cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bs06h
title: Data from: Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations

description: Northeast Africa has a long history of human habitation, with fossil-finds
 from the earliest anatomically modern humans, and housing ancient
 civilizations. The region is also the gate-way out of Africa, as well as a
 portal for migration into Africa from Eurasia via the Middle East and the
 Arabian Peninsula. We investigate the population history of northeast
 Africa by genotyping ~3.9 million SNPs in 221 individuals from 18
 populations sampled in Sudan and South Sudan and combine this data with
 published genome-wide data from surrounding areas. We find a strong
 genetic divide between the populations from the northeastern parts of the
 region (Nubians, central Arab populations, and the Beja) and populations
 towards the west and south (Nilotes, Darfur and Kordofan populations).
 This differentiation is mainly caused by a large Eurasian ancestry
 component of the northeast populations likely driven by migration of
 Middle Eastern groups followed by admixture that affected the local
 populations in a north-to-south succession of events. Genetic evidence
 points to an early admixture event in the Nubians, concurrent with
 historical contact between North Sudanese and Arab groups. We estimate the
 admixture in current-day Sudanese Arab populations to about 700 years ago,
 coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture
 that reached the Darfurian/Kordofanian populations some 400-200 years ago.
 In contrast to the northeastern populations, the current-day Nilotic
 populations from the south of the region display little or no admixture
 from Eurasian groups indicating long-term isolation and population
 continuity in these areas of northeast Africa.
description: Sudanese and South
 Sudanese genomic variationUncleaned plink (bed bim
 fam) files from 18 Sudanese and South Sudanese populations. Created using
 Illumina Human Omni 5M Exo SNP array.Sudan_plink.tar.gz
DOI: 10.5061/dryad.ns40k
title: Data from: Linkage disequilibrium and effective population size when generations overlap

description: Estimates of effective population size are critical for species of
 conservation concern. Genetic datasets can be used to provide robust
 estimates of this important parameter. However, the methods used to obtain
 these estimates assume that generations are discrete. We used simulated
 data to assess the influences of overlapping generations on estimates of
 effective size provided by the linkage disequilibrium method. Our
 simulations focus on two factors: the degree of reproductive skew
 exhibited by the focal species and the generation time, without
 considering sample size or the level of polymorphism at marker loci. In
 situations where a majority of reproduction is achieved by a small
 fraction of the population, the effective number of breeders can be much
 smaller than the per generation effective population size. The linkage
 disequilibrium in samples of newborns can provide estimates of the former
 size, while our results indicate that the latter size is best estimated
 using random samples of reproductively mature adults. Using samples of
 adults, the downwards bias was less than ~15% across our simulated life
 histories. As noted in previous assessments, precision of the estimate
 depends on the magnitude of effective size itself, with greater precision
 achieved for small populations.
description: Data Archive - Robinson
 & MoyerThis zipped archive
 contains simulated microsatellite datasets used to assess the influence of
 overlapping generations on estimates of LD-based estimates of effective
 population size. The file contains four additional zipped directories with
 SPIP simulation scripts, processed genotype files, outputs from LDNe, and
 spreadsheets summarizing the data.RobinsonMoyer-DataArchive.zip
DOI: 10.5061/dryad.6b2c9
title: Data from: Shark tooth weapons from the 19th century reflect shifting baselines in Central Pacific predator assemblies

description: The reefs surrounding the Gilbert Islands (Republic of Kiribati, Central
 Pacific), like many throughout the world, have undergone a period of rapid
 and intensive environmental perturbation over the past 100 years. A
 byproduct of this perturbation has been a reduction of the number of shark
 species present in their waters, even though sharks play an important in
 the economy and culture of the Gilbertese. Here we examine how shark
 communities changed over time periods that predate the written record in
 order to understand the magnitude of ecosystem changes in the Central
 Pacific. Using a novel data source, the shark tooth weapons of the
 Gilbertese Islanders housed in natural history museums, we show that two
 species of shark, the Spot-tail (Carcharhinus sorrah) and the Dusky (C.
 obscurus), were present in the islands during the last half of the 19th
 century but not reported in any historical literature or contemporary
 ichthyological surveys of the region. Given the importance of these
 species to the ecology of the Gilbert Island reefs and to the culture of
 the Gilbertese people, documenting these shifts in baseline fauna
 represents an important step toward restoring the vivid splendor of both
 ecological and cultural diversity.
description: Drew
 EtAlSharkToothWeaponPhotographs of shark
 toothed weapons in the Anthropology holdings of the Field Museum of
 Natural History (Chicago, IL USA)DrewEtAlSharkToothWeapon.zip
DOI: 10.5061/dryad.mq25897
title: Data from: Signatures of human-commensalism in the house sparrow genome

description: House sparrows (Passer domesticus) are a hugely successful anthrodependent
 species; occurring on nearly every continent. Yet, despite their ubiquity
 and familiarity to humans, surprisingly little is known about their
 origins. We sought to investigate the evolutionary history of the house
 sparrow and identify the processes involved in its transition to a
 human-commensal niche. We used a whole genome resequencing dataset of 120
 individuals from three Eurasian species, including three populations of
 Bactrianus sparrows, a non-commensal, divergent house sparrow lineage
 occurring in the Near East. Coalescent modelling supports a split between
 house and Bactrianus sparrow 11 Kya and an expansion in the house sparrow
 at 6 Kya, consistent with the spread of agriculture following the
 Neolithic revolution. Commensal house sparrows therefore likely moved into
 Europe with the spread of agriculture following this period. Using the
 Bactrianus sparrow as a proxy for a pre-commensal, ancestral house
 population, we performed a comparative genome scan to identify genes
 potentially involved with adaptation to an anthropogenic niche. We
 identified potential signatures of recent, positive selection in the
 genome of the commensal house sparrow that are absent in Bactrianus
 populations. The strongest selected region encompasses two major candidate
 genes; COL11A – which regulates craniofacial and skull development and
 AMY2A, part of the amylase gene family which has previously been linked to
 adaptation to high-starch diets in humans and dogs. Our work examines
 human-commensalism in an evolutionary framework, identifies genomic
 regions likely involved in rapid adaptation to this new niche and ties the
 evolution of this species to the development of modern human civilization.
description: Scripts for alignment,
 filtering and file conversionScripts for aligning
 reads, calling SNPs and converting files for downstream population genomic
 analyses. See README for more detailsfiltering_and_file_conversion.zipIndividual dataIndividual data stored as a csv file - necessary for R scripts bundled here. Information on species, population, location and sex.house_spanish_bac_data.csvPopulation structure scriptsR and shell scripts for analysing population structure. See README for more details.pop_structure_scripts.zipGenome scan scriptsR and shell scripts to perform genome scan analyses. See README for details on how to use scriptsgenome_scan.zipGenome scan dataFst, dxy, fd and LRH statistics for genome sliding windows. See readme for more information on how to interpret individual filesgenome_scan_data.zipdemographic_history_filesModel templates, parameter files, observed SFS and scripts needed to run demographic analyses.Outlier analysis data and scriptsCompressed archive contains R script for identifying clusters in outlier SNP regions. Outlier SNP data is also includedoutlier_analysis.zip
DOI: 10.5061/dryad.670716m
title: Data from: Two speed invasion: assisted and intrinsic dispersal of common mynas over 150-years of colonization

description: Aim: Despite the common myna’s widespread distribution, and the
 significant impact it has caused in parts of its non-native range, there
 have been no comprehensive genomic studies of its invasion of any region.
 We aimed to characterize the common myna invasion of the Australian
 continent to understand its population genetic landscape, introduction
 history, dispersal characteristics, and the interconnectedness between
 different source populations and invasive fronts. Location: Common mynas
 from 26 geographical locations spanning the Australian continent were
 utilized in this study. Taxon: Common myna (Acridotheres tristis).
 Methods: We used a reduced genome representation method (DArTseq) to
 generate thousands of single nucleotide polymorphism markers in 462 common
 mynas. We then applied population genomic techniques to identify the
 common myna’s population attributes such as gene flow, genetic diversity
 and effective dispersal, all of which are critical for understanding
 geographical range expansion of pest species. Results: We found
 significant genetic structuring across the common myna’s Australian
 distribution, indicating limited levels of effective dispersal amongst the
 populations founded from historic introductions in the 19th century. The
 historic introduction points were found to be genetically distinct, such
 that in the region on the invasion front where admixture did occur, myna
 populations exhibited higher genetic diversity than in the source
 populations. Significant isolation by distance was evident amongst
 populations derived from the same founding population, with genetic
 diversity decreasing moving away from the point of colonization, and in
 general, higher levels of gene flow from source to front than vice versa.
 Main conclusions: This study indicates that despite a 150-year
 colonization history of mynas in Australia, contemporary genetic structure
 still largely reflects human-mediated dispersal. However, expanding
 populations are now connecting and the consequent increased genetic
 diversity may improve evolutionary potential. These results suggest that
 more management focus should be directed towards the invasion fronts,
 rather than the large, historic source populations.
description: SNP data for all common
 myna samples used in this paperThe SNPs provided by
 DArT and the associated metadata for all common myna samples used in this
 paper. Explanations for the metadata can be found in the first tab of the
 spreadsheet. Note: data in the 'ScoringData_SilicoDArT' tab was
 not used in this study.OrderAppendix_1_DImy16-2231.xlsx
DOI: 10.60520/ieda/114188
title: LA-ICP-MS settings for trace element analysis of volcanic glass at University of Cologne - v2

description: ICP:MS-LA instrument (University of Cologne) settings V2 applied to analyze volcanic glass fragments of tephra layers.
DOI: 10.5061/dryad.3r0h560
title: Data from: Energy landscape for the insertion of amphiphilic nanoparticles into lipid membranes: a computational study

description: Amphiphilic, monolayer-protected gold nanoparticles (NPs) have been shown
 to enter cells via a non-endocytic, non-disruptive pathway that could be
 valuable for biomedical applications. The same NPs were also found to
 insert into a series of model cell membranes as a precursor to cellular
 uptake, but the insertion mechanism remains unclear. Previous simulations
 have demonstrated that an amphiphilic NP can insert into a single leaflet
 of a planar lipid bilayer, but in this configuration all charged end
 groups are localized to one side of the bilayer and it is unknown if
 further insertion is thermodynamically favorable. Here, we use atomistic
 molecular dynamics simulations to show that an amphiphilic NP can reach
 the bilayer midplane non-disruptively if charged ligands iteratively
 ``flip'' across the bilayer. Ligand flipping is a favorable
 process that relaxes bilayer curvature, decreases the nonpolar
 solvent-accessible surface area of the NP monolayer, and increases
 attractive ligand-lipid electrostatic interactions. Analysis of end group
 hydration further indicates that iterative ligand flipping can occur on
 experimentally relevant timescales. Supported by these results, we present
 a complete energy landscape for the non-disruptive insertion of
 amphiphilic NPs into lipid bilayers. These findings will help guide the
 design of NPs to enhance bilayer insertion and non-endocytic cellular
 uptake, and also provide physical insight into a possible pathway for the
 translocation of charged biomacromolecules.
description: dataSimulation input
 parameters, output configurations, and system preparation scripts needed
 to reproduce simulations performed in the main text. In addition, the
 processed data and instructions on the data was generated for each figure
 is included.
DOI: 10.5061/dryad.cb3t4
title: Data from: A new Magneto-Inductive tracking technique to uncover subterranean activity: what do animals do underground?

description: 1. Despite the importance of the subterranean ecotope, knowledge of
 underground movement and behaviour has been extremely limited. Previous
 technologies have relied upon techniques with very low spatial or temporal
 resolution, such as VHF telemetry. Rather incongruously therefore,
 relatively simple underground activity regimes have often been assumed,
 with insufficient attention to the ecological importance of burrow use. 2.
 We test the capability of Magneto-Inductive (MI) tracking, recording
 underground movement within a European badger sett over a two week period
 in February. These data allowed us to: quantify subterranean movement;
 extrapolate the three-dimensional burrow architecture; simultaneously
 track multiple individuals; and establish the function of specific
 movement patterns; demonstrating the technique's utility. Contrasting
 data generated using MI tracking, against the resolution achievable with
 VHF tracking, we establish how sampling frequency can influence the
 percecption of movement. 3. Taking 20 locational fixes per minute, MI
 collars operated for one year before on-board batteries failed, resulting
 in an average five billion data points per collar deployment.
 Socio-ecologically we found that rather than foraging continuously
 throughout the night, badgers returned to the sett an average of 2.2
 times, approximately every 3-4 hours. From burrow mapping, badgers tended
 to use peripheral chambers for ca. 45 minutes on these return visits,These
 outlying chambers were used less by day, when badgers selected deeper
 chambers, suggesting each chamber type fulfils a different function. This
 technology also exposed that badgers exhibited a far greater extent of
 underground movement than revealed by former technologies, which by
 comparison captured less than 0.5% of subterranean activity. Importantly,
 these high-resolution data showed that individuals left, returned to, and
 moved about the sett independently, with no tendency for synchronous
 subterranean activity. 4. In overview, magneto-inductive tracking proved
 relatively simple and cost effective to deploy, it provided very detailed
 and accurate subterranean fixes, and was robust enough for long-term field
 deployment. Furthermore, the capabilities of MI are highly transferable,
 enabling a better understanding of underground activity and the ecological
 importance of subterranean burrows for the conservation and management of
 a wide range of species.
description: Badger 1100
 DataBadger 1300
 DataBadger 1400
 DataBadger 2202
 Data
DOI: 10.5061/dryad.85fm181
title: Data from: Associations between age at first calving and subsequent lactation performance in UK Holstein and Holstein-Friesian dairy cows

description: Lactation records from 396,534 pedigree Holstein and Holstein-Friesian
 primiparous cows from 6,985 UK milk recorded herds, calving for the first
 time during the period between the 1st of January 2006 and the 31st of
 December 2008, were examined in order to determine the associations
 between age at first calving (AFC) and subsequent production, udder
 health, fertility and survivability parameters. Heifers were grouped by
 AFC into single month classes ranging from 21 to 42 months. Mixed effects
 multivariable regression modelling was used for data analysis. Mean and
 median AFC were 29.1 and 28 months respectively. Within the study, only
 48,567 heifers (12.3% of the studied population) calved for the first time
 at 24 months of age or younger. 162,157 heifers (40.9%) were 30 months or
 older at their first calving. An increased AFC was associated with
 increased first lactation milk, fat and protein yields. The lowest
 predicted mean 305-day yield (6,617kgs; 95% confidence interval (CI):
 6,546–6,687 kgs) was recorded for the 21 month AFC class, significantly
 lower than any other class. The 36 month AFC class had the highest
 predicted mean (7,774 kgs; 95% CI: 7,737–7,811 kgs). However, an increased
 AFC was also associated with increased calving interval and increased
 first lactation somatic cell count (SCC). Animals calving at 21 months had
 a predicted mean lactation SCC of 72,765 (95% CI: 68427–77378). Animals
 calving at 36 months of age had a predicted mean lactation SCC of 86,648
 (95% CI: 84,499–88,853). Importantly, an increased AFC was also associated
 with decreased lifetime daily milk yield and decreased likelihood of
 calving for a second successive time. Animals calving at 22 months of age
 had a predicted mean daily lifetime milk yield of 15.24 kgs (95% CI:
 15.06–15.35); animals calving at 36 months of age had a predicted mean
 daily lifetime milk yield of 12.83 kgs (95% CI: 12.76–12.91). Our results
 highlight the importance of achieving a lower age at first calving which
 was here associated with improved udder health, increased lifetime daily
 milk yield, improved reproductive performance and increased likelihood of
 calving for a second time.
description: AFC paper
 data
DOI: 10.5061/dryad.9n237
title: Data from: Placoderms and the evolutionary origin of teeth: a comment on Rücklin & Donoghue (2015)

description: [No description entered]
description: Anterior supragnathal of
 an Early Devonian arthrodire (ANU V244)PLY file of the anterior
 supragnathal (ASG) of an Early Devonian arthrodire (ANU
 V244).ASG_LowRes.zip
DOI: 10.5061/dryad.5n2bs6r
title: Data from: Population genomics of sorghum (Sorghum bicolor) across diverse agroclimatic zones of Niger

description: Improving adaptation of staple crops in developing countries is important
 to ensure food security. In the West African country of Niger, the staple
 crop sorghum (Sorghum bicolor) is cultivated across diverse agroclimatic
 zones, but the genetic basis of local adaptation has not been described.
 The objectives of this study were to characterize the genomic diversity of
 sorghum from Niger and to identify genomic regions conferring local
 adaptation to agroclimatic zones and farmer preferences. We analyzed 516
 Nigerien accessions for which local variety name, botanical race, and
 geographic origin were known. We discovered 144,299 single nucleotide
 polymorphisms (SNPs) using genotyping-by-sequencing (GBS). We performed
 discriminant analysis of principal components (DAPC), which identified six
 genetic groups, and performed a genome scan for loci with high
 discriminant loadings. The highest discriminant coefficients were on
 chromosome 9, near the putative ortholog of maize flowering time
 adaptation gene Vgt1. Next, we characterized differentiation among local
 varieties and used a genome scan of pairwise FST values to identify SNPs
 associated with specific local varieties. Comparison of varieties named
 for light- versus dark-grain identified differentiation near Tannin1, the
 major gene responsible for grain tannins. These findings could facilitate
 genomics-assisted breeding of locally-adapted and farmer-preferred sorghum
 varieties for Niger.
description: sorghum_germplasm_imputedCurrent genome version of sorghum (V3)sorghum_germplasm_niger.hmp.txt
DOI: 10.5061/dryad.0n205
title: Data from: Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds

description: The routine collection and use of genomic data are useful for effectively
 managing breeding programs for endangered populations. Linkage
 disequilibrium (LD) using high-density DNA markers has been widely used to
 determine population structures and predict the genomic regions that are
 associated with economic traits in beef cattle. The extent of LD also
 provides information about historical events, including past effective
 population size (Ne), and it allows inferences on the genetic diversity of
 breeds. The objective of this study was to estimate the LD and Ne in three
 Korean cattle breeds that are genetically similar but have different coat
 colors (Brown, Brindle and Jeju Black Hanwoo). Brindle and Jeju Black are
 endangered breeds with small populations, whereas Brown Hanwoo is the main
 breeding population in Korea. DNA samples from these cattle breeds were
 genotyped using the Illumina BovineSNP50 Bead Chip. We examined 13 cattle
 breeds, including European taurines, African taurines and indicines, and
 hybrids to compare their LD values. Brown Hanwoo consistently had the
 lowest mean LD compared to Jeju Black, Brindle and the other 13 cattle
 breeds (0.13, 0.19, 0.21 and 0.15–0.22 respectively). The high LD values
 of Brindle and Jeju Black contributed to small Ne values (53 and 60
 respectively), which were distinct from that of Brown Hanwoo (531) for 11
 generations ago. The differences in LD and Ne for each breed reflect the
 breeding strategy applied. The Ne for these endangered cattle breeds
 remain low; thus, effort is needed to bring them back to a sustainable
 tract.
description: Korean cattle 50K SNP
 dataThis compressed data
 contains our original 50K SNP data of three Korean cattle breeds and 13
 cattle breeds compiled from Bovine Hapmap data (Gautier et al.,
 2010).dryad.tar.gz