cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jm820mg
title: Data from: Fossils reveal the complex evolutionary history of the mammalian regionalized spine

description: A unique characteristic of mammals is a vertebral column with anatomically
 distinct regions, but when and how this trait evolved remains unknown.
 Here we reconstruct vertebral regions and their morphological disparity in
 the extinct forerunners of mammals, the non-mammalian synapsids, to
 elucidate the evolution of mammalian axial differentiation. Mapping
 patterns of regionalization and disparity (heterogeneity) across amniotes
 reveals that both traits increased during synapsid evolution. However, the
 onset of regionalization predates increased heterogeneity. Based on
 inferred homology patterns, we propose a “pectoral-first” hypothesis for
 region acquisition. Evolutionary shifts in forelimb function in
 non-mammalian therapsids drove increasing vertebral modularity prior to
 differentiation of the vertebral column for specialized functions in
 mammals.
description: Raw
 dataLinear and angular
 measurements from the vertebral columns of non-mammalian synapsids and
 extant amniotesDATA.zipTreeNexus file containing time-callibrated phylogenySynapsid tree_5.25.2018.nex
DOI: 10.5061/dryad.6v4h5
title: Data from: Collecting in collections: a PCR strategy and primer set for DNA barcoding of decades-old dried museum specimens

description: Natural history museums are vastly underutilized as a source of material
 for DNA analysis because of perceptions about the limitations of DNA
 degradation in older specimens. Despite very few exceptions, most DNA
 barcoding projects, which aim to obtain sequence data from all species,
 generally use specimens collected specifically for that purpose, instead
 of the wealth of identified material in museums, constrained by the lack
 of suitable PCR methods. Any techniques that extend the utility of museum
 specimens for DNA analysis therefore are highly valuable. This study first
 tested the effects of specimen age and PCR amplicon size on PCR success
 rates in pinned insect specimens, then developed a PCR primer set and
 amplification strategy allowing greatly increased utilization of older
 museum specimens for DNA barcoding. PCR success rates compare favourably
 with the few published studies utilizing similar aged specimens, and this
 new strategy has the advantage of being easily automated for
 high-throughput laboratory workflows. The strategy uses hemi-nested,
 degenerate, M13-tailed PCR primers to amplify two overlapping amplicons,
 using two PCRs per amplicon (i.e. four PCRs per DNA sample). Initial PCR
 products are reamplified using an internal primer and a M13 primer.
 Together the two PCR amplicons yield 559 bp of the COI gene from
 Coleoptera, Lepidoptera, Diptera, Hemiptera, Odonata and presumably also
 other insects. BARCODE standard-compliant data were recovered from 67% (56
 of 84) of specimens up to 25 years old, and 51% (102 of 197) of specimens
 up to 55 years old. Given the time, cost and specialist expertise required
 for fieldwork and identification, ‘collecting in collections’ is a viable
 alternative allowing researchers to capitalize on the knowledge captured
 by curation work in decades past.
description: AlignmentAlignment of 166 partial and complete DNA barcode (mitochondrial COI gene) sequences derived during testing of the PCR primers and amplification strategy described in this study. All sequences except one (ww01176, which is less than 200 nt in length, too short) have been deposited in GenBank, accession numbers KP688405 - KP688569.Final alignment.fasta
DOI: 10.5061/dryad.9f2d8
title: Data from: Evaluation of electronically supported nursing transfers between hospital and nursing home based on a test health telematics infrastructure: a case analysis

description: Background: Improper information transmission can lead to compromised
 patient safety and quality of life when patients are transferred from one
 setting to another. Electronic instruments may improve this situation,
 however, they are rarely used. Objective: The aim of this study therefore
 was to investigate the technical and organizational feasibility,
 usability, usefulness and completeness of an electronic instrument that is
 based on the German HL7 CDA standard for eNursing Summaries. Materials and
 methods: To this end, a test health telematics infrastructure, which
 included the German electronic health card, was established and nursing
 summary application was developed that allowed summary documents to be
 communicated between a hospital and a nursing home. The users were asked
 to evaluate the usability of the nursing summary application as well as to
 compare the usefulness and completeness of electronically and paper
 transmitted information. Results: This study demonstrated the feasibility
 of implementing an electronic nursing summary application that was based
 on the German HL7 CDA standard eNursing Summary and that was integrated in
 a test health telematics infrastructure. It could also be shown that the
 users rated this application as usable and that electronically supported
 patient transfers were superior to paper based ones. The use of the German
 electronic health card was regarded as a barrier by the users. Discussion:
 This study emphasizes the feasibility, relevance and barriers of
 electronically supported transfers of patients with nursing needs. Nurses
 working in hospitals and long-term care can integrate an application based
 on the HL7 CDA Standard ePfgebericht into their working processes and get
 better and more complete information. To ensure continuity of care in a
 sustainable manner in the future, the German HL7 CDA based eNursing
 Summary standard should become part of the German telematics
 infrastructure.
description: analysis_IsoMetricsanalysis_logbooksClinical_documentation_transfered_patientsanalysis_transfer_documents
DOI: 10.5061/dryad.487fq3m
title: Data from: Relative importance of competition and plant-soil feedback, their synergy, context dependency and implications for coexistence

description: Plants interact simultaneously with each other and with soil biota, yet
 the relative importance of competition versus plant soil feedback (PSF) on
 plant performance is poorly understood. Using a meta-analysis of 38
 published studies and 150 plant species, we show that effects of
 interspecific competition (either growing plants with a competitor or
 singly, or comparing inter- vs. intraspecific competition) and PSF
 (comparing home vs. away soil, live vs. sterile soil, or control vs.
 fungicide-treated soil) depended on treatments but were predominantly
 negative, broadly comparable in magnitude, and additive or synergistic.
 Stronger competitors experienced more negative PSF than weaker competitors
 when controlling for density (inter- to intraspecific competition),
 suggesting that PSF could prevent competitive dominance and promote
 coexistence. When competition was measured against plants growing singly,
 the strength of competition overwhelmed PSF, indicating that the relative
 importance of PSF may depend not only on neighbor identity but also
 density. We evaluate how competition and PSFs might interact across
 resource gradients; PSF will likely strengthen competitive interactions in
 high resource environments and enhance facilitative interactions in low
 resource environments. Finally, we provide a framework for filling key
 knowledge gaps and advancing our understanding of how these biotic
 interactions influence community structure.
description: Tables
 S1_S2Table S1 contains all
 the data necessary to repeat analyses and Table S2 presents
 results.
DOI: 10.5061/dryad.5mk37
title: Data from: Patterns of biodiverse, understudied groups do not mirror those of the surrogate groups that set conservation priorities: a case study from the Mid-Atlantic Coastal Plain of eastern North America

description: We conducted biodiversity inventories of lichens, woody plants, and sedges
 at 32 sites on the Mid-Atlantic Coastal Plain of eastern North America
 between November 2012 and June 2015. Each site comprised a single, uniform
 habitat, and sites were classified as: Coastal Plain Floodplain forest,
 Coastal Plain Flatwood swamp, Coastal Plain Oak-Pine forest, Maritime
 forest, Mixed Mesic Hardwood forest, or Tidal forest. We compared alpha
 diversity and community assemblages of each organismal group across the
 sites, and compared selected minimal reserve sets in order to visualize
 biodiversity patterns and assess whether specific components of vascular
 plants (sedges and woody plants) serve as an effective surrogate for
 lichens. Woody plants provide a direct substrate for lichen growth, but
 there was no significant correlation between the alpha diversity of these
 groups. For conserving maximal species richness among the studied groups,
 lichens outperformed the sedges and woody plants as the better surrogate
 group for building minimum reserve sets, even though vascular plants are
 more commonly used as a surrogate. Likewise, sedge alpha diversity was not
 correlated with lichens, or with woody plants. Although no group was an
 effective indicator for high alpha diversity sites of other organisms, a
 significant correlation between the community assemblages of lichens and
 woody plants suggests that protecting varied types of plant communities
 might serve as a workable surrogate for protecting lichens. The lack of
 congruence between species richness patterns across organismal groups
 suggests that the mechanisms that shape patterns of diversity are not
 identical, and that identifying and incorporating specific biodiversity
 indicators for understudied groups into conservation policy is necessary
 to ensure their protection.
description: data_packetThis is a zipped folder that contains the following spreadsheets used for analyses in this study: 1) site by species matrices for lichens (1 CSV file) and for vascular plants (1 CSV file). 2) Location data for study sites (1 XLSX file). 3) Georeferenced specimen data used to generate species lists for each site (1 XLSX file).Data_Packet
DOI: 10.5061/dryad.26443
title: Data from: A new method for testing evolutionary rate variation and shifts in phenotypic evolution

description: 1.Quantifying phenotypic evolutionary rates and their variation across
 phylogenetic trees is a major issue in evolutionary biology. A number of
 phylogenetic comparative methods (PCMs) currently perform such task.
 However, available PCMs can locate rate shifts pertaining to entire
 portions of the phylogeny, but not those expected to occur at the level of
 individual species and lineages, such as with the idea that body size
 changes more rapidly in insular vertebrates. Still, most PCMs cannot deal
 with fossil phylogenies, albeit fossils provide highly desirable
 information when it comes to understand trait variation and evolution.
 2.We developed a PCM based on phylogenetic ridge regression, which we
 named RRphylo, which assigns an evolutionary rate to each branch of the
 phylogeny, and is designed to locate rate shifts relating to entire
 clades, as well as to unrelated tree tips. We tested RRphylo on simulated
 trees and data to assess its performance under different conditions. Then,
 we repeated its application with two real case scenarios, the evolution of
 flight in ornithodirans and mammals, and body size evolution in insular
 mammals, which are usually subsumed to evolve under different range
 regimes than terrestrial and continental species, respectively. 3.RRphylo
 performs well across all different conditions. The simulation experiments
 demonstrated it has low Type I and Type II error rate. We found
 significant evidence that flight accelerates the rate of body size
 evolution in vertebrates, and that the acquisition of very large body size
 slows down the rate. Still, insular mammals body size evolution is not
 faster than in continental species. 4.RRphylo is a new PCM ideal to
 estimate variation and shift in the rate of phenotypic evolution with
 fossil data. In addition to testing evolutionary rate variation, it is
 open to a variety of further questions, such as the evolution of rates in
 time, the estimation of ancestral states, and the estimation of phenotypic
 trends over time.
description: Appendix_S1Body masses and wingspans of Pterosaurs with referencesAppendix_S2Ornithodirans body masses with referencesAppendix_S3Ornithodiran tree in Newick formatAppendix_S4Ornithodiran locomotory types
DOI: 10.5061/dryad.g4p30
title: Data from: The palaeogenetics of cat dispersal in the ancient world

description: The cat has long been important to human societies as a pest-control
 agent, object of symbolic value and companion animal, but little is known
 about its domestication process and early anthropogenic dispersal. Here we
 show, using ancient DNA analysis of geographically and temporally
 widespread archaeological cat remains, that both the Near Eastern and
 Egyptian populations of Felis silvestris lybica contributed to the gene
 pool of the domestic cat at different historical times. While the cat’s
 worldwide conquest began during the Neolithic period in the Near East, its
 dispersal gained momentum during the Classical period, when the Egyptian
 cat successfully spread throughout the Old World. The expansion patterns
 and ranges suggest dispersal along human maritime and terrestrial routes
 of trade and connectivity. A coat-colour variant was found at high
 frequency only after the Middle Ages, suggesting that directed breeding of
 cats occurred later than with most other domesticated animals.
description: Cat mtDNA
 fragmentsNine ND5 gene fragments
 were amplified via multiplex PCR and either sequenced by NGS in bulk
 following the “aMPlex Torrent” workflow, or reamplified individually by
 nested PCR and sequenced by pyrosequencing (see Ottoni et al, 2017, Nature
 Ecol Evol in press). The nine sequences obtained by “aMPlex Torrent” for
 each specimen were concatenated using a 10 N intervening spacer. For the
 specimen sequences that were obtained only by pyrosequencing, the N spacer
 was extended to allow alignment of all sequences. The coordinates of the
 fragments, excluding primers, numbered according to the Felis silvestris
 mtDNA reference sequence (NC001700) are: Frag_7: 12918-12961; Frag_2:
 13052-13102; Frag_8: 13263-13333; Frag_3: 13513-13569; Frag_4:
 13746-13807; Frag_1: 13945-13980; Frag_5: 14004-14012; Frag_9:
 14170-14228; Frag_6: 15071-15131.cats_TOTAL_to_deposit_mtDNA_final.fastaCat Taqpep gene fragmentsThree fragments allowing genotyping of the T139, D228 and W841 codons of the Taqpep genes controlling the Macquerel or Blotched Tabby coat color pattern were concatenated for each specimen using a 10 N intervening spacer. The coordinates of the fragments, excluding primers, numbered according to the Felis silvestris Taqpep gene (LOC101101437) from the genomic sequence NC018723 are: T139: 21887-21926; D228: 22154-22180; W841: 80673-80731.cats_TOTAL_to_deposit_NUCLEAR_final.fasta
DOI: 10.5061/dryad.bc260
title: Data from: Human cooperation based on punishment reputation

description: The threat of punishment usually promotes cooperation. However, punishing
 itself is costly, rare in non-human animals, and humans who punish often
 finish with low payoffs in economic experiments. The evolution of
 punishment has therefore been unclear. Recent theoretical developments
 suggest that punishment has evolved in the context of reputation games. We
 tested this idea in a simple helping game with observers and with
 punishment and punishment reputation (experimentally controlling for other
 possible reputational effects). We show that punishers fully compensate
 their costs as they receive help more often. The more likely defection is
 punished within a group, the higher the level of within-group cooperation.
 These beneficial effects perish if the punishment reputation is removed.
 We conclude that reputation is key to the evolution of punishment.
description: HumanCooperationBasedOnPunishment ReputationRawDataThis file contains raw data on the donors' decisions in function of the receivers' reputation (punishment score: "ReceiverPd", and punishment score relative to the group mean: "ReceiverPdScoreDev") for each round, group and treatment.dosSantosHumanCooperationAndPunishment.txt
DOI: 10.5061/dryad.022dv
title: Data from: The genetic structure of the plant pathogenic fungus Melampsora larici-populina on its wild host is extensively impacted by host domestication

description: Wild and cultivated plants represent very different habitats for
 pathogens, especially when cultivated plants bear qualitative resistance
 genes. Here, we investigated to what extent the population genetic
 structure of a plant pathogenic fungus collected on its wild host can be
 impacted by the deployment of resistant cultivars. We studied one of the
 main poplar diseases, poplar rust, caused by the fungus Melampsora
 larici-populina. A thousand fifty individuals sampled from several
 locations in France were phenotyped for their virulence profile (ability
 to infect or not the most deployed resistant cultivar ‘Beaupré’), and a
 subset of these was genotyped using 25 microsatellite markers. Bayesian
 assignment tests on genetic data clustered the 476 genotyped individuals
 into three genetic groups. Group 1 gathered most virulent individuals and
 displayed evidence for selection and drastic demographic changes resulting
 from breakdown of the poplar cultivar ‘Beaupré’. Group 2 comprised
 individuals corresponding to ancestral populations of M. larici-populina
 naturally occurring in the native range. Group 3 displayed the hallmarks
 of strict asexual reproduction, which has never previously been
 demonstrated in this species. We discuss how poplar cultivation has
 influenced the spatial and genetic structure of this plant pathogenic
 fungus, and has led to the spread of virulence alleles (gene swamping) in
 M. larici-populina populations evolving on the wild host.
description: Data-11691887MEC-10-1357Population genetic data (microsatellite loci) of a plant pathogenic fungi (Melampsora larici-populina) collected on its wild hosts. See ReadMe files and publication for details
DOI: 10.5061/dryad.7vp288f
title: Data from: Direct measurement of swimming and diving kinematics of giant Atlantic bluefin tuna (Thunnus thynnus)

description: Tunas possess a range of physiological and mechanical adaptations geared
 towards high performance swimming that are of considerable interest to
 physiologists, ecologists and engineers. Advances in biologging have
 provided significant improvements in understanding tuna migrations and
 vertical movement patterns, yet our understanding of the locomotion and
 swimming mechanics of these fish under natural conditions is limited. We
 equipped Atlantic bluefin tuna (Thunnus thynnus) with motion sensitive
 tags and video cameras to quantify the gaits and kinematics used by wild
 fish. Our data reveal significant variety in the locomotory activity of
 Atlantic bluefin tuna kinematics, ranging from continuous locomotion to
 two types of intermittent locomotion. The tuna sustained swimming speeds
 in excess of 3 m s-1 (1.2 body lengths s-1), while beating their tail at a
 frequency of ~1 Hz. While diving, some descents were entirely composed of
 passive glides, with slower descent rates featuring more gliding, while
 ascents were primarily composed of active swimming. The observed swimming
 behaviour of Atlantic bluefin tuna is consistent with theoretical models
 predicting such intermittent locomotion to result in mechanical and
 physiological advantages. Our results confirm that Atlantic bluefin tuna
 possess a number of behavioural specializations to increase their
 locomotory performance, which together with their unique physiology
 improve their capacity to use pelagic and mesopelagic habitats.
description: All Dives by Tuna
 #1This file includes all
 dives from the fish tagged with the CEFAS G6a tag that did not include a
 speed sensor.All_Dives_Tuna_Cefas.xlsxDetailed kinematic data for all dives of Tuna 2Each row represents a single ascent/descent of the tuna carrying a multi-sensor tag. All columns and their units are described in a separate sheet of the file.All_Dives_Tuna_CATS.Final.xlsx
DOI: 10.5061/dryad.q50m1
title: Data from: Timeframe of speciation inferred from secondary contact zones in the European tree frog radiation (Hyla arborea group)

description: Background: Hybridization between incipient species is expected to become
 progressively limited as their genetic divergence increases and
 reproductive isolation proceeds. Amphibian radiations and their secondary
 contact zones are useful models to infer the timeframes of speciation, but
 empirical data from natural systems remains extremely scarce. Here we
 follow this approach in the European radiation of tree frogs (Hyla arborea
 group). We investigated a natural hybrid zone between two lineages (Hyla
 arborea and Hyla orientalis) of Mio-Pliocene divergence (~5 My) for
 comparison with other hybrid systems from this group. Results: We found
 concordant geographic distributions of nuclear and mitochondrial gene
 pools, and replicated narrow transitions (~30 km) across two independent
 transects, indicating an advanced state of reproductive isolation and
 potential local barriers to dispersal. This result parallels the situation
 between H. arborea and H. intermedia, which share the same amount of
 divergence with H. orientalis. In contrast, younger lineages show much
 stronger admixture at secondary contacts. Conclusions: Our findings
 corroborate the negative relationship between hybridizability and
 divergence time in European tree frogs, where 5 My are necessary to
 achieve almost complete reproductive isolation. Speciation seems to
 progress homogeneously in this radiation, and might thus be driven by
 gradual genome-wide changes rather than single speciation genes. However,
 the timescale differs greatly from that of other well-studied amphibians.
 General assumptions on the time necessary for speciation based on evidence
 from unrelated taxa may thus be unreliable. In contrast, comparative
 hybrid zone analyses within single radiations such as our case study are
 useful to appreciate the advance of speciation in space and time.
description: Individual mitotypes and
 microsatellite genotypesGenetic data of the H.
 arborea/H. orientalis contact zones in southern Europe. Mitochondrial
 haplotypes (cyt-b) and genotypes of microsatellite genotypes (23 loci) for
 each individual. NA: missing data. Information on localities are available
 in supporting information of the publication.Data.xlsx