using the
 Illumina BovineSNP50 panel to understand their genetic diversity and
 population structure. In addition, we scanned genomes from eight breeds
 for signatures of diversifying selection. Our population structure
 analysis indicated six distinct breed groups, the most divergent being the
 Yakutian cattle from Siberia. Selection signals were shared (experimental
 P-value &lt; 0.01) with more than four breeds on chromosomes 6, 7, 13,
 16 and 22. The strongest selection signals in the Yakutian cattle were
 found on chromosomes 7 and 21, where a miRNA gene and genes related to
 immune system processes are respectively located. In general, genomic
 regions indicating selection overlapped with known QTL associated with
 milk production (e.g. on chromosome 19), reproduction (e.g. on chromosome
 24) and meat quality (e.g. on chromosome 7). The selection map created in
 this study shows that native cattle breeds and their genetic resources
 represent unique material for future breeding.
description: Genotype
 folderFolder contains
 genotypes as .ped file and corresponding .map file.Breed.data.7z
DOI: 10.5061/dryad.rh24n
title: Data from: Ecological speciation in sympatric palms: 2. pre- and post-zygotic isolation

description: We evaluated reproductive isolation in two species of palms (Howea) that
 have evolved sympatrically on Lord Howe Island (LHI, Australia). We
 estimated the strength of some pre- and post-zygotic mechanisms in
 maintaining current species boundaries. We found that flowering time
 displacement between species is consistent across in and ex situ common
 gardens and is thus partly genetically determined. On LHI, pre-zygotic
 isolation due solely to flowering displacement was 97% for H. belmoreana
 and 80% for H. forsteriana; this asymmetry results from H. forsteriana
 flowering earlier than H. belmoreana and being protandrous. As expected,
 only a few hybrids (here confirmed by genotyping) at both juvenile and
 adult stages could be detected in two sites on LHI, in which the two
 species grow intermingled (The Far Flats) or adjacently (Transit Hill).
 Yet, the distribution of hybrids was different between sites. At Transit
 Hill we found no hybrid adult trees, but 13.5% of younger palms examined
 there were of late hybrid classes. In contrast we found four hybrid adult
 trees, mostly of late hybrid classes, and only one juvenile F1 hybrid in
 the Far Flats. This pattern indicates that selection acts against hybrids
 between the juvenile and adult stages. An in situ reciprocal seed
 transplant between volcanic and calcareous soils also shows that early
 fitness components (up to 36 months) were affected by species and soil.
 These results are indicative of divergent selection in reproductive
 isolation, although it does not solely explain the current distribution of
 the two species on LHI.
description: Suppl_Info_Table_S1_AFLPresultsAFLPsFar Flat Raw Phenol CORRECTEDPhenologySydney_Raw PhenolPhenology 2Seed-Transplant_data record sheet-June 2013_HH copySeed transplantsSydney_Raw PhenolSeed transplants 2Silwood_Seed_Transplant_Final.xlsx
DOI: 10.5061/dryad.g08gb
title: Data from: Characteristics and outcomes of women utilizing emergency medical services for third-trimester pregnancy-related complaints in India: a prospective observational study

description: Objectives: Characterize the demographics, management, and outcomes of
 obstetric patients transported by emergency medical services (EMS).
 Design: Prospective observational study. Setting: Five Indian states
 utilizing a centralized EMS agency that transported 3.1 million pregnant
 women in 2014. Participants: This study enrolled a convenience sample of
 1684 women in third trimester of pregnancy calling with a
 “pregnancy-related” complaint for free-of-charge ambulance transport.
 Calls were deemed “pregnancy-related” if categorized by EMS dispatchers as
 “pregnancy”, “childbirth”, “miscarriage”, or “labor pains”. Interfacility
 transfers, patients absent upon ambulance arrival, and patients refusing
 care were excluded. Main outcome measures: Emergency medical technician
 (EMT) interventions, method of delivery, and death. Results: The median
 age enrolled was 23 years (IQR 21-25). Women were primarily from
 rural/tribal areas (1550/1684 (92.0%)) and lower economic strata
 (1177/1684 (69.9%)). Time from initial call to hospital arrival was longer
 for rural/tribal compared to urban patients (66 min (IQR 51-84) vs 56 min
 (IQR 42-73), respectively, p&lt;0.0001). EMTs assisted delivery in 44
 women, delivering the placenta in 33/44 (75%), performing transabdominal
 uterine massage in 29/33 (87.9%), and administering oxytocin in none (0%).
 There were 1411 recorded deliveries. Most women delivered at a hospital
 (1212/1411 (85.9%)), however 126/1411 (8.9%) delivered at home following
 hospital discharge. Follow-up rates at 48 hours, 7 days, and 42 days were
 95.0%, 94.4%, and 94.1%, respectively. Four women died, all within 48
 hours. The cesarean section rate was 8.2% (116/1411). On multivariate
 regression analysis, women transported to private hospitals versus
 government primary health centers were less likely to deliver by cesarean
 section (odds ratio 0.14 (0.05 to 0.43)). Conclusions: Pregnant women from
 vulnerable Indian populations use free-of-charge EMS for impending
 delivery, making it integral to the health care system. Future research
 and health system planning should focus on strengthening and expanding EMS
 as a component of EmONC.
description: Data for a Convenience
 Sample of Women Utilizing EMS for Obstetric Emergencies in
 IndiaThis data is from a
 convenience sample of women in their third-trimester who used EMS across
 five states in India over a six week period in 2014.Maternal Cohort -
 Dryad.xlsx
DOI: 10.5281/zenodo.15681968
title: Allostery is a widespread cause of loss-of-function variant pathogenicity - metadata

description: Supplemental data for the preprint: Liao, X., & Lehner, B. (2025). Allostery is a widespread cause of loss-of-function variant pathogenicity. bioRxiv, 2025-06.   



zenodo_final_jan2026.tar.gz (supplementary table 1): proteome-wide predictions of protein stability changes and corresponding ESM-1v scores for all variants.
DOI: 10.5061/dryad.87rc8
title: Data from: Fine-scale flight strategies of gulls in urban airflows indicate risk and reward in city living

description: Birds modulate their flight paths in relation to regional and global
 airflows in order to reduce their travel costs. Birds should also respond
 to fine-scale airflows, although the incidence and value of this remains
 largely unknown. We resolved the three-dimensional trajectories of gulls
 flying along a built-up coastline, and used computational fluid dynamic
 models to examine how gulls reacted to airflows around buildings. Birds
 systematically altered their flight trajectories with wind conditions to
 exploit updraughts over features as small as a row of low-rise buildings.
 This provides the first evidence that human activities can change patterns
 of space-use in flying birds by altering the profitability of the
 airscape. At finer scales still, gulls varied their position to select a
 narrow range of updraught values, rather than exploiting the strongest
 updraughts available, and their precise positions were consistent with a
 strategy to increase their velocity control in gusty conditions.
 Ultimately, strategies such as these could help unmanned aerial vehicles
 negotiate complex airflows. Overall, airflows around fine-scale features
 have profound implications for flight control and energy use, and
 consideration of this could lead to a paradigm-shift in the way ecologists
 view the urban environment.
description: Ornithodolite
 dataThis file contains the
 Ornithodolite data from gulls soaring over two sites that border Swansea
 Bay.Flight paths for CFD
 modellingThis workbook contains
 two worksheets that detail (i) wind data (collected from balloon ascents)
 and (ii) summary data from birds gliding over hotels that border Swansea
 Bay. These data were used to estimate the wind fields around these flight
 paths, when combined with CFD model outputs. This file is also described
 in the README file for the Ornithodolite data.WindDataThe excel file "WindData" includes the 2D (averaged wind vector components) along the Y,Z axis. Data are available for each session where the positions of gulls soaring over the seafront hotels were recorded.Glide_polarThis contains the MATLAB code to estimate the glide polar for a fixed wing gull.
DOI: 10.5281/zenodo.18386427
title: Allostery is a widespread cause of loss-of-function variant pathogenicity - metadata

description: Supplemental data for the preprint: Liao, X., & Lehner, B. (2025). Allostery is a widespread cause of loss-of-function variant pathogenicity. bioRxiv, 2025-06.   



zenodo_final_jan2026.tar.gz (supplementary table 1): proteome-wide predictions of protein stability changes and corresponding ESM-1v scores for all variants.
DOI: 10.5061/dryad.kh654
title: Data from: Alternative reproductive tactics in context: how demography, ecology, and behavior affect male mating success

description: Exploitation of sexual signals by predators or parasites increases costs
 to signalers, creating opportunities for establishment of alternative
 reproductive tactics (ARTs). In field crickets, males calling may attract
 acoustically-orienting parasitoid flies. Alternatively, males behaving as
 satellites forgo calling and attempt to intercept females attracted to
 callers. We modeled the contribution of calling vs. satellite behavior to
 male reproductive success in the larger context of variation in ecology
 (parasitism rate, background mortality), demography (density, sex ratio),
 and female behavior (phonotaxis, mating choosiness). Male mating success
 was most influenced by number of females (standardized effect size 0.42),
 then female choosiness (0.33), background mortality (-0.31), number of
 males (-0.28), and parasitism rate (-0.21). Smallest effects were
 phonotaxis (0.10) and satellite behavior (-0.09). Although satellite
 behavior ameliorated negative effects of parasitism, its comparative
 effect was slight. ARTs seem most likely to evolve and persist when a
 single selection pressure on signaling is particularly strong.
description: Fully-crossed Model
 OutputSee read-me
 file.