cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v3n85
title: Data from: Free-ranging farm cats: home range size and predation on a livestock unit in Northwest Georgia

description: This study’s objective was to determine seasonal and diurnal vs. nocturnal
 home range size, as well as predation for free-ranging farm cats at a
 livestock unit in Northwest Georgia. Seven adult cats were tracked with
 attached GPS units for up to two weeks for one spring and two summer
 seasons from May 2010 through August 2011. Three and five cats were
 tracked for up to two weeks during the fall and winter seasons,
 respectively. Feline scat was collected during this entire period. Cats
 were fed a commercial cat food daily. There was no seasonal effect (P
 &gt; 0.05) on overall (95% KDE and 90% KDE) or core home range size
 (50% KDE). Male cats tended (P = 0.08) to have larger diurnal and
 nocturnal core home ranges (1.09 ha) compared to female cats (0.64 ha).
 Reproductively intact cats (n = 2) had larger (P &lt; 0.0001) diurnal
 and nocturnal home ranges as compared to altered cats. Feline scat
 processing separated scat into prey parts, and of the 210 feline scats
 collected during the study, 75.24% contained hair. Of these 158 scat
 samples, 86 contained non-cat hair and 72 contained only cat hair. Other
 prey components included fragments of bone in 21.43% of scat and teeth in
 12.86% of scat. Teeth were used to identify mammalian prey hunted by these
 cats, of which the Hispid cotton rat (Sigmodon hispidus) was the primary
 rodent. Other targeted mammals were Peromyscus sp., Sylvilagus sp. and
 Microtus sp. Invertebrates and birds were less important as prey, but all
 mammalian prey identified in this study consisted of native animals. While
 the free-ranging farm cats in this study did not adjust their home range
 seasonally, sex and reproductive status did increase diurnal and nocturnal
 home range size. Ultimately, larger home ranges of free-ranging cats could
 negatively impact native wildlife.
description: Cat GPS data by cat,
 season, and day/nightFree-ranging cat GPS
 data for 2010-2011 by cat, season, and day/nightAll cat GPS data by cat,
 season, daynight.xlsxCat home range data
 (m2)Free-ranging cat home
 range data calculated by 95%, 90% and 50% kernel density
 estimationsCat HR data KDE
 11-6-13.xlsxCat Home Range (ha) by
 sex and repro status.xlsFree-ranging cat home
 range data (ha) by sex and reproductive status2010-2011 Cat Home Range by sex
 and repro status.xls.xlsbCat scat processing
 dataFree-ranging cat scat
 data with processed components, including bones, teeth, and
 hairKitts-Morgan Cat Project scat
 processing .xlsx
DOI: 10.5281/zenodo.18390841
title: Gallium-Assisted Platinum Isolation – Formation of Multiple Active Species in Ga-Pt Liquid Metal Catalysts
DOI: 10.5061/dryad.70ph0
title: Data from: The parasite’s long arm: a tapeworm parasite induces behavioural changes in uninfected group members of its social host

description: Parasites can induce alterations in host phenotypes in order to enhance
 their own survival and transmission. Parasites of social insects might not
 only benefit from altering their individual hosts, but also from inducing
 changes in uninfected group members. Temnothorax nylanderi ant workers
 infected with the tapeworm Anomotaenia brevis are known to be chemically
 distinct from nestmates and do not contribute to colony fitness, but are
 tolerated in their colonies and well cared-for. Here, we investigated how
 infected workers affect colony aggression by manipulating the presence of
 tapeworm-infected workers and analysing whether their absence or presence
 resulted in behavioural alterations in their nestmates. We report a
 parasite-induced shift in colony aggression, shown by lower aggression of
 uninfected nestmates from parasitized colonies towards conspecifics,
 potentially explaining the tolerance towards infected ants. We also
 demonstrate that tapeworm-infected workers showed a reduced flight
 response and higher survival, while their presence caused a decrease in
 survival of uninfected nestmates. This anomalous behaviour within infected
 ants, coupled with their increased survival, could facilitate the
 parasites’ transmission to its definitive hosts, woodpeckers. We conclude
 that parasites exploiting individuals that are part of a society not only
 induce phenotypic changes within their individual hosts, but in uninfected
 group members as well.
description: Data_Beros et al.
 06.10.2015Data: Escape,
 Aggression, Acceptance, Survival
DOI: 10.5281/zenodo.18390840
title: Gallium-Assisted Platinum Isolation – Formation of Multiple Active Species in Ga-Pt Liquid Metal Catalysts
DOI: 10.5061/dryad.4gh70
title: Data from: Genome-wide association analysis for blood lipid traits measured in three pig populations revealed a substantial level of genetic heterogeneity

description: Serum lipids are associated with myocardial infarction and cardiovascular
 disease in humans. Here we dissected the genetic architecture of blood
 lipid traits by applying genome-wide association studies (GWAS) in 1,256
 pigs from Laiwu, Erhualian and Duroc × (Landrace × Yorkshire) populations,
 and a meta-analysis of GWAS in more than 2,400 pigs from five diverse
 populations. A total of 22 genomic loci surpassing the suggestive
 significance level were detected on 11 pig chromosomes (SSC) for six blood
 lipid traits. Meta-analysis of GWAS identified 5 novel loci associated
 with blood lipid traits. Comparison of GWAS loci across the tested
 populations revealed a substantial level of genetic heterogeneity for
 porcine blood lipid levels. We further evaluated the causality of nine
 polymorphisms nearby or within the APOB gene on SSC3 for serum LDL-C and
 TC levels. Of the 9 polymorphisms, an indel showed the most significant
 association with LDL-C and TC in Laiwu pigs. But the significant
 association was not identified in the White Duroc × Erhualian F2 resource
 population, in which the QTL for LDL-C and TC was also detected on SSC3.
 This indicates that population-specific signals may exist for the SSC3
 QTL. Further investigations are warranted to validate this assumption.
description: Genotype and phenotype
 primary dataFiles include genotype
 (*_gens.ped & *_gens.map) and phenotype (*_phens.txt) for the GWAS and
 single marker association analysis (SMA). In GWAS file, the alleles are
 recoded as 1 and 2. In SMA file, a total of nine mutations were genotyped.
 All missing data of genotype files are recoded as 0, and missing data of
 phenotype files as NA.Primary_data.zip
DOI: 10.5061/dryad.b2t2f
title: Data from: Detecting adaptive evolution in phylogenetic comparative analysis using the Ornstein-Uhlenbeck model

description: Phylogenetic comparative analysis is an approach to inferring evolutionary
 process from a combination of phylogenetic and phenotypic data. The last
 few years have seen increasingly sophisticated models employed in the
 evaluation of more and more detailed evolutionary hypotheses, including
 adaptive hypotheses with multiple selective optima and hypotheses with
 rate variation within and across lineages. The statistical performance of
 these sophisticated models has received relatively little systematic
 attention, however. We conducted an extensive simulation study to quantify
 the statistical properties of a class of models toward the simpler end of
 the spectrum that model phenotypic evolution using Ornstein–Uhlenbeck
 processes. We focused on identifying where, how, and why these methods
 break down so that users can apply them with greater understanding of
 their strengths and weaknesses. Our analysis identifies three key
 determinants of performance: a discriminability ratio, a signal-to-noise
 ratio, and the number of taxa sampled. Interestingly, we find that
 model-selection power can be high even in regions that were previously
 thought to be difficult, such as when tree size is small. On the other
 hand, we find that model parameters are in many circumstances difficult to
 estimate accurately, indicating a relative paucity of information in the
 data relative to these parameters. Nevertheless, we note that accurate
 model selection is often possible when parameters are only weakly
 identified. Our results have implications for more sophisticated methods
 inasmuch as the latter are generalizations of the case we study.
description: Cressler_Butler_King_App_ASupplementary plotsCressler_Butler_King_App_BGeneralized additive model regression detailsSimulation study codeCodes for exactly reproducing the results of this simulation studysimstudy.zip
DOI: 10.5061/dryad.h13vg
title: Data from: Patterns and drivers of intraspecific variation in avian life history along elevational gradients: a meta-analysis

description: Elevational gradients provide powerful natural systems for testing
 hypotheses regarding the role of environmental variation in the evolution
 of life-history strategies. Case studies have revealed shifts towards
 slower life histories in organisms living at high elevations yet no
 synthetic analyses exist of elevational variation in life-history traits
 for major vertebrate clades. We examined (i) how life-history traits
 change with elevation in paired populations of bird species worldwide, and
 (ii) which biotic and abiotic factors drive elevational shifts in life
 history. Using three analytical methods, we found that fecundity declined
 at higher elevations due to smaller clutches and fewer reproductive
 attempts per year. By contrast, elevational differences in traits
 associated with parental investment or survival varied among studies.
 High-elevation populations had shorter and later breeding seasons, but
 longer developmental periods implying that temporal constraints contribute
 to reduced fecundity. Analyses of clutch size data, the trait for which we
 had the largest number of population comparisons, indicated no evidence
 that phylogenetic history constrained species-level plasticity in trait
 variation associated with elevational gradients. The magnitude of
 elevational shifts in life-history traits were largely unrelated to
 geographic (altitude, latitude), intrinsic (body mass, migratory status),
 or habitat covariates. Meta-population structure, methodological issues
 associated with estimating survival, or processes shaping range boundaries
 could potentially explain the nature of elevational shifts in life-history
 traits evident in this data set. We identify a new risk factor for montane
 populations in changing climates: low fecundity will result in lower
 reproductive potential to recover from perturbations, especially as fewer
 than half of the species experienced higher survival at higher elevations.
description: Avian Life History Trait
 DatasetCore dataset upon which
 the study was based. Details of contents described in the ReadMe
 file.ALHTDataset.csvALHTTreesFileFile containing 500 phylogenetic trees for the taxa included in tests of phylogenetic signal in responses of clutch size to elevational differences as described in the README file associated with the main data file.
DOI: 10.5061/dryad.c8g52
title: Data from: Development of circadian oscillators in neurosphere cultures during adult neurogenesis

description: Circadian rhythms are common in many cell types but are reported to be
 lacking in embryonic stem cells. Recent studies have described possible
 interactions between the molecular mechanism of circadian clocks and the
 signaling pathways that regulate stem cell differentiation. Circadian
 rhythms have not been examined well in neural stem cells and progenitor
 cells that produce new neurons and glial cells during adult neurogenesis.
 To evaluate circadian timing abilities of cells undergoing neural
 differentiation, neurospheres were prepared from the mouse subventricular
 zone (SVZ), a rich source of adult neural stem cells. Circadian rhythms in
 mPer1 gene expression were recorded in individual spheres, and cell types
 were characterized by confocal immunofluorescence microscopy at early and
 late developmental stages in vitro. Circadian rhythms were observed in
 neurospheres induced to differentiate into neurons or glia, and rhythms
 emerged within 3–4 days as differentiation proceeded, suggesting that the
 neural stem cell state suppresses the functioning of the circadian clock.
 Evidence was also provided that neural stem progenitor cells derived from
 the SVZ of adult mice are self-sufficient clock cells capable of producing
 a circadian rhythm without input from known circadian pacemakers of the
 organism. Expression of mPer1 occurred in high frequency oscillations
 before circadian rhythms were detected, which may represent a role for
 this circadian clock gene in the fast cycling of gene expression
 responsible for early cell differentiation.
description: PLoS ONE
 DataPLoS ONE
 Repository.zip
DOI: 10.5061/dryad.802
title: Data from: Delimiting Species Using DNA and Morphological Variation and Discordant Species Limits in Spiny Lizards (Sceloporus)

description: Haplotype phylogenies based on DNA sequence data are increasingly being
 used to test traditional species-level taxonomies based on morphology.
 However, few studies have critically compared species limits based on
 morphological and DNA data, and the methods used to delimit species using
 either type of data are only rarely explained. In this paper, we review
 three approaches for species delimitation (tree-based with DNA data and
 tree-based and character-based with morphological data) and propose
 explicit protocols for each. We then compare species limits inferred from
 these approaches, using morphological and mtDNA data for the Yarrow's
 spiny lizard (Sceloporus jarrovii), a traditionally polytypic species from
 the southwestern United States and Mexico. All three approaches support
 division of S. jarrovii into five species, but only two species are the
 same among the three approaches. We find the greatest support for the five
 species that are delimited based on mtDNA data, and we argue that mtDNA
 data may have important (and previously unappreciated) advantages for
 species delimitation. Because different data and approaches can disagree
 so extensively, our results demonstrate that the methodology of species
 delimitation is a critical issue in systematics.
description: Appendix
 1-1apdx1-1.pdfAppendix 1-2apdx1-2.pdfAppendix 3-4apndx3-4.pdfAppendix 3-5apndx3-5.pdfAppendix 3-6apndx3-6.pdfAppendix 3-7apndx3-7.pdfAppendix 3-8apndx3-8.pdfAppendix 1-3apdx1-3.pdfAppendix 1-4apdx1-4.pdfAppendix 2-1apndx2-1.pdfAppendix 2-2apndx2-2.pdfAppendix 2-3apndx2-3.pdfAppendix 3-1apndx3-1.pdfAppendix 3-2apndx3-2.pdfAppendix 3-3apndx3-3.pdf
DOI: 10.5061/dryad.8023
title: Data from: Multiplex preamplification PCR and microsatellite validation allows accurate single nucleotide polymorphism (SNP) genotyping of historical fish scales

description: Incorporating historical tissues into the study of ecological,
 conservation, and management questions can broaden the scope of population
 genetic research by enhancing our understanding of evolutionary processes
 and anthropogenic influences on natural populations. Genotyping historical
 and low-quality samples has been plagued by challenges associated with low
 amounts of template DNA and the potential for preexisting DNA
 contamination among samples. We describe a two-step process designed to
 (i) accurately genotype large numbers of historical low-quality scale
 samples in a high-throughput format and (ii) screen samples for
 preexisting DNA contamination. First, we describe how an efficient
 multiplex preamplification PCR of 45 single nucleotide polymorphisms
 (SNPs) can generate highly accurate genotypes with low failure and error
 rates in subsequent SNP genotyping reactions of individual historical
 scales from sockeye salmon (Oncorhynchus nerka). Second, we demonstrate
 how the method can be modified for the amplification of microsatellite
 loci to detect preexisting DNA contamination. A total of 760 individual
 historical scale and 182 contemporary fin clip samples were genotyped and
 screened for contamination. Genotyping failure and error rates were
 exceedingly low and similar for both historical and contemporary samples.
 Preexisting contamination in 21% of the historical samples was
 successfully identified by screening the amplified microsatellite loci.
 The potential for automation, low failure and error rates, and ability to
 multiplex both the preamplification and subsequent genotyping reactions
 combine to make the protocol ideally suited for efficiently genotyping
 large numbers of potentially contaminated low-quality sources of DNA.
description: Combined_Invalidated_SEGEG65Genotypic data from historical sockeye salmon scales representing harvests occurring in the Egegik Fishing District in Bristol Bay, AK in 1965. SNP genotypes were generated with Taqman Assays in Fluidigm 96.96 Dynamic Arrays that were read on a Fluidigm Biomark instrument.Combined_Invalidated_SEGEG93Genotypic data from historical sockeye salmon scales representing harvests occurring in the Egegik Fishing District in Bristol Bay, AK in 1993. SNP genotypes were generated with Taqman Assays in Fluidigm 96.96 Dynamic Arrays that were read on a Fluidigm Biomark instrument.
DOI: 10.5061/dryad.5q7kf
title: Data from: Dissemination, divergence and establishment of H7N9 influenza viruses in China

description: Since 2013 the occurrence of human infections by a novel avian H7N9
 influenza virus in China has demonstrated the continuing threat posed by
 zoonotic pathogens. Although the first outbreak wave that was centred on
 eastern China was seemingly averted, human infections recurred in October
 2013. It is unclear how the H7N9 virus re-emerged and how it will develop
 further; potentially it may become a long-term threat to public health.
 Here we show that H7N9 viruses have spread from eastern to southern China
 and become persistent in chickens, which has led to the establishment of
 multiple regionally distinct lineages with different reassortant
 genotypes. Repeated introductions of viruses from Zhejiang to other
 provinces and the presence of H7N9 viruses at live poultry markets have
 fuelled the recurrence of human infections. This rapid expansion of the
 geographical distribution and genetic diversity of the H7N9 viruses poses
 a direct challenge to current disease control systems. Our results also
 suggest that H7N9 viruses have become enzootic in China and may spread
 beyond the region, following the pattern previously observed with H5N1 and
 H9N2 influenza viruses.
description: Phylogenetic trees of
 H7N9 and related influenza A virusesDryad_FigS1-S4_TableS1.pdf
DOI: 10.15468/dl.bc6zgg
title: Occurrence Download

description: A dataset containing 2663 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-75.00561 6.00141,-75.00296 5.99464,-74.98619 5.99276,-74.97888 6.00204,-74.98115 6.0132,-74.99111 6.01984,-75.00119 6.02034,-75.01128 6.01207,-75.00989 6.00279,-75.00561 6.00141))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 2663 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001626-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8029
title: Data from: Development of 54 novel SNP assays for sockeye and coho salmon and assessment of available SNPs to differentiate stocks within the Columbia River

description: Single nucleotide polymorphisms (SNPs) have potential for broad
 application in population and conservation genetics, but availability of
 these markers are limited in many non-model species. In this study,
 genomic and expressed sequence tagged (EST) sequences from closely related
 salmonids (Chinook salmon, and rainbow trout) were used to design primers
 for amplification and sequencing of sockeye (Oncorhynchus nerka) and coho
 (O. kisutch) salmon DNA for SNP discovery. One-hundred and six primer sets
 were designed and tested for amplification in each species. An
 ascertainment panel of 32 diverse individuals from each species was used
 as template for PCR amplification and Sanger sequencing. In total 21,647
 bases of consensus sequence were screened in sockeye salmon and 20,784
 bases in coho salmon with 93 and 149 SNP sites identified, respectively.
 Sixty four SNP sites were chosen for assay development and 54 of the
 assays were validated by comparison of genotype and sequence data (O.
 nerka = 23; O. kisutch = 31). These validated SNP assays along with 142
 other available SNP assays (O. nerka = 103 [126 total]; O. kisutch = 30[61
 total]) were used to genotype collections of O. nerka (N = 5) and O.
 kisutch (N = 4) from various sites in the Columbia River to evaluate the
 utility of these markers in this region. Results from factorial
 correspondence analysis (FCA) indicate that these SNP markers are capable
 of distinguishing O. nerka populations, but O. kisutch collections were
 less distinct due to their common ancestry.
description: Sequence
 alignments.zip file contains
 aligned sequence data from which SNPs were identified and assays were
 created.Fasta
 aligned.zipObserved SNPs and
 Genotype dataDescribes observed SNPs
 from sequence alignments. Also included are genotype data from which
 descriptive statistics and FCA plots were created.Dryad-data.xls
DOI: 10.15468/dl.nka3j6
title: Occurrence Download

description: A dataset containing 3741 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Teleogryllus emma"
 ]
}

 The dataset includes 3741 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001627-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fr075
title: Data from: Predicting ground temperatures across European landscapes

description: 1. Ambient temperatures in natural environments can vary widely over short
 distances, especially on rugged ground where exposure to solar radiation
 depends on slope and aspect. Temperatures can also fluctuate rapidly,
 reaching values not revealed by climate data. Such fine-scale variation
 raises challenges for modelling species distributions under changing
 climates. 2. To avoid misunderstanding current species distributions and
 future changes, temperatures must be modelled at high resolutions. Most
 existing methods either require extensive parameterisation or are
 pre-parameterised for restricted localities and current conditions; here
 we describe a more versatile method intended for European landscapes under
 a wide range of scenarios. 3. The availability of high-resolution
 topographic data makes possible the use of projected solar irradiation to
 help predict local diurnal ground temperatures. Using time series from 83
 points across Europe, we fitted statistical models for soil surface
 temperature based on geographical characteristics of the sites along with
 atmospheric variables obtained from a publicly-available database. The
 sites ranged from 40°N to 60°N and 2°W to 25°E, and from 43m to 1500m in
 elevation. 4. We compare models for monthly mean and daily afternoon
 temperatures, for open and tree-covered habitats. The effect of topography
 was greatest for the daily predictions, and generally more important in
 open than in tree-covered sites. Tests with data collected from other
 European locations in a different time period suggest that our models can
 predict monthly means with an error standard deviation of 2.7°C. We
 provide an R function that implements our models on the basis of
 readily-available data. 5. Our mean-temperatures model should be useful
 for understanding organisms’ niches, dispersal possibilities and community
 dynamics, and for predicting species’ refugia, range shifts and
 opportunities for adaptation under projected climate change.
description: Microclimate
 dataRecorded soil
 temperatures for two sets of sites in Europe, from two different periods.
 Accompanied by summaries of modelled climate data from public
 sources.MCMdata_public_full.xlsx