cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g4000
title: Data from: A pantropical analysis of the impacts of forest degradation and conversion on local temperature

description: Temperature is a core component of a species’ fundamental niche. At the
 fine scale over which most organisms experience climate (mm to ha),
 temperature depends upon the amount of radiation reaching the Earth’s
 surface, which is principally governed by vegetation. Tropical regions
 have undergone widespread and extreme changes to vegetation, particularly
 through the degradation and conversion of rainforests. Since most
 terrestrial biodiversity is in the tropics, and many of these species
 possess narrow thermal limits, it is important to identify local thermal
 impacts of rainforest degradation and conversion. We collected
 pan-tropical, site-level (&lt; 1 ha) temperature data from the
 literature to quantify impacts of land-use change on local temperatures,
 and to examine whether this relationship differed above-ground relative to
 below-ground and between wet and dry seasons. We found that local
 temperature in our sample sites was higher than primary forest in all
 human-impacted land-use types (N = 113,894 day-time temperature
 measurements from 25 studies). Warming was pronounced following conversion
 of forest to agricultural land (minimum +1.6°C, maximum +13.6°C), but
 minimal and non-significant when compared to forest degradation (e.g. by
 selective logging; minimum +1°C, maximum +1.1°C). The effect was buffered
 below-ground (minimum buffering 0°C, maximum buffering 11.4°C), whereas
 seasonality had minimal impact (maximum buffering 1.9°C). We conclude that
 forest-dependent species that persist following conversion of rainforest
 have experienced substantial local warming. Deforestation pushes these
 species closer to their thermal limits, making it more likely that
 compounding effects of future perturbations, such as severe droughts and
 global warming, will exceed species’ tolerances. By contrast, degraded
 forests and below-ground habitats may provide important refugia for
 thermally-restricted species in landscapes dominated by agricultural land.
description: Local temperature in
 different land-use types (.csv format)This file includes
 site-level temperature data collated from the literature, where studies
 considered at least two different land-use types using a consistent
 methodology. See the Methods in the associated article for more detail.
 Data are included in the exact format used for analyses, which in some
 cases means they were aggregated to a coarser spatial or temporal
 resolution. For finer scale data it is recommended to refer to the
 original data sources, which are cited both within the data file and
 within the article (Table 2).SeniorRA_et_al_data_2017-06-28.csvLocal temperature in different land-use types (.Rds format)The same dataset, in an .Rds format suitable for quick and easy loading into R using the function 'readRDS' .SeniorRA_et_al_data_2017-06-28.Rds
DOI: 10.5061/dryad.mf202
title: Data from: Parasite metacommunities: evaluating the roles of host community composition and environmental gradients in structuring symbiont communities within amphibians

description: 1. Ecologists increasingly report the structures of metacommunities for
 free-living species, yet far less is known about the composition of
 symbiont communities through space and time. Understanding the drivers of
 symbiont community patterns has implications ranging from emerging
 infectious disease to managing host microbiomes. 2. Using symbiont
 communities from amphibian hosts sampled from wetlands of California, USA,
 we quantified the effects of spatial, habitat filtering, and host
 community components on symbiont occupancy and overall metacommunity
 structure. 3. We built upon a statistical method to describe metacommunity
 structure that accounts for imperfect detection in survey data – detection
 error-corrected elements of metacommunity structure (DECEMS) – by adding
 an analysis to identify covariates of community turnover. We applied our
 model to a metacommunity of 8 parasite taxa observed in 3571 Pacific
 chorus frogs (Pseudacris regilla) surveyed from 174 wetlands over 5 years.
 4. Symbiont metacommunity structure varied across years, showing nested
 structure in three years and random structure in two years. Species
 turnover was most consistently influenced by spatial and host community
 components. Occupancy generally increased in more southeastern wetlands,
 and snail (intermediate-host) community composition had strong effects on
 most symbiont taxa. 5. We have used sophisticated but accessible
 statistical methods to reveal that spatial components - which influence
 colonization - and host community composition - which mediates
 transmission - both drive symbiont community composition in this system.
 These methods allow us to associate broad patterns of community turnover
 to local, species-level effects, ultimately improving our understanding of
 spatial community dynamics.
description: Mihaljevic_etal_JAE_SMData and code for "Parasite metacommunities: Evaluating the roles of host community composition and environmental gradients in structuring symbiont communities within amphibians." A README file is included to explain each element of the .ZIP file.
DOI: 10.5061/dryad.bb46h5s
title: Data from: EFHC1, implicated in juvenile myoclonic epilepsy, functions at the cilium and synapse to modulate dopamine signaling

description: Neurons throughout the mammalian brain possess non-motile cilia,
 organelles with varied functions in sensory physiology and cellular
 signaling, yet their roles in these neurons are poorly understood. To shed
 light into their functions, we studied EFHC1, an evolutionarily conserved
 protein required for motile cilia function and linked to a common form of
 inherited epilepsy in humans, juvenile myoclonic epilepsy (JME). We
 demonstrate that C. elegans EFHC1 functions within specialized non-motile
 mechanosensory cilia, where it regulates neuronal activation and dopamine
 signaling. EFHC1 also localizes at the synapse, where it further modulates
 dopamine signaling in cooperation with the orthologue of an R-type
 voltage-gated calcium channel. Our findings unveil a previously
 undescribed dual-regulation of neuronal excitability at sites of neuronal
 sensory input (cilium) and neuronal output (synapse). Such a distributed
 regulatory mechanism may be essential for establishing neuronal activation
 thresholds under physiological conditions, and when impaired, may
 represent a novel pathomechanism for epilepsy.
description: EFHC1-data_2019-02-04The zip file contains all the data used to generate the figures in the associated manuscript. It is organized with folders containing different data types (from different kinds of experiments). It is further divided into folders containing data used to generate specific figures.
DOI: 10.15468/dl.2sss5t
title: Occurrence Download

description: A dataset containing 88 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Morocco",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Opuntia ficus-indica",
 "Year 1500-2026"
 ]
}

 The dataset includes 88 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000469-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8431
title: Data from: Monotreme ossification sequences and the riddle of mammalian skeletal development

description: The developmental differences between marsupials, placentals and
 monotremes are thought to be reflected in differing patterns of
 postcranial development and diversity. However, developmental polarities
 remain obscured by the rarity of monotreme data. Here I present the first
 postcranial ossification sequences of the monotreme echidna and platypus,
 and compare these with published data from other mammals and amniotes.
 Strikingly, monotreme stylopodia (humerus, femur) ossify after the more
 distal zeugopodia (radius/ulna, tibia/fibula), resembling only the
 European mole among all amniotes assessed. European moles also share
 extreme humeral adaptations to rotation digging and/or swimming with
 monotremes, suggesting a causal relationship between adaptation and
 ossification heterochrony. Late femoral ossification with respect to
 tibia/fibula in monotremes and moles points towards developmental
 integration of the serially homologous fore-and hind limb bones. Monotreme
 cervical ribs and coracoids ossify later than in most amniotes but are
 similarly timed as homologous ossifications in therians, where they are
 lost as independent bones. This loss may have been facilitated by a
 developmental delay of coracoids and cervical ribs at the base of mammals.
 The monotreme sequence, although highly derived, resembles placentals more
 than marsupials. Thus, marsupial postcranial development, and potentially
 related diversity constraints, may not represent the ancestral mammalian
 condition.
description: data
DOI: 10.5061/dryad.r0p00
title: Data from: Genomic variation across the Yellow-rumped Warbler species complex

description: Populations that have experienced long periods of geographic isolation
 will diverge over time. The application of high-throughput sequencing
 technologies to study the genomes of related taxa now allows us to
 quantify, at a fine scale, the consequences of this divergence across the
 genome. Throughout a number of studies, a notable pattern has emerged. In
 many cases, estimates of differentiation across the genome are strongly
 heterogeneous; however, the evolutionary processes driving this striking
 pattern are still unclear. Here we quantified genomic variation across
 several groups within the Yellow-rumped Warbler species complex (Setophaga
 spp.), a group of North and Central American wood warblers. We showed that
 genomic variation is highly heterogeneous between some taxa and that these
 regions of high differentiation are relatively small compared to those in
 other study systems. We found that the clusters of highly differentiated
 markers between taxa occur in gene-rich regions of the genome and exhibit
 low within-population diversity. We suggest these patterns are consistent
 with selection, shaping genomic divergence in similar genomic regions
 across the different populations. Our study also confirms previous results
 relying on fewer genetic markers that several of the phenotypically
 distinct groups in the system are also genomically highly differentiated,
 likely to the point of full species status.
description: SNP variants across
 yellow-rumped warbler complexVariant calls for 37,518
 polymorphic SNPs assayed across the yellow-rumped warbler complex.
 "sitenum" in "README" files correspond to the site
 information reported in Table 1 of the main manuscript. See main text for
 information about mapping, variant calling, and
 filtering.YRWA.Ref.GATK.filtered.snps.dryad.vcf
DOI: 10.5061/dryad.8bs2b
title: Data from: Endoskeletal structure in Cheirolepis (Osteichthyes, Actinopterygii), an early ray-finned fish

description: As the sister lineage of all other actinopterygians, the Middle to Late
 Devonian (Eifelian–Frasnian) Cheirolepis occupies a pivotal position in
 vertebrate phylogeny. Although the dermal skeleton of this taxon has been
 exhaustively described, very little of its endoskeleton is known, leaving
 questions of neurocranial and fin evolution in early ray-finned fishes
 unresolved. The model for early actinopterygian anatomy has instead been
 based largely on the Late Devonian (Frasnian) Mimipiscis, preserved in
 stunning detail from the Gogo Formation of Australia. Here, we present
 re-examinations of existing museum specimens through the use of
 high-resolution laboratory- and synchrotron-based computed tomography
 scanning, revealing new details of the neuro-cranium, hyomandibula and
 pectoral fin endoskeleton for the Eifelian Cheirolepis trailli. These new
 data highlight traits considered uncharacteristic of early
 actinopterygians, including an uninvested dorsal aorta and imperforate
 propterygium, and corroborate the early divergence of Cheirolepis within
 actinopterygian phylogeny. These traits represent conspicuous differences
 between the endoskeletal structure of Cheirolepis and Mimipiscis.
 Additionally, we describe new aspects of the parasphenoid, vomer and
 scales, most notably that the scales display peg-and-socket articulation
 and a distinct neck. Collectively, these new data help clarify primitive
 conditions within ray-finned fishes, which in turn have important
 implications for understanding features likely present in the last common
 ancestor of living osteichthyans.
description: Cheirolepis
 otico-occipitalPLY file of the
 otico-occipital portion of the braincase of
 Cheirolepis.Supp_1.plyCheirolepis ethmoidPLY file of the ethmoid portion of the braincase of Cheirolepis.Supp_2.plyCheirolepis hyomandibulaPLY file of the hyomandibula of Cheirolepis.Supp_3.plyCheirolepis fin endoskeletonPLY file of the left pectoral fin endoskeleton of Cheirolepis.Supp_4.plyHowqualepis braincasePLY file of the mould of the braincase of Howqualepis.Supp_5.ply
DOI: 10.5061/dryad.30tk6
title: Data from: Genome-wide SNP data unveils the globalization of domesticated pigs

description: Background: Pigs were domesticated independently in Eastern and Western
 Eurasia early during the agricultural revolution, and have since been
 transported and traded across the globe. Here, we present a worldwide
 survey on 60K genome-wide single nucleotide polymorphism (SNP) data for
 2093 pigs, including 1839 domestic pigs representing 122 local and
 commercial breeds, 215 wild boars, and 39 out-group suids, from Asia,
 Europe, America, Oceania and Africa. The aim of this study was to infer
 global patterns in pig domestication and diversity related to demography,
 migration, and selection. Results: A deep phylogeographic division
 reflects the dichotomy between early domestication centers. In the core
 Eastern and Western domestication regions, Chinese pigs show
 differentiation between breeds due to geographic isolation, whereas this
 is less pronounced in European pigs. The inferred European origin of pigs
 in the Americas, Africa, and Australia reflects European expansion during
 the sixteenth to nineteenth centuries. Human-mediated introgression, which
 is due, in particular, to importing Chinese pigs into the UK during the
 eighteenth and nineteenth centuries, played an important role in the
 formation of modern pig breeds. Inbreeding levels vary markedly between
 populations, from almost no runs of homozygosity (ROH) in a number of
 Asian wild boar populations, to up to 20% of the genome covered by ROH in
 a number of Southern European breeds. Commercial populations show moderate
 ROH statistics. For domesticated pigs and wild boars in Asia and Europe,
 we identified highly differentiated loci that include candidate genes
 related to muscle and body development, central nervous system,
 reproduction, and energy balance, which are putatively under artificial
 selection. Conclusions: Key events related to domestication, dispersal,
 and mixing of pigs from different regions are reflected in the 60K SNP
 data, including the globalization that has recently become full circle
 since Chinese pig breeders in the past decades started selecting Western
 breeds to improve local Chinese pigs. Furthermore, signatures of ongoing
 and past selection, acting at different times and on different genetic
 backgrounds, enhance our insight in the mechanism of domestication and
 selection. The global diversity statistics presented here highlight
 concerns for maintaining agrodiversity, but also provide a necessary
 framework for directing genetic conservation.
description: Description_data_GSE_Global_pigsTable describing the samples. Note that the submitted data includes a few animals that were removed from the paper due to additional constraints applied in the review process.GSE_global_pigs.mapPLINK MAP file, describing the SNPs used.GSE_global_pigs.pedGenotype data used in PLINK PED file format.
DOI: 10.5061/dryad.692jb15
title: Data from: Integrated population modeling provides the first empirical estimates of vital rates and abundance for polar bears in the Chukchi Sea

description: Large carnivores are imperiled globally, and characteristics making them
 vulnerable to extinction (e.g., low densities and expansive ranges) also
 make it difficult to estimate demographic parameters needed for
 management. Here we develop an integrated population model to analyze
 capture-recapture, radiotelemetry, and count data for the Chukchi Sea
 subpopulation of polar bears (Ursus maritimus), 2008–2016. Our model
 addressed several challenges in capture-recapture studies for polar bears
 by including a multievent structure reflecting location and life history
 states, while accommodating state uncertainty. Female breeding probability
 was 0.83 (95% credible interval [CRI] = 0.71–0.90), with litter sizes of
 2.18 (95% CRI = 1.71–2.82) for age-zero and 1.61 (95% CRI = 1.46–1.80) for
 age-one cubs. Total adult survival was 0.90 (95% CRI = 0.86–0.92) for
 females and 0.89 (95% CRI = 0.83–0.93) for males. Spring on-ice densities
 west of Alaska were 0.0030 bears/km2 (95% CRI = 0.0016–0.0060), similar to
 1980s-era density estimates although methodological differences complicate
 comparison. Abundance of the Chukchi Sea subpopulation, derived by
 extrapolating density from the study area using a spatially-explicit
 habitat metric, was 2,937 bears (95% CRI = 1,552–5,944). Our findings are
 consistent with other lines of evidence suggesting the Chukchi Sea
 subpopulation has been productive in recent years, although it is
 uncertain how long this will continue given sea-ice loss due to climate
 change.
description: Regehr2018_PolarBear_IPM_GOFR code and JAGS model to run the Integrated Population Model and goodness-of-fit for Chukchi Sea polar bearsRegehr2018_jags_dataData for the Integrated Population ModelRegehr2018_state_initsInitial values for the Integrated Population ModelRegehr2018_PolarBear_NR code for density extrapolation and abundance estimation for Chukchi Sea polar bearsRegehr2018_dextrp_dataData for density extrapolation and abundance estimationRegehr2018_PolarBear_recruitmentR code for separate recruitment analyses for Chukchi Sea polar bearsRegehr2018_C1perAF_dataData for separate recruitment analyses
DOI: 10.5061/dryad.b8kb0
title: Data from: Using sensitivity analysis to identify key factors for the propagation of a plant epidemic

description: Identifying the key factors underlying the spread of a disease is an
 essential but challenging prerequisite to design management strategies. To
 tackle this issue, we propose an approach based on sensitivity analyses of
 a spatiotemporal stochastic model simulating the spread of a plant
 epidemic. This work is motivated by the spread of sharka, caused by Plum
 pox virus, in a real landscape. We first carried out a broad-range
 sensitivity analysis, ignoring any prior information on six
 epidemiological parameters, to assess their intrinsic influence on model
 behaviour. A second analysis benefited from the available knowledge on
 sharka epidemiology and was thus restricted to more realistic values. The
 broad-range analysis revealed that the mean duration of the latent period
 is the most influential parameter of the model, whereas the
 sharka-specific analysis uncovered the strong impact of the connectivity
 of the first infected orchard. In addition to demonstrating the interest
 of sensitivity analyses for a stochastic model, this study highlights the
 impact of variation ranges of target parameters on the outcome of a
 sensitivity analysis. With regard to sharka management, our results
 suggest that sharka surveillance may benefit from paying closer attention
 to highly-connected patches whose infection could trigger serious
 epidemics.
description: Data &
 scripts_v2ZIP folder containing
 all scripts, data and simulation results used in this
 study.
DOI: 10.5061/dryad.dc04s
title: Data from: Characterization of the gray whale Eschrichtius robustus genome and a genotyping array based on single-nucleotide polymorphisms in candidate genes

description: Genetic and genomic approaches have much to offer in terms of ecology,
 evolution, and conservation. To better understand the biology of the gray
 whale Eschrichtius robustus (Lilljeborg, 1861), we sequenced the genome
 and produced an assembly that contains ∼95% of the genes known to be
 highly conserved among eukaryotes. From this assembly, we annotated 22,711
 genes and identified 2,057,254 single-nucleotide polymorphisms (SNPs).
 Using this assembly, we generated a curated list of candidate genes
 potentially subject to strong natural selection, including genes
 associated with osmoregulation, oxygen binding and delivery, and other
 aspects of marine life. From these candidate genes, we queried 92
 autosomal protein-coding markers with a panel of 96 SNPs that also
 included 2 sexing and 2 mitochondrial markers. Genotyping error rates,
 calculated across loci and across 69 intentional replicate samples, were
 low (0.021%), and observed heterozygosity was 0.33 averaged over all
 autosomal markers. This level of variability provides substantial
 discriminatory power across loci (mean probability of identity of 1.6 ×
 10−25 and mean probability of exclusion &gt;0.999 with neither parent
 known), indicating that these markers provide a powerful means to assess
 parentage and relatedness in gray whales. We found 29 unique multilocus
 genotypes represented among our 36 biopsies (indicating that we
 inadvertently sampled 7 whales twice). In total, we compiled an individual
 data set of 28 western gray whales (WGSs) and 1 presumptive eastern gray
 whale (EGW). The lone EGW we sampled was no more or less related to the
 WGWs than expected by chance alone. The gray whale genomes reported here
 will enable comparative studies of natural selection in cetaceans, and the
 SNP markers should be highly informative for future studies of gray whale
 evolution, population structure, demography, and relatedness.
description: Eschrichtius robustus
 genome annotationGray whale (Eschrichtius
 robustus) genome annotation in gff format. MAKER 2.28b was used to
 annotate the genome assembly. Scaffolds with a minimum size of 1000bp from
 the genome assembly were used to produce the final annotation. Assembly
 and annotation were conducted on individual ER-14-168.Eschrichtius_robustus.all.maker.gffEschrichtius robustus annotated proteinsGray whale (Eschrichtius robustus) annotated proteins from MAKER 2.28b in fasta format. Assembly and annotation were conducted on individual ER-14-168.Eschrichtius_robustus.all.maker.proteins.fastaEschrichtius robustus annotated transcriptsGray whale (Eschrichtius robustus) annotated transcripts from MAKER 2.28b in fasta format. Assembly and annotation were conducted on individual ER-14-168.Eschrichtius_robustus.all.maker.transcripts.fasta