cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pvmcvdngk
title: Migratory divides coincide with reproductive barriers across replicated avian hybrid zones above the Tibetan Plateau

description: Migratory divides are proposed to be catalysts for speciation across a
 diversity of taxa. However, it is difficult to test the relative
 contributions of migratory behavior vs. other divergent traits to
 reproductive isolation. Comparing hybrid zones with and without migratory
 divides offers a rare opportunity to directly examine the contribution of
 divergent migratory behavior to reproductive barriers. We show that across
 replicate sampling transects of two pairs of barn swallow (Hirundo
 rustica) subspecies, strong reproductive isolation coincided with a
 migratory divide spanning 20 degrees of latitude. A third subspecies pair
 exhibited no evidence for a migratory divide and hybridized extensively.
 Within migratory divides, overwintering habitats were associated with
 assortative mating, implicating a central contribution of divergent
 migratory behavior to reproductive barriers. The remarkable geographic
 coincidence between migratory divides and genetic breaks supports a
 longstanding hypothesis that the Tibetan Plateau is a substantial barrier
 contributing to the diversity of Siberian avifauna.
description: Included in the dataset: 1. Script for running
 geographic cline analysis using HZAR in R 2. Metadata
 for all samples, including sampling date, location, and phenotype
 information 3. SNPs (0/1/2 format) for 1288 individuals
 across 12,383 loci meeting quality filtering 4. Draft
 reference genome for the barn swallow, used for sequence
 alignment
DOI: 10.5061/dryad.m905qftwz
title: The morphological diversity of the quadrate bone in squamate reptiles as revealed by high-resolution computed tomography and geometric morphometrics

description: We examined the morphological diversity of the quadrate bone in squamate
 reptiles (i.e. lizards, snakes, amphisbaenians). The quadrate is the
 principal splanchnocranial element involved in suspending the lower jaw
 from the skull, and its shape is of particular interest because it is
 potentially affected by several factors, such as phylogenetic history,
 allometry, ecology, skull kinesis and hearing capabilities (e.g. presence
 or absence of a tympanic ear). Due to its complexity, the quadrate bone is
 also considered one of the most diagnostic elements in fragmentary fossil
 taxa. We describe quadrates from 38 species spread across all major
 squamate clades, using qualitative and quantitative (e.g. geometric
 morphometrics) methods. We test for possible correlations between shape
 variation and factors such as phylogeny, size, ecology and
 presence/absence of a tympanum. Our results show that the shape of the
 quadrate is highly evolutionarily plastic, with very little of the
 diversity explained by phylogenetic history. Size variation (allometric
 scaling) is similarly unable to explain much shape diversity in the
 squamate quadrate. Ecology (terrestrial/fossorial/aquatic) and presence of
 a tympanic ear are more significant, but together explain only about 20%
 of the diversity observed. Other unexplored and more analytically complex
 factors, such as skull biomechanics, likely play additional major roles in
 shaping the quadrates of lizards and snakes.
DOI: 10.5061/dryad.80gb5mkn3
title: Data from: Geography alone cannot explain Tetranychus truncatus (Acari: Tetranychidae) population abundance and genetic diversity in the context of the center–periphery hypothesis

description: The center–periphery hypothesis (CPH) states that the genetic diversity,
 genetic flow and population abundance of a species are highest at the
 center of the species’geographic distribution. However, most CPH studies
 have focused on geographic distance and have ignored ecological and
 historical effects. Studies using niche models to define the center and
 periphery of a distribution and the interactions among
 geographical, ecological and historical gradients have rarely been done in
 the framework of the CPH, especially in biogeographical studies
 of animal species. Here, we examined the CPH for a widely
 distributed arthropod, Tetranychus truncatus (Acari: Tetranychidae), in
 eastern China using three measurements: geographic distance to
 the center of the distribution (geography), ecological
 suitability based on current climate data  (ecology), and
 historical climate data from the last glacial maximum (history). We
 found that the relative abundances of different populations were
 more strongly related to ecology than to geography and history. Genetic
 diversity within populations and genetic differentiation among
 populations based on mitochondrial marker were only
 significantly related to history. However, the genetic diversity
 and population differentiation based on microsatellites were
 significantly related to all three CPH measurements. Overall, population
 abundance and genetic pattern cannot be explained very well by geography
 alone. Our results show that ecological gradients explain the variation in
 population abundance better than geographic gradients and
 historical factors, and that current and historical factors strongly
 influence the spatial patterns of genetic variation. This
 study highlights the importance of examining more than just
 geography when assessing the CPH.
description: In each
 location, spider mite samples for genetic analysis were collected and
 soaked in 95% ethanol for DNA extraction in the lab. DNA was extracted
 using Qiagen DNeasy Blood and Tissue Kits following the standard protocol
 (Qiagen Valencia, CA, USA). Microsatellite
 variation was genotyped at 14 loci developed by Ge et al. (2013) (TUFG6,
 TUFG12, TUFG33, TUFG18, TUFG169, TUFG130N) and Zhang et al. (2016)
 (TUGZ155, TUFZ4, TUFZ3, TUFZ 34, TUFZ30, TUFZ60, TUFZ23). PCR was
 performed using the protocol described by Zhang et al. (2016). Fragment
 lengths were sequenced in an ABI 3170 automated sequencer using LIZ-500
 size standard. All allele scores were manually checked for quality and
 consistency.
description: Microsatellite type of Tetranychus truncatus populations from
 China using 14 loci
DOI: 10.34740/kaggle/dsv/14642893
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.66t1g1jxs
title: Variable prediction accuracy of polygenic scores within an ancestry group

description: Fields as diverse as human genetics and sociology are increasingly using
 polygenic scores based on genome-wide association studies (GWAS) for
 phenotypic prediction. However, recent work has shown that polygenic
 scores have limited portability across groups of different genetic
 ancestries, restricting the contexts in which they can be used reliably
 and potentially creating serious inequities in future clinical
 applications. Using the UK Biobank data, we demonstrate that even within a
 single ancestry group (i.e., when there are negligible differences in
 linkage disequilibrium or in causal alleles frequencies), the prediction
 accuracy of polygenic scores can depend on characteristics such as the
 socio-economic status, age or sex of the individuals in which the GWAS and
 the prediction were conducted, as well as on the GWAS design. Our findings
 highlight both the complexities of interpreting polygenic scores and
 underappreciated obstacles to their broad use.
description: This repository contains summary statistics for all association
 tests (including GWAS and effect re-estimations for sets of
 pre-ascertained SNPs) that were performed in this study.
 The directory "gwas_by_sample_characteristics" stores
 data corresponding to Figures 1, 2, and Appendix-figures 1-5,13-15, and
 Appendix-table 2. The directory
 "standard_vs_sibling_gwas" stores data corresponding to Figure
 3, and Appendix-figures 11, 12, 16. Additional README
 files can be found within each directory.
DOI: 10.5061/dryad.9ghx3ffd0
title: Data from: Joint evolution of dispersal and connectivity

description: Functional connectivity, the realized flow of individuals between the
 suitable sites of a heterogeneous landscape, is a prime determinant of the
 maintenance and evolution of populations in fragmented habitats. While a
 large body of literature examines the evolution of dispersal propensity,
 it is less known how evolution shapes functional connectivity via traits
 that influence the distribution of the dispersers. Here we use a simple
 model to demonstrate that, in a heterogeneous environment with clustered
 and solitary sites (i.e., with variable structural connectivity), the
 evolutionarily stable population contains strains that are strongly
 differentiated in their pattern of connectivity (local vs global
 dispersal), but not necessarily in the fraction of dispersed individuals.
 Also during evolutionary branching, selection is disruptive predominantly
 on the pattern of connectivity rather than on dispersal propensity itself.
 Our model predicts diversification along a hitherto neglected axis of
 dispersal strategies and highlights the role of the solitary sites – the
 more isolated and therefore seemingly less important patches of habitat –
 in maintaining global dispersal that keeps all sites connected.
description: This zip folder contains code and data files provided as
 electronic enhancements to the paper "Joint evolution of dispersal
 and connectivity" by P. Karisto and E. Kisdi, published in
 Evolution. Content of the zip folder:<br> - Six
 Mathematica notebooks containing the model analysis<br>   
  monomorphic_boundary_analysis_annotated.nb<br>   
  monomorphic_singularities_annotated.nb<br>   
  isocline_plots_annotated.nb<br>   
  direction_of_disruptive_selection_annotated.nb<br>   
  dimorphic_singularities_annotated.nb<br>   
  canonical_equation_annotated.nb<br> - The data file data_file.csv
 with the coordinates of dimorphic singularities of the form
 ((d1,0),(d2,q2)) with q2&lt;1 (cited in Section 5 of the Electronic
 Appendix of the paper, published on the website of the journal
 Evolution)
DOI: 10.5061/dryad.c866t1g34
title: Payment For Ecosystem Services (PES); A Holistic Tool For Sustainable Forest Management-A Case Study From Pakistan

description: Economic valuation of ecosystem services is a new concept in forest
 management. Economic valuation provides basis for payment for ecosystem
 services (PES). Therefore, objective of this study was to evaluate
 eco-tourism and carbon stock services of the Maindam valley, District
 Swat, Pakistan. For the carbon stock calculation, a sample size of 155
 plots of 0.1 hectare (Ha) was taken using preliminary survey at 95%
 confidence interval and 10% allowable error. The data for tourism services
 was collected from owners of all the hotels, 100 tourists and key
 informants of the area at 10% sampling intensity on pretested
 questionnaire for twenty years period (1997-2017). Results showed that
 Miandam valley has carbon stock worth US$ 16,306,000 while the value of
 eco-tourism was US$ 1,578,458 on annual basis. The results also showed
 that trend of tourism has drastically declined after the 9/11 incident for
 foreigners and locals and the situation was further deteriorated during
 the era of Talibanization or militancy from 2008-2011. This study
 recommends implementation of PES strategy at the rate of 5%, thus a total
 of US$ 78,922 can be earned from eco-tourism and carbon crediting in the
 study area annually which could play important role in sustainable forest
 management.
DOI: 10.5061/dryad.b2rbnzs93
title: Evolution of phenotypic plasticity: genetic differentiation and additive genetic variation for induced defense in wild arugula Eruca sativa

description: Phenotypic plasticity is the primary mechanism of organismal resilience to
 abiotic and biotic stress, and genetic differentiation in plasticity can
 evolve if stresses differ among populations. Inducible defense is a common
 form of adaptive phenotypic plasticity and long-standing theory predicts
 that its evolution is shaped by costs of the defensive traits, costs of
 plasticity, and a trade-off in allocation to constitutive versus induced
 traits. We used a common-garden to study the evolution of defense in two
 native populations of wild arugula Eruca sativa (Brassicaceae) from
 contrasting desert and Mediterranean habitats that differ in attack by
 caterpillars and aphids. We report genetic differentiation and additive
 genetic variance for phenology, growth, and three defensive traits (toxic
 glucosinolates, anti-nutritive protease inhibitors, and physical trichome
 barriers) as well their inducibility in response to the plant hormone
 jasmonic acid. The two populations were strongly differentiated for
 plasticity in nearly all traits. There was little evidence for costs of
 defense or plasticity, but constitutive and induced traits showed a
 consistent additive genetic trade-off within each population for the three
 defensive traits. We conclude that these populations have evolutionarily
 diverged in inducible defense and retain ample potential for the future
 evolution of phenotypic plasticity in defense.
DOI: 10.5061/dryad.kh189321s
title: Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers

description: Hosting unique and important plant germplasms, the Qinghai-Tibet Plateau
 (QTP), as the third pole of the world, and Xinjiang, located in the centre
 of the Eurasian continent, are major distribution areas of perennial
 Triticeae grasses, especially the
 widespread Elymus species. Elymus
 excelsus Turcz. ex Griseb, a perennial forage grass with strong
 tolerance to environmental stresses, such as drought, cold and soil
 impoverishment, can be appropriately used for grassland establishment due
 to its high seed production. To provide basic information for collection,
 breeding strategies and utilization of E.
 excelsus germplasm, microsatellite markers (SSR) were employed in
 the present study to determine the genetic variation and population
 structure of 25 wild accessions of E. excelsus from
 Xinjiang (XJC) and the QTP, including Sichuan (SCC) and Gansu (GSC) of
 western China. Based on the 159 polymorphic bands amplified by 35 primer
 pairs developed from three related species, the average values of the
 polymorphic information content (PIC), marker index (MI), resolving power
 (Rp), Nei’s genetic diversity (H) and Shannon’s diversity index (I) of
 each pair of primers were 0.289, 1.348, 1.897, 0.301 and 0.459,
 respectively, validating that these SSR markers can also be used for the
 evaluation of genetic diversity of E.
 excelsus germplasms, and demonstrating the superior versatility
 of EST-SSR vs. G-SSR. We found a relatively moderate differentiation
 (Fst = 0.151) among the XJC, SCC and GSC geo-groups, and
 it is worth noting that, the intra-group genetic diversity of the SCC
 group (He = 0.197) was greater than that of the GSC
 (He = 0.176) and XJC (He = 0.148)
 groups. Both the Unweighted Pair Group Method with Arithmetic (UPGMA)
 clustering and principal coordinates analysis (PCoA) divided the 25
 accessions into three groups, whereas the Bayesian STRUCTURE analysis
 suggested that E. excelsus accessions fell into four
 main clusters. Besides, this study suggested that geographical distance
 and environmental variables (annual mean precipitation and average
 precipitation in growing seasons), especially for QTP accessions, should
 be combined to explain the population genetic differentiation among the
 divergent geographical regions. These data provided comprehensive
 information about these valuable E. excelsus germplasm
 resources for the protection and collection of germplasms and for breeding
 strategies in areas of Xinjiang and QTP in western China.
description: A microsatellite data including EST-SSRs and G-SSRs
DOI: 10.5061/dryad.05qfttdz7
title: Xylomelum occidentale (Proteaceae) accesses relatively mobile soil organic phosphorus without releasing carboxylates

description: 1. Hundreds of Proteaceae species in Australia and South Africa typically
 grow on phosphorus (P)-impoverished soils, exhibiting a
 carboxylate-releasing P-mobilising strategy. In the Southwest Australian
 Biodiversity Hotspot, two Xylomelum (Proteaceae) species are widely
 distributed, but restricted within that distribution. 2. We grew X.
 occidentale in hydroponics at 1 μM P. Leaves, seeds, rhizosheath and bulk
 soil were collected in natural habitats. 3. Xylomelum occidentale did not
 produce functional cluster roots and occupied soils that are somewhat less
 P-impoverished than those in typical Proteaceae habitats in the region.
 Based on measurements of foliar manganese concentrations (a proxy for
 rhizosphere carboxylate concentrations) and P fractions in bulk and
 rhizosheath soil, we conclude that X. occidentale accesses organic P,
 without releasing carboxylates. Solution 31P-NMR revealed which organic P
 forms X. occidentale accessed. 4. Xylomelum occidentale uses a strategy
 that differs fundamentally from that typical in Proteaceae, accessing soil
 organic P without carboxylates. We surmise that this novel strategy is
 likely expressed also in co-occurring non-Proteaceae that lack a
 carboxylate-exuding strategy, and plants in similar habitats. These
 co-occurring species are unlikely to benefit from mycorrhizal
 associations, because plant-available soil P concentrations are too low.
 5. Synthesis. Our findings show the first field evidence of effectively
 utilising soil organic P by X. occidentale without carboxylate exudation
 and explain their relatively restricted distribution in an old
 P-impoverished landscape, contributing to a better understanding of how
 diverse P-acquisition strategies coexist in a megadiverse ecosystem.
description: Soil chemical data. Soils were field-collected from natural
 habitats of <em>Xylomelum occidentale</em>. Soil data in this
 file include: pH, EC, total phosphorus (P), organic P, inorganic P. resin
 P, total carbon, soil organic matter, and soil organic carbon. This
 soil_chemical_data.csv file was created using Microsoft Excel
 2013.
description: Leaf chemistry data: elemental concentrations. Leaves were
 field-collected from natural habitats of <em>Xylomelum
 </em>species. This leaf_chemistry_data.csv file was created using
 Microsoft Excel 2013.
DOI: 10.5061/dryad.rr4xgxd54
title: A classification framework for Bacillus anthracis defined by global genomic structure

description: Bacillus anthracis, the causative agent of anthrax, is a considerable
 global health threat affecting wildlife, livestock, and the general
 public. In this study whole-genome sequence analysis of over 350 B.
 anthracis isolates was used to establish a new high-resolution global
 genotyping framework that is both biogeographically informative, and
 compatible with multiple genomic assays. The data presented in this study
 shed new light on the diverse global dissemination of this species and
 indicate that many lineages may be uniquely suited to the geographic
 regions in which they are found. In addition, we demonstrate that plasmid
 genomic structure for this species is largely consistent with chromosomal
 population structure, suggesting vertical inheritance in this bacterium
 has contributed to its evolutionary persistence. This classification
 methodology is the first based on population genomic structure for this
 species and has potential use for local and broader institutions seeking
 to understand both disease outbreak origins and recent introductions. In
 addition, we provide access to a newly developed genotyping script as well
 as the full whole genome sequence analyses output for this study, allowing
 future studies to rapidly employ and append their data in the context of
 this global collection. This framework may act as a powerful tool for
 public health agencies, wildlife disease laboratories, and researchers
 seeking to utilize and expand this classification scheme for further
 investigations into B. anthracis evolution.
DOI: 10.5061/dryad.mw6m905sz
title: Data from: Distribution maps of cetacean and seabird populations in the North-East Atlantic

description: Distribution maps of cetaceans and seabirds at basin and monthly scales
 are needed for conservation and marine management. These are usually
 created from standardised and systematic aerial and vessel surveys, with
 recorded animal densities interpolated across study areas. However, as
 individual surveys have restricted spatial and temporal coverage,
 distribution maps at basin and monthly scales have previously not been
 possible. This study develops an alternative approach consisting of (1)
 collating diverse survey data to maximise spatial and temporal coverage,
 (2) using detection functions to estimate variation in the surface area
 covered (km2) among these surveys, standardising measurements of effort
 and animal densities, (3) developing species distribution models (SDM)
 that overcome issues with heterogeneous and uneven coverage. 2.68 million
 km of survey data in the North-East Atlantic between 1980 and 2018 were
 collated and standardised. SDM using Generalized Linear Models (GLM) and
 General Estimating Equations (GEE) in a hurdle-model were developed.
 Distribution maps were then created for 12 cetacean and 12 seabird species
 at 10 km and monthly resolution. Qualitative and quantitative assessments
 indicated good model performance. This study provides the largest-ever
 collation and standardisation of diverse survey data for cetaceans and
 seabirds and the most comprehensive distribution maps of these taxa in the
 North-East Atlantic. These distribution maps have numerous applications
 including the identification of important areas needing protection and the
 quantification of overlap between vulnerable species and anthropogenic
 activities. This study demonstrates how the analysis of existing and
 diverse survey data can meet conservation and marine management needs.
description: Distribution maps were created from Species Distribution Models
 using 1790375km and 1143587km of cetacean and seabird at-sea surveys,
 respectively.
description: Distribution maps at monthly and 10km for 24 species of cetacean
 and seabird species in the North-East Atlantic.
 <strong>Format –</strong> ASCII files can be viewed
 in either ArcGIS or R. <strong>Name
 –</strong> filename includes species name and month (01 to
 12). <strong>Units –</strong> Number of
 animals per km<sup>2</sup>
 <strong>Resolution –</strong> 10 x 10 km
 <strong>Coordinate System –</strong> WGS 84 UTM 30N
 (EPSG:32630)