cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k3j9kd564
title: Experimentally elevated testosterone shortens telomeres across years in a free-living songbird

description: Reproductive investment often comes at a cost to longevity, but the
 mechanisms that underlie these long-term effects are not well understood.
 In male vertebrates, elevated testosterone has been shown to increase
 reproductive success, but simultaneously decrease survival. One factor
 that may contribute to or serve as a biomarker of these long-term effects
 of testosterone on longevity is telomeres, which are often positively
 related to lifespan and have been shown to shorten in response to
 reproduction. In this longitudinal study, we measured the effects of
 experimentally elevated testosterone on telomere shortening in
 free-living, male dark-eyed juncos (Junco hyemalis carolinensis), a system
 in which the experimental elevation of testosterone has previously been
 shown to increase reproductive success and reduce survival. We found a
 small, significant effect of testosterone treatment on telomeres, with
 testosterone-treated males exhibiting significantly greater telomere
 shortening with age than controls. These results are consistent with the
 hypothesis that increased telomere shortening may be a long-term cost of
 elevated testosterone exposure. As both testosterone and telomeres are
 conserved physiological mechanisms, our results suggest that their
 interaction may apply broadly to the long-term costs of reproduction in
 male vertebrates.
DOI: 10.15468/dl.e5hud4
title: Occurrence Download

description: A dataset containing 3752 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Kerivoula"
 ]
}

 The dataset includes 3752 records from 92 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002754-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25338/b89s53
title: Data for project: A quantitative investigation into the impact of partially automated vehicles on vehicle miles travelled in California

description: We investigate travel changes in partially automated electric vehicles.
 Partial automation can control vehicle speed and steering using sensors
 that monitor the external environment. We use survey results from survey
 responses including 940 users of partial automation, including 628 who
 have Tesla Autopilot and 312 with systems from other automakers. Autopilot
 users report using automation more than users of other partial automation
 systems. Autopilot has the largest impact on travel, notably 36% of
 Autopilot users reporting more long-distance travel. Respondents who are
 younger, have a lower household income, use automation in a greater
 variety of traffic, roads, and weather conditions, and those who have
 pro-technology attitudes and outdoor lifestyles are more likely to report
 doing more long-distance travel. We use propensity score matching to
 investigate whether automation causes any increase in respondents’ annual
 vehicle miles travelled. For simplicity, we focus only on the impact of
 Tesla Autopilot and find that automation causes an increase of 4888 more
 miles driven per year.
description: In this study, we primarily use a cohort survey of PEV owners in California administered by the authors in November 2019. Respondents had been previously surveyed by the PH&EV Research Center between 2015 and 2018 as part of the four phases of the ‘eVMT survey’ when they originally bought the PEV tracked in the repeat survey in 2019 (households may have other PEVs in their fleet). Respondents for the four phases of the eVMT survey were sampled from the pool of PEV buyers who had applied for the state rebate from the California Vehicle Rebate Program (CVRP). More than 25,000 PEV owners were surveyed between 2015 and 2018. 15,000 of these respondents gave consent to be re-contacted and were invited for the repeat survey in 2019. 4,925 PEV owners responded to the repeat survey. The sample is a convenience sample. Most survey respondents have several vehicles in their household. For the purpose of this study we consider the vehicle most frequently used by the survey taker. We ask survey respondents how they use this vehicle, whether it has automation, and how often they use the automated features of the vehicle.
description: Please note the data only contains three sociodemographic variables for households. The data was reduced so that is includes no more than three indirect identifiers of households to align with guidance on preparing human subject data.
DOI: 10.5061/dryad.51c59zw7f
title: Data from: Dynamics of bird assemblages in response to temporally and spatially variable resources in arid Australia

description: Bird assemblages in arid Australia are often characterised as being highly
 variable through time in response to boom and bust dynamics, although the
 importance of habitat in structuring assemblages at a local scale is also
 recognised. We use a novel approach to investigate the importance of
 rainfall variability in structuring bird assemblages in a resource-limited
 environment. Monthly bird surveys were conducted at ten plots for
 eight years at a botanical and zoological park in central Australia,
 including five irrigated plots within a fenced area and five natural plots
 outside. Irrigation – used to promote growth, flowering, and fruiting of
 plants – created an artificial resource-enhanced environment against which
 the response of birds to natural fluctuations in season and rainfall were
 compared. Species richness was generally maintained at a higher level in
 resource-enhanced plots during dry times but was higher in natural sites
 when rainfall was high, mainly due to increases in granivores and
 insectivores. Honeyeaters were consistently more abundant at
 irrigated sites. Rainfall was important in structuring bird assemblages at
 all plots; however, assemblages were more stable in irrigated plots and
 did not respond as dramatically to a period of very high rainfall. The
 comparative smoothing of fluctuations in the composition and abundance of
 birds in irrigated areas highlights the importance of primary
 productivity, normally tied to rainfall, in driving temporal change in
 arid-zone bird communities. There was also evidence that different plots
 in differing habitats supported distinct bird assemblages and that this
 spatial distinctiveness persisted irrespective of rainfall and determined,
 to some extent, the response to rainfall. Our study is one of few
 long-term studies of arid bird assemblages and highlights the importance
 of both long-term cycles of productivity driven by rain and season as well
 as site differences in the dynamics of arid zone bird communities. These
 insights are particularly valuable as climate change further exacerbates
 rainfall variability worldwide and initiatives to conserve avifauna in
 increasingly extreme environments may be required.
description: Data represent 30-minute area searches conducted simultaneously
 at 10 sites by citizen scientists. Surveys were conducted on 94 occasions
 between February 2004 and December 2011. Five sites were inside the Alice
 Springs Desert Park in an area that is irrigated and maintained as a
 botanical/zoological garden and five are outside the park in surrounding
 bushland and are natural (with no irrigation).
description: Labels are in the form Feb04I1 and represent the month of survey,
 year of survey, 'treatment' I/N, site number.
 I = Irrigated sites N = Natural sites (no
 irrigation)
DOI: 10.5061/dryad.qjq2bvqfh
title: Complete mitochondrial genome of the Caribbean reef shark, Carcharhinus perezi (Carcharhinformes: Carcharhinidae)

description: The Caribbean reef shark Carcharhinus perezi is a medium to large-bodied
 coastal and reef-associated predator found throughout the subtropical and
 tropical waters of the Atlantic Ocean and Caribbean Sea, although its
 populations are increasingly threatened by overfishing. We describe the
 first mitochondrial genome sequence for this species, using Illumina MiSeq
 sequencing of an individual from The Bahamas. We report the mitogenome
 sequence of the Caribbean reef shark to be 16,709 bp and composed two rRNA
 genes, 22 tRNA genes, 13 protein-coding genes, two non-coding genes; the
 control region and the origin of light-strand replication. We discuss the
 implications of this new information on future monitoring efforts and
 conservation measures such as marine protected areas, and urge future
 mitochondrial studies of sharks to expand their reach into the Atlantic
 Ocean.
description: Mitochondrial DNA genome sequence data for Caribbean reef shark
 C. perezi.  We
 describe the complete mitochondrial genome of the Caribbean reef shark. A
 2 mm muscle sample was taken from a live, mature female individual (177 cm
 total length, identification tag: 39093) sampled from the waters off Great
 Exumas, The Commonwealth of The Bahamas (23.726984 N, -76.033982 W) on
 February 20, 2019 (the shark was released alive). The sample was
 immediately frozen, and later transported to the Center for Genome
 Innovation (CGI) at the University of Connecticut (USA) for genomic DNA
 extraction. Genomic
 DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen,
 Hilden, Germany) following manufacturer protocol.  Genomic DNA (deposited
 and stored at the CGI) was quantified, purity ratios determined using the
 NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA,
 USA).  To further assess DNA quality, genomic DNA was analyzed on the
 Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA, USA)
 using the Genomic DNA assay.  Whole genome shotgun libraries were made
 using the Illumina Nextera XT library preparation kit following
 manufacturer protocol (Illumina, San Diego, CA).  Libraries were validated
 for length and adapter dimer removal using the Agilent TapeStation 4200
 D1000 High Sensitivity assay (Agilent Technologies, Santa Clara, CA, USA)
 then quantified and normalized using the dsDNA High Sensitivity Assay for
 Qubit 3.0 (Life Technologies, Carlsbad, CA, USA).  Libraries were prepared
 for sequencing on the Illumina MiSeq using version 2 chemistry for paired
 end 250bp reads.
DOI: 10.5061/dryad.nzs7h44qv
title: Paleoecology of naticid-molluscan prey interaction during the Late Jurassic (Oxfordian) in Kutch, India: Evolutionary implications

description: We document and quantify one of the oldest predator-prey interactions
 between naticid gastropods and molluscan prey, based on drill holes in
 shells, from the Late Jurassic (Oxfordian) beds of Kutch, western India.
 Previously, many workers recorded naticid-like drill holes on prey taxa
 from the Triassic and the Jurassic, but in the absence of associated
 naticid body fossils, they remained equivocal. The present gastropod
 community is dominated by turritellines (98% of the sample) which form the
 TDA (turritelline-dominated assemblage) and the naticid drilling predation
 is almost entirely restricted to turritellines among gastropods.
 Confamilial naticid predation takes place occasionally. Within the bivalve
 community, corbulids and nuculids are most abundant and are drilled more
 often than other taxa. These observations indicate that prey selection was
 opportunistic and solely based on availability. Drilling intensities at
 both assemblage and lower taxon levels are low. Behavioural stereotypy of
 naticid predation in some cases is moderately high. Turritellines are
 often the preferred prey of naticid gastropods since the late Early
 Cretaceous. These two groups form a recurrent association reflecting
 prey-predator interaction. Here we suggest that both turritellines and
 naticids evolved during the Jurassic and the prey-predator interaction
 between them was established shortly thereafter. Among bivalves, corbulids
 also became important prey of naticids in the same spatiotemporal
 framework. Corbulids are older than naticids and first appeared during the
 Middle Jurassic. After their first encounter with naticids, corbulids
 evolved conchiolin layers within the valves to resist predation.
DOI: 10.5281/zenodo.18345203
title: Elevated in-situ Vp/Vs preceding hydraulic-fracturing-induced earthquakes
DOI: 10.5281/zenodo.18396545
title: Elevated in-situ Vp/Vs preceding hydraulic-fracturing-induced earthquakes
DOI: 10.5061/dryad.c59zw3r6m
title: Tumour suppressor genes fasta files for orthologous groups and hierarchical orthologous groups

description: Cetaceans are the longest-living species of mammals and the largest in the
 history of the planet. They have developed mechanisms against diseases
 such cancer, although the underlying molecular bases of these remain
 unknown. The goal of this study was to investigate the role of natural
 selection in the evolution of 1077 tumour suppressor genes (TSGs) in
 cetaceans. We used a comparative genomic approach to analyse two sources
 of molecular variation in the form of dN/dS rates and gene copy number
 variation. We found a signal of positive selection in the ancestor of
 cetaceans within the CXCR2 gene, an important regulator of DNA-damage,
 tumour dissemination, and immune system. Further, in the ancestor of
 baleen whales, we found six genes exhibiting positive selection relating
 to such diseases as breast carcinoma, lung neoplasm (ADAMTS8) and
 leukaemia (ANXA1). The TSGs turnover rate (gene gain and loss) was almost
 2.4-fold higher in cetaceans as compared to other mammals, and noticeably
 even faster in baleen whales. The molecular variants in TSGs found in
 baleen whales, combined with the faster gene turnover rate, could have
 favoured the evolution of their particular traits of anti-cancer
 resistance, gigantism and longevity. Additionally, we report 71 genes with
 duplications, of which 11 genes are linked to longevity (e.g. NOTCH3 and
 SIK1) and are important regulators of senescence, cell proliferation and
 metabolism. Overall, these results provide evolutionary evidence that
 natural selection in tumour suppressor genes could act on species with
 large body sizes and extended life span, providing novel insights into the
 genetic basis of disease resistance. 
description: Homology inference We inferred homologous
 relationships between the 1077 tumour suppressor genes described for
 humans, which are available from publically accessible databases (Tumor
 Suppressor Gene Database, https://bioinfo.uth.edu/TSGene/ and the Tumor
 Associate Gene, http://www.binfo.ncku.edu.tw/TAG/GeneDoc.php) (supplementary table 2), and the other 14 species included in our study using the program OMA standalone v.2.3.1 [37]. OMA standalone is a graph-based method that infers homology using strict pairwise sequence comparisons “all-against-all" based on evolutionary distances. It also has a survey of the relationships between species, which for this study were included a priori. We inferred two types of groupings: 1) OMA Groups (OG), containing the sets of orthologous genes (supplementary file 1), and 2) Hierarchical Orthologous Groups (HOGs, supplementary file 2). Briefly, tHOGs are those genes that have descended from a single ancestral gene within a species against which gene duplications and losses can be contrasted. This algorithm has previously shown high precision, minimising the errors in orthology assignment in comparison with other homology inference methods [38,39]. Using these HOGs groups, the number of copies of tumour suppressor genes was obtained on a per species basis.
DOI: 10.5061/dryad.k3j9kd565
title: Prosocial and antisocial choices in a monogamous cichlid with biparental care

description: Human society is cooperative and characterized
 by spontaneous prosociality. Comparative studies on
 endotherm vertebrates suggest that social interdependence causes the
 evolution of proactive prosociality. To test the generality of this
 hypothesis, we modified a prosocial choice task for application to the
 convict cichlid, Amatitlania nigrofasciata, a monogamous
 fish with biparental care and a strong pair bond. We show that subject
 males learned to favor prosocial choices when their mates were the
 recipients in neighboring tank. When the neighboring tank was empty, males
 chose at random. Furthermore, in the absence of their mates, males also
 behaved prosocially towards a stranger female. However, if the subjects’
 mate was also visible in a third tank, or if a male was the potential
 recipient, subjects made antisocial choices. In conclusion, fish may show
 both spontaneous prosocial and antisocial behaviors,
 according to their social relationships with conspecifics and the overall
 social context.
DOI: 10.5061/dryad.vmcvdncrw
title: Data from: An Appalachian population of neochoristoderes (Diapsida: Choristodera) elucidated through fossil evidence and ecological niche modeling

description: Four neochoristoderan vertebral centra are described from the latest
 Cretaceous of New Jersey. One specimen was recovered from the basal
 transgressive lag of the Navesink Formation in the area of Holmdel Park,
 New Jersey, and two others were recovered nearby and likely were derived
 from the same horizon. The fourth was recovered from the Marshalltown
 sequence in the vicinity of the Ellisdale Dinosaur Site. These vertebrae
 expand the geographic range of Late Cretaceous neochoristoderes in North
 America by over 2000 km further east, and represent the first
 neochoristoderan remains from the Atlantic coastal plain. To discern
 whether neochoristodere remains are to be expected in New Jersey, and
 elucidate why neochoristoderes are apparently so rare in Appalachia, we
 implemented ecological niche modeling to predict the range of suitable
 habitat for Champsosaurus, the only known genus of Late Cretaceous
 neochoristoderes. We found that in Appalachia, the ideal habitat of
 Champsosaurus likely existed slightly further north and west than the
 Atlantic coastal plain, and New Jersey is likely on or near the margin of
 this suitable habitat space. These results suggest that the occurrence of
 neochoristoderes in New Jersey is consistent with the habitat requirements
 of known Late Cretaceous neochoristoderes. These vertebrae therefore may
 represent the southern margin of a population of neochoristoderes that
 lived further inland, where latest Cretaceous sediments are not preserved.
 The continued recovery of material from Late Cretaceous deposits along the
 Atlantic coast, and review of existing collections, is encouraged to
 clarify the true distribution of neochoristoderes in Appalachia.
description: The occurrence datasets from the Palaeobiology Database (PBDB)
 were downloaded on the 18th of February 2020. These are: (1) occurrence
 datasets for <em>Champsosaurus</em> from the Campanian and
 Maastrichtian; and (2) fossil occurrences from the Campanian Maastrichtian
 (for the reconstruction of sedimentary outcrop). Please refer to the
 details listed at the top of each document for a breakdown of how the data
 were searched, and what variables they contain.
DOI: 10.5061/dryad.12jm63xxb
title: Considering sampling bias in close-kin mark-recapture (CKMR) abundance estimates of Atlantic salmon

description: Genetic methods for the estimation of population size can be powerful
 alternatives to conventional methods. Close-kin mark-recapture (CKMR) is
 based on the principles of conventional mark-recapture, but instead of
 being physically marked, individuals are marked through their close kin.
 The aim of this study was to evaluate the potential of CKMR for the
 estimation of spawner abundance in Atlantic salmon and how age, sex,
 spatial, and temporal sampling bias may affect CKMR estimates. Spawner
 abundance in a wild population was estimated from genetic samples of
 adults returning in 2018 and of their potential offspring collected in
 2019. Adult samples were obtained in two ways. First, adults were sampled
 and released alive in the breeding habitat during spawning surveys.
 Second, genetic samples were collected from out-migrating smolts PIT
 tagged in 2017 and registered when returning as adults in 2018. CKMR
 estimates based on adult samples collected during spawning surveys were
 somewhat higher than conventional counts. Uncertainty was small
 (CV&lt;0.15), due to the detection of a high number of
 parent-offspring-pairs. Sampling of adults was age- and size-biased and
 correction for those biases resulted in moderate changes in the CKMR
 estimate. Juvenile dispersal was limited, but spatially balanced sampling
 of adults rendered CKMR estimates robust to spatially biased sampling of
 juveniles. CKMR estimates based on returning PIT tagged adults were
 approximately twice as high as estimates based on samples collected during
 spawning surveys. We suggest that estimates based on PIT tagged fish
 reflect the total abundance of adults entering the river, while estimates
 based on samples collected during spawning surveys reflect the abundance
 of adults present in the breeding habitat at the time of spawning. Our
 study showed that CKMR can be used to estimate spawner abundance in
 Atlantic salmon, with a moderate sampling effort, but a carefully designed
 sampling regime is required.
description: See paper for methods.
description: See README file.