cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f9m27
title: Data from: Multilocus phylogeography reveals nested endemism in a gecko across the monsoonal tropics of Australia

description: Multilocus phylogeography can uncover taxonomically unrecognized lineage
 diversity across complex biomes. The Australian monsoonal tropics includes
 vast, ecologically intact savanna-woodland plains interspersed with
 ancient sandstone uplands. Though recognized in general for its high
 species richness and endemism, the biodiversity of the region remains
 underexplored due to its remoteness. This is despite a high rate of
 ongoing species discovery, especially in wetter regions and for
 rock-restricted taxa. To provide a baseline for ongoing comparative
 analyses, we tested for phylogeographic structure in an ecologically
 generalized and widespread taxon, the gecko Heteronotia binoei. We apply
 coalescent analyses to multilocus sequence data (mitochondrial DNA and
 eight nuclear DNA introns) from individuals sampled extensively and at
 fine scale across the region. The results demonstrate surprisingly deep
 and geographically nested lineage diversity. Several intraspecific clades
 previously shown to be endemic to the region were themselves found to
 contain multiple, short-range lineages. To infer landscapes with
 concentrations of unique phylogeographic diversity, we probabilistically
 estimate the ranges of lineages from point data and then, combining these
 estimates with the nDNA species tree, estimate phyloendemism across the
 region. Highest levels of phyloendemism occur in northern Top End,
 especially on islands, across the topographically complex Arnhem
 escarpment, and across the sandstone ranges of the western Gulf region.
 These results drive home that deep phylogeographic structure is prevalent
 in tropical low-dispersal taxa, even ones that are ubiquitous across
 geography and habitats.
description: Heteronotia_binoei_phylogeneticsAlignments and phylogenies for northern lineages of Heteronotia binoeiHeteronotia_binoei_PEGIS raster layer for phylogenetic endemism within Heteronotia binoei
DOI: 10.34810/data2691
title: Replication data for: "Link between graphene features and the resulting functionality of quasi-Van der Waals Zn3P2"

description: "-Zn3P2, made from earth-abundant elements, is a promising candidate for thin-film solar cells but faces limitations due, to difficulties in achieving n-type doping and its large lattice mismatch with commercial substrates and a high thermal expansion coefficient, causing defects and cracks. Graphene substrates can address these challenges thanks to its weak Van der Waals interactions with Zn3P2 allowing for mechanical transfer of the thin film and a strain-free growth. This study compares five graphene substrates for quasi-Van der Waals epitaxial (q-VdWe) growth of polycrystalline Zn3P2 thin films using molecular beam epitaxy. Surface features like steps and wrinkles on graphene were identified as main nucleation sites for Zn3P2, provided the graphene has minimal point defects. The highest-quality thin films, with the largest grain sizes, were grown on H-CVD graphene on the Si-face of 6H-SiC, featuring solely terraces of atomic height. All substrates showed comparable growth windows for crystalline Zn3P2, with higher growth temperatures improving crystal quality, as indicated by enhanced photoluminescence. Cryo-cathodoluminescence measurements revealed spatially localized sub-bandgap emissions, potentially linked to localized strain fields at grain boundaries of up to ±3% as identified by cross-sectional transmission electron microscopy. This work provides insights into advantages and drawbacks of utilising q-VdWe to produce Zn3P2 thin films for solar cell applications and highlights the roles of graphene substrate choice and growth parameters on Zn3P2 film quality."
DOI: 10.5061/dryad.4t20n
title: Data from: Genomic variation in recently collected maize landraces from Mexico

description: The present dataset comprises 36,931 SNPs genotyped in 46 maize landraces
 native to Mexico as well as the teosinte subspecies Zea maiz ssp.
 Parviglumis and ssp. Mexicana. These landraces were collected directly
 from farmers mostly between 2006 and 2010. We accompany these data with a
 short description of the variation within each landrace, as well as maps,
 principal component analyses and neighbor joining trees showing the
 distribution of the genetic diversity relative to landrace, geographical
 features and maize biogeography. High levels of genetic variation were
 detected for the maize landraces (HE = 0.234 to 0.318 (mean 0.311), while
 slightly lower levels were detected in Zea m. mexicana and Zea m.
 parviglumis (HE = 0.262 and 0.234, respectively). The distribution of
 genetic variation was better explained by environmental variables given by
 the interaction of altitude and latitude than by landrace identity. This
 dataset is a following up product of the Global Native Maize Project, an
 initiative to update the data on Mexican maize landraces and their wild
 relatives, and to generate information that is necessary for implementing
 the Mexican Biosafety Law.
description: Scripts for analyses and
 plotsContent:
 'admixtureplot.R' to plot admixture analyses,
 'maices_estimatingpopgenstats_wrapall.R' R code for estimating
 He, Ho, and Fst, 'maices_PCAs_plots.html' and
 'maices_PCAs_plots.Rmd' show a Rmarkdown document used to plot
 the PCA, NJ trees and maps. 'runadmixture.sh' code used to run
 admixture. These scripts need the data and metada available at the
 DataandMetadata.zip section of this repositorybin.zipAdmixture outputContains the log, .Q, .P and se files of the admixture analyses. For command line used and code for plotting see the Scripts section of this repo.admixture.zipData and Meta'data/SNPs' contains SNP data provided in plink and gds format along with a README of how each file was produced. 'data/spatial' contains the shapefiles used for the maps. Please uncompress each one before use. 'meta/maizteocintle_SNP50k_meta_extended.txt' is a text file containing sampling locality, lat, long, and other metadata of each of the samples. Columns correspond to the data collected as part of the Global Maize Proyect and are further detailed at http://www.biodiversidad.gob.mx/genes/pdf/proyecto/Anexo13_Base %20de%20datos/Contenido%20y%20observaciones%20de%20la%20BdeD.pdfDataandMeta.zip
DOI: 10.5061/dryad.d4841
title: Data from: Challenges in the estimation of extinction from molecular phylogenies: a response to Beaulieu and O'Meara

description: Time-calibrated phylogenies that contain only living species have been
 widely used to study the dynamics of speciation and extinction. Concerns
 about the reliability of phylogenetic extinction estimates were raised by
 Rabosky (2010), where I suggested that unaccommodated heterogeneity in
 speciation rate could lead to positively biased extinction estimates. In a
 recent article, Beaulieu and O'Meara (2015) correctly point out
 several technical errors in the execution of my 2010 study and concluded
 that phylogenetic extinction estimates are robust to speciation rate
 heterogeneity under a range of model parameters. I demonstrate that
 Beaulieu and O'Meara underestimated the magnitude of speciation rate
 variation in real phylogenies and consequently did not incorporate
 biologically meaningful levels of rate heterogeneity into their
 simulations. Using parameter values drawn from the recent literature, I
 find that modest levels of heterogeneity in speciation rate result in a
 consistent, positive bias in extinction estimates that are exacerbated by
 phylogenetic tree size. This bias, combined with the inherent lack of
 information about extinction in molecular phylogenies, suggests that
 extinction rate estimates from phylogenies of extant taxa only should be
 treated with caution.
description: Simulation and analysis
 codeZipped archive of all
 data and scripts necessary to perform the analyses in Rabosky (2015),
 organized in order of the figures in the manuscript. Directory
 "fig_1_2_analyses" does the analysis of clade age and speciation
 rate, "fig_3" does analysis of phylogenetic tree balance, and
 "fig_4_5" does simulations and analysis of extinction rates when
 speciation rate heterogeneity is present.rabosky_evo_dryad.zip
DOI: 10.5061/dryad.mc736
title: Data from: Phylogenomics and historical biogeography of the monocot order Liliales: out of Australia and through Antarctica

description: We present the first phylogenomic analysis of relationships among all ten
 families of Liliales, based on 75 plastid genes from 35 species in 29
 genera, and 97 additional plastomes stratified across angiosperm lineages.
 We used a supermatrix approach to extend our analysis to 58 of 64 genera
 of Liliales, and calibrated the resulting phylogeny against 17 fossil
 dates to produce a new timeline for monocot evolution. Liliales diverged
 from other monocots 124 Mya and began splitting into separate families 113
 Mya. Our data support an Australian origin for Liliales, with close
 relationships between three pairs of lineages (Corsiaceae/Campynemataceae,
 Philesiaceae/Ripogonaceae, tribes Alstroemerieae/Luzuriageae) in South
 America and Australia or New Zealand reflecting teleconnections of these
 areas via Antarctica. Long-distance dispersal (LDD) across the Pacific and
 Tasman Sea led to re-invasion of New Zealand by two lineages (Luzuriaga,
 Ripogonum); LDD allowed Campynemanthe to colonize New Caledonia after its
 submergence until 37 Mya. LDD permitted Colchicaceae to invade East Asia
 and Africa from Australia, and re-invade Africa from Australia. Periodic
 desert greening permitted Gloriosa and Iphigenia to colonize Southeast
 Asia overland from Africa, and Androcymbium–Colchicum to invade the
 Mediterranean from South Africa. Melanthiaceae and Liliaceae crossed the
 Bering land-bridge several times from the Miocene to the Pleistocene.
description: Alignments of 75
 chloroplast coding regions for 135 AngiospermsNexus file containing a
 concatenated alignment of 75 coding regions for 33 species of Liliales and
 other 102 Angiosperms.135_Angiosperm_75CDS.nexXML BEAST file for divergence times estimationXML file for divergence times estimation analysis with BEAST v1.8.0.Liliales_2Genes_angiosperm.xml
DOI: 10.5061/dryad.cp25h
title: Data from: Genetic variation and association mapping for 12 agronomic traits in indica rice

description: Background: Increasing rice (Oryza sativa L.) yield is a crucial challenge
 for modern agriculture. The ideal plant architecture is considered to be
 critical to enhance rice yield. Elite plant morphological traits should
 include compact plant type, short stature, few unproductive tillers, thick
 and sturdy stems and erect leaves. To reveal the genetic variations of
 important morphological traits, 523 germplasm accessions were genotyped
 using the Illumina custom-designed array containing 5,291 single
 nucleotide polymorphisms (SNPs) and phenotyped in two independent
 environments. Genome-wide association studies were performed to uncover
 the genotypic and phenotypic variations using a mixed linear model.
 Results: In total, 126 and 172 significant loci were identified and these
 loci explained an average of 34.45 % and 39.09 % of the phenotypic
 variance in two environments, respectively, and 16 of 298 (~5.37 %) loci
 were detected across the two environments. For the 16 loci, 423 candidate
 genes were predicted in a 200-kb region (±100 kb of the peak SNP).
 Expression-level analyses identified four candidate genes as the most
 promising regulators of tiller angle. Known (NAL1 and Rc) and new
 significant loci showed pleiotropy and gene linkage. In addition, a long
 genome region covering ~1.6 Mb on chromosome 11 was identified, which may
 be critical for rice leaf architecture because of a high association with
 flag leaf length and the ratio of flag leaf length and width. The pyramid
 effect of the elite alleles indicated that these significant loci could be
 beneficial for rice plant architecture improvements in the future.
 Finally, 37 elite varieties were chosen as breeding donors for further
 rice plant architectural modifications. Conclusions: This study detected
 multiple novel loci and candidate genes related to rice morphological
 traits, and the work demonstrated that genome-wide association studies are
 powerful strategies for uncovering the genetic variations of complex
 traits and identifying candidate genes in rice, even though the linkage
 disequilibrium decayed slowly in self-pollinating species. Future research
 will focus on the biological validation of the candidate genes, and elite
 varieties will also be of interest in genome selection and breeding by
 design.
description: Genotype
 data5291 SNPs of 523
 accessions
DOI: 10.5061/dryad.gh208
title: Data from: Izumo1 and Juno: the evolutionary origins and coevolution of essential sperm-egg binding partners

description: Reproductive proteins are among the most rapidly evolving classes of
 proteins. For a subset of these, rapid evolution is driven by positive
 Darwinian selection despite vital, well-conserved, reproductive functions.
 Izumo1 is the only essential sperm–egg fusion protein currently known on
 mammalian sperm, and its egg receptor (Juno; formerly Folr4) was recently
 discovered. Male knockout mice for Izumo1 and female knockout mice for
 Juno are both healthy but sterile. Here, both sperm–egg binding proteins
 are shown to be evolving under positive selection. Within mammals,
 coevolution of Izumo1 and Juno is also uncovered, suggesting that similar
 forces have shaped the evolutionary histories of these binding partners
 within Mammalia. Additionally, genomic analyses reveal an ancient origin
 for the Izumo gene family, initially reported as conserved exclusively in
 mammals. Newly identified Izumo1 orthologues could serve reproductive
 functions in birds, fish and reptiles. Surprisingly, these same analyses
 support Juno's presence in mammals alone, suggesting a recent
 mammalian-specific duplication and neofunctionalization of the ancestral
 folate receptor. Despite the indispensability of their reproductive
 interaction, and their apparent coevolution within Mammalia, this binding
 pair arose through strikingly different evolutionary forces.
description: RSOS_Grayson_2015Zip archive containing trees, alignments and supplementary figures.
DOI: 10.5061/dryad.hr0km
title: Data from: Diversity and evolution of the primate skin microbiome

description: Skin microbes play a role in human body odour, health and disease.
 Compared to gut microbes we know comparatively little about the changes in
 the composition of skin microbes in response to evolutionary changes in
 hosts, or more recent behavioral and cultural changes in humans. No
 studies have used sequence-based approaches to consider the skin microbe
 communities of gorillas and chimpanzees, for example. Comparison of the
 microbial associates of non-human primates with those of humans offers
 unique insights into both the ancient and modern features of our skin
 associated microbes. Here we describe the microbes found on the skin of
 humans, chimpanzees, gorillas, rhesus macaques and baboons. We focus on
 the bacterial and Archaeal residents in the axilla using high throughput
 sequencing of the 16S rRNA gene. We find that human skin microbial
 communities are unique relative to those of other primates, both in terms
 of their diversity and composition. These differences appear to reflect
 both ancient shifts during millions of years of primate evolution and more
 recent changes due to modern hygiene.
description: PrimateArmpitOTUsheetThis data file is the raw OTU chart of our primate armpit samples.PrimateArmpitL2This files contains operational taxonomic units at the phyla level (L2) from our primate armpit samples after rarefaction at 1,000 reads.PrimateArmpitL6This files contains operational taxonomic units at the genera level (L6) from our primate armpit samples after rarefaction at 1,000 reads.
DOI: 10.6084/m9.figshare.31151326
title: Phenotype data for the 300FG and 500FG cohorts

description: Differences of immune responses are observed between males and females, influenced by genetic, hormonal, and environmental factors. The sex-specific genetic effects on cytokine production however remain underexplored. This study aimed to identify sex-specific quantitative trait loci (QTLs) affecting cytokine production in response to diverse infectious antigens. We performed sex-stratified cytokine QTL (cQTLs) mapping in two population-based cohorts from Tanzania and the Netherlands. In the Tanzanian cohort, twelve genome-wide significant cytokine QTLs were identified, with seven observed in males and five in females. In the Dutch cohort, twelve genome-wide significant cQTLs were identified, with six cQTLs each in males and females. Colocalization analysis confirmed that all twelve genome-wide cQTLs from the Tanzanian cohort are sex-specific, while in the Dutch cohort ten genome-wide cQTL variants are modulated in a sex-specific manner. Furthermore, pathway and phenotype enrichment analyses linked the identified cQTL variants to relevant immune functions and sex-biased traits. Our study highlights the importance of sex-stratified genetic analyses when investigating the genetic basis of cytokine production in humans. We show that sex-specific cQTLs may underlie observed phenotypic differences between males and females and that accounting for such effects can inform the development of personalized medical treatments for sex-biased diseases.
DOI: 10.6084/m9.figshare.31151326.v1
title: Phenotype data for the 300FG and 500FG cohorts

description: Differences of immune responses are observed between males and females, influenced by genetic, hormonal, and environmental factors. The sex-specific genetic effects on cytokine production however remain underexplored. This study aimed to identify sex-specific quantitative trait loci (QTLs) affecting cytokine production in response to diverse infectious antigens. We performed sex-stratified cytokine QTL (cQTLs) mapping in two population-based cohorts from Tanzania and the Netherlands. In the Tanzanian cohort, twelve genome-wide significant cytokine QTLs were identified, with seven observed in males and five in females. In the Dutch cohort, twelve genome-wide significant cQTLs were identified, with six cQTLs each in males and females. Colocalization analysis confirmed that all twelve genome-wide cQTLs from the Tanzanian cohort are sex-specific, while in the Dutch cohort ten genome-wide cQTL variants are modulated in a sex-specific manner. Furthermore, pathway and phenotype enrichment analyses linked the identified cQTL variants to relevant immune functions and sex-biased traits. Our study highlights the importance of sex-stratified genetic analyses when investigating the genetic basis of cytokine production in humans. We show that sex-specific cQTLs may underlie observed phenotypic differences between males and females and that accounting for such effects can inform the development of personalized medical treatments for sex-biased diseases.
DOI: 10.34894/lryytv
title: Jedidiah Morse, The American Gazetteer (Boston 1797) [ALTO word format]

description: This dataset contains the digitalised text of Jedidiah Morse's &lt;em&gt;The American Gazetteer&lt;/em&gt; (Boston 1797). The text was digitalised using scans provided by the John Adams Library at the Boston Public Library (&lt;a href="https://archive.org/details/americangazettee00mors" target="_blank"&gt;Internet Archive&lt;/a&gt;) and the HTR software &lt;a href="http://www.transkribus.eu/" target="_blank"&gt;Transkribus&lt;/a&gt;.&lt;br&gt;&lt;br&gt;
This dataset contains the files in ALTO (word) format.
DOI: 10.5061/dryad.pn85t
title: Data from: Evolution of stickleback in 50 years on earthquake-uplifted islands

description: How rapidly can animal populations in the wild evolve when faced with
 sudden environmental shifts? Uplift during the 1964 Great Alaska
 Earthquake abruptly created freshwater ponds on multiple islands in Prince
 William Sound and the Gulf of Alaska. In the short time since the
 earthquake, the phenotypes of resident freshwater threespine stickleback
 fish on at least three of these islands have changed dramatically from
 their oceanic ancestors. To test the hypothesis that these freshwater
 populations were derived from oceanic ancestors only 50 y ago, we
 generated over 130,000 single-nucleotide polymorphism genotypes from more
 than 1,000 individuals using restriction site-associated DNA sequencing
 (RAD-seq). Population genomic analyses of these data support the
 hypothesis of recent and repeated, independent colonization of freshwater
 habitats by oceanic ancestors. We find evidence of recurrent gene flow
 between oceanic and freshwater ecotypes where they co-occur. Our data
 implicate natural selection in phenotypic diversification and support the
 hypothesis that the metapopulation organization of this species helps
 maintain a large pool of genetic variation that can be redeployed rapidly
 when oceanic stickleback colonize freshwater environments. We find that
 the freshwater populations, despite population genetic analyses clearly
 supporting their young age, have diverged phenotypically from oceanic
 ancestors to nearly the same extent as populations that were likely
 founded thousands of years ago. Our results support the intriguing
 hypothesis that most stickleback evolution in fresh water occurs within
 the first few decades after invasion of a novel environment.
description: batch_1.structure_1000-rep1Subset of 1000 loci for individuals from 21 populations formatted for Structure.batch_1.structure_1000-rep2Subset of 1000 loci for individuals from 21 populations formatted for Structure.batch_1.structure_1000-rep3Subset of 1000 loci for individuals from 21 populations formatted for Structure.
DOI: 10.57841/casdc.0007101
title: 实现千米级Bi2212长线制备