cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dd91b
title: Data from: Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs

description: Knowledge on the genetic epidemiology of disorders in the dog population
 has implications for both veterinary medicine and sustainable breeding.
 Limited data on frequencies of genetic disease variants across breeds
 exists, and the disease heritage of mixed breed dogs remains poorly
 explored to date. Advances in genetic screening technologies now enable
 comprehensive investigations of the canine disease heritage, and generate
 health-related big data that can be turned into action. We pursued
 population screening of genetic variants implicated in Mendelian disorders
 in the largest canine study sample examined to date by examining around
 83,000 mixed breed and 18,000 purebred dogs representing 330 breeds for
 152 known variants using a custom-designed beadchip microarray. We further
 announce the creation of MyBreedData (www.mybreeddata.com), an online
 updated inherited disorder prevalence resource with its foundation in the
 generated data. We identified the most prevalent, and rare, disease
 susceptibility variants across the general dog population while providing
 the first extensive snapshot of the mixed breed disease heritage. Around 2
 in 5 dogs carried at least one copy of a tested disease variant. Most
 disease variants are shared by both mixed breeds and purebreds, while
 breed- or line-specificity of others is strongly suggested. Mixed breed
 dogs were more likely to carry a common recessive disease, whereas
 purebreds were more likely to be genetically affected with one, providing
 DNA-based evidence for hybrid vigor. We discovered genetic presence of 22
 disease variants in at least one additional breed in which they were
 previously undescribed. Some mutations likely manifest similarly
 independently of breed background; however, we emphasize the need for
 follow up investigations in each case and provide a suggested validation
 protocol for broader consideration. In conclusion, our study provides
 unique insight into genetic epidemiology of canine disease risk variants,
 and their relevance for veterinary medicine, breeding programs and animal
 welfare.
description: Full genotype
 datasetCustom Illumina®
 Infinium HD microarray generated genotypes for 152 Mendelian disease
 variants in 100K canids. Information on breed and each sample's
 geographic region of origin also included. A1 = wild type allele; A2 =
 disease allele.Full_genotype_dataset.xlsx
DOI: 10.5061/dryad.rp2js
title: Data from: Digging their own macroevolutionary grave: Fossoriality as an evolutionary dead-end in snakes

description: The tree of life is highly asymmetrical in its clade wise species richness
 and this has often been attributed to variation in diversification rates
 either across time or lineages. Variations across lineages are usually
 associated with traits that increase lineage diversification. Certain
 traits can also hinder diversification by increasing extinction and such
 traits are called evolutionary dead-ends. Ecological specialization has
 usually been considered as an evolutionary dead-end. However, recent
 analyses of specializations along single axes have provided mixed support
 for this model. Here, we test if fossoriality, a trait that forces
 specialization at multiple axes, acts as an evolutionary dead-end in
 squamates (lizards and snakes) using recently developed phylogenetic
 comparative methods. We show that fossoriality is an evolutionary dead-end
 in snakes but not in lizards. Fossorial snakes exhibit reduced speciation
 and increased extinction compared to non-fossorial snakes. Our analysis
 also indicates that transition rates from fossoriality to non-fossoriality
 in snakes are significantly lower than transition rates from
 non-fossoriality to fossoriality. Overall our results suggest that broad
 scale ecological interactions that lead to specialization at multiple axes
 limit diversification.
description: Appendix
 S1_Table1_Snake_microhabitat_dataMicrohabitat data
 described as fossorial and non-fossorial along with references for 1256
 species of snakesAppendix_S1_Table_SuppInfo_Snake_microhabitat_data_22Dec.xlsxAppendix_S2_Table2_Lizard_microhabitat_dataMicrohabitat data described as fossorial and non-fossorial compiled for 822 species of lizards from the GARD database (http://www.gardinitiative.org/data.html).Appendix_S2_Table_SuppInfo_Lizard_microhabitat_data.xlsxAppendix_S3_SupportingInfoSupporting information containing results of model selection and parameter estimation from the BiSSE, HiSSE and STRAPP analyses carried out on the snake and lizard microhabitat data.Appendix_S4_supplementary methodsThe file describes the methods used to evaluate the effect of tip ratio bias on HISSE along with the results of the analyses.
DOI: 10.5061/dryad.d1k50
title: Data from: Phenotypic integration and the evolution of signal repertoires: a case study of treefrog acoustic communication

description: Animal signals are inherently complex phenotypes with many interacting
 parts combining to elicit responses from receivers. The pattern of
 interrelationships between signal components reflects the extent to which
 each component is expressed, and responds to selection, either in concert
 with or independently of others. Furthermore, many species have complex
 repertoires consisting of multiple signal types used in different
 contexts, and common morphological and physiological constraints may
 result in interrelationships extending across the multiple signals in
 species’ repertoires. The evolutionary significance of interrelationships
 between signal traits can be explored within the framework of phenotypic
 integration, which offers a suite of quantitative techniques to
 characterize complex phenotypes. In particular, these techniques allow for
 the assessment of modularity and integration, which describe,
 respectively, the extent to which sets of traits covary either
 independently or jointly. Although signal and repertoire complexity are
 thought to be major drivers of diversification and social evolution, few
 studies have explicitly measured the phenotypic integration of signals to
 investigate the evolution of diverse communication systems. We applied
 methods from phenotypic integration studies to quantify integration in the
 two primary vocalization types (advertisement and aggressive calls) in the
 treefrogs Hyla versicolor, Hyla cinerea, and Dendropsophus ebraccatus. We
 recorded male calls and calculated standardized phenotypic
 variance–covariance (P) matrices for characteristics within and across
 call types. We found significant integration across call types, but the
 strength of integration varied by species and corresponded with the
 acoustic similarity of the call types within each species. H. versicolor
 had the most modular advertisement and aggressive calls and the least
 acoustically similar call types. Additionally, P was robust to changing
 social competition levels in H. versicolor. Our findings suggest new
 directions in animal communication research in which the complex
 relationships among the traits of multiple signals are a key consideration
 for understanding signal evolution.
description: Dendropsophus ebraccatus
 call dataCall data for
 Dendropsophus ebraccatus. See Readme file for more
 detailsDendropsophusebraccatus.txtHyla cinerea call dataCall data for Hyla cinerea. See Readme file for more detailsHylacinerea.txtHyla versicolor call dataCall data for Hyla versicolor. For more details see Readme file.Hylaversicolor.txt
DOI: 10.5061/dryad.4pd33
title: Data from: Assessing cetacean surveys throughout the Mediterranean Sea: a gap analysis in environmental space

description: Heterogeneous data collection in the marine environment has led to large
 gaps in our knowledge of marine species distributions. To fill these gaps,
 models calibrated on existing data may be used to predict species
 distributions in unsampled areas, given that available data are
 sufficiently representative. Our objective was to evaluate the feasibility
 of mapping cetacean densities across the entire Mediterranean Sea using
 models calibrated on available survey data and various environmental
 covariates. We aggregated 302,481 km of line transect survey effort
 conducted in the Mediterranean Sea within the past 20 years by many
 organisations. Survey coverage was highly heterogeneous geographically and
 seasonally: large data gaps were present in the eastern and southern
 Mediterranean and in non-summer months. We mapped the extent of
 interpolation versus extrapolation and the proportion of data nearby in
 environmental space when models calibrated on existing survey data were
 used for prediction across the entire Mediterranean Sea. Using model
 predictions to map cetacean densities in the eastern and southern
 Mediterranean, characterised by warmer, less productive waters, and more
 intense eddy activity, would lead to potentially unreliable
 extrapolations. We stress the need for systematic surveys of cetaceans in
 these environmentally unique Mediterranean waters, particularly in
 non-summer months.
description: Mediterranean gap
 analysis in environmental spaceThis .zip folder
 contains the data and an R script to reproduce the gap analysis documented
 in Mannocci et al. 2018.Data_Scientific_Reports.zip
DOI: 10.5061/dryad.8fk81
title: Data from: Genomic characterisation of the indigenous Irish Kerry cattle breed

description: Kerry cattle are an endangered landrace heritage breed of cultural
 importance to Ireland. In the present study we have used genome-wide SNP
 array data to evaluate genomic diversity within the Kerry population and
 between Kerry cattle and other European breeds. Patterns of genetic
 differentiation and gene flow among breeds using phylogenetic trees with
 ancestry graphs highlighted historical gene flow from the British
 Shorthorn breed into the ancestral population of modern Kerry cattle.
 Principal component analysis (PCA) and genetic clustering emphasised the
 genetic distinctiveness of Kerry cattle relative to comparator British and
 European cattle breeds. Modelling of genetic effective population size
 (Ne) revealed a demographic trend of diminishing Ne over time and that
 recent estimated Ne values for the Kerry breed may be less than the
 threshold for sustainable genetic conservation. In addition, analysis of
 genome-wide autozygosity (FROH¬) showed that genomic inbreeding has
 increased significantly during the 20 years between 1992 and 2012.
 Finally, signatures of selection revealed genomic regions subject to
 natural and artificial selection as Kerry cattle adapted to the climate,
 physical geography and agro-ecology of southwest Ireland.
description: KY92-KY12_SNP_dataKerry cattle (KY92 and KY12 population samples) Illumina® Bovine SNP50 BeadChip SNP genotype data in PLINK format.
DOI: 10.5061/dryad.kj2d3
title: Data from: Designing efficient hybrid strategies for information spreading in scale-free networks

description: Designing a spreading strategy is one of the critical issues strongly
 affecting spreading efficiency in complex networks. In this paper, to
 improve the efficiency of information spreading in scale-free networks, we
 propose four hybrid strategies by combing two basic strategies, i.e., (1)
 the LS (in which information is preferentially spread from the
 Large-degree vertices to the Small-degree ones) and (2) the SL (in which
 information is preferentially spread from the Small-degree vertices to the
 Large-degree ones). The objective in combining the two basic LS and SL
 strategies is to fully exploit the advantages of both strategies. To
 evaluate the spreading efficiency of the proposed four hybrid strategies,
 we first propose an information spreading model. Then, we introduce the
 details of the proposed hybrid strategies that are formulated by combining
 LS and SL. Third, we build a set of scale-free network structures by
 differently configuring the relevant parameters. In addition, finally, we
 conduct various Monte Carlo experiments to examine the spreading
 efficiency of the proposed hybrid strategies in different scale-free
 network structures. Experimental results indicate that the proposed hybrid
 strategies are effective and efficient for spreading information in
 scale-free networks.
description: Experimental
 ResultsThe Monte Carlo
 experimental results of spreading time in different complex
 networks.
DOI: 10.5061/dryad.873c4
title: Data from: The European Paromomyidae (Primates, Mammalia): taxonomy, phylogeny, and biogeographic implications

description: Plesiadapiforms represent the first radiation of Primates, appearing near
 the Cretaceous-Paleogene boundary. Eleven families of plesiadapiforms are
 recognized, including the Paromomyidae. Four species of paromomyids from
 the early Eocene have been reported from Europe: Arcius fuscus, Arcius
 lapparenti, and Arcius rougieri from France, and Arcius zbyszewskii from
 Portugal. Other Arcius specimens from the early Eocene are known from
 Masia de l’Hereuet (Spain), Abbey Wood (England), and Sotteville-sur-Mer
 (Normandy, France). A cladistic analysis of the European paromomyids has
 never previously been published. A total of 53 dental characters were
 analyzed for the four Arcius species and the specimens from Spain,
 England, and Normandy. The results of a parsimony analysis using TNT agree
 with previous conceptions of A. zbyszewskii as the most primitive member
 of the genus. Also consistent with existing hypotheses, Arcius rougieri is
 positioned as the sister taxon of A. fuscus and A. lapparenti, and the
 results suggest that the fossil from Normandy is A. zbyszewskii. However,
 the English fossil pertains to a primitive lineage, rather than grouping
 with A. lapparenti as had been suggested; as such it is recognized here as
 a distinct species (Arcius hookeri). The Spanish fossils cluster together
 with the French species, but do not show the previously proposed special
 relationship with A. lapparenti, and are sufficiently distinct to be
 placed in a new species (Arcius ilerdensis). Arcius is recovered as
 monophyletic, which is consistent with a single migration event from North
 America to Europe around the earliest Eocene though the Greenland land
 bridge.
description: Phylogenetic hypotheses
 of relationships of Arcius including A. ilerdensisFive most parsimonious
 trees once Arcius ilerdensis n. sp. is included. The strict consensus for
 these five trees is shown in Figure 10.4.LopezTorresandSilcoxFigureS1_2col.tifTerminologyDefinitions of hypoflexid, prehypoflexid cristid, postvallid, and protoconid-metaconid notch.Supplemental Data 1.docxNewick treesNewick format for trees from Figures 10, 11 and S1.Table 2.docxMatrixMatrix of 53 dental characters and 13 paromomyid speciesSupplemental Data 3.xlsx
DOI: 10.5061/dryad.87rb0
title: Data from: Estimating national population sizes: methodological challenges and applications illustrated in the common nightingale, a declining songbird in the UK

description: 1. Estimation of national population size can be important for setting
 conservation priorities but its methodology has received little critical
 attention. Sites for highly aggregated species are often prioritised if
 they contain 1% of national or biogeographical populations but the utility
 of this approach for other species is unclear. 2. To make recommendations
 for study design, we present methods used to estimate the UK population
 size of the common nightingale Luscinia megarhynchos. We assess the
 sensitivity of the population estimate to the analytical method used and
 identify sites of national importance for this territorial songbird. 3.
 Survey effort was directed by prior knowledge of the species’ distribution
 and the survey design maximised detectability by focussing on the period
 of greatest song output. We used three different statistical methods to
 account for detectability, estimating that 55–65% of the national
 population was detected during surveys. 4. Birds in areas not known to
 contain the species accounted for 13–23% of the population estimate.
 Methods to account for these individuals contributed the greatest
 uncertainty to the results, due to the difficulty of surveying a very
 large sample of random sites and consequent need to stratify the sample.
 5. The 12 derived estimates ranged between 5094 and 5938 territorial
 males, with the confidence limits ranging from 4764 to 6534. Site
 delimitation, using clustering based on nearest-neighbour distances,
 identified one site clearly of national importance and several others
 potentially nationally important, depending on the population threshold
 and clustering distance used. 6. Synthesis and applications. National
 population estimation is difficult and requires that species-specific
 variability in detectability and individuals present outside surveyed
 areas are accurately accounted for through survey design and statistical
 analysis. Accounting for these sources of error will not always be
 possible and will hamper efforts to assess true population size and
 consequently to determine whether sites, however defined, exceed critical
 thresholds of importance. Resources may be better invested in other
 activities, for example in generating population trends based on relative
 indices. The latter are generally easier to produce, potentially more
 robust and arguably more suitable for many conservation applications.
description: Data from Hewson et al
 2018 J Applied EcolExcel workbook
 containing four spreadsheets: 1) Data from tetrads selected for the BTO UK
 Nightingale survey in 2012; 2) Predicted Nightingale abundance from
 National Breeding Atlas for all other tetrads falling in 10km squares
 occupied by the species; 3) Recording history by territory*visit and visit
 covariates (start time, duration and date); 4) Habitat data for
 territories, where availableHewson et al 2018
 dataset.xlsx
DOI: 10.5061/dryad.s2d3c
title: Data from: Oldest known multituberculate stapes suggests an asymmetric bicrural pattern as ancestral for Multituberculata

description: Middle ear ossicles (malleus, incus, stapes) are known only for few
 multituberculate taxa, and three different stapedial morphotypes have been
 suggested: (1) slender, columelliform and microperforate, (2) robust and
 rod-like, and (3) bicrural. Reinvestigation of Upper Jurassic
 (Kimmeridgian) mammalian petrosals from the Guimarota coal mine in central
 Portugal (Western Europe) revealed an asymmetric bicrural stapes (ABS) in
 the paulchoffatiid Pseudobolodon oreas. The middle ear bones displaced
 inside the osseous vestibule were detected by a microCT analysis. The
 Kimmeridgian age of the Guimarota stapes exceeds the stapes from the Early
 Cretaceous (Barremian) of Asia (about 122-124 ma) by ~30 ma, and is only
 slightly younger than the stapes of the recently described Oxfordian
 euharamiyid Arboroharamiya allinhopsoni. The Guimarota stapes indicates
 that the stapes of Lambdopsalis, described as columelliform and
 microperforate (small stapedial foramen), does not represent a general
 condition for multituberculates. The stapes of Pseudobolodon is bicrural,
 the anterior crus sits centrally on the oval footplate, and the stapedial
 head is simple and smaller than the footplate. We hypothesize that the ABS
 evolved from the symmetric bicrural stapes (SBS) of non-mammaliaform
 cynodonts. The ABS appears to be the ancestral morphotype of the mammalian
 SBS, and the mammalian columelliform imperforate stapes (CIS).
description: Pseudobolodon_ear_region_IstackCT-image stack of the vestibule of Pseudobolodon oreas (specimen Gui Mam 77). For settings and resolution of the scan please see README.pdf file.Pseudobolodon_GuiMam77_stapes_incus_malleus_frags3D surface model of the middle ear ossicles of Pseudobolodon oreas created with software Avizo 8 (STL-file).
DOI: 10.5061/dryad.g1d2s
title: Data from: Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex

description: Heterotrophic plants provide excellent opportunities to study the effects
 of altered selective regimes on genome evolution. Plastid genome
 (plastome) studies in heterotrophic plants are often based on one or a few
 highly divergent species or sequences as representatives of an entire
 lineage, thus missing important evolutionary-transitory events. Here we
 present the first infraspecific analysis of plastome evolution in any
 heterotrophic plant. By combining genome skimming and targeted sequence
 capture, we address hypotheses on the degree and rate of plastome
 degradation in a complex of leafless orchids (Corallorhiza striata) across
 its geographic range. Plastomes provide strong support for relationships
 and evidence of reciprocal monophyly between C. involuta and the
 endangered C. bentleyi. Plastome degradation is extensive, occurring
 rapidly over a few million years, with evidence of differing rates of
 substitution among the two principal clades of the complex. Genome
 skimming and targeted sequence capture differ widely in coverage depth
 overall, with depth in targeted sequence capture datasets varying
 immensely across the plastome as a function of GC content. These findings
 will help fill a knowledge gap in models of heterotrophic plastid genome
 evolution, and have implications for future studies in heterotrophs.
description: Corallorhiza_allNexus format alignment of captured plastomes of the Corallorhiza striata complex, with Corallorhiza trifida and Calypso bulbosa as outgroup taxa
DOI: 10.5061/dryad.hq8m7
title: Data from: Quadrupedal locomotor simulation: producing more realistic gaits using dual-objective optimisation

description: In evolutionary biomechanics it is often considered that gaits should
 evolve to minimise the energetic cost of travelling a given distance. In
 gait simulation this goal often leads to convincing gait generation.
 However, as the musculoskeletal models used get increasingly
 sophisticated, it becomes apparent that such a single goal can lead to
 extremely unrealistic gait patterns. In this paper we explore the effects
 of requiring adequate lateral stability and show how this both increases
 energetic cost and the realism of the generated walking gait in a high
 biofidelity chimpanzee musculoskeletal model. We also explore the effects
 of changing the footfall sequences in the simulation so it mimics both the
 diagonal sequence walking gaits that primates typically use and also the
 lateral sequence walking gaits that are much more widespread among
 mammals. It is apparent that adding a lateral stability criterion has an
 important effect on the footfall phase relationship suggesting that
 lateral stability may be one of the key drivers behind the observed
 footfall sequences in quadrupedal gaits. The observation that single
 optimisation goals are no longer adequate for generating gait in current
 models has important implications for the use of biomimetic virtual robots
 to predict the locomotor patterns in fossil animals.
description: Supplementary
 InformationZIP file containing the
 3D bone segments, the model definitions, and the movie files generated by
 the simulator.