cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.010sq3j
title: Data from: First record of the Mesozoic scroll coprolites: classification, characteristics, elemental composition and probable producers

description: Multiple, small, cylindrical scroll coprolites having rounded and tapering
 ends and pertaining to a new ichnotaxon have been recovered from the Upper
 Triassic Tiki Formation of India. This is the first record of scroll
 coprolites from the Mesozoic. Based on cross‐sectional geometry, external
 surface textures, and internal morphology, these coprolites are subdivided
 into three morphotypes. The coprolites contain several kinds of undigested
 food material in the form of ganoid fish scales, teeth, lower jaw and
 skeletal remains of various osteichthyans, chondrichthyans,
 archosauriforms and indeterminate reptiles. These inclusions are embedded
 in the groundmass separated by thin mucosal layers. The groundmass
 contains abundant gas vesicles, and secondarily‐filled shrinkage cracks.
 EDS analysis shows that the overall composition of the coprolites reflects
 Ca, P, C and O, suggesting calcium phosphate mineralogy, though other
 elements such as Fe, Mn, Al, Si are present in lesser proportions. Based
 on their similarity with the scrolled faeces of extant euryhaline
 hammerhead sharks, it is deduced that these coprolites were produced by
 euryhaline hybodontid sharks. At least two hybodontid taxa, Lonchidion and
 Pristrisodus, show high prevalence in the Tiki vertebrate fauna,
 suggesting that these were the possible producers. As the coprolite
 inclusions contain remains of other aquatic animals, these carnivorous
 hybodonts constituted the dominant predators of the Tiki aquatic
 ecosystem.
description: Rakshit et al._Appendix
 1_R1Appendix 1. Tikicopros
 triassicus igen et isp. nov. Details of the scroll coprolites collected
 from the Upper Triassic Tiki Formation of India. Colour code follows The
 Rock Color Chart Committee (1980). Abbreviations used: H, holotype; L,
 length measured along longitudinal axis; WL, maximum width measured along
 long axis in transverse section; WS, maximum width measured along short
 axis in transverse section. Explanation of abbreviations used given in
 Fig. 3A.
DOI: 10.5061/dryad.rc504
title: Data from: Dispersal and group formation dynamics in a rare and endangered temperate forest bat (Nyctalus lasiopterus, Chiroptera: Vespertilionidae)

description: For elusive mammals like bats, colonization of new areas and colony
 formation are poorly understood, as is their relationship with the genetic
 structure of populations. Understanding dispersal and group formation
 behaviors is critical not only for a better comprehension of mammalian
 social dynamics, but also for guiding conservation efforts of rare and
 endangered species. Using nuclear and mitochondrial markers, we studied
 patterns of genetic diversity and differentiation among and within
 breeding colonies of giant noctule bats (Nyctalus lasiopterus), their
 relation to a new colony still in formation, and the impact of this
 ongoing process on the regionwide genetic makeup. Nuclear differentiation
 among colonies was relatively low and mostly nonsignificant. Mitochondrial
 variation followed this pattern, contrasting with findings for other
 temperate bat species. Our results suggest that this may indicate a recent
 population expansion. On average, female giant noctules were not more
 closely related to other colony members than to foreign individuals. This
 was also true for members of the newly forming colony and those of
 another, older group sampled shortly after its formation, suggesting that
 contrary to findings for other temperate bats, giant noctule colonies are
 not founded by relatives. However, mother–daughter pairs were found in the
 same populations more often than expected under random dispersal. Given
 this indication of philopatry, the lack of mitochondrial differentiation
 among most colonies in the region is probably due to the combination of a
 recent population expansion and group formation events.
description: HVI_II_212_834_grpConcatenated and aligned Nyctalus lasiopterus mitochodrial control regions HVI and HVIII, 437 and 397 bp long respectively. Total size 834 bp. 212 individuals.MicrosCorrect_GENEPOPNyctalus lasiopetrus genotype file. Genepop format. 214 individuals, five populations. 11 microsatellite markers per individual.MicrosCorrect_FSTAT-FSTATNyctalus lasiopetrus genotype file. FSTAT format. 214 individuals, five populations. 11 microsatellite markers per individual.MicrosCorrect_FSTAT-FSTAT-POPULATION NAMESFSTAT genotype file population names.DifferetiationCalcR script for population differentiation and overall allelic richness calculation from uploaded Genepop and Fstat files containning 214 Nyctalus lasiopterus genotypes from 5 populations. Required packages: hierfstat; diveRsity.
DOI: 10.5061/dryad.m7t63
title: Data from: Why there are no essential genes on plasmids

description: Mobile genetic elements such as plasmids are important for the evolution
 of prokaryotes. It has been suggested that there are differences between
 functions coded for by mobile genes and those in the “core” genome and
 that these differences can be seen between plasmids and chromosomes. In
 particular, it has been suggested that essential genes, such as those
 involved in the formation of structural proteins or in basic metabolic
 functions, are rarely located on plasmids. We model competition between
 genotypically varying bacteria within a single population to investigate
 whether selection favors a chromosomal location for essential genes. We
 find that in general, chromosomal locations for essential genes are indeed
 favored. This is because the inheritance of chromosomes is more stable
 than that for plasmids. We define the “degradation” rate as the rate at
 which chance genetic processes, for example, mutation, deletion, or
 translocation, render essential genes nonfunctioning. The only way in
 which plasmids can be a location for functioning essential genes is if
 chromosomal genes degrade faster than plasmid genes. If the two
 degradation rates are equal, or if plasmid genes degrade faster than
 chromosomal genes, functioning essential genes will be found only on
 chromosomes.
description: BasicHousekeepingMathematica fileBasicHousekeeping2Mathematica fileSize_Of_mpstarMathematica file
DOI: 10.5061/dryad.665np
title: Data from: Population genetic structure of serotine bats (Eptesicus serotinus) across Europe and implications for the potential spread of bat rabies (European bat lyssavirus EBLV-1)

description: Understanding of the movements of species at multiple scales is essential
 to appreciate patterns of population connectivity and in some cases, the
 potential for pathogen transmission. The serotine bat (Eptesicus
 serotinus) is a common and widely distributed species in Europe where it
 frequently harbours European bat lyssavirus type 1 (EBLV-1), a virus
 causing rabies and transmissible to humans. In the United Kingdom, it is
 rare, with a distribution restricted to south of the country and so far
 the virus has never been found there. We investigated the genetic
 structure and gene flow of E. serotinus across the England and continental
 Europe. Greater genetic structuring was found in England compared with
 continental Europe. Nuclear data suggest a single population on the
 continent, although further work with more intensive sampling is required
 to confirm this, while mitochondrial sequences indicate an east–west
 substructure. In contrast, three distinct populations were found in
 England using microsatellite markers, and mitochondrial diversity was very
 low. Evidence of nuclear admixture indicated strong male-mediated gene
 flow among populations. Differences in connectivity could contribute to
 the high viral prevalence on the continent in contrast with the United
 Kingdom. Although the English Channel was previously thought to restrict
 gene flow, our data indicate relatively frequent movement from the
 continent to England highlighting the potential for movement of EBLV-1
 into the United Kingdom.
description: Genotypes of individuals
 analysedAllelic profile for each
 of the 699 individuals analysed for 10 microsatellites. The format follows
 the three digits coding used by the program Genepop, with #000000
 indicating missing data.Genotypes.xlsGeographical coordinates of the sites sampledLocation and sample size of each site. Most of the sites in England are private properties.coordinates genetic samples.xlsUnique mitochondrial haplotypesFASTA file containing the sequences of unique mitochondrial DNAmtDNA haplotypes.fasta
DOI: 10.15468/dl.w6nzys
title: Occurrence Download

description: A dataset containing 21912 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phryma"
 ]
}

 The dataset includes 21912 records from 405 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000694-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j51d02h
title: Data from: Histopathology of diffusion imaging abnormalities in cerebral amyloid angiopathy

description: Objective: we sought to determine the underlying mechanism for altered
 white matter diffusion tensor imaging (DTI) measures at the
 histopathologic level in patients with cerebral amyloid angiopathy (CAA).
 Methods: formalin-fixed intact hemispheres from nine CAA cases and two
 elderly controls were scanned at 3 tesla MRI, including a
 diffusion-weighted sequence. DTI measures (i.e. fractional anisotropy (FA)
 and mean diffusivity (MD)) and histopathology measures were obtained from
 two tracts: the anterior thalamic radiation (ATR) and inferior
 longitudinal fasciculus (ILF). Results: FA was reduced in both tracts and
 MD was increased in CAA cases compared to controls. Regional FA was
 significantly correlated with tissue rarefaction, myelin density, axonal
 density, and white matter microinfarcts. MD correlated significantly with
 tissue rarefaction, myelin density, and white matter microinfarcts, but
 not axonal density. FA and MD did not correlate with oligodendrocytes,
 astrocytes, or gliosis. Multivariate analysis revealed that tissue
 rarefaction (β=-0.32±0.12, p=0.009) and axonal density (β=0.25±0.12,
 p=0.04) were both independently associated with FA, whereas myelin density
 was independently associated with MD (β=-0.32±0.12, p=0.013). Finally, we
 found an association between increased MD in the frontal white matter and
 CAA severity in the frontal cortex (p=0.035). Conclusions: these results
 suggest that overall tissue loss, and in particular axonal and myelin
 loss, are major components underlying CAA-related alterations in DTI
 properties observed in living patients. The findings allow for a more
 mechanistic interpretation of DTI parameters in small vessel disease and
 for mechanism-based selection of candidate treatments to prevent vascular
 cognitive impairment.
description: Supplementary Table
 1
DOI: 10.5061/dryad.2bm7d
title: Data from: Selection on an antagonistic behavioral trait can drive rapid genital coevolution in the burying beetle, Nicrophorus vespilloides

description: Male and female genital morphology varies widely across many taxa, and
 even among populations. Disentangling potential sources of selection on
 genital morphology is problematic because each sex is predicted to respond
 to adaptations in the other due to reproductive conflicts of interest. To
 test how variation in this sexual conflict trait relates to variation in
 genital morphology we used our previously developed artificial selection
 lines for high and low repeated mating rates. We selected for high and low
 repeated mating rates using monogamous pairings to eliminate
 contemporaneous female choice and male-male competition. Male and female
 genital shape responded rapidly to selection on repeated mating rate. High
 and low mating rate lines diverged from control lines after only 10
 generations of selection. We also detected significant patterns of male
 and female genital shape coevolution among selection regimes. We argue
 that because our selection lines differ in sexual conflict, these results
 support the hypothesis that sexually antagonistic coevolution can drive
 the rapid divergence of genital morphology. The greatest divergence in
 morphology corresponded with lines in which the resolution of intrasexual
 conflict over mating rate was biased in favor of male interests.
description: Hopwood-Head-genitals_coevolve_2016Full data associated with: "Selection on an antagonistic behavioral trait can drive rapid genital coevolution in the burying beetle, Nicrophorus vespilloides". Description of data headings is included in Excel worksheets.
DOI: 10.5061/dryad.q2m38
title: Data from: Opposite effects of anthelmintic treatment on microbial infection at individual versus population scales

description: Parasitic worms modulate host immune responses in ways that affect
 microbial co-infections. For this reason, anthelmintic therapy may be a
 potent tool for indirectly controlling microbial pathogens. However, the
 population-level consequences of this type of intervention on co-infecting
 microbes are unknown. We evaluated the effects of anthelmintic treatment
 on bovine tuberculosis (BTB) acquisition, mortality after infection, and
 pathogen fitness in free-ranging African buffalo. We found that treatment
 had no effect on the probability of BTB infection, but buffalo survival
 after infection was ninefold higher among treated individuals. These
 contrasting effects translated into an approximately eightfold increase in
 the reproductive number of BTB for anthelmintic-treated compared with
 untreated buffalo. Our results indicate that anthelmintic treatment can
 enhance the spread of microbial pathogens in some real-world situations.
description: pre-treatment_wormswormsifngneutrophilsBTBriskmortalitymortality_BTBneg
DOI: 10.5061/dryad.mr62h68
title: Data from: The importance of individual heterogeneity for interpreting faecal glucocorticoid metabolite levels in wildlife studies

description: 1. Being a non-invasive and inexpensive method, the analysis of faecal
 corticosteroid metabolites (FCM) is increasingly being applied in wildlife
 research. Various environmental factors have been shown to influence FCM
 levels, but most studies did not account for inter-individual variance,
 which we hypothesized may substantially affect the results. 2. We combined
 FCM analysis with genetic analysis to identify the sex and individual of
 samples collected in three consecutive winters, with repeated samples per
 individual, across the entire range of an endangered population of
 capercaillie (Tetrao urogallus) in Southwestern Germany. Using generalized
 additive mixed models, we modelled FCM levels as a function of sex, season
 and environmental covariates at two spatial scales (sampling location and
 home range scales). We compared two models: one including information on
 the individual animal, and the other excluding this information (i.e.
 naïve model) to assess the influence of individual effects on the results
 obtained. 3. Most of the variance (44.0% and 45.1% at the sampling and
 home range scale, respectively) was explained by the inter-individual
 differences, and only very little (4.0% and 5.1%, respectively) by the
 environmental predictors. When ignoring individual effects, the model
 results changed considerably, with other, previously non-informative
 predictors, becoming significant. 4. In the full models, accounting for
 inter-individual variance, no effect was found of weather conditions, at
 either scale. FCM levels were negatively correlated with habitat quality,
 at the sampling location, whereas human recreation at the home range scale
 led to elevated FCM levels. In the naïve models, two additional predictors
 appeared significant: one weather variable at local scales and two at home
 range scale. In all models, seasonal FCM patterns differed significantly
 between males and females. 5. Synthesis and applications. Our results
 highlight the importance of considering the effects of individual
 heterogeneity when studying FCM in wildlife research, as ignoring
 information on the individual might lead to erroneous conclusions.
 Combining FCM analyses with genetic analyses can be an efficient approach
 to adequately address this issue.21-Feb-2018
description: FCM
 dataData of FCM analysis of
 the paper: The importance of individual heterogeneity for interpreting
 faecal glucocorticoid metabolite levels in wildlife studies. J. Coppes,
 J-L. Kämmerle, M. Willert, A. Kohnen, R. Palme3, V.
 BraunischCoppes_etal_2018_JAE_Data_Dryad.xlsx
DOI: 10.5061/dryad.cv853
title: Data from: Effects of extreme weather on two sympatric Australian passerine bird species

description: Despite abundant evidence that natural populations are responding to
 climate change, there are few demonstrations of how extreme climatic
 events (ECEs) affect fitness. Climate warming increases adverse effects of
 exposure to high temperatures, but also reduces exposure to cold ECEs.
 Here, we investigate variation in survival associated with severity of
 summer and winter conditions, and whether survival is better predicted by
 ECEs than mean temperatures using data from two coexisting bird species
 monitored over 37 years in southwestern Australia, red-winged fairy-wrens,
 Malurus elegans and white-browed scrubwrens, Sericornis frontalis. Changes
 in survival were associated with temperature extremes more strongly than
 average temperatures. In scrubwrens, winter ECEs were associated with
 survival within the same season. In both species, survival was associated
 with body size, and there was evidence that size-dependent mortality was
 mediated by carry-over effects of climate in the previous season. For
 fairy-wrens, mean body size declined over time but this could not be
 explained by size-dependent mortality as the effects of body size on
 survival were consistently positive. Our study demonstrates how ECEs can
 have individual-level effects on survival that are not reflected in
 long-term morphological change, and the same climatic conditions can
 affect similar-sized, coexisting species in different ways.
description: Gardner et
 al.data.PhilTransBRaw
 data
DOI: 10.5061/dryad.82gn0
title: Data from: Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling

description: Transcription-regulating long non-coding RNAs (lncRNAs) have the potential
 to control the site-specific expression of thousands of target genes.
 Previously, we showed that Evf2, the first described ultraconserved
 lncRNA, increases the association of transcriptional activators (DLX
 homeodomain proteins) with key DNA enhancers but represses gene
 expression. In this report, mass spectrometry shows that the Evf2-DLX1
 ribonucleoprotein (RNP) contains the SWI/SNF-related chromatin remodelers
 Brahma-related gene 1 (BRG1, SMARCA4) and Brahma-associated factor
 (BAF170, SMARCC2) in the developing mouse forebrain. Evf2 RNA colocalizes
 with BRG1 in nuclear clouds and increases BRG1 association with key DNA
 regulatory enhancers in the developing forebrain. While BRG1 directly
 interacts with DLX1 and Evf2 through distinct binding sites, Evf2 directly
 inhibits BRG1 ATPase and chromatin remodeling activities. In vitro studies
 show that both RNA-BRG1 binding and RNA inhibition of BRG1
 ATPase/remodeling activity are promiscuous, suggesting that context is a
 crucial factor in RNA-dependent chromatin remodeling inhibition. Together,
 these experiments support a model in which RNAs convert an active enhancer
 to a repressed enhancer by directly inhibiting chromatin remodeling
 activity, and address the apparent paradox of RNA-mediated stabilization
 of transcriptional activators at enhancers with a repressive outcome. The
 importance of BRG1/RNA and BRG1/homeodomain interactions in
 neurodevelopmental disorders is underscored by the finding that mutations
 in Coffin–Siris syndrome, a human intellectual disability disorder,
 localize to the BRG1 RNA-binding and DLX1-binding domains.
description: Mass Spectrometry
 Data.Evf2++ Evf2TSTSMass spectrometry
 sequencing of DLX1 complexes isolated by affinity purification of mouse
 E13.5 embryonic brain ganglionic eminence nuclear extracts. Complexes are
 analyzed from Evf2+/+ (wildtype) and Evf2TSTS (lacking the Evf2 long
 noncoding RNA) mice, and shown in two Excel sheets.
DOI: 10.5061/dryad.46092
title: Data from: Sea-level driven glacial-age refugia and post-glacial mixing on subtropical coasts, a palaeohabitat and genetic study

description: Using a novel combination of palaeohabitat modelling and genetic mixture
 analyses, we identify and assess a sea-level-driven recolonization process
 following the Last Glacial Maximum (LGM). Our palaeohabitat modelling
 reveals dramatic changes in estuarine habitat distribution along the coast
 of California (USA) and Baja California (Mexico). At the LGM (approx. 20
 kya), when sea level was approximately 130 m lower, the palaeo-shoreline
 was too steep for tidal estuarine habitat formation, eliminating this
 habitat type from regions where it is currently most abundant, and
 limiting such estuaries to a northern and a southern refugium separated by
 1000 km. We assess the recolonization of estuaries formed during post-LGM
 sea-level rise through examination of refugium-associated alleles and
 approximate Bayesian computation in three species of estuarine fishes.
 Results reveal sourcing of modern populations from both refugia, which
 admix in the newly formed habitat between the refuges. We infer a dramatic
 peak in habitat area between 15 and 10 kya with subsequent decline.
 Overall, this approach revealed a previously undocumented dynamic and
 integrated relationship between sea-level change, coastal processes and
 population genetics. These results extend glacial refugial dynamics to
 unglaciated subtropical coasts and have significant implications for
 biotic response to predicted sea-level rise.
description: PRSB_qyc_forDIYABC_3popsinput data file for DIYABC v. 2 for Quietula y-caudaPRSB_fpa_forDIYABC_3pops_withoutFMA8,15input data file for DIYABC for Fundulus parvipinnisPRSB_gmi_forDIYABC_3popsinput data file for DIYABC for Gillichthys mirabilisMicrosatellite allele copy number dataallele copy number data for all 3 species used for the genetic Discriminant Function Analysis ('genetic DFA). Microsatellite fragment lengths are alleles, and individuals can have 0 copies of an allele, 1 copy of an allele (heterozygous) or 2 copies of an allele (homozygous).Microsatellite presence-absence data for DRYAD.xlsxforTraining_ModernPolygonAttributesHabitat attribute data (based on polygons meeting slope/bathymetry requirements in ArcGIS) for the modern (0 +/- 5 mbpsl) depth bin. These data were used to train the discriminant function analysis ('habitat DFA') to identify variables that predict presence (yes) or absence (no) of our focal species.Habitat Attribute DataPolygon attribute data on which the DFA and GLMs were performed to assess the habitat models.AreaPerTime26Aug2015_prsb.csvFMA28Apr2013_CONVERT_5Feb2014_STRUCTUREMicrosatellite data in input file for STRUCTURE for Fundulus parvipinnisGMA_30July2013_CONVERT_pac5Feb2014_STRUCTUREMicrosatellite data in STRUCTURE format for Gillichthys mirabilisQMA_26August2013_PACb_CONVERT_5Feb2014_STRUCTUREMicrosatellite data in STRUCTURE format for Quietula y-cauda