cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gt377
title: Data from: A critical evaluation of how ancient DNA bulk bone metabarcoding complements traditional morphological analysis of fossil assemblages

description: When pooled for extraction as a bulk sample, the DNA within
 morphologically unidentifiable fossil bones can, using next-generation
 sequencing, yield valuable taxonomic data. This method has been proposed
 as a means to rapidly and cost-effectively assess general ancient DNA
 preservation at a site, and to investigate temporal and spatial changes in
 biodiversity; however, several caveats have yet to be considered. We
 critically evaluated the bulk bone metabarcoding (BBM) method in terms of
 its: (i) repeatability, by quantifying sampling and technical variance
 through a nested experimental design containing sub-samples and replicates
 at several stages; (ii) accuracy, by comparing morphological and molecular
 family-level identifications; and (iii) overall utility, by applying the
 approach to two independent Holocene fossil deposits, Bat Cave (Kangaroo
 Island, Australia) and Finsch's Folly (Canterbury, New Zealand). For
 both sites, bone and bone powder sub-sampling were found to contribute
 significantly to variance in molecularly identified family assemblage,
 while the contribution of library preparation and sequencing was almost
 negligible. Nevertheless, total variance was small. Sampling over 80%
 fewer bones than was required to morphologically identify the taxonomic
 assemblages, we found that the families identified molecularly are a
 subset of the families identified morphologically and, for the most part,
 represent the most abundant families in the fossil record. In addition, we
 detected a range of extinct, extant and endangered taxa, including some
 that are rare in the fossil record. Given the relatively low sampling
 effort of the BBM approach compared with morphological approaches, these
 results suggest that BBM is largely consistent, accurate, sensitive, and
 therefore widely applicable. Furthermore, we assessed the overall benefits
 and caveats of the method, and suggest a workflow for palaeontologists,
 archaeologists, and geneticists that will help mitigate these caveats. Our
 results show that DNA analysis of bulk bone samples can be a universally
 useful tool for studying past biodiversity, when integrated with existing
 morphology-based approaches. Despite several limitations that remain, the
 BBM method offers a cost-effective and efficient way of studying fossil
 assemblages, offering complementary insights into evolution, extinction,
 and conservation.
description: BC_FF_filtered_fasta_filesFASTA files of filtered Illumina NGS reads for both sequencing runs, for both Bat Cave and Finsch's Folly bulk bone pools, and bulk bone powder sub-samples (extracts). MB numbers in the file names refer to the extract (see Supplementary Information Table IV in the online version of the article for details regarding which extracts were sub-sampled from the same bulk bone pool). These are all the sequence reads, not just unique reads.
DOI: 10.5061/dryad.8k823
title: Data from: Fixational eye movements predict visual sensitivity

description: During steady fixation, observers make small fixational saccades at a rate
 of around 1-2 per second. Presentation of a visual stimulus triggers a
 biphasic modulation in fixational saccade rate – an initial inhibition
 followed by a period of elevated rate and a subsequent return to baseline.
 Here we show that, during passive viewing, this rate signature is highly
 sensitive to small changes in stimulus contrast. By training a linear
 support vector machine to classify trials in which a stimulus is either
 present or absent, we directly compared the contrast sensitivity of
 fixational eye movements with individuals’ psychophysical judgements.
 Classification accuracy closely matched psychophysical performance and
 predicted individuals’ threshold estimates with less bias and overall
 error than those obtained using specific features of the signature.
 Performance of the classifier was robust to changes in the training set
 (novel subjects and/or contrasts) and good prediction accuracy was
 obtained with a practicable number of trials. Our results indicate a tight
 coupling between the sensitivity of visual perceptual judgements and
 fixational eye control mechanisms. This raises the possibility that
 fixational saccades could provide a novel and objective means of
 estimating visual contrast sensitivity without the need for observers to
 make any explicit judgement.
description: Data from: Fixational
 eye movements predict visual sensitivityData for 7 subjects and
 a file describing the data [MATLAB necessary for .mat and .m
 files]forDryad.zip
DOI: 10.5061/dryad.8m1v1
title: Data from: Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

description: Goats and sheep are versatile domesticates that have been integrated into
 diverse environments and production systems. Natural and artificial
 selection have shaped the variation in the two species but, natural
 selection has played the major role amongst indigenous flocks. To
 investigate signals of natural selection, we analyzed genotype data
 generated using the caprine and ovine 50K SNP BeadChips from Barki goats
 and sheep that are indigenous to a hot arid environment in Egypt's
 Coastal Zone of the Western Desert. We identify several candidate regions
 under selection that spanned 119 genes. A majority of the genes are
 involved in multiple signaling and, signal transduction pathways in a wide
 variety of cellular and biochemical processes. In particular, selection
 signatures spanning several genes which directly or indirectly influence
 traits for adaptation to hot arid environments, such as thermo-tolerance
 (melanogenesis) (FGF2, GNAI3, PLCB1), body size and development (BMP2,
 BMP4, GJA3, GJB2), energy and digestive metabolism (several MYH, TRHDE,
 ALDH1A3) and nervous and autoimmune response (GRIA1, IL2, IL7, IL21,
 IL1R1) are identified. We also identified eight common candidate genes
 under selection in the two species and a shared selection signature that
 spanned a conserved syntenic segment to bovine chromosome 12 on caprine
 and ovine chromosome 12 and 10 respectively, providing, most likely,
 evidence for selection in a common environment in two different but
 closely related species. Our study highlights the importance of indigenous
 livestock as model organisms for investigating selection sweeps and
 genome-wide association mapping.
description: Plink file data for
 Barki Ruminants (sheep and goats)The data contains SNP
 genotype data for Barki sheep and goats that can be used in
 Plink.plinkBarkiRuminants.zip
DOI: 10.5061/dryad.58k0t
title: Data from: Giving taxonomic significance to morphological variability in the bivalve Ptychomya Agassiz

description: The taxonomic significance of the morphological variability present in the
 genus Ptychomya Agassiz has remained obscure due to inadequacy of the
 traditional qualitative approach to account for complex patterns of
 variation. In this work, we focus on solving the distinction between
 intra- and interspecific variability in Ptychomya from Hauterivian marine
 beds of the Neuquén Basin (west-central Argentina), a longstanding and
 unresolved palaeontological issue, using the quantitative framework
 provided by geometric morphometrics and multivariate statistics. The
 species Ptychomya koeneni Behrendsen and several subspecies had been
 recognized in the studied succession by former authors based on
 qualitative morphological descriptions. We tested two hypotheses: (1) that
 there exist morphological discontinuities between hypothesized species
 that mark their boundaries; and (2) that morphology follows a pattern of
 geographical variation, suitable for recognition of subspecies. We find
 two morphological groups in the studied sample, with a significant
 morphological gap between them, supporting the idea that there are at
 least two species in the studied succession, Ptychomya cf. koeneni and
 Ptychomya coihuicoensis Weaver. On the other hand, we found no
 correspondence between morphological and geographical distributions,
 leading to the conclusion that the named subspecies are invalid taxa. This
 study highlights the potential of this methodological approach for solving
 the taxonomy of this notorious genus of pandemic distribution during the
 Cretaceous.
description: Ptychomya
 contoursDigitalized contours
 (JPG) of shell outlines and ribbing patterns in left lateral view of 60
 specimens belonging to the bivalve genus Ptychomya, from the upper
 Hauterivian of the Neuquén Basin, west-central
 Argentina.Data
 Ptychomya.rar
DOI: 10.5061/dryad.29fp0
title: Data from: A study of applicability of SNP chips developed for bovine and ovine species to whole-genome analysis of reindeer Rangifer tarandus

description: Two sets of commercially available single nucleotide polymorphisms (SNPs)
 developed for cattle (BovineSNP50 BeadChip) and sheep (OvineSNP50
 BeadChip) have been trialed for whole-genome analysis of 4 female samples
 of Rangifer tarandus inhabiting Russia. We found out that 43.0% of bovine
 and 47.0% of Ovine SNPs could be genotyped, while only 5.3% and 2.03% of
 them were respectively polymorphic. The scored and the polymorphic SNPs
 were identified on each bovine and each ovine chromosome, but their
 distribution was not unique. The maximal value of runs of homozygosity
 (ROH) was 30.93Mb (for SNPs corresponding to bovine chromosome 8) and
 80.32Mb (for SNPs corresponding to ovine chromosome 7). Thus, the SNP
 chips developed for bovine and ovine species can be used as a powerful
 tool for genome analysis in reindeer R. tarandus.
description: Data_file_Russian_ReindeerWhole-genome analysis of four female samples of Rangifer tarandus inhabiting Russia (Suppl_Bovine_Russian_Reindeer and Suppl_Ovine_Russian_Reindeer): 1-column -Chromosome; 2 column - SNP; 3- column –Control; 4 column-Allele1; 5 column –Allele2; 6 column -Number of homozygous animals1; 7 column -Number of heterozygous animals; 8 column -Number of homozygous animals2; 9 column -Observed heterozygosity; 10 column- Expected heterozygosity; 11-Hardy-Weinberg equilibrium; 12-Number of animals.
DOI: 10.5061/dryad.n5509
title: Data from: Increased land use by Chukchi Sea polar bears in relation to changing sea ice conditions

description: Recent observations suggest that polar bears (Ursus maritimus) are
 increasingly using land habitats in some parts of their range, where they
 have minimal access to their preferred prey, likely in response to loss of
 their sea ice habitat associated with climatic warming. We used location
 data from female polar bears fit with satellite radio collars to compare
 land use patterns in the Chukchi Sea between two periods (1986–1995 and
 2008–2013) when substantial summer sea-ice loss occurred. In both time
 periods, polar bears predominantly occupied sea-ice, although land was
 used during the summer sea-ice retreat and during the winter for maternal
 denning. However, the proportion of bears on land for &gt; 7 days
 between August and October increased between the two periods from 20.0% to
 38.9%, and the average duration on land increased by 30 days. The majority
 of bears that used land in the summer and for denning came to Wrangel and
 Herald Islands (Russia), highlighting the importance of these northernmost
 land habitats to Chukchi Sea polar bears. Where bears summered and denned,
 and how long they spent there, was related to the timing and duration of
 sea ice retreat. Our results are consistent with other studies supporting
 increased land use as a common response of polar bears to sea-ice loss.
 Implications of increased land use for Chukchi Sea polar bears are
 unclear, because a recent study observed no change in body condition or
 reproductive indices between the two periods considered here. This result
 suggests that the ecology of this region may provide a degree of
 resilience to sea ice loss. However, projections of continued sea ice loss
 suggest that polar bears in the Chukchi Sea and other parts of the Arctic
 may increasingly use land habitats in the future, which has the potential
 to increase nutritional stress and human-polar bear interactions.
description: Chukchi Sea Polar Bear
 Locations (2008-2013)These data are the
 locations (latitude and longitude) of polar bears in the Chukchi Sea that
 were used in the analysis by Rode et al. The data include the date and
 time of the location, the unique identifier of the bear the locations are
 from, and the accuracy classification of the location. Location accuracy
 is based on Argos error classes (3,2,1,0,A,B). If a location was obtained
 from GPS, its accuracy is labeled as 'GPS'.CS_Data2008-2013.csv
DOI: 10.5061/dryad.57f3t
title: Data from: The dipnoan buccal pump reconstructed in 3D and implications for air breathing in Devonian lungfishes

description: Lungfishes are known for, and indeed take their name from, their bimodal
 respiratory abilities. All three extant genera can use their lungs to
 extract oxygen from the atmosphere, although their reliance upon this
 capability differs among taxa. Lungs are considered primitive for the
 Osteichthyes, however the distinctive buccal pump mode of air gulping
 exhibited by extant lungfishes appears to be a specialization. It is
 associated with a number of derived skeletal characters (cranial ribs,
 long parasphenoid stalk, midline gap between palatal tooth plates) that
 first appeared during the Devonian. These have been described
 individually, but in no Devonian lungfish has their three-dimensional (3D)
 spatial relationship been reconstructed and analyzed. Here we present the
 3D morphology of Rhinodipterus, a Mid-Late Devonian lungfish from
 Australia and Europe, based on synchrotron tomography and conventional
 microtomography scans. Unlike less crownward contemporaneous lungfishes
 such as Griphognathus and Chirodipterus, Rhinodipterus has a full set of
 skeletal buccal pump components that can be directly compared to those of
 extant lungfishes, suggesting that it made more extensive use of air
 breathing than other Gogo or Bergisch Gladbach genera. This is interesting
 in relation to the environmental context as Gogo and Bergisch Gladbach are
 both marine, contrasting with the frequently hypoxic tropical to
 subtropical fresh water environments inhabited by modern lungfishes. The
 evolution of buccal pump-supported lung ventilation was evidently not
 necessarily associated with a transition to non-marine habitats.
description: SI:1 Rhinodipterus
 buccal pump complex in 3DReconstruction animation
 of the dipnoan buccal pump complex in 3D, using combined elements from R.
 kimberleyensis WAM 09.6.149 (skull, mandible, anocleithrum), and R.
 ulrichi NRM P6609a (pectoral girdle, occipital, cranial
 rib).SI1
 Rhino_BPcomplex_3D_movie.aviSI:2 Characters and
 matrixCharacters and matrix
 used for cladistic analysis for position of Rhinodipterus
 kimberleyensisSI2 Appendix_S1_AMC
 copy.txtSI:3 Corrected codings
 from analysis of Pardo et al. (2014)Detailed responses to
 erroneous codings incorporated into the cladistic analysis of Pardo et al
 (2014), now corrected in the current analysis.SI3 Corrected
 codings.docx
DOI: 10.5061/dryad.8tm76
title: Data from: Genealogical working distributions for Bayesian model testing with phylogenetic uncertainty

description: Marginal likelihood estimates to compare models using Bayes factors
 frequently accompany Bayesian phylogenetic inference. Approaches to
 estimate marginal likelihoods have garnered increased attention over the
 past decade. In particular, the introduction of path sampling (PS) and
 stepping-stone sampling (SS) into Bayesian phylogenetics has tremendously
 improved the accuracy of model selection. These sampling techniques are
 now used to evaluate complex evolutionary and population genetic models on
 empirical data sets, but considerable computational demands hamper their
 widespread adoption. Further, when very diffuse, but proper priors are
 specified for model parameters, numerical issues complicate the
 exploration of the priors, a necessary step in marginal likelihood
 estimation using PS or SS. To avoid such instabilities, generalized SS
 (GSS) has recently been proposed, introducing the concept of “working
 distributions” to facilitate - or shorten - the integration process that
 underlies marginal likelihood estimation. However, the need to fix the
 tree topology currently limits GSS in a coalescent-based framework. Here,
 we extend GSS by relaxing the fixed underlying tree topology assumption.
 To this purpose, we introduce a “working” distribution on the space of
 genealogies, that enables estimating marginal likelihoods while
 accommodating phylogenetic uncertainty. We propose two different “working”
 distributions that help GSS to outperform PS and SS in terms of accuracy
 when comparing demographic and evolutionary models applied to synthetic
 data and real-world examples. Further, we show that the use of very
 diffuse priors can lead to a considerable overestimation in marginal
 likelihood when using PS and SS, while still retrieving the correct
 marginal likelihood using both GSS approaches. The methods used in this
 paper are available in BEAST, a powerful user-friendly software package to
 perform Bayesian evolutionary analyses.
description: Supplementary
 informationSupplementary
 information to ``Genealogical working distributions for Bayesian model
 testing with phylogenetic uncertainty'' by Guy Baele, Philippe
 Lemey and Marc A. SuchardBaele_SuppMat.pdf
DOI: 10.5061/dryad.751cv
title: Data from: Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

description: Interspecies hybridization has been recently recognized as potentially
 common in wild animals, but the extent to which it shapes modern genomes
 is still poorly understood. Distinguishing historical hybridization events
 from other processes leading to phylogenetic discordance among different
 markers requires a well-resolved species tree that considers all modes of
 inheritance, and overcomes systematic problems due to rapid lineage
 diversification by sampling large genomic character sets. Here we assessed
 genome-wide phylogenetic variation across a diverse mammalian family,
 Felidae (cats). We combined genotypes from a genome-wide SNP array with
 additional autosomal, X- and Y-linked variants to sample ~150 kilobases of
 nuclear sequence, in addition to complete mitochondrial genomes generated
 using light-coverage Illumina sequencing. We present the first robust
 felid timetree that accounts for unique maternal, paternal, and biparental
 evolutionary histories. Signatures of phylogenetic discordance were
 abundant in the genomes of modern cats, in many cases indicating
 hybridization as the most likely cause. Comparison of big cat whole-genome
 sequences revealed a substantial reduction of X-linked divergence times
 across several large recombination coldspots, which were highly enriched
 for signatures of selection-driven post-divergence hybridization between
 the ancestors of the snow leopard and lion lineages. These results
 highlight the mosaic origin of modern felid genomes and the influence of
 sex chromosomes and sex-biased dispersal in post-speciation gene flow. A
 complete resolution of the Tree of Life will require comprehensive genomic
 sampling of biparental and sex-limited genetic variation to identify and
 control for phylogenetic conflict caused by ancient admixture and
 sex-biased differences in genomic transmission.
description: Felidae_SNPmatrix_Dryad
DOI: 10.5518/1501
title: Subchondral bone morphology of ankle in healthy and arthritic joints.

description: This dataset contains the morphological parameters of arthritic and non-diseased ankle bones, and donor characteristics for the non-diseased tissues. Non-diseased specimens were collected from a tissue bank, and had no history of lower limb trauma or OA, and the arthritic tissues were collected from donors undergoing ankle replacement or fusion surgery for ankle osteoarthritis.
DOI: 10.5061/dryad.qs552
title: Data from: Identification of migratory bird flyways in North America using community detection on biological networks

description: Migratory behavior of waterfowl populations in North America has
 traditionally been broadly characterized by four north-south flyways, and
 these flyways have been central to the management of waterfowl populations
 for more than 80 years. However, previous flyway characterizations are not
 easily updated with current bird movement data and fail to provide
 assessments of the importance of specific geographical regions to the
 identification of flyways. Here, we developed a network model of migratory
 movement for four waterfowl species —mallard (Anas platyrhnchos), northern
 pintail (A. acuta), American green-winged teal (A. carolinensis), and
 Canada goose (Branta canadensis) — in North America using bird band and
 recovery data. We then identified migratory flyways using a community
 detection algorithm and characterize the importance of smaller geographic
 regions in identifying flyways using a novel metric, the consolidation
 factor. We identified four main flyways for mallards, northern pintails,
 and American green-winged teal with the flyway identification in Canada
 geese exhibiting higher complexity. For mallards, flyways were relatively
 consistent through time. However, consolidation factors revealed that for
 mallards and green-winged teal the presumptive Mississippi flyway was
 potentially a zone of high mixing between other flyways. Our results
 demonstrate that the network approach provides a robust method for flyway
 identification that is widely applicable given the relatively minimal data
 requirements and is easily updated with future movement data to reflect
 changes in flyway definitions and management goals.
description: Band encounter data from
 hunter recovered mallards (MALL), northern pintails (NOPI), American
 green-winged teal (AGWT), and Canada geese (CAGO) between 2004 and 2013 in
 North America.Included fields are the
 band number (BAND), species (SPEC), banding date (BMONTH, BDAY, BYEAR),
 recovery date (RMONTH, RDAY, RYEAR), banding location reported at the node
 level (BNODELAT, BNODELONG), and recovery location reported at the node
 level (RNODELAT, RNODELONG). For information on requesting the full band
 and encounter data, please go to
 https://www.pwrc.usgs.gov/BBL/homepage/datarequest.cfm.BandData_2014Feb12.csv
DOI: 10.15468/dl.dudyzw
title: Occurrence Download

description: A dataset containing 136 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((6.2486 43.93459,6.37107 43.85137,6.45155 43.8766,6.49004 43.92703,6.46554 44.02146,6.40781 44.08684,6.32908 44.08307,6.27309 44.03781,6.19087 44.029,6.07715 43.93711,5.8812 43.89804,5.87945 43.86399,6.03341 43.87408,6.2486 43.93459))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Buddleja davidii"
 ]
}

 The dataset includes 136 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001655-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.