cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8gh60
title: Data from: Down-regulation of Rad51 activity during meiosis in yeast prevents competition with Dmc1 for repair of double-strand breaks

description: Interhomolog recombination plays a critical role in promoting proper
 meiotic chromosome segregation but a mechanistic understanding of this
 process is far from complete. In vegetative cells, Rad51 is a highly
 conserved recombinase that exhibits a preference for repairing double
 strand breaks (DSBs) using sister chromatids, in contrast to the
 conserved, meiosis-specific recombinase, Dmc1, which preferentially
 repairs programmed DSBs using homologs. Despite the different preferences
 for repair templates, both Rad51 and Dmc1 are required for interhomolog
 recombination during meiosis. This paradox has recently been explained by
 the finding that Rad51 protein, but not its strand exchange activity,
 promotes Dmc1 function in budding yeast. Rad51 activity is inhibited in
 dmc1Δ mutants, where the failure to repair meiotic DSBs triggers the
 meiotic recombination checkpoint, resulting in prophase arrest. The
 question remains whether inhibition of Rad51 activity is important during
 wild-type meiosis, or whether inactivation of Rad51 occurs only as a
 result of the absence of DMC1 or checkpoint activation. This work shows
 that strains in which mechanisms that down-regulate Rad51 activity are
 removed exhibit reduced numbers of interhomolog crossovers and
 noncrossovers. A hypomorphic mutant, dmc1-T159A, makes less stable
 presynaptic filaments but is still able to mediate strand exchange and
 interact with accessory factors. Combining dmc1-T159A with up-regulated
 Rad51 activity reduces interhomolog recombination and spore viability,
 while increasing intersister joint molecule formation. These results
 support the idea that down-regulation of Rad51 activity is important
 during meiosis to prevent Rad51 from competing with Dmc1 for repair of
 meiotic DSBs.
description: PGENETICS_D_13_01530R2_ReCombine_data
DOI: 10.5061/dryad.1718129
title: Data from: Phylogenetic diversity, types of endemism and the evolutionary history of New World bats

description: New World bats represent over one third of global bat species and
 encompass the widest adaptive radiation among bats. Modern bat diversity
 in the Americas resulted from a mixture of migrations and colonisations of
 different taxa throughout the Cenozoic. Traditionally, these taxa are
 conceived as either South or North American, based on the location of
 their centres of diversification. To better understand the spatial and
 temporal processes behind modern biogeographic patterns of New World bat
 fauna, we investigated phylogenetic diversity (PD) and endemism (PE) for
 325 American bat species using distribution maps and a species-level
 phylogenetic supertree of bats. Randomisation tests were used to evaluate
 the statistical significance of our results, and to derive a categorical
 analysis of neo- and palaeo-endemism (CANAPE) to deconstruct significant
 endemism into its different components. PD and PE showed different
 patterns than those previously reported for New World bats based on
 traditional measures of diversity. We found multiple centres of
 significant endemism across the New World for most bat families, extending
 the hypothesis of dual centres of diversification, previously proposed for
 Emballonuridae, Phyllostomidae and Mormoopidae, to Molossidae and
 Vespertilionidae. Our results indicate that Central America and southern
 North America played important roles in the diversification of New World
 bats, as did the Andes in the diversification of Vespertilionidae in South
 America.
description: EmballonuridaeMolossidaeMormoopidaeNatalidaePhyllostomidaeVespertilionidae
DOI: 10.5061/dryad.kg3d57r
title: Data from: An evaluation of transferability of ecological niche models

description: Ecological niche modeling (ENM) is used widely to study species’
 geographic distributions. ENM applications frequently involve transferring
 models calibrated with environmental data from one region to other regions
 or times that may include novel environmental conditions. When novel
 conditions are present, transferability implies extrapolation, whereas, in
 absence of such conditions, transferability is an interpolation step only.
 We evaluated transferability of models produced using 11 ENM algorithms
 from the perspective of interpolation and extrapolation in a virtual
 species framework. We defined fundamental niches and potential
 distributions of 16 virtual species distributed across Eurasia. To
 simulate real situations of incomplete understanding of species’
 distribution or existing fundamental niche (environmental conditions
 suitable for the species contained in the study area; NF), we divided
 Eurasia into six regions and used 1-5 regions for model calibration and
 the rest for model evaluation. The models produced with the 11 ENM
 algorithms were evaluated in environmental space, to complement the
 traditional geographic evaluation of models. None of the algorithms
 accurately estimated the existing fundamental niche (NF) given one region
 in calibration, and model evaluation scores decreased as the novelty of
 the environments in the evaluation regions increased, so we recommend
 quantifying environmental similarity between calibration and transfer
 regions prior to model transfer, providing an avenue for assessing
 uncertainty of model transferability. Different algorithms had different
 sensitivities to completeness of knowledge of NF, with implications for
 algorithm selection. If the goal is to reconstruct fundamental niches,
 users should choose algorithms with limited extrapolation when NF is well
 known, or choose algorithms with increased extrapolation when NF is poorly
 known. Our assessment can inform applications of ecological niche modeling
 transference to anticipate species invasions into novel areas, disease
 emergence in new regions, and forecasts of species distributions under
 future climate conditions.
description: Environmental variables
 used to generate the ENMsEnvironmental variables
 used to generate the ENMs, including the raw layers and the PCA layers
 calculated from the raw datasets.bio_2.5m_Eurasia.zipVirtual speciesNine virtual species generated via NicheA (http://nichea.sourceforge.net/).VS.zipSeperated virtual species6 regions for each virtual species, which were separated based on the areas of the potential distribution of each species.Split.zipREADME
DOI: 10.5061/dryad.n1q6527
title: Data from: Blooms of aberrant planktic foraminifera across the K/Pg boundary in the Western Tethys: causes and evolutionary implications

description: Here we report a detailed study of the different categories and types of
 abnormal morphologies in planktic foraminifera recognizable in the
 lowermost Danian mainly from the El Kef and Aïn Settara sections, Tunisia.
 Various types of abnormalities in the test morphology were identified,
 including protuberances near the proloculus, abnormal chambers, double or
 twinned ultimate chambers, multiple ultimate chambers, abnormal apertures,
 distortion in test coiling, morphologically abnormal tests, attached twins
 or double tests, and general monstrosities. Detailed biostratigraphic and
 quantitative studies of the Tunisian sections documented a major
 proliferation of aberrant planktic foraminifera (between approximately 5
 and 18% in relative abundance) during the first 200Kyr of the Danian,
 starting immediately after the Cretaceous/Paleogene (K/Pg) boundary mass
 extinction (spanning from the Guembelitria cretacea Zone to the lower part
 of the P. pseudobulloides Zone). This contrasts with the proportionately
 low frequency of aberrant tests (generally &lt; 2%) identified within
 the uppermost Maastrichtian, suggesting more stable environmental
 conditions during the last ~50-100Kyr of the Cretaceous. Two main pulses
 with abundant aberrant tests were recognized in the earliest Danian, the
 one recorded in the well-known K/Pg boundary clay being the more intense
 of those (maxima of &gt;18%). These main pulses of aberrants coincide
 approximately with relevant quantitative and evolutionary turnovers in the
 planktic foraminiferal assemblages. In this paper we explore the relation
 of these high values of the foraminiferal abnormality index with the
 environmental changes induced by the meteorite impact of Chicxulub in
 Yucatan, Mexico, and the massive eruptions of the Deccan Traps, India.
description: Arenillas et al.
 supplementary Material
DOI: 10.5061/dryad.380n3
title: Data from: De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens

description: Noccaea caerulescens of the Brassicaceae family has become the key model
 plant among the metal hyperaccumulator plants. Populations/accessions of
 N. caerulescens from geographic locations with different soil metal
 concentrations differ in their ability to hyperaccumulate and
 hypertolerate metals. Comparison of transcriptomes in several accessions
 provides candidates for detailed exploration of the mechanisms of metal
 accumulation and tolerance and local adaptation. This can have
 implications in the development of plants for phytoremediation and
 improved mineral nutrition. Transcriptomes from root and shoot tissues of
 four N. caerulescens accessions with contrasting Zn, Cd and Ni
 hyperaccumulation and tolerance traits were sequenced with Illumina
 Hiseq2000. Transcriptomes were assembled using the Trinity de novo
 assembler and were annotated and the protein sequences predicted. The
 comparison against the BUSCO plant early release dataset indicated
 high-quality assemblies.The predicted protein sequences have been
 clustered into ortholog groups with closely related species. The data
 serve as important reference sequences in whole transcriptome studies, in
 analyses of genetic differences between the accessions and other species,
 and for primer design.
description: GAk32 transcriptome
 annotationAnnotation of the GAK32
 (Ganges accession) de novo assembly. Annotation was performed using the
 Trinotate pipeline. Ortholog clustering was performed using OrthoFinder.
 Ortholog groups and the corresponding A. thaliana TAIR codes have been
 combined with the Trinotate annotation.GAk32_annotation_final.xlsxLCk32 transcriptome annotationAnnotation of the LCK32 (La Calamine accession) de novo assembly. Annotation was performed using the Trinotate pipeline. Ortholog clustering was performed using OrthoFinder. Ortholog groups and the corresponding A thaliana TAIR codes have been combined with the Trinotate annotation.LCk32_annotation_final.xlsxLEk32 transcriptome annotationAnnotation of the LEK32 (Lellingen accession) de novo assembly. Annotation was performed using the Trinotate pipeline. Ortholog clustering was performed using OrthoFinder. Ortholog groups and the corresponding A thaliana TAIR codes have been combined with the Trinotate annotation.LEk32_annotation_final.xlsxMPk32 transcriptome annotationAnnotation of the MPK32 (Monte Prinzera accession) de novo assembly. Annotation was performed using the Trinotate pipeline. Ortholog clustering was performed using OrthoFinder. Ortholog groups and the corresponding A thaliana TAIR codes have been combined with the Trinotate annotation.MPk32_annotation_final.xlsxFasta files of ortholog groupsA zip archive containing the fasta files of the protein sequences clustered into ortholog groups by OrthoFinder.fasta.zipPython code - taxonomic groupPython code to extract the taxonomic group after blast search.python_tax_code.py
DOI: 10.5061/dryad.n276d
title: Data from: Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations

description: Restoration of lost species ranges to their native distribution is key for
 the survival of endangered species. However, reintroductions often fail
 and long-term genetic consequences are poorly understood. Alpine ibex
 (Capra ibex) are wild goats that recovered from &lt;100 individuals to
 ~50,000 within a century by population reintroductions. We analyzed the
 population genomic consequences of the Alpine ibex reintroduction
 strategy. We genotyped 101'822 genome-wide single nucleotide
 polymorphism loci in 173 Alpine ibex, the closely related Iberian ibex
 (Capra pyrenaica) and domestic goat (Capra hircus). The source population
 of all Alpine ibex maintained genetic diversity comparable to Iberian
 ibex, which experienced less severe bottlenecks. All reintroduced Alpine
 ibex populations had individually and combined lower levels of genetic
 diversity than the source population. The reintroduction strategy
 consisted of primary reintroductions from captive-breeding and secondary
 reintroductions from established populations. This step-wise
 reintroduction strategy left a strong genomic footprint of population
 differentiation, which increased with subsequent rounds of
 reintroductions. Furthermore, analyses of genome-wide runs of homozygosity
 showed recent inbreeding primarily in individuals of reintroduced
 populations. We showed that despite the rapid census recovery, Alpine ibex
 carry a persistent genomic signature of their reintroduction history. We
 discuss how genomic monitoring can serve as an early indicator of
 inbreeding.
description: raw SNP
 fileThis is the raw SNP file
 used for all analyses. It was produced using GATK and pre-filtered using
 vcftools (i.e. minimal genotyping rate of 0.45 and a maximal normalized
 coverage of 2). This includes SNPs which are not within 90bp of cut sites
 (hence SNPs located on R2 reads are included here). For analyses presented
 in the manuscript, further filters were applied. See methods part in the
 manuscript.DRYAD.raw.SNPfile.gz
DOI: 10.5061/dryad.f7248
title: Data from: Long-term in situ persistence of biodiversity in tropical sky-islands revealed by landscape genomics

description: Tropical mountains are areas of high species richness and endemism. Two
 historical phenomena may have contributed to this: (1) fragmentation and
 isolation of habitats may have promoted the genetic differentiation of
 populations and increased the possibility of allopatric divergence and
 speciation, and; (2) the mountain areas may have allowed long-term
 population persistence during global climate fluctuations. These two
 phenomena have been studied using either species occurrence data or
 estimating species divergence times. However, only few studies have used
 intraspecific genetic data to analyse the mechanisms by which endemism may
 emerge at the microevolutionary scale. Here, we use landscape analysis of
 genomic SNP data sampled from two high-elevation plant species from an
 archipelago of tropical sky-islands (the Transmexican Volcanic Belt) to
 test for population genetic differentiation, synchronous demographic
 changes and habitat persistence. We show that genetic differentiation can
 be explained by the degree of glacial habitat connectivity among
 mountains, and that mountains have facilitated the persistence of
 populations throughout glacial/interglacial cycles. Our results support
 the ongoing role of tropical mountains as cradles for biodiversity by
 uncovering cryptic differentiation and limits to gene flow.
description: Juniperus raw
 demultiplexed data (.fq)Fastq files for each of
 the Juniperus samples.Berberis alpina raw
 demultiplexed data (.fq)Fastq files for each B.
 alpina sampleassembled
 ddRADdataContains data and
 scripts of the section *Sequencing output, de novo assembly and loci
 filtering of RAD data* of the manuscript.processing_ddRADdata.zipdata and scripts for the aSFS analysisData and scripts for the *Comparative demographic inference using the aggregate site frequency spectrum* section of the manuscript.aSFS.zipData and scripts for population genomics and SDMContains data and scripts for the sections *Population genomic statistics and population differentiation*, *Timberline-alpine grassland distribution of glacial and interglacial periods* and *Landscape genomics analyses* of the manuscript.PopGenomicsIBR.zip
DOI: 10.5061/dryad.7j9t5
title: Data from: The impact of gene expression variation on robustness and evolvability of a developmental gene regulatory network

description: Regulatory interactions buffer development against genetic and
 environmental perturbations, but adaptation requires phenotypes to change.
 We investigated the relationship between robustness and evolvability
 within the gene regulatory network underlying development of the larval
 skeleton in the sea urchin Strongylocentrotus purpuratus. We find
 extensive variation in gene expression in this network throughout
 development in a natural population, some of which has a heritable genetic
 basis. Switch-like regulatory interactions predominate during early
 development, buffer expression variation, and may promote the accumulation
 of cryptic genetic variation affecting early stages. Regulatory
 interactions during later development are typically more sensitive
 (linear), allowing variation in expression to affect downstream target
 genes. Variation in skeletal morphology is associated primarily with
 expression variation of a few, primarily structural, genes at terminal
 positions within the network. These results indicate that the position and
 properties of gene interactions within a network can have important
 evolutionary consequences independent of their immediate regulatory role.
description: Expression
 DataThese files contain
 expression data, both in its pre-processed form and the actual data we
 used to generate the results. We've also included the scripts used to
 process the Illumina data as described in the supplementary
 materials.expression.zipMorphology DataThese folders contain text versions of the morphology data (morphological landmark locations) as well scripts used to transform these data into length data used in the analyses. The file "allResults_26Aug.csv" contains the final transformed data (the location in space of each morphological landmark). "AveMeasures_aveCulture.txt" has averaged data that was used in the 2B-PLS analyses. Due to size restrictions, we cannot upload the raw images, however we are happy to provide them on request.morphology_processing.zip
DOI: 10.5061/dryad.b6928
title: Data from: Serial monitoring of circulating tumor DNA in patients with primary breast cancer for detection of occult metastatic disease

description: Metastatic breast cancer is usually diagnosed after becoming symptomatic,
 at which point it is rarely curable. Cell‐free circulating tumor DNA
 (ctDNA) contains tumor‐specific chromosomal rearrangements that may be
 interrogated in blood plasma. We evaluated serial monitoring of ctDNA for
 earlier detection of metastasis in a retrospective study of 20 patients
 diagnosed with primary breast cancer and long follow‐up. Using an approach
 combining low‐coverage whole‐genome sequencing of primary tumors and
 quantification of tumor‐specific rearrangements in plasma by droplet
 digital PCR, we identify for the first time that ctDNA monitoring is
 highly accurate for postsurgical discrimination between patients with
 (93%) and without (100%) eventual clinically detected recurrence.
 ctDNA‐based detection preceded clinical detection of metastasis in 86% of
 patients with an average lead time of 11 months (range 0–37 months),
 whereas patients with long‐term disease‐free survival had undetectable
 ctDNA postoperatively. ctDNA quantity was predictive of poor survival.
 These findings establish the rationale for larger validation studies in
 early breast cancer to evaluate ctDNA as a monitoring tool for early
 metastasis detection, therapy modification, and to aid in avoidance of
 overtreatment.
description: ddPCR-dropletIntensitiesDroplet digital PCR result files: raw unprocessed droplet intensity data and normalized data (see publication for details).
DOI: 10.5061/dryad.226d0
title: Data from: A review of the lichens of the Dare Regional Biodiversity Hotspot in the Mid-Atlantic Coastal Plain of North Carolina, eastern North America

description: The results of a large-scale biodiversity inventory of lichens (including
 lichenicolous and allied fungi) in the Dare Regional Biodiversity Hotspot
 (DRBH) are presented. The DRBH is a region within the Mid-Atlantic Coastal
 Plain (MACP) of eastern North America that was recently delineated based
 on its unique and diverse lichen communities relative to other areas of
 the Atlantic Coast. Drawing on 4,952 newly generated voucher specimens
 from 49 sites, patterns of biodiversity and biogeography are presented and
 discussed within the context of both the DRBH and the broader MACP.
 Relationships between natural communities, vegetation, and lichen
 communities are discussed, as are threats to the lichen biota. A series of
 conservation actions are presented together with avenues for future study.
 In addition, supplementary resources are provided in the form of: (a) a
 checklist of DRBH lichens, lichenicolous fungi, and allied fungi; (b) keys
 to DRBH lichens and lichenicolous and allied fungi; and (c) formal
 descriptions of the following species new to science that were discovered
 during the inventory: Albemarlea pamlicoensis gen. et. sp. nov., Arthonia
 agelastica sp. nov. (on Lecanora louisianae B. de Lesd.), Arthonia
 hodgesii sp. nov. (on Graphis lineola), Arthonia stevensoniana sp. nov.
 (on Haematomma accolens), Lichenochora haematommatum sp. nov. (on
 Haematomma persoonii), Megalaria alligatorensis sp. nov., Minutoexcipula
 miniatoexcipula sp. nov. (on Pertusaria epixantha), Trichosphaerella
 buckii sp. nov. (on Punctelia rudecta).
description: Data_packetThis is a zipped folder that contains the following items:1) dataset, input file, and results for analyses of community similarity between different habitat types. 2) table of distribution patterns of the species studied. 3) tabular summary of northern/southern distribution limits of the species studied. 4) dataset, input file, and results for analyses of collector similarity between Buck (B), Harris (H) and Lendemer (L). 5) dataset, input file, and results for analyses of community similarity between sites. 6) dataset and tabular summary of species traits scored for this study. 7) dataset and tabular summary of for site data, taxonomic diversity, species data, and species occurence. 8) dataset of existing vouchers from CNALH (both original download and cleaned data 9) csv files for each species used to produce distribution maps compiled figures with four maps per plate.
DOI: 10.5061/dryad.000bq75
title: Data from: A well-preserved respiratory system in a Silurian ostracod

description: Ostracod crustaceans are diverse and ubiquitous in aqueous environments
 today but relatively few known species have gills. Ostracods are the most
 abundant fossil arthropods but examples of soft-part preservation,
 especially of gills, are exceptionally rare. A new ostracod, Spiricopia
 aurita (Myodocopa), from the marine Silurian Herefordshire Lagerstätte
 (430 Mya), UK, preserves appendages, lateral eyes and gills. The
 respiratory system includes five pairs of gill lamellae with hypobranchial
 and epibranchial canals that conveyed hemolymph. A heart and associated
 vessels had likely evolved in ostracods by the mid-Silurian.
description: Spiricopia
 VAXMLVAXML / STL dataset for
 Spiricopia holotype. See www.spiers-software.org for VAXML specification
 and free VAXML viewerSpiricopiaVAXML.zip
DOI: 10.15468/dl.gcnnaj
title: Occurrence Download

description: A dataset containing 2764 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Geometry POLYGON((-148.44 59.27,-118.08 59.27,-118.08 69.77,-148.44 69.77,-148.44 59.27))",
 "HasCoordinate is true",
 "License is one of (CC-BY-NC 4.0, CC-BY 4.0, CC0 1.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Ochrophyta"
 ]
}

 The dataset includes 2764 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000404-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.