cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.apf89t
title: Occurrence Download

description: A dataset containing 6658 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-101.3031 19.44734, -101.1508 19.44823, -101.1522 19.56503, -101.3041 19.56257, -101.3031 19.44734))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6658 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000558-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.17rh3
title: Data from: Tournament ABC analysis of the western palaearctic population history of an oak gallwasp, Synergus umbraculus

description: Approximate Bayesian computation (ABC) is a powerful and widely used
 approach in inference of population history. However, the computational
 effort required to discriminate among alternative historical scenarios
 often limits the set that is compared to those considered more likely a
 priori. While often justifiable, this approach will fail to consider
 unexpected but well-supported population histories. We used a hierarchical
 tournament approach, in which subsets of scenarios are compared in a first
 round of ABC analyses and the winners are compared in a second analysis,
 to reconstruct the population history of an oak gallwasp, Synergus
 umbraculus (Hymenoptera, Cynipidae) across the Western Palaearctic. We
 used 4233 bp of sequence data across 7 loci to explore the relationships
 between four putative Pleistocene refuge populations in Iberia, Italy, the
 Balkans, and Western Asia. We compared support for 148 alternative
 scenarios in eight pools, each pool comprising all possible rearrangements
 of four populations over a given topology of relationships, with or
 without founding of one population by admixture and with or without an
 unsampled ‘ghost’ population. We found very little support for the
 directional ‘out of the east’ scenario previously inferred for other
 gallwasp community members. Instead, the best-supported models identified
 Iberia as the first regional population to diverge from the others in the
 late Pleistocene, followed by divergence between the Balkans and Western
 Asia, and founding of the Italian population through late Pleistocene
 admixture from Iberia and the Balkans. We compare these results with what
 is known for other members of the oak gall community, and consider the
 strengths and weaknesses of using a tournament approach to explore
 phylogeographic model space.
description: DIYABC sequence datafile
 for Synergus umbraculusSequence data for seven
 loci for Synergus umbraculus populations from four putative refugial
 populations, in a format allowing analysis in DIYABC v1.0.4.46beta
 24 pops
 combeast.txt
DOI: 10.5061/dryad.7c550
title: Data from: Vicariance, long-distance dispersal, and regional extinction–recolonization dynamics explain the disjunct circumpolar distribution of the arctic-alpine plant Silene acaulis

description: PREMISE OF THE STUDY: Many arctic-alpine species have vast geographic
 ranges, but these may encompass substantial gaps whose origins are poorly
 understood. Here we address the phylogeographic history of Silene acaulis,
 a perennial cushion plant with a circumpolar distribution except for a
 large gap in Siberia. METHODS: We assessed genetic variation in a
 range-wide sample of 103 populations using plastid DNA (pDNA) sequences
 and AFLPs (amplified fragment length polymorphisms). We constructed a
 haplotype network and performed Bayesian phylogenetic analyses based on
 plastid sequences. We visualized AFLP patterns using principal coordinate
 analysis, identified genetic groups using the program structure, and
 estimated genetic diversity and rarity indices by geographic region. KEY
 RESULTS: The history of the main pDNA lineages was estimated to span
 several glaciations. AFLP data revealed a distinct division between
 Beringia/North America and Europe/East Greenland. These two regions shared
 only one of 17 pDNA haplotypes. Populations on opposite sides of the
 Siberian range gap (Ural Mountains and Chukotka) were genetically distinct
 and appear to have resulted from postglacial leading-edge colonizations.
 We inferred two refugia in North America (Beringia and the southern Rocky
 Mountains) and two in Europe (central-southern Europe and northern
 Europe/East Greenland). Patterns in the East Atlantic region suggested
 transoceanic long-distance dispersal events. CONCLUSIONS: Silene acaulis
 has a highly dynamic history characterized by vicariance, regional
 extinction, and recolonization, with persistence in at least four refugia.
 Long-distance dispersal explains patterns across the Atlantic Ocean, but
 we found no evidence of dispersal across the Siberian range gap.
description: sa_AFLP_458ind_335charAFLP data matrix (0;1). See description in the readMe file.sa_pDNA_107ind_3190charpDNA sequence file in nexus format. See description in ReadMe file.
DOI: 10.15468/dl.4su3d3
title: Occurrence Download

description: A dataset containing 6658 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-101.3031 19.44734, -101.1508 19.44823, -101.1522 19.56503, -101.3041 19.56257, -101.3031 19.44734))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6658 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000559-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.85c0s
title: Data from: Using genomic location and coalescent simulation to investigate gene tree discordance in Medicago L.

description: Several well-documented evolutionary processes are known to cause conflict
 between species-level phylogenies and gene-level phylogenies. Three of the
 most challenging processes for species tree inference are incomplete
 lineage sorting, hybridization and gene duplication, which may result in
 unwarranted comparisons of paralogous genes. Several existing methods have
 dealt with these processes but none has yet been able to untangle all
 three at once. Here, we propose a stepwise method by which these processes
 can be discerned using information on genomic location coupled with
 coalescent simulations. In the first step, highly discordant genes within
 genomic blocks (putative paralogs) are identified and excluded from the
 data set and, in the second step, blocks of linked genes are grouped
 according to their hybrid history. Existing multispecies coalescent
 software can then be applied to recover the principal tree(s) that make up
 the species tree/network without violating the underlying model. The
 potential of the approach is evaluated on simulated data derived from a
 species network composed of nine species, of which one is of hybrid
 origin, and displaying a single-gene duplication that leads to paralogous
 comparisons. We apply our method to an empirical set of 12 genes from 7
 species sampled in the plant genus Medicago that display phylogenetic
 discordance. We identify the causes of the discordance and demonstrate
 that the Medicago orbicularis lineage experienced an episode of ancient
 hybridization. Our results show promise as a new way to explore
 phylogenetic sequence data that can significantly improve species tree
 inference in presence of hybridization and undetected paralogy or other
 causes leading to extremely discordant gene trees.
description: Supp_Fig_1supplementary figure 1Supp_Fig_2supplementary figure 2Supp_Fig_3supplementary figure 3Supp_Fig_4supplementary figure 4Supp_Fig_5supplementary figure 5Supp_Fig_6supplementary figure 6Supp_Fig_7supplementary figure 7Supp_Table_1supplementary table 1Supplementary_figure_legendssupplementary figure legendsNexus_filesNexus files of 12 gene alignments
DOI: 10.5061/dryad.vj7nr
title: Data from: Molecular evolution accompanying functional divergence of duplicated genes along the plant starch biosynthesis pathway

description: Background: Starch is the main source of carbon storage in the
 Archaeplastida. The Starch Biosynthesis Pathway (SBP) emerged from
 cytosolic glycogen metabolism shortly after plastid endosymbiosis and was
 redirected to the plastid stroma during the green lineage divergence. The
 SBP is a complex network of genes, most of which are members of large
 multigene families. While some gene duplications occurred in the
 Archaeplastida ancestor, most were generated during the SBP redirection
 process, and the remaining few paralogs were generated through
 compartmentalization or tissue specialization during the evolution of the
 land plants. In the present study, we tested models of duplicated gene
 evolution in order to understand the evolutionary forces that have led to
 the development of SBP in angiosperms. We combined phylogenetic analyses
 and tests on the rates of evolution along branches emerging from major
 duplication events in six gene families encoding SBP enzymes. Results: We
 found evidence of positive selection along branches following cytosolic or
 plastidial specialization in two starch phosphorylases and identified
 numerous residues that exhibited changes in volume, polarity or charge.
 Starch synthases, branching and debranching enzymes functional
 specializations were also accompanied by accelerated evolution. However,
 none of the sites targeted by selection corresponded to known functional
 domains, catalytic or regulatory. Interestingly, among the 13 duplications
 tested, 7 exhibited evidence of positive selection in both branches
 emerging from the duplication, 2 in only one branch, and 4 in none of the
 branches. Conclusions: The majority of duplications were followed by
 accelerated evolution targeting specific residues along both branches.
 This pattern was consistent with the optimization of the two sub-functions
 originally fulfilled by the ancestral gene before duplication. Our results
 thereby provide strong support to the so-called “Escape from Adaptive
 Conflict” (EAC) model. Because none of the residues targeted by selection
 occurred in characterized functional domains, we propose that enzyme
 specialization has occurred through subtle changes in affinity, activity
 or interaction with other enzymes in complex formation, while the basic
 function defined by the catalytic domain has been maintained.
description: AGT_AlignmentDBE_AlignmentGBSS&SS_AlignmentPGM_AlignmentPHO_AlignmentSBE_AlignmentAGT_TreeDBE_TreeGBSS&SS_TreePGM_TreePHO_TreeSBE_Tree
DOI: 10.5061/dryad.fk2rm
title: Data from: Grazing effects on surface energy fluxes in a desert steppe on the Mongolian Plateau

description: Quantifying the surface energy fluxes of grazed and ungrazed steppes is
 essential to understand the roles of grasslands in local and global
 climate and in land use change. We used paired eddy-covariance towers to
 investigate the effects of grazing on energy balance (EB) components: net
 radiation (Rn), latent heat (LE), sensible heat (H), and soil heat (G)
 fluxes on adjacent grazed and ungrazed areas in a desert steppe of the
 Mongolian Plateau for a two-year period (2010-2012). Near 95% of Rn was
 partitioned as LE and H, whereas the contributions of G and other
 components of the EB were 5% at an annual scale. H dominated the energy
 partitioning and shared ~50% of Rn. When comparing the grazed and the
 ungrazed desert steppe, there was remarkably lower Rn and a lower H, but
 higher G at the grazed site than at the ungrazed site. Both reduced
 available energy (Rn˗G) and H through grazing indicated a “cooling effect”
 feedback onto the local climate. Grazing reduced the dry year LE but
 enhanced the wet year LE. Energy partitioning of LE/Rn was positively
 correlated with the canopy conductivity, leaf area index, and soil
 moisture. H/Rn was positively correlated with the vapor pressure deficit
 but negatively correlated with the soil moisture. Boosted regression tree
 results showed that LE/Rn was dominated by soil moisture in both years and
 at both sites, while grazing shifted the H/Rn domination from temperature
 to soil moisture in the wet year. Grazing not only caused a LE shift
 between the dry and the wet year, but also triggered a decrease in the
 H/Rn because of changes in vegetation and soil properties, indicating that
 the ungrazed area had a greater resistance while the grazed area had a
 greater sensitivity of EB components to the changing climate.
description: Fig1_dataFig1_dataFig2_dataFig2_dataFig3_dataFig3_dataFig4_dataFig4_dataFig5_dataFig5_dataFig6_dataFig6_dataFig7_dataFig7_dataFig8_dataFig8_dataFig9_dataFig9_data
DOI: 10.5061/dryad.0d7t0
title: Data from: Regional-scale spatial heterogeneity in the Late Paleocene paratropical forests of the U.S. Gulf Coast

description: The study of spatial patterns in biotic compositional variability in deep
 time is key to understanding the macroecological response of species
 assemblages to global change. Globally warm climatic phases are marked by
 the expansion of megathermal climates into currently extra-tropical areas.
 However, there is currently little information on whether vegetation in
 these ‘paratropical’ regions resembled spatially modern tropical or
 extra-tropical biomes. In this paper we explore spatial heterogeneity in
 extra-tropical megathermal vegetation, using sporomorph (pollen and spore)
 data from the Late Paleocene Calvert Bluff and Tuscahoma formations of the
 formerly paratropical US Gulf Coast (Texas, Mississippi and Alabama). The
 dataset comprises 139 sporomorph taxa recorded from 56 samples. Additive
 diversity partitioning, non-metric multidimensional scaling, and cluster
 analysis show compositional heterogeneity both spatially and
 lithologically within the US Gulf Coastal Plain (GCP) microflora. We then
 use sporomorph data from Holocene lake cores to compare spatial patterns
 in the Late Paleocene GCP to modern tropical and extra-tropical biomes.
 Distance decay analysis of the Holocene data reveals a higher rate of
 spatial turnover in tropical versus extra-tropical vegetation types,
 consistent with a latitudinal gradient in floral compositional
 heterogeneity. The specific combination of rate and scale dependency of
 distance decay in the Holocene assemblages prevented us from associating
 the Late Paleocene GCP with any particular modern biome. Our results
 demonstrate the importance of spatial scale, taphonomy and lithology in
 determining patterns of spatial heterogeneity, and show the potential of
 the fossil sporomorph record for studying spatial patterns and processes
 in deep time.
description: Supp_Table_1Community matrix of US Gulf Coast pollen and spore data. Rows are samples, columns are taxa, data are given as taxon counts. The data are derived from sampled outcrops and sediment cores. The file was created in MS Excel 2008.Supp_Figure_1Large scale version of Text-Figure 7, with sample and taxon names included. Figure shows two-way cluster analysis plot of US Gulf Coast pollen and spore data.Supp_Tab2Fig2Details of Holocene pollen data used in the analysis. Supplement Table 2 gives location, age and citation details for the Holocene lake cores used. Supplement Figure 2 shows the locations of the core sites on maps of North and South America. All data are from the literature, and most was downloaded from the Neotoma database (http://www.neotomadb.org/).Supp_File_RcodeAnnotated R code used to analyse data.
DOI: 10.5061/dryad.0t2d1
title: Data from: Hybridization and adaptation to introduced balloon vines in an Australian soapberry bug

description: Contemporary adaptation of plant feeding insects to introduced hosts
 provides clear cases of ecologically based population divergence. In most
 cases the mechanisms permitting rapid differentiation are not well known.
 Here we study morphological and genetic variation associated with recent
 shifts by the Australian soapberry bug Leptocoris tagalicus onto two
 naturalized Neotropical balloon vines, Cardiospermum halicacabum and C.
 grandiflorum that differ in time since introduction. Our results show that
 these vines have much larger fruits than the native hosts (Whitewood tree
 –Atalaya hemiglauca– and Woolly Rambutan –Alectryon tomentosus–) and that
 bugs living on them have evolved significantly longer beaks and new
 allometries. Genetic analyses of mitochondrial haplotypes and amplified
 fragment length polymorphic (AFLP) markers indicate that the lineage of
 bugs on the annual vine C. halicacabum, the older introduction, is
 intermediate between the two subspecies of L. tagalicus found on native
 hosts. Moreover, where the annual vine and Whitewood tree co-occur
 together, the morphology and genomic composition of the bugs are similar
 to those occurring in allopatry. These results show that hybridization
 provided the genetic elements underlying the strongly differentiated
 ‘Halicacabum bugs’. In contrast, the bugs feeding on the recently
 introduced perennial balloon vine (C. grandiflorum) showed no evidence of
 admixture, and are genetically indistinguishable from the nearby
 populations on a native host.
description: AFLP_dataDNA_sequencesAtalaya_ENMGrandiflorum_ENMHalicacabum_ENMTomentosus_ENMBug_morphologyHost_morphologyHost_dataHostfruit_sizedata.txtmorphological datamorphodata_allhosts_RR-codesRcodes
DOI: 10.5061/dryad.b32jm
title: Data from: Do singles or couples live healthier lifestyles? trends in Queensland between 2005-2014

description: Objectives: To compare the frequency of and trends in healthy lifestyle
 factors between singles and couples. Methods: Cross-sectional data from
 annual surveys conducted from 2005-2014 were used. The pooled sample
 included 15,001 Australian adults (mean age: 52.9 years, 50% male, 74%
 couples) who participated in the annual Queensland Social Survey via
 computer-assisted telephone interviews. Relationship status was
 dichotomised into single and couple. Binary logistic regression was used
 to assess associations between relationship status, and the frequency of
 and trends in healthy lifestyle factors. Results: Compared to singles,
 couples were significantly more likely to be a non-smoker (OR = 1.82), and
 meet recommendations for limited fast food (OR = 1.12), alcohol
 consumption (OR = 1.27) and fruit and vegetable intake (OR = 1.24). Fruit
 and vegetable intake was not significantly associated with relationship
 status after adjusting for the other healthy lifestyle factors. Conversly,
 couples were significantly less likely to be within a normal weight range
 (OR = 0.81). In both singles and couples, the trend data revealed
 significant declines in the rates of normal weight (singles: OR = 0.97,
 couples: OR = 0.97) and viewing TV for less than 14 hours per week
 (singles: OR = 0.85, couples: OR = 0.84), whilst non-smoking rates
 significantly increased (singles: OR = 1.12, couples: OR = 1.03). The BMI
 trend was no longer significant when adjusting for health behaviours.
 Further, in couples, rates of meeting recommendations for physical
 activity and fruit/vegetable consumption significantly decreased (OR =
 0.97 and OR = 0.95, respectively), as did rates of eating no fast food (OR
 = 0.96). These trends were not significant when adjusting for the other
 healthy lifestyle factors. In singles, rates of meeting alcohol
 recommendations significantly increased (OR = 1.08). Conclusions: Health
 behaviour interventions are needed in both singles and couples, but
 relationship status needs to be considered in interventions targeting
 alcohol, fast food, smoking and BMI. Further research is needed to
 understand why health behaviours differ by relationship status in order to
 further improve interventions.
description: manuscript
 PONE-D-16-44696R1 PLOS ONE dataSociodemographic and
 health-related variables used in the analyses.
DOI: 10.5061/dryad.1409
title: Data from: Contrasting patterns of genetic diversity at three different genetic markers in a marine mammal metapopulation

description: Many studies use genetic markers to explore population structure and
 variability within species. However, only a minority use more than one
 type of marker and, despite increasing evidence of a strong link between
 heterozygosity and individual fitness, few ask whether diversity
 correlates with population trajectory. To address these issues, we
 analysed data from the Steller's sea lion, Eumetiopias jubatus, where
 three stocks are distributed over a vast geographic range and where both
 genetic samples and detailed demographic data have been collected from
 many diverse breeding colonies. To previously published mtDNA and
 microsatellite datasets we have added new data for Amplified Fragment
 Length Polymorphism (AFLP) markers, comprising 238 loci scored in 285 sea
 lions sampled from 23 natal rookeries. Genotypic diversity was low
 relative to most vertebrates, with only 37 loci (15.5%) being polymorphic.
 Moreover, contrasting geographic patterns of genetic diversity were found
 at the three markers, with Nei's gene diversity tending to be higher
 for AFLPs and microsatellites in rookeries of the western and Asian
 stocks, while the highest mtDNA values were found in the eastern stock.
 Overall, and despite strongly contrasting demographic histories, after
 applying phylogenetic correction we found little correlation between
 genetic diversity and either colony size or demography. In contrast, we
 were able to show a highly significant positive relationship between AFLP
 diversity and current population size across diverse pinniped species,
 even though equivalent analyses did not reveal significant trends for
 either microsatellites or mtDNA
description: Dryad data
 file.xlsDatafile containing
 AFLP, microsatellite and mtDNA datafiles.
DOI: 10.5061/dryad.gd365jq4
title: Data from: Phylogenetic footprints of an Antarctic radiation: the Trematominae (Notothenioidei, Teleostei)

description: The teleost suborder Notothenioidei is restricted to the Southern Ocean
 and has been described as a species flock spanning the whole of it. Within
 the suborder, the subfamily Trematominae is important for coastal
 Antarctic ecosystems. The eleven Trematomus species occupy a large range
 of ecological niches. The genus is monophyletic if the genus Pagothenia
 (two additional species) and Cryothenia amphitreta, also nested within it,
 are included. Although the Trematominae have received much interest, the
 relationships among these fourteen species are still unclear. Several
 recent studies have tried to resolve these interrelationships; however no
 complete and clear picture has emerged, probably because of the use of a
 low number of insufficiently variable markers. The only common results
 places T. scotti as the sister-group of the rest of the subfamily and T.
 loennbergi close to T. lepidorhinus. We use here more variable markers.
 Four nuclear markers, two of which are new, and a mitochondrial marker for
 the biggest trematomine sampling ever gathered (14 species, 78 specimens).
 We found that several nuclear haplotypes are shared by several species
 (mostly in very closely related species). The haplotype patterns coupled
 with the cytogenetics of the subfamily suggest that a phenomenon of
 incomplete lineage sorting is likely to be at play. Using a calibration
 linked to fossil evidence, we evaluate the relative ages of each clade
 within the Trematominae to assess the proximity of the speciation events
 to one another. The main trematomine diversification was recent and
 sudden.
description: Trematomus_radiation_BEASTXML file used for the *BEAST analysis