cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mr67p
title: Data from: Diversification in a biodiversity hotspot: landscape correlates of phylogeographic patterns in the African spotted reed frog

description: The Eastern Afromontane Biodiversity Hotspot is known for microendemism
 and exceptional population genetic structure. The region's landscape
 heterogeneity is thought to limit gene flow between fragmented populations
 and create opportunities for regional adaptation, but the processes
 involved are poorly understood. Using a combination of phylogeographic
 analyses and circuit theory, I investigate how characteristics of
 landscape heterogeneity including regional distributions of slope, rivers
 and streams, habitat and hydrological basins (drainages) impact genetic
 distance among populations of the endemic spotted reed frog (Hyperolius
 substriatus), identifying corridors of connectivity as well as barriers to
 dispersal. Results show that genetic distance among populations is most
 strongly correlated to regional and local hydrologic structure and the
 distribution of suitable habitat corridors, not isolation by distance.
 Contrary to expectations, phylogeographic structure is not coincident with
 the two montane systems, but instead corresponds to the split between the
 region's two major hydrological basins (Zambezi and East Central
 Coastal). This results in a paraphyletic relationship for the Malawian
 Highlands populations with respect to the Eastern Arc Mountains and
 implies that the northern Malawian Highlands are the diversity centre for
 H. substriatus. Although the Malawian Highlands collectively hold the
 greatest genetic diversity, individual populations have lower diversity
 than their Eastern Arc counterparts, with an overall pattern of decreasing
 population diversity from north to south. Through the study of
 intraspecific differentiation across a mosaic of ecosystem and geographic
 heterogeneity, we gain insight into the processes of diversification and a
 broader understanding of the role of landscape in evolution.
description: Multilocus dataset for
 species tree analysesedited sequence data for
 ND2, C-myc, and POMC for Hyperolius
 substriatus/puncticulatusmultilocus_for_Dryad.nexCurrent_TMM_ascCurrent Bioclim variables (30 arc second resolution) clipped to the extent of Tanzania, Malawi, and MozambiqueLGM_TMM_ascLGM bioclim layers (30 arc sec resolution) of Tanzania, Malawi, and Mozambique
DOI: 10.5061/dryad.rv08j
title: Data from: Signals of selection in conditionally expressed genes in the diversification of three horned beetles species

description: Species radiations may be facilitated by phenotypic differentiation
 already present within populations, such as those arising through
 sex-specific development or developmental processes biased toward
 particular reproductive or trophic morphs. We sought to test this
 hypothesis by utilizing a comparative transcriptomic approach to contrast
 among and within-species differentiation using three horned beetle species
 in the genus Onthophagus. These three species exhibit differences along
 three phenotypic axes reflective of much of the interspecific diversity
 present within the genus: horn location, polarity of sexual dimorphism,
 and degree of nutritional sensitivity. Our approach combined de novo
 transcript assembly, assessment of amino acid substitutions (dN/dS) across
 orthologous gene pairs, and integration of gene function and conditional
 gene expression data. We identified 17 genes across the three species
 pairs related to axis patterning, development, and metabolism with dN/dS
 &gt;1 and detected elevated dN/dS in genes related to metabolism and
 biosynthesis in the most closely related species pair, which is
 characterized by a loss of nutritional polyphenism and a reversal of
 sexual dimorphism. Further, we found that genes that are conditionally
 expressed (i.e. as a function of sex, nutrition, or body region) within
 one of our focal species also showed significantly stronger signals of
 positive or relaxed purifying selection between species divergent along
 the same morphological axis (i.e. polarity of sexual dimorphism, degree of
 nutritional sensitivity, or location of horns). Our findings thus reveal a
 positive relationship between intraspecific differentiation due to
 condition-specific development and genetic divergences among species.
description: Fasta files of original
 transcriptome assemblies for the three speciesThese are the original
 transcriptome assembly files prior to the filtering and ORF prediction
 described in the paper.original_assemblies.tar.gzFunctional Annotation TableGene annotation of the 2010 orthologous genes for each species. The table includes best blast hit to NCBI nr database, Gene Ontology (GO) categories, and pfam domains.AnnotationTable.txtFasta file of the 2010 orthologs for each of the three speciesOrtholog identification and alignment are described in the paper. Briefly, clusters of orthologous genes (with a single member from each species) were identified using blast and mcl clustering. Alignments were made using MUSCLE.Ortholog2010setSequences.faPairwise dN, dS, dN/dS data for the 2010 orthologsPairwise dN, dS, and dN/dS were calculated for each ortholog using PAML. See paper and the scripts and commands for additional details.dN.dS_data.txtScripts and commands for the generation of the PAML resultsscripts_and_commands.tar.gz
DOI: 10.5061/dryad.408d6f0
title: Data from: Big data analysis of genes associated with neuropsychiatric disorders in an Alzheimer's disease animal model

description: Alzheimer’s disease is a neurodegenerative disease characterized by the
 impairment of cognitive function and loss of memory, affecting millions of
 individuals worldwide. With the dramatic increase in the prevalence of
 Alzheimer’s disease, it is expected to impose extensive public health and
 economic burden. However, this burden is particularly heavy on the
 caregivers of Alzheimer’s disease patients eliciting neuropsychiatric
 symptoms that include mood swings, hallucinations, and depression.
 Interestingly, these neuropsychiatric symptoms are shared across symptoms
 of bipolar disorder, schizophrenia, and major depression disorder. Despite
 the similarities in symptomatology, comorbidities of Alzheimer’s disease
 and these neuropsychiatric disorders have not been studied in the
 Alzheimer’s disease model. Here, we explore the comprehensive changes in
 gene expression of genes that are associated with bipolar disorder,
 schizophrenia, and major depression disorder through the microarray of an
 Alzheimer’s disease animal model, the forebrain specific PSEN double
 knockout mouse. To analyze the genes related with these three
 neuropsychiatric disorders within the scope of our microarray data, we
 used selected 1207 of a total of 45,037 genes that satisfied our selection
 criteria. These genes were selected on the basis of 14 Gene Ontology terms
 significantly relevant with the three disorders which were identified by
 previous research conducted by the Psychiatric Genomics Consortium. Our
 study revealed that the forebrain specific deletion of Alzheimer’s disease
 genes can significantly alter neuropsychiatric disorder associated genes.
 Most importantly, most of these significantly altered genes were found to
 be involved with schizophrenia. Taken together, we suggest that the
 synaptic dysfunction by mutation of Alzheimer’s disease genes can lead to
 the manifestation of not only memory loss and impairments in cognition,
 but also neuropsychiatric symptoms.
description: mRNA microarray within
 hippocampus and cortex brain regions of PSEN12 double knockout
 miceThe wild type and PSEN
 dKO mice were sacrificed at the ages of 7 and 18 months. The complete
 mouse brain structure was removed and immediately prepared by being frozen
 on dry ice. The cortex and hippocampus were dissected and stored at -80°C
 until RNA isolation. Total RNA was isolated using the Trizol reagent.
 Messenger RNA expression profiling was performed using Affymetrix Mouse
 Genome 430 2.0 array chip containing 764,885 probe sets from 28,132 genes
 (Ensembl) or from 19,734 putative full-length transcripts (GenBank and Ref
 Seq).
DOI: 10.5061/dryad.rp257gt
title: Data from: Ancestral hybridization yields evolutionary distinct hybrids lineages and species boundaries in crocodiles, posing unique conservation conundrums

description: Interspecific hybridization can lead to adaptation and speciation,
 especially in the context of recent radiations. The emblematic Crocodylus
 (true crocodiles) is the most broadly distributed, ecologically diverse,
 and species-rich crocodylian genus. Nonetheless, their within-species
 evolutionary processes are poorly resolved mainly due to their potential
 for hybridization. Notably, the evolutionary outcomes when hybridization
 is ancient and involves long-lived species, like crocodiles, remain
 largely unexplored. Here, we evaluate the genomic admixture between the
 American (Crocodylus acutus) and the Morelet’s (Crocodylus moreletii)
 species, and demonstrate that this hybridization system challenges the
 definition of species boundaries and poses a triple conservation
 conundrum: what has been recognized as C. acutus is actually two distinct
 species, therefore its taxonomic reassessment is needed; we identified two
 evolutionary distinct hybrids lineages, which are genetically discernible
 from the parental species; the remaining C. moreletii populations evidence
 its likely extinction as a species and/or evolution via hybridization.
 Hence, the crocodiles’ distinct species and hybrids lineages warrant
 recognition and need urgent conservation efforts.
description: microsatellite genotypes
 table Genotypes for 374
 crocodile individuals obtained in the study based on 12 polymorphic
 microsatellites loci microsatellite
 genotypes.csv SNPs data
 Acutus_moreletii_SNPs.vcf - This file includes 12879 SNP markers identified in <em>Crocodylus</em> <em>acutus</em> and <em>C. moreletii</em> from Mexico. Acutus_moreletii_SNPs.vcf
DOI: 10.5061/dryad.c3k7s
title: Data from: Repeated invasions into the twilight zone: evolutionary origins of a novel assemblage of fishes from deep Caribbean reefs

description: Mesophotic and deeper reefs of the tropics are poorly known and
 underexplored ecosystems worldwide. Collectively referred to as the
 ‘twilight zone’, depths below ~30–50 m are home to many species of reef
 fishes that are absent from shallower depths, including many undescribed
 and endemic species. We currently lack even a basic understanding of the
 diversity and evolutionary origins of fishes on tropical mesophotic reefs.
 Recent submersible collections in the Caribbean have provided new
 specimens that are enabling phylogenetic reconstructions that incorporate
 deep-reef representatives of tropical fish genera. Here, we investigate
 evolutionary depth transitions in the family Gobiidae (gobies), the most
 diverse group of tropical marine fishes. Using divergence-time estimation
 coupled with stochastic character mapping to infer the timing of
 shallow-to-deep habitat transitions in gobies, we demonstrate at least
 four transitions from shallow to mesophotic depths. Habitat transitions
 occurred in two broad time periods (Miocene, Pliocene–Pleistocene), and
 may have been linked to the availability of underutilized niches, as well
 as the evolution of morphological/behavioural adaptations for life on deep
 reefs. Further, our analysis shows that at least three evolutionary
 lineages that invaded deep habitats subsequently underwent speciation,
 reflecting another unique mode of radiation within the Gobiidae. Lastly,
 we synthesize depth distributions for 95 species of Caribbean gobies,
 which reveal major bathymetric faunal breaks at the boundary between
 euphotic and mesophotic reefs. Ultimately, our study is the first rigorous
 investigation into the origin of Caribbean deep-reef fishes and provides a
 framework for future studies that utilize rare, deep-reef specimens.
description: AlignmentFileNexus alignment of 257 species of gobies, including deep-reef taxa.BEAST_OutputA posterior distribution of phylogenetic trees resulting from a BEAST2 analysis.Beast2_InputInput XML file for BEAST2 analysis.
DOI: 10.5061/dryad.f0k4j
title: Data from: Prevalence, diversity, and host associations of Bartonella strains in bats from Georgia (Caucasus)

description: Bartonella infections were investigated in seven species of bats from four
 regions of the Republic of Georgia. Of the 236 bats that were captured,
 212 (90%) specimens were tested for Bartonella infection. Colonies
 identified as Bartonella were isolated from 105 (49.5%) of 212 bats
 Phylogenetic analysis based on sequence variation of the gltA gene
 differentiated 22 unique Bartonella genogroups. Genetic distances between
 these diverse genogroups were at the level of those observed between
 different Bartonella species described previously. Twenty-one reference
 strains from 19 representative genogroups were characterized using four
 additional genetic markers. Host specificity to bat genera or families was
 reported for several Bartonella genogroups. Some Bartonella genotypes
 found in bats clustered with those identified in dogs from Thailand and
 humans from Poland.
description: Urushadze et al (2017)
 PLOS NTDData files used in
 Urushadze et al (2017) PLOS NTD "Prevalence, Diversity, and Host
 Associations of Bartonella Strains in Bats from Georgia (Caucasus)."
 Includes Excel tables containing data on collected bat specimens,
 bacterial isolates, sequences, and statistical analyses, Excel tables
 containing data on phylogenetic model selection, phylogenetic trees in
 Nexus format, parameter log files from Bayesian phylogenetic analyses, and
 supplementary documents (Appendix and supplementary
 text).
DOI: 10.5061/dryad.rd736
title: Data from: Drones count wildlife more accurately and precisely than humans

description: Knowing how many individuals are in a wildlife population allows informed
 management decisions to be made. Ecologists are increasingly using
 technologies, such as remotely piloted aircraft (RPA; commonly known as
 “drones,” unmanned aerial systems or unmanned aerial vehicles), for
 wildlife monitoring applications. Although RPA are widely touted as a
 cost-effective way to collect high-quality wildlife population data, the
 validity of these claims is unclear. Using life-sized, replica seabird
 colonies containing a known number of fake birds, we assessed the accuracy
 of RPA-facilitated wildlife population monitoring compared to the
 traditional ground-based counting method. The task for both approaches was
 to count the number of fake birds in each of 10 replica seabird colonies.
 We show that RPA-derived data are, on average, between 43% and 96% more
 accurate than the traditional ground-based data collection method. We also
 demonstrate that counts from this remotely sensed imagery can be
 semi-automated with a high degree of accuracy. The increased accuracy and
 increased precision of RPA-derived wildlife monitoring data provides
 greater statistical power to detect fine-scale population fluctuations
 allowing for more informed and proactive ecological management.
description: Main
 datasetThis dataset contains
 the true number of birds for each colony, as well as the ground counts,
 RPA-derived manual counts and RPA-derived semi-automated counts for each
 colony. This dataset was used for all analyses.MASTER_AllCountData.csvRPA-derived imagery of bird coloniesCompressed folder containing photographs of each colony (n=10) at each sample height (n=4).Colony_imagery.zipSemi-automated aerial image counting approach - archived source code and datasetThis is a DOI for the source code and dataset used for the semi-automated aerial image counting approach which has been archived on figshare and released under a Creative Commons Attribution 4.0 International License. The current version of the code is available via Bitbucket (https://bitbucket.org/trungtpham/bird-detection).R script for analysesScript used to analyse ground counts, RPA-derived manual counts and RPA-derived semi-automated counts.MASTER_analysisScript_v1.4.R
DOI: 10.5061/dryad.d5f1r
title: Data from: Space can substitute for time in predicting climate-change effects on biodiversity

description: “Space-for-time” substitution is widely used in biodiversity modeling to
 infer past or future trajectories of ecological systems from contemporary
 spatial patterns. However, the foundational assumption—that drivers of
 spatial gradients of species composition also drive temporal changes in
 diversity—rarely is tested. Here, we empirically test the space-for-time
 assumption by constructing orthogonal datasets of compositional turnover
 of plant taxa and climatic dissimilarity through time and across space
 from Late Quaternary pollen records in eastern North America, then
 modeling climate-driven compositional turnover. Predictions relying on
 space-for-time substitution were ∼72% as accurate as “time-for-time”
 predictions. However, space-for-time substitution performed poorly during
 the Holocene when temporal variation in climate was small relative to
 spatial variation and required subsampling to match the extent of spatial
 and temporal climatic gradients. Despite this caution, our results
 generally support the judicious use of space-for-time substitution in
 modeling community responses to climate change.
description: Blois_etal_2013_PNAS_DataPlease refer to the 'README' fileBlois_etal_2013_DATA_CODE.zip
DOI: 10.15468/dl.xep8tj
title: Occurrence Download

description: A dataset containing 565 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Abronia graminea"
 ]
}

 The dataset includes 565 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000489-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3g57k
title: Data from: Utilizing descriptive statements from the Biodiversity Heritage Library to expand the Hymenoptera Anatomy Ontology

description: Hymenoptera, the insect order that includes sawflies, bees, wasps, and
 ants, exhibits an incredible diversity of phenotypes, with over 145,000
 species described in a corpus of textual knowledge since Carolus Linnaeus.
 In the absence of specialized training, often spanning decades, however,
 these articles can be challenging to decipher. Much of the vocabulary is
 domain-specific (e.g., Hymenoptera biology), historically without a
 comprehensive glossary, and contains much homonymous and synonymous
 terminology. The Hymenoptera Anatomy Ontology was developed to surmount
 this challenge and to aid future communication related to hymenopteran
 anatomy, as well as provide support for domain experts so they may
 actively benefit from the anatomy ontology development. As part of HAO
 development, an active learning, dictionary-based, natural language
 recognition tool was implemented to facilitate Hymenoptera anatomy term
 discovery in literature. We present this tool, referred to as the
 ‘Proofer’, as part of an iterative approach to growing phenotype-relevant
 ontologies, regardless of domain. The process of ontology development
 results in a critical mass of terms that is applied as a filter to the
 source collection of articles in order to reveal term occurrence and
 biases in natural language species descriptions. Our results indicate that
 taxonomists use domain-specific terminology that follows taxonomic
 specialization, particularly at superfamily and family level groupings and
 that the developed Proofer tool is effective for term discovery,
 facilitating ontology construction.
description: cluster analysis
 R-scriptSummarized R-script used
 in data analysis.doclust.Rg2 data fileData file used in analysis where term occurrence is &gt; 2.g2.txttaxon groupingsGroups file used to constrain analysis R analysis.groups.csvall result treesAll result trees from analysis including: summary files of all trees, and R-out files from each analysis.result_trees.zipscript_modifications_for_mxModifications for mx used in producing matrices.JHR_articlesJournal of Hymenoptera Research articles used in analysis with corresponding mx identifiers.termsTerms found in mx database with identifier. These identifier numbers correspond to the term (character) numbers used in analysis.
DOI: 10.5061/dryad.m96d0
title: Data from: Spatial patterns of plant litter in a tidal freshwater marsh and implications for marsh persistence

description: The maintenance of marsh platform elevation under conditions of sea level
 rise is dependent on mineral sediment supply to marsh surfaces and
 conversion of above- and below-ground plant biomass to soil organic
 material. These physical and biological processes interact within the
 tidal zone, resulting in elevation-dependent processes contributing to
 marsh accretion. Here we explore spatial pattern in a variable related to
 above-ground biomass, plant litter, to reveal its role in the maintenance
 of marsh surfaces. Plant litter persisting through the dormant season
 represents the more recalcitrant portion of plant biomass, and as such has
 an extended period of influence on ecosystem processes. We conducted a
 field and remote sensing analysis of plant litter height, above-ground
 biomass, vertical cover, and stem density (collectively termed plant
 litter structure) at a tidal freshwater marsh located within the Potomac
 River estuary. LiDAR and field observations show that plant litter
 structure becomes more prominent with increasing elevation. Spatial
 patterns in litter structure exhibit stability from year to year and
 correlate with patterns in soil organic matter content, revealed by
 measuring the loss on ignition of surface sediments. The amount of mineral
 material embedded within plant litter decreases with increasing elevation,
 representing an important trade-off with litter structure. Therefore, at
 low elevations where litter structure is short and sparse, the role of
 plant litter is to capture sediment; at high elevations where litter
 structure is tall and dense, above-ground litter contributes organic
 matter to soil development. This organic matter contribution has the
 potential to eclipse that of below-ground biomass as the root to shoot
 ratio of dominant species at high elevations is low compared to that of
 dominant species at low elevations. Because of these tradeoffs in mineral
 and organic matter incorporation into soil across elevation gradients, the
 rate of marsh surface elevation change is remarkably consistent across
 elevation. Because of the role of plant litter in marsh ecosystem
 processes, monitoring and assessment of these dynamic geomorphic marsh
 landscapes might be streamlined through the measurement of plant litter
 structure, either via LiDAR technologies or field observation.
description: LiDAR and field data for
 Dyke MarshLiDAR point files
 (Ground and All Points) collected in 2012; RTK GPS point files collected
 in 2012 and 2013; Field data on plant litter and surface soils; and some
 derived data from the LiDAR survey at the locations of plots and RTK
 elevations.Elmore_et_al_Archive.zip