cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9qt14
title: Data from: Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern

description: The North America deserts were impacted by both Neogene plate tectonics
 and Quaternary climatic fluctuations, yet it remains unclear how these
 events influenced speciation in this region. We tested published
 hypotheses regarding the timing and mode of speciation, population
 structure, and demographic history of the Mojave Fringe-toed Lizard (Uma
 scoparia), a sand dune specialist endemic to the Mojave Desert of
 California and Arizona. We sampled 109 individual lizards representing 22
 insular dune localities, obtained DNA sequences for 14 nuclear loci, and
 found that U. scoparia has low genetic diversity relative to the U. notata
 species complex, comparable to that of chimpanzees and southern elephant
 seals. Analyses of genotypes using Bayesian clustering algorithms did not
 identify discrete populations within U. scoparia. Using
 Isolation-with-Migration (IM) models and a novel coalescent-based
 hypothesis testing approach, we estimated that U. scoparia diverged from
 U. notata in the Pleistocene epoch. The Likelihood Ratio Test and the
 Akaike Information Criterion consistently rejected nested speciation
 models that included parameters for migration and population growth of U.
 scoparia. We reject the Neogene vicariance hypothesis for the speciation
 of U. scoparia, and define this species as a single evolutionarily
 significant unit for conservation purposes.
description: DNA Sequence
 DataDiploid nuclear DNA
 sequence data in fasta format.Sequences.zipPHASEInput and output files for PHASE v2.1.RAxMLInput, output, and gene tree files from RAxML v7.3.0.MrBayesInput, output, and gene tree files from MrBayes v3.2.2.StructuramaInput and output files for Structurama v2.0.GenelandInput files and R script for Geneland v4.0.3.IM and IMaInput and output files for IM and IMa.IM.zipCoalescent SimulationsTree files simulated with Mesquite v2.75 and chi-square test.CoalescentSimulations.zipBEASTInput and output from the Extended Bayesian Skyline Plot implemented in BEAST v1.7.5.
DOI: 10.5061/dryad.vh0h80g
title: Data from: A genomic reference panel for Drosophila serrata

description: Here we describe a collection of re-sequenced inbred lines of Drosophila
 serrata, sampled from a natural population situated deep within the
 species endemic distribution in Brisbane, Australia. D. serrata is a
 member of the speciose montium group whose members inhabit much of south
 east Asia and has been well studied for aspects of climatic adaptation,
 sexual selection, sexual dimorphism, and mate recognition. We sequenced
 110 lines that were inbred via 17-20 generations of full-sib mating at an
 average coverage of 23.5x with paired-end Illumina reads. 15,228,692
 biallelic SNPs passed quality control after being called using the Joint
 Genotyper for Inbred Lines (JGIL). Inbreeding was highly effective and the
 average levels of residual heterozygosity (0.86%) were well below
 theoretical expectations. As expected, linkage disequilibrium decayed
 rapidly, with r2 dropping below 0.1 within 100 base pairs. With the
 exception of four closely related pairs of lines which may have been due
 to technical errors, there was no statistical support for population
 substructure. Consistent with other endemic populations of other
 Drosophila species, preliminary population genetic analyses revealed high
 nucleotide diversity and, on average, negative Tajima’s D values. A
 preliminary GWAS was performed on a cuticular hydrocarbon trait, 2-MeC28
 revealing 4 SNPs passing Bonferroni significance residing in or near
 genes. One gene Cht9 may be involved in the transport of CHCs from the
 site of production (oenocytes) to the cuticle. Our panel will facilitate
 broader population genomic and quantitative genetic studies of this
 species and serve as an important complement to existing D. melanogaster
 panels that can be used to test for the conservation of genetic
 architectures across the Drosophila genus.
description: dsgrp_snps_for_gwas.txtCompressed SNP file for DsGRP lines
DOI: 10.5061/dryad.1kc982n5
title: Data from: Variation in the level of aggression, chemical and genetic distance among three supercolonies of the Argentine ant in Europe

description: In their invasive ranges, Argentine ant populations often form one
 geographically vast supercolony, genetically and chemically uniform within
 which there is no intraspecific aggression. Here we present regional
 patterns of intraspecific aggression, cuticular hydrocarbons and
 population genetics of 18 nesting-sites across Corsica and the French
 mainland. Aggression tests confirm the presence of a third European
 supercolony, the Corsican supercolony, which exhibits moderate to high
 levels of aggression, depending on nesting-sites, with the Main
 supercolony, and invariably high levels of aggression with the Catalonian
 supercolony. The chemical analyses corroborated the behavioral data, with
 workers of the Corsican supercolony showing moderate differences in
 cuticular hydrocarbons compared to workers of the European Main
 supercolony and strong differences compared to workers of the Catalonian
 supercolony. Interestingly, there were also clear genetic differences
 between workers of the Catalonian supercolony and the two other
 supercolonies at both nuclear and mitochondrial markers, but only very
 weak genetic differentiation between nesting-sites of the Corsican and
 Main supercolonies (FST = 0.06). A detailed comparison of the genetic
 composition of supercolonies also revealed that, if one of the last two
 supercolonies derived from the other, it is the Main supercolony that
 derived from the Corsican supercolony rather than the reverse. Overall,
 these findings highlight the importance of conducting more qualitative and
 quantitative analyses of the level of aggression between supercolonies,
 which has to be correlated with genetic and chemical data.
description: Confrontation_between_the_Catalonian_and_Corsican_supercoloniesConfrontation_between_the_Main_and_Corsican_supercoloniesConfrontation_within_the Corsican_supercolonyHAPLOTYPESVariation_in_the_level_of aggression_data_ver3Microsatellites, CHC and behavioral data
DOI: 10.5061/dryad.kg26j
title: Data from: Predicting rice hybrid performance using univariate and multivariate GBLUP models based on North Carolina mating design II

description: Genomic selection (GS) is more efficient than traditional phenotype-based
 methods in hybrid breeding. The present study investigated the predictive
 ability of genomic best linear unbiased prediction models for rice hybrids
 based on the North Carolina mating design II, in which a total of 115
 inbred rice lines were crossed with 5 male sterile lines. Using 8 traits
 of the 575 (115 × 5) hybrids from two environments, both univariate (UV)
 and multivariate (MV) prediction analyses, including additive and
 dominance effects, were performed. Using UV models, the prediction results
 of cross-validation indicated that including dominance effects could
 improve the predictive ability for some traits in rice hybrids.
 Additionally, we could take advantage of GS even for a low-heritability
 trait, such as grain yield per plant (GY), because a modest increase in
 the number of top selection could generate a higher, more stable mean
 phenotypic value for rice hybrids. Thus this strategy was used to select
 superior potential crosses between the 115 inbred lines and those between
 the 5 male sterile lines and other genotyped varieties. In our MV
 research, an MV model (MV-ADV) was developed utilizing a MV relationship
 matrix constructed with auxiliary variates. Based on joint analysis with
 multi-trait (MT) or with multi-environment, the prediction results
 confirmed the superiority of MV-ADV over an UV model, particularly in the
 MT scenario for a low-heritability target trait (such as GY), with highly
 correlated auxiliary traits. For a high-heritability trait (such as
 thousand-grain weight), MT prediction is unnecessary, and UV prediction is
 sufficient.
description: Phenotype
 dataEight traits of all the
 hybrids and their inbred parentsSNP
 dataSNP data of 120 rice
 inbred lines
DOI: 10.5061/dryad.4271s
title: Data from: Short distance migrants travel as far as long distance migrants in lesser black-backed gulls Larus fuscus

description: Migration strategies differ greatly among and within avian populations.
 The associated trade-offs and fitness consequences of diverse strategies
 and how they persist are pertinent questions in migration research.
 Migration is a costly endeavour, presumably compensated for by better
 survival conditions in the non-breeding area. One way to assess the cost
 of alternative strategies is to investigate the investment in movement
 across the entire annual cycle, an assessment made increasingly feasible
 with improvements in tracking technology. Our study focuses on lesser
 black-backed gulls, generalist seabirds that exploit a broad range of
 resources, exhibit diverse migration strategies and have potentially
 altered migration strategies in response to human activities and climate
 change. We used GPS tracking to quantify lesser black-backed gulls’
 movement throughout their annual cycle and compare trade-offs among four
 migration strategies. The annual cumulative distance travelled by long
 distance migrants wintering in west Africa, over 4000 km from their
 breeding colony, did not differ significantly from individuals of the same
 breeding colony wintering only a few hundred kilometres away in Great
 Britain. Short distance migrants returned to the colony first, and long
 distance migrants returned last. Sex and wing length were not correlated
 with maximum range, cumulative distance travelled or timing. Individuals
 spent only a small proportion of their time in flight and spent on average
 17% of their time at sea throughout an annual cycle, suggesting a reliance
 on inland resources for many individuals. Analysing movement throughout
 the annual cycle can change our perspective and understanding of
 consequences of different migration strategies. Our study shows that a
 range of migration strategies coexists and we propose that the long term
 costs and benefits of these strategies balance out. Diversity in migration
 strategies may contribute to the resilience of this species in the face of
 ongoing anthropogenic impact on the environment.
description: Shamoun-Baranes et al.
 (2016)This file includes the
 longitude and latitude data for each of the gulls included in our
 analyses, re-sampled at a 20 minute interval. Individuals are identified
 using a unique three digit code (BirdID) and bird-year subsets are each
 assigned a separate identifier (Subset). In addition to the coordinate
 data, cumulative distance travelled (CumulativeDistance) and distance from
 the colony (ColonyDistance) are also provided for each
 subset.
DOI: 10.5061/dryad.8f1bt
title: Data from: HDAC1/2-dependent P0 expression maintains paranodal and nodal integrity independently of myelin stability through interactions with neurofascins

description: The pathogenesis of peripheral neuropathies in adults is linked to
 maintenance mechanisms that are not well understood. Here, we elucidate a
 novel critical maintenance mechanism for Schwann cell (SC)–axon
 interaction. Using mouse genetics, ablation of the transcriptional
 regulators histone deacetylases 1 and 2 (HDAC1/2) in adult SCs severely
 affected paranodal and nodal integrity and led to
 demyelination/remyelination. Expression levels of the HDAC1/2 target gene
 myelin protein zero (P0) were reduced by half, accompanied by altered
 localization and stability of neurofascin (NFasc)155, NFasc186, and loss
 of Caspr and septate-like junctions. We identify P0 as a novel binding
 partner of NFasc155 and NFasc186, both in vivo and by in vitro adhesion
 assay. Furthermore, we demonstrate that HDAC1/2-dependent P0 expression is
 crucial for the maintenance of paranodal/nodal integrity and axonal
 function through interaction of P0 with neurofascins. In addition, we show
 that the latter mechanism is impaired by some P0 mutations that lead to
 late onset Charcot-Marie-Tooth disease.
description: Underlying data main and
 supplementary figures2 Excel files with
 underlying data of Figs. 1CEFGH, 2AD, 3AGH, 4AB, 5BEGI, 6F, 7F, 9BE,
 S1ABC, S2BCD, S3ABCDE, S5, S6A, S7BC, S17BE, S18, and 2 video for Fig
 1DDryad.zip
DOI: 10.5061/dryad.q6f6qd7
title: Data from: Pseudo-parallel patterns of disjunctions in an Arctic-alpine plant lineage

description: Disjunct distributions have intrigued biologists for centuries.
 Investigating these biogeographic patterns provides insight into
 speciation and biodiversity at multiple spatial and phylogenetic scales.
 Some disjunctions have been intensively studied, yet others have been
 largely overlooked and remain poorly understood. Among the lesser-known
 disjunction patterns is that between the mountain ranges of western North
 America. Flora and fauna endemic to the mountains of this region provide
 important systems for investigating causes and results of disjunctions,
 given the relatively recent geological formation of this area and the
 intense climatic fluctuations that have occurred since its formation. In
 Micranthes (Saxifragaceae), which has high rates of montane endemism, two
 species, M. bryophora and M. tolmiei, show this biogeographical pattern.
 By reconstructing a time-calibrated phylogeny based on 518 low-copy
 nuclear markers and including multiple populations of each species from
 the Coast Ranges, Cascades, Sierra Nevada, and Rocky Mountains, this study
 provides a biogeographical and temporal framework for the evolution of
 Micranthes in western North America. Strongly supported east-west
 differentiated clades are recovered for M. bryophora and M. tolmiei in
 both maximum likelihood and coalescent-based species tree reconstructions.
 Biogeographic analysis suggests different patterns of dispersal for both
 taxa and the dating analyses recovered contrasting ages for each clade.
 Due to both the different geographic patterns and the timing of the
 initial diversification of each taxon corresponding to different geologic
 and climatic events, the disjunction patterns shown for these taxa are
 suggested to be an example of biogeographical pseudocongruence.
description: Nuclear_alignments_518genesConcatenated alignment (.phy format) of 518 orthologous nuclear genes.Plastid_alignmentAlignment of plastid sequencesRAxML_bestTrees_genetreesSingle .fasta file containing all 518 nuclear gene trees inferred using RAxML.
DOI: 10.5061/dryad.bc80r
title: Data from: Evolution of floral diversity: genomics, genes and gamma

description: A salient feature of flowering plant diversification is the emergence of a
 novel suite of floral features coinciding with the origin of the most
 species-rich lineage, Pentapetalae. Advances in phylogenetics,
 developmental genetics and genomics, including new analyses presented
 here, are helping to reconstruct the specific evolutionary steps involved
 in the evolution of this clade. The enormous floral diversity among
 Pentapetalae appears to be built on a highly conserved ground plan of
 five-parted (pentamerous) flowers with whorled phyllotaxis. By contrast,
 lability in the number and arrangement of component parts of the flower
 characterize the early-diverging eudicot lineages subtending Pentapetalae.
 The diversification of Pentapetalae also coincides closely with ancient
 hexaploidy, referred to as the gamma whole-genome triplication, for which
 the phylogenetic timing, mechanistic details and molecular evolutionary
 consequences are as yet not fully resolved. Transcription factors
 regulating floral development often persist in duplicate or triplicate in
 gamma-derived genomes, and both individual genes and whole transcriptional
 programmes exhibit a shift from broadly overlapping to tightly defined
 expression domains in Pentapetalae flowers. Investigations of these
 changes associated with the origin of Pentapetalae can lead to a more
 comprehensive understanding of what is arguably one of the most important
 evolutionary diversification events within terrestrial plants.
description: Chanderbali et
 al_Gamma_DataGenes_Genomes_Gamma.tar
DOI: 10.5061/dryad.v12f25n
title: Data from: Evaluating internal model strength and performance of myoelectric prosthesis control strategies

description: Ongoing developments in myoelectric prosthesis control have provided
 prosthesis users with an assortment of control strategies that vary in
 reliability and performance. Many studies have focused on improving
 performance by providing feedback to the user, but have overlooked the
 effect of this feedback on internal model development, which is key to
 improving long-term performance. In this work, the strength of internal
 models developed for two commonly used myoelectric control strategies: raw
 control with raw feedback (using a regression-based approach), and
 filtered control with filtered feedback (using a classifier-based
 approach), were evaluated using two psychometric measures: trial-by-trial
 adaptation and just-noticeable-difference. The performance of both
 strategies was also evaluated using a Schmidt’s style target acquisition
 task. Results obtained from 24 able-bodied subjects showed that although
 filtered control with filtered feedback had better short-term performance
 in path efficiency (p &lt; 0.05), raw control with raw feedback
 resulted in stronger internal model development (p &lt; 0.05), which
 may lead to better long-term performance. Despite inherent noise in the
 control signals of the regression controller, these findings suggest that
 rich feedback associated with regression control may be used to improve
 human understanding of the myoelectric control system.
description: Psychophysics and
 performance tests for 24 able-bodied subjectsA Matlab structure
 holding data from 24 able-bodied subjects testing two commonly used
 myoelectric prosthesis control strategies.Subjects.mat
DOI: 10.5061/dryad.g3vm8
title: Data from: Demography and selection shape transcriptomic divergence in field crickets

description: Gene flow, demography, and selection can result in similar patterns of
 genomic variation and disentangling their effects is key to understanding
 speciation. Here, we assess transcriptomic variation to unravel the
 evolutionary history of Gryllus rubens and G. texensis, cryptic field
 cricket species with highly divergent mating behavior. We infer their
 demographic history and screen their transcriptomes for footprints of
 selection in the context of the inferred demography. We find strong
 support for a long history of bidirectional gene flow, which ceased during
 the late Pleistocene, and a bottleneck in G. rubens consistent with a
 peripatric origin of this species. Importantly, comparing the observed FST
 distribution with distributions from coalescent simulations under various
 demographic scenarios indicates that gene flow (without selection)
 strongly shaped patterns of genetic divergence. Genetic divergence at FST
 outlier loci could thus falsely be attributed to selection when not
 accounting for demographic history. We uncovered a subset of loci with
 signatures of selection, many of which are candidates for controlling
 variation in mating behavior. Our results underscore the importance of
 gene flow and demography in overall levels of genetic divergence and
 highlight that simultaneously examining demography and selection
 facilitates a more complete understanding of genetic divergence during
 speciation.
description: 17-0611.R1 data
 filesdata corresponding to:
 "Demography and selection shape transcriptomic divergence in field
 crickets". See readme for list and description of
 files.17-0611R1_Data.rar
DOI: 10.5061/dryad.7g1tb
title: Data from: Preservation of uropygial gland lipids in a 48-million-year-old bird

description: Although various kinds of organic molecules are known to occur in fossils
 and rocks, most soft tissue preservation in animals is attributed to
 melanin or porphyrins. Lipids are particularly stable over time—as
 diagenetically altered ‘geolipids’ or as major molecular constituents of
 kerogen or fossil ‘geopolymers’—and may be expected to be preserved in
 certain vertebrate tissues. Here we analysed lipid residues from the
 uropygial gland of an early Eocene bird using pyrolysis gas chromatography
 mass spectroscopy. We found a pattern of aliphatic molecules in the fossil
 gland that was distinct from the host oil shale sediment matrix and from
 feathers of the same fossil. The fossil gland contained abundant
 n-alkenes, n-alkanes and alkylbenzenes with chain lengths greater than 20,
 as well as functionalized long-chain aldehydes, ketones, alkylnitriles and
 alkylthiophenes that were not detected in host sediment or fossil
 feathers. By comparison with modern bird uropygial gland wax esters, we
 show that these molecular fossils are likely derived from endogenous wax
 ester fatty alcohols and fatty acids that survived initial decay and
 underwent early diagenetic geopolymerization. These data demonstrate the
 high fidelity preservation of the uropygial gland waxes and showcase the
 resilience of lipids over geologic time and their potential role in the
 exceptional preservation of lipid-rich tissues of macrofossils.
description: Mass spectrometry data
 filesPyrolysis GC-MS and
 GC-MS wax ester analysis raw datafiles for fossils and modern gland
 specimensOReilly et al
 data.zip
DOI: 10.5061/dryad.4fq355k
title: Data from: Impact of local forest composition on soil fungal communities in a mixed boreal forest

description: [No abstract entered]
description: sequencesfungal ITS sequencesSoil chemical analysesSoil chemical analysessoilchar.csvfunguild resultsfunguild.csvdescription of samplescarsample.csvR codeR_code