cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.683h4j5
title: Data from: Multilocus phylogeny and revised classification for mountain dragons of the genus Japalura s.l. (Reptilia: Agamidae: Draconinae) from Asia

description: Although the genus Japalura s.l. has long been recognized as paraphyletic
 based on limited genetic sampling, its problematic taxonomy has not been
 revised, and phylogenetic relationships among the majority of congeners
 remain unknown. Here we utilize a densely sampled dataset of both
 multilocus genetic and morphological data to provide the first
 phylogenetic inference of relationships among Japalura s.l.species. Our
 results show that Japalura s.l. is paraphyletic, consisting of four major
 clades that are scattered across the phylogeny of the subfamily
 Draconinae: the first clade from the western, central and middle-eastern
 Trans-Himalayas, the second clade from the far eastern Trans-Himalayas,
 the third clade from East Asia and the last clade from Indochina. To
 address this widespread paraphyly of the genus and to stabilize the
 taxonomy within the family Draconinae, we revise the current taxonomy and
 split Japalura s.l. into four genera. By doing so, we recognize two
 existing generic names, Japalura sensu stricto and Pseudocalotes,
 resurrect one name available in the literature, Diploderma, and describe
 one new genus, Cristidorsa gen. nov. We discuss phylogenetic relationships
 and taxonomy within Japalura s.l. and present a diagnostic key to all
 recognized genera of the subfamily Draconinae.
description: Final topology from
 RaxML Analyses based on concatenated data setRAxML_bipartitions.BootstrapTOPOLOGY.pdfFinal topology from Bayesian analyses on concatenated datasetAugust25_2017.con.pdfFinal alignmentsFinal_Concatenated_Datadryad.nexMorphological data for PCA and DAPC analysesPCA_continuous_only_2017.xlsx
DOI: 10.5061/dryad.14625
title: Data from: Particle backtracking improves breeding subpopulation discrimination and natal-source identification in mixed populations

description: We provide a novel method to improve the use of natural tagging approaches
 for subpopulation discrimination and source-origin identification in
 aquatic and terrestrial animals with a passive dispersive phase. Our
 method integrates observed site-referenced biological information on
 individuals in mixed populations with a particle-tracking model to retrace
 likely dispersal histories prior to capture (i.e., particle backtracking).
 To illustrate and test our approach, we focus on western Lake Erie’s
 yellow perch (Perca flavescens) population during 2006–2007, using
 microsatellite DNA and otolith microchemistry from larvae and juveniles as
 natural tags. Particle backtracking showed that not all larvae collected
 near a presumed hatching location may have originated there, owing to
 passive drift during the larval stage that was influenced by strong river-
 and wind-driven water circulation. Re-assigning larvae to their most
 probable hatching site (based on probabilistic dispersal trajectories from
 the particle backtracking model) improved the use of genetics and otolith
 microchemistry to discriminate among local breeding subpopulations. This
 enhancement, in turn, altered (and likely improved) the estimated
 contributions of each breeding subpopulation to the mixed population of
 juvenile recruits. Our findings indicate that particle backtracking can
 complement existing tools used to identify the origin of individuals in
 mixed populations, especially in flow-dominated systems.
description: 2006collectionsitesCollection site information for larval yellow perch during 20062007collectionsitesCollection site information for larval yellow perch during 20072006_and_2007_YP_Chem_Gen_dataMicrosatellite and otolith microchemical data for larval and juvenile yellow perch from 2006 and 2007
DOI: 10.5061/dryad.5k05t
title: Data from: A new giant titanosaur sheds light on body mass evolution among sauropod dinosaurs

description: Titanosauria was the most diverse and successful lineage of sauropod
 dinosaurs. This clade had its major radiation during the middle Early
 Cretaceous and survived up to the end of that period. Among sauropods,
 this lineage has the most disparate values of body mass, including the
 smallest and largest sauropods known. Although recent findings have
 improved our knowledge on giant titanosaur anatomy, there are still many
 unknown aspects about their evolution, especially for the most gigantic
 forms and the evolution of body mass in this clade. Here we describe a new
 giant titanosaur, which represents the largest species described so far
 and one of the most complete titanosaurs. Its inclusion in an extended
 phylogenetic analysis and the optimization of body mass reveals the
 presence of an endemic clade of giant titanosaurs inhabited Patagonia
 between the Albian and the Santonian. This clade includes most of the
 giant species of titanosaurs and represents the major increase in body
 mass in the history of Titanosauria.
description: Nexus
 fileNexus file with the data
 matixCarballido et
 al_Patagotitan.nexTNT
 fileData matrix in .tnt
 formatCarballido et
 al_Patagotitan.tnt
DOI: 10.5061/dryad.7tb6b
title: Data from: Maternal body condition influences magnitude of anti-predator response in offspring

description: Organisms exhibit plasticity in response to their environment, but there
 is large variation even within populations in the expression and magnitude
 of response. Maternal influence alters offspring survival through size
 advantages in growth and development. However, the relationship between
 maternal influence and variation in plasticity in response to predation
 risk is unknown. We hypothesized that variation in the magnitude of
 plastic responses between families is at least partly due to maternal
 provisioning and examined the relationship between maternal condition, egg
 provisioning and magnitude of plastic response to perceived predation risk
 (by dragonfly larvae: Aeshna spp.) in northern leopard frogs (Lithobates
 pipiens). Females in better body condition tended to lay more (clutch
 size) larger (egg diameter) eggs. Tadpoles responded to predation risk by
 increasing relative tail depth (morphology) and decreasing activity
 (behaviour). We found a positive relationship between morphological effect
 size and maternal condition, but no relationship between behavioural
 effect size and maternal condition. These novel findings suggest that
 limitations imposed by maternal condition can constrain phenotypic
 variation, ultimately influencing the capacity of populations to respond
 to environmental change.
description: Maternal Investment
 DataRaw data from maternal
 investment experiments including: 1) Maternal mass and snout-urostyle
 lengths, clutch mass and size, egg mass and size, 2) tadpole morphology
 measurements, 3) tadpole tank activities (% active/tank), and 4) tadpole
 mass and stage.
DOI: 10.5061/dryad.qk461
title: Data from: The evolution of morphological diversity in continental assemblages of Passerine birds

description: Understanding geographic variation in the species richness and lineage
 composition of regional biotas is a long standing goal in ecology. Why do
 some evolutionary lineages proliferate while others do not, and how do new
 colonists fit into an established fauna? Here, we analyse the
 morphological structure of assemblages of passerine birds in four
 biogeographic regions to examine the relative influence of colonization
 history and niche-based processes on regional communities of passerine
 birds. Using morphological traits related to habitat choice, foraging
 technique and movement, we quantify the morphological spaces occupied by
 different groups of passerine birds. We quantify morphological overlap
 between groups by multivariate discriminant analysis and null model
 analyses of trait dispersion. Finally, we use subclade disparity through
 time to assess the temporal component of morphological evolution. We find
 mixed support for the prediction, based on priority, that first colonisers
 constrain subsequent colonisers. Indeed, our results show that the
 assembly of regional communities is idiosyncratic with regards to the
 diversification of new clades and the filling of morphospace.
description: Passerine bird
 morphological measurementsAverage morphological
 measurements and distributions of 1,579 passerine bird species included in
 the study “THE EVOLUTION OF MORPHOLOGICAL DIVERSITY IN CONTINENTAL
 ASSEMBLAGES OF PASSERINE BIRD” by Jønsson KA, Lessard JP, Ricklefs RE.
 Species names are matched to the bird tree of life
 (birdtree.org).data_morphospace_FINAL.xls
DOI: 10.5061/dryad.2fk71
title: Data from: Detection of human disease conditions by single-cell morpho-rheological phenotyping of blood

description: Blood is arguably the most important bodily fluid and its analysis
 provides crucial health status information. A first routine measure to
 narrow down diagnosis in clinical practice is the differential blood
 count, determining the frequency of all major blood cells. What is lacking
 to advance initial blood diagnostics is an unbiased and quick functional
 assessment of blood that can narrow down the diagnosis and generate
 specific hypotheses. To address this need, we introduce the continuous,
 cell-by-cell morpho-rheological (MORE) analysis of diluted whole blood,
 without labeling, enrichment or separation, at rates of 1,000 cells/sec.
 In a drop of blood we can identify all major blood cells and characterize
 their pathological changes in several disease conditions in vitro and in
 patient samples. This approach takes previous results of mechanical
 studies on specifically isolated blood cells to the level of application
 directly in blood and adds a functional dimension to conventional blood
 analysis.
description: Data.xlsx, complete
 collection of the analized dataData.xlsxData.zip, Part 1 of 31, archive of RT-DC raw dataData.zip.001Data.zip, Part 2 of 31Data.zip.002Data.zip, Part 3 of 31Data.zip.003Data.zip, Part 4 of 31Data.zip.004Data.zip, Part 5 of 31Data.zip.005Data.zip, Part 6 of 31Data.zip.006Data.zip, Part 7 of 31Data.zip.007Data.zip, Part 8 of 31Data.zip.008Data.zip, Part 9 of 31Data.zip.009Data.zip, Part 10 of 31Data.zip.010Data.zip, Part 11 of 31Data.zip.011Data.zip, Part 12 of 31Data.zip.012Data.zip, Part 13 of 31Data.zip.013Data.zip, Part 14 of 31Data.zip.014Data.zip, Part 15 of 31Data.zip.015Data.zip, Part 16 of 31Data.zip.016Data.zip, Part 17 of 31Data.zip.017Data.zip, Part 18 of 31Data.zip.018Data.zip, Part 19 of 31Data.zip.019Data.zip, Part 20 of 31Data.zip.020Data.zip, Part 21 of 31Data.zip.021Data.zip, Part 22 of 31Data.zip.022Data.zip, Part 23 of 31Data.zip.023Data.zip, Part 24 of 31Data.zip.024Data.zip, Part 25 of 31Data.zip.025Data.zip, Part 26 of 31Data.zip.026Data.zip, Part 27 of 31Data.zip.027Data.zip, Part 28 of 31Data.zip.028Data.zip, Part 29 of 31Data.zip.029Data.zip, Part 30 of 31Data.zip.030Data.zip, Part 31 of 31Data.zip.031
DOI: 10.5061/dryad.f6m02
title: Data from: Reef-specific patterns of gene expression plasticity in eastern oysters (Crassostrea virginica)

description: Understanding the interaction between phenotypic plasticity and
 evolutionary processes is important for predicting a species’ response to
 changing environment. Strong recurrent selection each generation may be an
 important process in highly fecund species with broad dispersal and
 extensive early mortality. We tested whether selection was associated with
 spatial divergence in gene expression plasticity for osmoregulation in the
 eastern oyster (Crassostrea virginica). We collected adult oysters from
 high and low salinity reefs within a single estuary and after 9 weeks of
 acclimation at 10 and 30 salinity, measured gene expression in 24 oysters
 using next-generation RNA sequencing technology. The oysters had
 significantly different expression (DE) in response to salinity treatments
 for 7936 (18.9%) transcripts overall, with planned contrasts showing 8×
 more DE in oysters from the high-salinity reef and 15× more DE between
 reefs when tested at 10 salinity. The reef-by-treatment interaction was
 also genomically pervasive (5858 DE transcripts, 13.9%). Inter-reef F ST
 for transcript SNPs averaged 0.0025 with the top 1% between 0.29 and 0.73.
 Transcripts containing “outlier” SNPs were significantly enriched for
 osmoregulatory genes and showed patterns of variation consistent with
 selection on the low-salinity reef. Both phenotypic plasticity and
 recurrent selection seem to be important factors determining the realized
 niche of oysters within estuaries.
description: FASTA Sequences for the
 Annotated Reference Transcriptome of the Eastern OysterThe FASTA file consists
 of the annotated reference transcriptome cDNA sequences used to map sample
 reads. The reference transciprtome was generated by collapsing two
 previously published transcriptomes (Eierman and Hare 2014, Zhang et al.
 2014) using Cd-hit-est (Li and Godzik 2006) as described in the
 publication (Eierman and Hare 2015).Eierman_Hare_2015_JOH_Transcriptome_Sequences.fastaAnnotation File for the Annotated Reference Transcriptome of the Eastern OysterThe Excel file provides the annotation information, including original source transcriptome, for each contig in the reference transcriptome. The ReadMe files describes the content of each Excel file column.Eierman_Hare_2015_JOH_Transcriptome_Annotation.xlsxFiltered, mapped RNA-seq reads from eastern oysters in merged bam fileThe file is a merged bam file. It contains the reads that mapped to the annotated reference transcriptome for all 24 sample oysters. The ReadMe file indicates that source population and treatment salinity for each sample oyster.All_samples_JOH_Eierman_Hare.bam
DOI: 10.5061/dryad.rg18034
title: Data from: Testing an hypothesis of hybrid zone movement for toads in France

description: Hybrid zone movement may result in substantial unidirectional
 introgression of selectively neutral material from the local to the
 advancing species, leaving a genetic footprint. This genetic footprint is
 represented by a trail of asymmetric tails and displaced cline centres in
 the wake of the moving hybrid zone. A peak of admixture linkage
 disequilibrium is predicted to exist ahead of the centre of the moving
 hybrid zone. We test these predictions of the movement hypothesis in a
 hybrid zone between common (Bufo bufo) and spined toads (B. spinosus),
 using 31 nuclear and one mtDNA SNPs along a transect in the northwest of
 France. Average effective selection in Bufo hybrids is low and clines vary
 in shape and centre. A weak pattern of asymmetric introgression is
 inferred from cline discordance of seven nuclear markers. The dominant
 direction of gene flow is from B. spinosus to B. bufo and is in support of
 southward movement of the hybrid zone. Conversely, a peak of admixture
 linkage disequilibrium north of the hybrid zone suggests northward
 movement. These contrasting results can be explained by reproductive
 isolation of the B. spinosus and B. bufo gene pools at the southern (B.
 spinosus) side of the hybrid zone. The joint occurrence of asymmetric
 introgression and admixture linkage disequilibrium can also be explained
 by the combination of low dispersal and random genetic drift due to low
 effective population sizes.
description: 01_DistanceDistance calculations populations transect02_SNP_design_transcriptomeScript, in-, and output for SNP design based on transcriptome data. Some large files are stored in the main directory02_Step1_01_README_Raw_data_Bufo02_Step1_02_Filtered_dataScripts, in-, and output for transcriptome data filtering. Some of the large files are in the main directory.02_Step1_02_README_filtered_data02_Step1_03_Assembled_dataScripts, in-, and output for the assembled transcriptome data03_Genepop_HW_LDScript, in-, and output for Hardy Weinberg and pairwise linkage disequilibrium calculations with Genepop in R04_StructureStructure in-, and output and R scripts to generate the figures in the main text and supplements05_Admixture_LDScripts, in-, and output for admixture linkage disequilibrium calculations following Barton & Gale 199306_HZARScripts, in-, and output files for HZAR analyses.07_HIestScript, in-, and output for HIestfiltered_bufo_forward_pairedfiltered_bufo_reverse_pairedfiltered_spinosus_forward_pairedfiltered_spinosus_reverse_pairedfiltered_ZFG-15-11_1_13136_AGTCAA_L001_R1_001filtered_ZFG-15-11_1_13136_AGTCAA_L001_R2_001filtered_ZFG-15-11_13_13148_GTCCGC_L001_R1_001filtered_ZFG-15-11_13_13148_GTCCGC_L001_R2_001
DOI: 10.5061/dryad.g12f9
title: Data from: Crop-to-wild gene flow and its fitness consequences for a wild fruit tree: towards a comprehensive conservation strategy of the wild apple in Europe

description: Crop-to-wild gene flow can reduce the fitness and genetic integrity of
 wild species. Malus sylvestris, the European crabapple fruit tree, in
 particular is threatened by the disappearance of its habitat and by gene
 flow from its domesticated relative, Malus domestica. With the aims of
 evaluating threats for M. sylvestris and of formulating recommendations
 for its conservation, we studied here, using microsatellite markers and
 growth experiments: i) hybridization rates in seeds and trees from a
 French forest and in seeds used for replanting crabapples in agrosystems
 and in forests, ii) the impact of the level of M. domestica ancestry on
 individual fitness tree, and iii) pollen dispersal abilities in
 relationship with crop-to-wild gene flow. We found substantial
 contemporary crop-to-wild gene flow in crabapple tree populations and
 superior fitness of hybrids compared to wild seeds and seedlings. Using
 paternity analyses, we showed that pollen dispersal could occur up to 4 km
 and decreased with tree density. The seed network furnishing the wild
 apple reintroduction agroforestry programs was found to suffer from poor
 genetic diversity, introgressions, and species misidentification. Overall,
 our findings indicate supported threats for the European wild apple
 steering us to provide precise recommendations for its conservation.
description: Crop-to-wild_gene_flow_and_its_consequences_data
DOI: 10.5061/dryad.g7j86
title: Data from: Mating patterns and pollinator mobility are critical traits in forest fragmentation genetics

description: Most woody plants are animal-pollinated, but the global problem of habitat
 fragmentation is changing the pollination dynamics. Consequently, the
 genetic diversity and fitness of the progeny of animal-pollinated woody
 plants sired in fragmented landscapes tend to decline due to shifts in
 plant-mating patterns (for example, reduced outcrossing rate, pollen
 diversity). However, the magnitude of this mating-pattern shift should
 theoretically be a function of pollinator mobility. We first test this
 hypothesis by exploring the mating patterns of three ecologically
 divergent eucalypts sampled across a habitat fragmentation gradient in
 southern Australia. We demonstrate increased selfing and decreased pollen
 diversity with increased fragmentation for two small-insect-pollinated
 eucalypts, but no such relationship for the mobile-bird-pollinated
 eucalypt. In a meta-analysis, we then show that fragmentation generally
 does increase selfing rates and decrease pollen diversity, and that more
 mobile pollinators tended to dampen these mating-pattern shifts. Together,
 our findings support the premise that variation in pollinator form
 contributes to the diversity of mating-pattern responses to habitat
 fragmentation.
description: Eucalypt
 adultsthe microsatellite
 genotypes of each sampled adult treeEucalyptus
 progenymicrosatellite genotypes
 for all progeny
DOI: 10.5061/dryad.6nc5572
title: Data from: The effects of rainforest fragment area on the strength of plant-pathogen interactions

description: Pathogenic interactions between fungi and plants facilitate plant species
 coexistence and tropical rainforest diversity. Such interactions, however,
 may be affected by forest fragmentation as fungi are susceptible to
 anthropogenic disturbance. To examine how fragmentation affects
 fungus-induced seed and seedling mortality, we sowed seeds of six plant
 species in soils collected from 21 forest fragments. We compared seedling
 establishment in unmanipulated soils to soils treated with fungicides.
 Fungicides increased germination of Toona ciliata seeds and decreased
 mortality of Syzygium rubicundum and Olea dioica seedlings. The
 fungus-induced mortality of one of these species, S. rubicundum, decreased
 with decreasing fragment size, indicating that its interactions with
 pathogenic fungi may weaken as fragments become smaller. We provide
 evidence that a potential diversity-maintaining plant-fungus interaction
 weakens in small forest fragments and suggest that such disruptions may
 have important long-term consequences for plant diversity. We, however,
 emphasize the need for further research across rainforest plant
 communities to better understand the future of diversity in fragmented
 rainforest landscapes.
description: germination and
 mortality dataPlease see
 READMEgermination and
 mortality.csv
DOI: 10.15468/dl.bepgpq
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acromyrmex crassispinus",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2025",
 "DecimalLatitude is greater than or equal to -60.0",
 "DecimalLatitude is less than or equal to 40.0",
 "DecimalLongitude is greater than or equal to -90.0",
 "DecimalLongitude is less than or equal to 55.0",
 "HasCoordinate is true"
 ]
}

 The dataset includes 29 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000625-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.