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

description: A dataset containing 133729 records in GBIF matching the query:
SELECT
 '430' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= -100.71036946873933
 AND decimalLongitude &lt;= -89.91112128543796
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 133729 records were derived from 220 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002315-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.qfttdz0dc
title: Anuran limbs reflect microhabitat and distal, later-developing bones are more evolutionarily labile

description: Tetrapod limbs have been used as a model system to investigate how
 selective pressures and constraints shape morphological evolution. Anurans
 have had many independent transitions to various microhabitats, allowing
 us to dissect how these factors influence limb morphology. Furthermore,
 anurans provide a unique system to test the generality of developmental
 constraints proposed in mammals, namely that later-developing limb bones
 are under less constraint and show more variation. We used micro-computed
 tomography scans of 236 species from 52 of 55 families, geometric
 morphometrics, and modern phylogenetic comparative methods to examine how
 limb bones are related to microhabitat, phylogeny, allometry, and
 developmental timing. Although there was significant phylogenetic signal,
 anuran limb shape showed a relationship with microhabitat and to a lesser
 extent, body size. We found that distal bones had higher evolutionary
 rates than proximal bones, providing evidence that developmental
 constraints are reduced in later-developing bones. Distal bones also
 showed increased selection related to allometry and microhabitat,
 providing an additional explanation for higher evolutionary rates. By
 looking at the evolution of limb shape across a diverse clade, we
 demonstrated that multiple factors have shaped anuran limbs and that
 greater evolutionary lability in later-developing limb bones is likely a
 general trend among tetrapods.
description: Dataset for Stepanova and Womack 2020 publication in Evolution
 contains (1) landmark data for each bone in the fore- and hindlimb as
 separate tps files, (2) Supplemental Datatable to be used as the
 classifiers in analysis, also contains references for microhabitat of each
 species, and (3) R scripts for all analyses.
DOI: 10.5061/dryad.1g1jwsts2
title: Data from: Anticipated climate warming effects on bull trout habitats and populations across the interior Columbia River basin

description: A warming climate could profoundly affect the distribution and abundance
 of many fishes. Bull trout Salvelinus confluentus may be especially
 vulnerable to climate change given that spawning and early rearing are
 constrained by cold water temperatures creating a patchwork of natal
 headwater habitats across river networks. Because the size and
 connectivity of patches also appear to influence the persistence of local
 populations, climate warming could lead to increasing fragmentation of
 remaining habitats and accelerated decline of this species. We modeled the
 relationships between (1) the lower elevation limits of small bull trout
 and mean annual air temperature and (2) latitude and longitude across the
 species’ potential range within the interior Columbia River basin of the
 USA. We used our results to explore the implications of the climate
 warming expected in the next 50 or more years. We found a strong
 association between the lower elevation limits of bull trout distributions
 and longitude and latitude; this association was consistent with the
 patterns in mean annual air temperature. We concluded that climate does
 strongly influence regional and local bull trout distributions, and we
 estimated bull trout habitat response to a range of predicted climate
 warming effects. Warming over the range predicted could result in losses
 of 18–92% of thermally suitable natal habitat area and 27–99% of large
 (.10,000-ha) habitat patches, which suggests that population impacts may
 be disproportionate to the simple loss of habitat area. The predicted
 changes were not uniform across the species’ range, and some populations
 appear to face higher risks than others. These results could provide a
 foundation for regional prioritization in conservation management,
 although more detailed models are needed to prioritize actions at local
 scales.
description: This dataset is electrofishing surveys along an elevation
 gradient, by stream, of juvenile (&lt;150 mm) bull trout to identify
 the lower elevation limits of natal habitats. Each site was sampled for at
 least 45 m of stream length. We obtained these observations directly from
 biologists responsible for fish inventory or monitoring and from published
 or archived data sets with clearly defined and controlled sampling
 methods.
description: This is the dataset used in Rieman et al. 2007. Anticipated
 climate warming effects on bull trout habitats and populations across the
 Interior Columbia River Basin. <i>Transactions of the American
 Fisheries Society</i> 136: 1552– 1565. See methods section in the
 paper for additional details.
DOI: 10.5061/dryad.w3r2280mv
title: Subducted lithospheric boundary tomographically imaged beneath arc-continent collision in Eastern Indonesia

description: We use travel-times from a temporary seismic deployment of 30 broadband
 seismometers and a national catalog of arrival times to construct a finite
 frequency teleseismic P-wave tomographic model of the upper mantle beneath
 astern Indonesia, where subduction of the Indo-Australian plate beneath
 the Banda Arc transitions to arc-continent collision. The change in
 tectonics is due to a change from oceanic to continental lithosphere in
 the lower plate as inferred from geologic mapping and geophysical,
 geochemical, and geodetic measurements. At this inferred transition, we
 seismically image the subducted continent-ocean boundary at upper mantle
 depths that links volcanism on Flores to amagmatic orogenesis on Timor.
 Our tomographic images reveal a relatively high velocity feature within
 the upper mantle, which we interpret as the subducted Indo-Australian
 slab. The slab appears continuous yet deformed as a result of the change
 in buoyancy due to the composition of the incoming continental
 lithosphere. Accordingly, there is a difference in dip angle between the
 oceanic and continental sections of the slab albeit not a gap or
 discontinuity. We suggest the slab has deformed without tearing to
 accommodate structural and kinematic changes across the continent-ocean
 boundary as the two sections of the slab diverge. These results suggest
 that deformation in tectonic collisions can be localized along a
 continent-ocean boundary, even at depth. We propose that future slab
 tearing may develop where we observe slab deformation in our study region
 and that a similar process may take place in collisions generally.
description: Our dataset consists of ~20,000 arrival times of teleseismic P
 and PP waves recorded across Indonesia (Table 1). We manually picked P and
 PP arrival times from 207 events recorded across the YS network of 31
 broadband stations (Miller et al., 2016) between 2014 and 2017 for a total
 of 9,838 travel time residuals (Figure 2). To this we added 10,117
 automatically picked arrivals from 339 events recorded across 59 stations
 from the AU, IA, and II broadband seismic networks between 2010 and 2018
 (Table 1, Figure 2). These data were provided by the Meteorological,
 Climatological, and Geophysical Agency (BMKG) headquartered in Jakarta,
 Indonesia. Automatic arrivals were picked using SeisComP3 software using a
 short-term-average/long-term-average
 (<i>sta</i>/<i>lta</i>) trigger on broadband data
 filtered between 0.7-2.0 Hz. We obtained travel-time residuals using
 predictions from the global one-dimensional velocity model
 <i>iasp91</i> (Kennett and Engdahl, 1991). To improve the
 quality of the manually picked residuals, we employed the
 cross-correlation optimization scheme of VanDecar and Crosson (1990) in
 four non-overlapping bandpasses (Table 1). Only measurements with
 cross-correlation coefficients ≥ 0.8 were used in the inversion. After
 pruning, all delays were demeaned per event.
DOI: 10.5281/zenodo.18395224
title: LINGUISTIC RELATIONS BETWEEN LANGUAGE UNITS

description:  This article examines the issue of linguistic relations among language units from the perspective of modern linguistics. The study analyzes the nature of paradigmatic and syntagmatic relations between phonetic, lexical, and grammatical units. In addition, the interdependence of language units within the linguistic system, their functional characteristics in the process of speech, as well as the relationship between form and meaning are discussed. The analysis demonstrates that linguistic relations among language units constitute a crucial factor in the formation of language as an integrated and coherent system.
DOI: 10.5281/zenodo.18395225
title: LINGUISTIC RELATIONS BETWEEN LANGUAGE UNITS

description:  This article examines the issue of linguistic relations among language units from the perspective of modern linguistics. The study analyzes the nature of paradigmatic and syntagmatic relations between phonetic, lexical, and grammatical units. In addition, the interdependence of language units within the linguistic system, their functional characteristics in the process of speech, as well as the relationship between form and meaning are discussed. The analysis demonstrates that linguistic relations among language units constitute a crucial factor in the formation of language as an integrated and coherent system.
DOI: 10.5061/dryad.sqv9s4n1b
title: Wildlife roadkill patterns in a fragmented landscape of the Western Amazon

description: One of the most evident and direct effects of roads on wildlife is the
 death of animals by vehicle collision. Understanding the spatial patterns
 behind roadkill helps to plan mitigation measures to reduce the impacts of
 roads on animal populations. However, although roadkill patterns have been
 extensively studied in temperate zones, the potential impacts of roads on
 wildlife in the Neotropics have received less attention and are
 particularly poorly understood in the Western Amazon. Here, we present the
 results of a study on roadkill in the Amazon region of Ecuador; a region
 that is affected by a rapidly increasing development of road
 infrastructure. Over the course of 50 days, in the wet season between
 September and November 2017, we searched for road-killed vertebrates on
 15.9 km of roads near the city of Tena, Napo province, for a total of 1590
 surveyed kilometers. We recorded 593 dead specimens, predominantly
 reptiles (237 specimens, 40%) and amphibians (190, 32%), with birds (102,
 17%) and mammals (64, 11%) being less common. Recorded species were
 assigned to three functional groups; based on their movement behavior and
 habitat use (‘slow’, ‘intermediate’ and ‘fast’). Using Ripley’s K
 statistical analyses and 2D HotSpot Identification Analysis, we found
 multiple distinct spatial clusters or hotspots, where roadkill was
 particularly frequent. Factors that potentially determined these clusters,
 and the prevalence of roadkill along road segments in general, differed
 between functional groups, but often included land cover variables such as
 native forest and waterbodies, and road characteristics such as speed
 limit (i.e. positive effect on roadkill frequency). Our study, which
 provides a first summary of species that are commonly found as roadkill in
 this part of the Amazon region, contributes to a better understanding of
 the negative impacts of roads on wildlife and is an important first step
 towards conservation efforts to mitigate these impacts.
DOI: 10.5061/dryad.hqbzkh1ch
title: Data from: One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark

description: With recent advances in sequencing technology, genomic data are changing
 how important conservation management decisions are made. Applications
 such as Close-Kin Mark-Recapture demand large amounts of data to estimate
 population size and structure, and their full potential can only be
 realised through ongoing improvements in genotyping strategies. Here we
 introduce DArTcap, a cost-efficient method that combines DArTseq and
 sequence capture, and illustrate its use in a high resolution population
 analysis of Glyphis garricki, a rare, poorly known and threatened
 euryhaline shark. Clustering analyses and spatial distribution of kin
 pairs from four different regions across northern Australia and one in
 Papua New Guinea, representing its entire known range, revealed that each
 region hosts at least one distinct population. Further structuring is
 likely within Van Diemen Gulf, the region that included the most rivers
 sampled, suggesting additional population structuring would be found if
 other rivers were sampled. Coalescent analyses and spatially explicit
 modelling suggest that G. garricki experienced a recent range expansion
 during the opening of the Gulf of Carpentaria following the conclusion of
 the Last Glacial Maximum. The low migration rates between neighbouring
 populations of a species that is found only in restricted coastal and
 riverine habitats show the importance of managing each population
 separately, including careful monitoring of local and remote anthropogenic
 activities that may affect their environments. Overall we demonstrated how
 a carefully chosen SNP panel combined with DArTcap can provide highly
 accurate kinship inference and also support population structure and
 historical demography analyses, therefore maximising cost-effectiveness.
description: Genotyping data was collected using DArTseq and DArTcap protocols
 from Diversity Arrays Technology Metadata was collated
 during field work
description: The files provided can be used as described in Supplemental
 Information S1
DOI: 10.5061/dryad.2rbnzs7jx
title: Skull shape data for 188 species of living Carnivora

description: There are 5 files. Two include 2D coordinates used to quantify cranium and
 mandible shape for a sample of 188 averaged Carnivora species. These
 coordinates are in .NTS format. Another file is the phylogenetic tree
 employed for this study in nexus format. In Excel there is museum catalog
 list of all the specimens included in the study while
 the text file RoutineR.txt include most of the scripts employed
 in this study with examples on how to run simulations and other
 analyses. 
description: The shape coordinates were obtained from a larger sample of
 digital images via TPSDig subsequently averaged. The
 phylogeny was obtained using the 10kTree project while ecological data in
 Excel were obtained via literature review. The R
 routine file was obtained from the history of R data workspace.
description: Note that the 2D coordinates are obtained after averaging
 specimens per species using Generalised Procrustes Analysis. As a result
 these are shape coordinates whose centroid size does not reflect the
 averaged size of the species. The centroid size values (ordered following
 the same order as the .NTS files and the phylogeny) are available from the
 R workspace using the object CScra [averaged size of the cranial data] and
 CSmand [averaged size of mandible data]. Ecological categories for each
 species are also available in the R workspace using the object
 "diet".
DOI: 10.5061/dryad.z34tmpg99
title: Reference transcriptome and Alignments of candidate gene

description: Recently diverged taxa with contrasting phenotypes offer opportunities for
 unravelling the genetic basis of phenotypic variation in nature. Horseshoe
 bats are a speciose group that exhibit a derived form of high duty cycle
 echolocation in which the inner ear is finely tuned to echoes of the
 narrowband call frequency. Here, by focusing on three recently diverged
 subspecies of the intermediate horseshoe bat (Rhinolophus affinis) that
 display divergent echolocation call frequencies, we aim to identify
 candidate loci putatively involved in hearing frequency variation. We used
 de novo transcriptome sequencing of two mainland taxa (himalayanus and
 macrurus) and one island taxon (hainanus) to compare expression profiles
 of thousands of genes. By comparing taxa with divergent call frequencies
 (around 15 kHz difference), we identified 252 differentially expressed
 genes (DEGs), of which six have been shown to be involved in hearing or
 deafness in human/mouse. To obtain further validation of these results, we
 applied quantitative reverse transcription-PCR to the candidate gene
 FBXL15 and found a broad association between the level of expression and
 call frequency across taxa. The genes identified here represent strong
 candidate loci associated with hearing frequency variation in bats.
description: We
 performed <i>de novo</i> transcriptome assembly based on all
 trimmed reads using TRINITY with default parameters. Redundant transcripts
 were removed using CD-HIT-EST based on a 95% sequence similarity
 threshold. Transcripts with the longest open reading frames (ORFs) were
 kept using TRANSDECODER (http://transdecoder.github.io). Functional
 annotation was conducted using the TRINOTATE r20190821 pipeline
 (http://trinotate.github.io/) by searching against UniProtKB/Swiss-Prot
 and Pfam database (accessed 2th February 2019) using BLASTp and BLASTx
 [42] (<i>E-value</i> &lt; 10<sup>-5</sup>).
 Gene Ontology (GO) terms were retrieved for transcripts with a positive
 BLAST hit. Only transcripts functionally annotated were included in the
 final reference transcriptome. We screened
 the candidate genes
 (<em>FBXL15, </em><i>GATA2</i>,
 <i>CLDN11</i>, <i>CKB</i>,
 <i>CCDC88C</i>, and <i>SLC1A3</i>) for amino acid
 differences, either among the three <i>R. affinis
 </i>subspecies, or the three <i>R. ferrumequinum</i>
 geographical populations.
DOI: 10.5061/dryad.5x69p8d0w
title: Data from: Trial marriage model – female mate choice under male interference

description: In sexually reproducing animals, the process of mate choice by females is
 often mixed with the process of male-male competition. Current models of
 female male choice focus mainly on how females identify the higher quality
 of males, but neglect the effect of male-male competition on the mate
 choice of females. Therefore, it remains controversial what is the
 relative importance of two processes in forming a social bond. We propose
 a new “trial marriage” model for females’ mate choice. The model assumes
 that females unconditionally accept any male they first encounter as their
 mating partner, and then conditionally switch mates to a new male of
 higher quality than their current partner when male-male competition
 occurs. This model was tested in the green weevil, Hypomeces squamosus, by
 exploring how females switched mates when males’ mating interference was
 experimentally induced. The likelihood that females switched mates, as
 well as their conditional acceptance criteria of a new mate, was both
 raised with the intensity of males’ mating interference that was
 manipulated in an enhanced encounter rate experiment, and in male
 introduction or stepwise removal experiments. These experimental findings
 confirm that a “trial marriage” strategy occurs during females’ mate
 choice. Compared with other strategies, it is more beneficial for females
 to choose a better mate without paying the costs of identifying males as
 suggested by the “trial marriage” strategy. More importantly, by using the
 current partner quality as the conditional acceptance threshold of new
 mates, females can choose better males in future encounters with potential
 mates. In the green weevils, males’ preference for larger females and the
 higher possibility of the largest male winning an interference are mixed
 together when males’ mating interference reaches a higher intensity.
 Therefore, the consequence of a male interference will determine which
 male could be chosen by a female. Under this condition, conditional
 acceptance of the winner becomes the most beneficial strategy of females
 in choosing their mates. We thus suggest that the “trial marriage”
 strategy would be more efficient when males’ mating interference becomes
 the determinant factor of females’ mate choice.
description: This dataset had been collected in the field. It has not been
 processed.
DOI: 10.5061/dryad.wdbrv15kd
title: Macroinvertebrate communities in streams with contrasting water sources in the Japanese Alps

description: Data on macroinvertebrate community structure and environmental
 conditions across groundwater and snowmelt fed stream systems in
 the northern Japanese Alps.
DOI: 10.15468/dl.zbhscf
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "CatalogNumber" : [
 "is one of (K-M001043813, K-M001043815, K-M000954389, K-M000977970)"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002334-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.