cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b3g67
title: Data from: New material of Palaeoamasia kansui (Embrithopoda, Mammalia) from the Eocene of Turkey and a phylogenetic analysis of Embrithopoda at the species level

description: Since the discovery of the megaherbivore Arsinoitherium zitteli Beadnell
 (early Oligocene of Egypt), the extinct order Embrithopoda has remained an
 enigmatic group, with disputed affinities among ungulates. In this study,
 new specimens of Palaeoamasia kansui from the early Palaeogene of Turkey
 are described and a synthetic dental terminology is proposed for
 embrithopods. Based on 130 cranial–mandibular and dental characters, the
 first phylogenetic analysis of embrithopods is carried out in aim to
 enhance the position of Palaeoamasia within embrithopods. The monophyly of
 Embrithopoda is confirmed, following the topology (Phenacolophus
 (Namatherium (Arsinoitheriinae, Palaeamasiinae))). However, phylogenetic
 relationships between Eurasian embrithopods (Palaeoamasiinae:
 Palaeoamasia, Crivadiatherium and Hypsamasia) remain unresolved. The
 integration of all embrithopod genera within a cladistic analysis
 encompassing a wider taxonomic sample (Condylarthra,
 Afrotheria/Paenungulata and Laurasiatheria) also supports Embrithopoda as
 being monophyletic, but questions the position of both Phenacolophus and
 Namatherium within Embrithopoda. Finally, possible faunal exchange events
 are proposed based on three hypothesized scenarios between Eurasia and
 Arabia–Africa during the early Palaeogene.
description: File 1LIST OF CRANIAL AND
 DENTAL CHARACTERS USED IN THE CLADISTIC ANALYSISFile 2DATA MATRIX OF 130
 CHARACTERS (10 CRANIAL-MANDIBULAR, 120 DENTAL) APPLIED ON 14 TERMINAL TAXA
 (PERISSODACTYLS, HYRACOID, PROBOSCIDEANS, EMBRITHOPODS, AND
 PHENACOLOPHUS). THE THREE OUTGROUPS ARE A PRIORI XENICOHIPPUS,
 ARENAHIPPUS, AND RADINSKYAFile 3TABLE OF MEAN SIZE
 VALUES OF STUDIED TAXAFile 4CHARACTER DISTRIBUTION
 OF THE STRICT CONSENSUS TREE
DOI: 10.5061/dryad.8f74d
title: Data from: Forests as promoters of terrestrial life history strategies in East African amphibians

description: Many amphibian lineages show terrestrialization of their reproductive
 strategy and breeding is partially or completely independent of water. A
 number of causal factors have been proposed for the evolution of
 terrestrialized breeding. While predation has received repeated attention
 as a potential factor, the influence of others such as habitat has never
 been tested using appropriate data or methods. Using a dataset that
 comprises 180 amphibian species from various East African habitats, we
 tested whether species occurring in different habitats show different
 patterns of terrestrialization in their breeding strategy. We recovered a
 significant association between terrestrialized breeding strategies and
 forest habitats. In general, forest seems to act as a facilitator,
 providing a permissive environment for the evolution of terrestrialized
 breeding strategies. However, while terrestrial oviposition is strongly
 correlated with lowland and montane forest habitat, complete terrestrial
 development is significantly correlated with montane forest only,
 indicating different selective pressures acting at different steps towards
 complete terrestrial development.
description: Input data for
 pGLSCoding for both habitat
 and breeding biology used in the phylogenetic generalized squares (pGLS)
 analysis using the R package "ape". The file contains all the
 different input files used in this study saved as different tabs inside
 the excel file. see README file and supplementary materials of publication
 for more details.pGLS_input.xlsxInput data for BayesTraits DISCRETECoding for both habitat and breeding biology used in the BayesTraits DISCRETE analysis. The file contains all the different input files used in this study saved as different tabs inside the excel file. see README and supplementary materials for more details.BayesTraits_input.xlsxSequence Alignment for East African AmphibiansSequence alignment file in fasta format used for the phylogenetic reconstruction implemented in this study. see README and supplementary materials in publication for more details.East_Africa.fastaPhylogeny of East African AmphibiansPhylogeny as newick format used in the analyses of this study. See README file and supplementary materials of publication for more detailsEast_Africa.tre
DOI: 10.5061/dryad.tf5f3
title: Data from: Phylogeography of sea oats (Uniola paniculata), a dune-building coastal grass in southeastern North America

description: We tested the hypothesis that Uniola paniculata populations are divided
 into eastern and western lineages, with the primary geographic break at
 the southern tip of Florida, as observed in codistributed animal taxa. We
 asked whether the geographic distribution of chloroplast DNA (cpDNA)
 variation in U. paniculata corresponds to 1) genetic structure in nuclear
 variation reported in previous studies, and 2) the geographic distribution
 of morphological adaptive traits reported in previous studies. We sampled
 66 populations and performed phylogeographic analyses using sequence
 variations in maternally inherited cpDNA. We reconstructed the
 intraspecific phylogenetic network with TCS software and identified
 phylogeographic breaks in the species using Monmonier’s algorithm.
 Analyses identified 6 cpDNA haplotypes and 2 major lineages: eastern
 (Atlantic) and western (Gulf), with a phylogeographic break at the
 southern tip of Florida. The data suggest U. paniculata survived the last
 glacial maximum (LGM) in southern refugia. Following the LGM, differential
 leading-edge recolonization explains the current distribution of
 haplotypes into 2 lineages. Populations containing a haplotype from
 outside its native range are likely due to human-mediated transplantation.
 The genetic structure of cpDNA variation has weak correlation with nuclear
 DNA variation, and there is partial concordance between the geographic
 distribution of cpDNA and morphological variation.
description: Supplementary Table
 S1Uniola paniculata
 populations, their geographical locations, haplotype group and the
 restoration status of the site.Supplementary Table
 S2The
 twenty-five primer pairs that successfully amplified multiple Uniola
 paniculata samples, the author/developer of each primer pair, and whether
 or not that primer pair was informative
DOI: 10.5061/dryad.h8c79
title: Data from: Computational design of protein-based inhibitors of Plasmodium vivax subtilisin-like 1 protease

description: Background: Malaria remains a major global health concern. The development
 of novel therapeutic strategies is critical to overcome the selection of
 multiresistant parasites. The subtilisin-like protease (SUB1) involved in
 the egress of daughter Plasmodium parasites from infected erythrocytes and
 in their subsequent invasion into fresh erythrocytes has emerged as an
 interesting new drug target. Findings: Using a computational approach
 based on homology modeling, protein–protein docking and mutation scoring,
 we designed protein–based inhibitors of Plasmodium vivax SUB1 (PvSUB1) and
 experimentally evaluated their inhibitory activity. The small peptidic
 trypsin inhibitor EETI-II was used as scaffold. We mutated residues at
 specific positions (P4 and P1) and calculated the change in free-energy of
 binding with PvSUB1. In agreement with our predictions, we identified a
 mutant of EETI-II (EETI-II-P4LP1W) with a Ki in the medium micromolar
 range. Conclusions: Despite the challenges related to the lack of an
 experimental structure of PvSUB1, the computational protocol we developed
 in this study led to the design of protein-based inhibitors of PvSUB1. The
 approach we describe in this paper, together with other examples,
 demonstrates the capabilities of computational procedures to accelerate
 and guide the design of novel proteins with interesting therapeutic
 applications.
description: PvSUB1 homology
 3D-modelPlasmodium vivax
 Subtilisin 1 (Genbank N° FJ536584) homology model generated by the
 modeling software Modeller and cited in Bastianelli et al, Plos One In
 press 2014).PvSUB1_3DModel.pdb
DOI: 10.5061/dryad.v4m56
title: Data from: Towards the description of livestock mobility in Sahelian Africa: some results from a survey in Mauritania

description: Understanding spatio-temporal patterns of host mobility is a key factor to
 prevent and control animal and human diseases. This is utterly important
 in low-income countries, where animal disease epidemics have strong
 socio-economic impacts. In this article we analyzed a livestock mobility
 database, whose data have been collected by the Centre National d’Elevage
 et de Recherches Vétérinaires (CNERV) Mauritania, to describe its patterns
 and temporal evolution. Data were collected through phone and face-to-face
 interviews in almost all the regions in Mauritania over a period of
 roughly two weeks during June 2015. The analysis has shown the existence
 of two mobility patterns throughout the year: the first related to routine
 movements from January to August; the second strictly connected to the
 religious festivity of Tabaski that in 2014 occurred at the beginning of
 October. These mobility patterns are different in terms of animals
 involved (fewer cattle and dromedaries are traded around Tabaski), the
 means of transportation (the volume of animals moved by truck raises
 around Tabaski) and destinations (most of the animals are traded
 nationally around Tabaski). Due to the differences between these two
 periods, public health officers, researchers and other stakeholders should
 take account of the time of the year when implementing vaccination
 campaigns or creating surveillance networks.
description: Datadryad2 Excel Worksheets. The first contains the result of the origin- destination survey. The second the geographical coordinates of the locations indicated in the survey
DOI: 10.5061/dryad.h9m07
title: Data from: NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss

description: Background: Key innovations have facilitated novel niche utilization, such
 as the movement of the algal predecessors of land plants into terrestrial
 habitats where drastic fluctuations in light intensity, ultraviolet
 radiation and water limitation required a number of adaptations. The NDH
 (NADH dehydrogenase-like) complex of Viridiplantae plastids participates
 in adapting the photosynthetic response to environmental stress,
 suggesting its involvement in the transition to terrestrial habitats.
 Although relatively rare, the loss or pseudogenization of plastid NDH
 genes is widely distributed across diverse lineages of photoautotrophic
 seed plants and mutants/transgenics lacking NDH function demonstrate
 little difference from wild type under non-stressed conditions. This study
 analyzes large transcriptomic and genomic datasets to evaluate the
 persistence and loss of NDH expression across plants. Results: Nuclear
 expression profiles showed accretion of the NDH gene complement at key
 transitions in land plant evolution, such as the transition to land and at
 the base of the angiosperm lineage. While detection of transcripts for a
 selection of non-NDH, photosynthesis related proteins was independent of
 the state of NDH, coordinate, lineage-specific loss of plastid NDH genes
 and expression of nuclear-encoded NDH subunits was documented in Pinaceae,
 gnetophytes, Orchidaceae and Geraniales confirming the independent and
 complete loss of NDH in these diverse seed plant taxa. Conclusion: The
 broad phylogenetic distribution of NDH loss and the subtle phenotypes of
 mutants suggest that the NDH complex is of limited biological significance
 in contemporary plants. While NDH activity appears dispensable under
 favorable conditions, there were likely sufficiently frequent episodes of
 abiotic stress affecting terrestrial habitats to allow the retention of
 NDH activity. These findings reveal genetic factors influencing
 plant/environment interactions in a changing climate through 450 million
 years of land plant evolution.
description: alignments_for_phylogenyThe data folder contains three sequence alignments used to construct phylogenetic trees of Geraniales, Gymnospermae and Orchidaceae in this study.
DOI: 10.5061/dryad.1012q
title: Data from: Multilevel selection with kin and non-kin groups, experimental results with Japanese quail (Coturnix japonica)

description: An experiment was conducted comparing multilevel selection in Japanese
 quail for 43 days weight and survival with birds housed in either kin (K)
 or random (R) groups. Multilevel selection significantly reduced mortality
 (6.6% K vs. 8.5% R) and increased weight (1.30 g/MG K vs. 0.13 g/MG R)
 resulting in response an order of magnitude greater with Kin than Random.
 Thus multilevel selection was effective in reducing detrimental social
 interactions, which contributed to improved weight gain. The observed
 rates of response did not differ significantly from expected,
 demonstrating that current theory is adequate to explain multilevel
 selection response. Based on estimated genetic parameters, group selection
 would always be superior to any other combination of multilevel selection.
 Further, near optimal results could be attained using multilevel selection
 if 20% of the weight was on the group component regardless of group
 composition. Thus in nature the conditions for multilevel selection to be
 effective in bringing about social change maybe common. In terms of a
 sustainability of breeding programs, multilevel selection is easy to
 implement and is expected to give near optimal responses with reduced
 rates of inbreeding as compared to group selection, the only requirement
 is that animals be housed in kin groups.
description: Kin selection
 dataRaw data weight by hatch
 and minigeneration and method of selectionkin vs random
 groupmeans used to generate
 graphs of selection responseKin selection
 response_figure groups size 16 currentExcel program to find
 expected responses to individual and kin selection
DOI: 10.5061/dryad.mq2ff
title: Data from: A synthesis of empirical plant dispersal kernels

description: Dispersal is fundamental to ecological processes at all scales and levels
 of organization, but progress is limited by a lack of information about
 the general shape and form of plant dispersal kernels. We addressed this
 gap by synthesizing empirical data describing seed dispersal and fitting
 general dispersal kernels representing major plant types and dispersal
 modes. A comprehensive literature search resulted in 107 papers describing
 168 dispersal kernels for 144 vascular plant species. The data covered 63
 families, all the continents except Antarctica, and the broad vegetation
 types of forest, grassland, shrubland and more open habitats (e.g.
 deserts). We classified kernels in terms of dispersal mode (ant,
 ballistic, rodent, vertebrates other than rodents, vehicle or wind), plant
 growth form (climber, graminoid, herb, shrub or tree), seed mass and plant
 height. We fitted 11 widely used probability density functions to each of
 the 168 data sets to provide a statistical description of the dispersal
 kernel. The exponential power (ExP) and log-sech (LogS) functions
 performed best. Other 2-parameter functions varied in performance. For
 example, the log-normal and Weibull performed poorly, while the 2Dt and
 power law performed moderately well. Of the single-parameter functions,
 the Gaussian performed very poorly, while the exponential performed
 better. No function was among the best-fitting for all data sets. For 10
 plant growth form/dispersal mode combinations for which we had &gt;3
 data sets, we fitted ExP and LogS functions across multiple data sets to
 provide generalized dispersal kernels. We also fitted these functions to
 subdivisions of these growth form/dispersal mode combinations in terms of
 seed mass (for animal-dispersed seeds) or plant height (wind-dispersed)
 classes. These functions provided generally good fits to the grouped data
 sets, despite variation in empirical methods, local conditions, vegetation
 type and the exact dispersal process. Synthesis. We synthesize the rich
 empirical information on seed dispersal distances to provide standardized
 dispersal kernels for 168 case studies and generalized kernels for plant
 growth form/dispersal mode combinations. Potential uses include the
 following: (i) choosing appropriate dispersal functions in mathematical
 models; (ii) selecting informative dispersal kernels for one's
 empirical study system; and (iii) using representative dispersal kernels
 in cross-taxon comparative studies.
description: Plant dispersal
 dataPlantdispersaldata.csv
DOI: 10.5061/dryad.489s0
title: Data from: Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline

description: This study presents genetic evidence that whale sharks, Rhincodon typus,
 are comprised of at least two populations that rarely mix and is the first
 to document a population expansion. Relatively high genetic structure is
 found when comparing sharks from the Gulf of Mexico with sharks from the
 Indo-Pacific. If mixing occurs between the Indian and Atlantic Oceans, it
 is not sufficient to counter genetic drift. This suggests whale sharks are
 not all part of a single global meta-population. The significant
 population expansion we found was indicated by both microsatellite and
 mitochondrial DNA. The expansion likely happened during the Holocene, when
 tropical species could expand their range due to sea level rise
 eliminating dispersal barriers. However, the historic trend of population
 increase may have reversed recently. Declines in genetic diversity are
 found for 6 consecutive years at Ningaloo Reef in Australia. The declines
 in genetic diversity being seen now are likely due to commercial-scale
 harvesting of whale sharks and collision with boats in past decades in
 other countries in the Indo-Pacific. Whale shark hunting is banned in
 Australia but continues in other countries despite bans in places like
 China. The study findings have implications for models of population
 connectivity for whale sharks and advocate for continued focus on
 effective protection of the world’s largest fish at multiple spatial
 scales.
description: Microsatellites genotype
 from 406 whale sharks14 microsatellites
 genotype from 406 whale sharks collected in 7 different location
 worldwide. 0 represents missing values. Description of each
 microsatellites with multiplex detail is included in the supplementary
 material of the publication. Genemapper was used to read the lenght of
 each allele.Vignaud etl al.
 2014-WS410-7pops-14loci.xlsxWhale Sharks Control
 region raw 506 individualsThis excel dataset can
 be saved in .fasta - Locations and year of collection are described when
 available. 'N' means unknown, while '-' indicates gap.
 Additional sequences can be found on genebank from Castro et al. 2007, but
 seems to be reversed. Analysis performed in Vignaud et al. 2014 used
 modified dataset to remove N and large gaps as described in the
 methods.Vignaudetal2014WhaleSharksCRseq-506.xlsx
DOI: 10.5061/dryad.n0432
title: Data from: Emerging patterns of genetic variation in the New Zealand endemic scallop Pecten novaezelandiae

description: Both historical and contemporary processes influence the genetic structure
 of species, but the relative roles of such processes are still difficult
 to access. Population genetic studies of species with recent evolutionary
 histories such as the New Zealand endemic scallop Pecten novaezelandiae
 (&lt;1 Ma) permit testing of the effects of recent processes affecting
 gene flow and shaping genetic structure. In addition, studies encompassing
 the entire distributional range of species can provide insight into
 colonization processes. Analyses of genetic variation in P. novaezelandiae
 (952 individuals from 14 locations, genotyped at 10 microsatellite loci)
 revealed a weak but significant regional structure across the
 distributional range of the species, as well as latitudinal gradients of
 genetic diversity and differentiation: estimates of migration rates
 supported these patterns. Our results suggest that the observed genetic
 structure and latitudinal gradients reflect a stepping-stone model of
 colonization (north to south) and emerging divergence of populations as a
 result of ongoing limitations to gene flow and insufficient time to reach
 migration–drift equilibrium. The low levels of interpopulation and
 interregional genetic differentiation detected over hundreds of kilometres
 reflect the recent evolutionary history of P. novaezelandiae and stand in
 contrast to patterns reported for other evolutionary older species at the
 same spatial scale. The outcomes of this study contribute to a better
 understanding of evolutionary processes influencing the genetic variation
 of species and provide vital information on the genetic structure of P.
 novaezelandiae.
description: Genotype
 dataGenotype data used in
 the manuscript "Emerging patterns of genetic variation in the New
 Zealand endemic scallop Pecten novaezelandiae". The file contains
 data for each sample with the locality and microsatellite genotypes for
 all individuals.MolEcolData.txtR Script Linear RegressionsR Script for Linear Regression analyses (Latitudinal gradients) from the manuscript "Emerging patterns of genetic variation in the New Zealand endemic scallop Pecten novaezelandiae"R Console Linear Regressions.txtGeographic coordinates GenelandGeographic coordinates used for Geneland analysis in the manuscript "Emerging patterns of genetic variation in the New Zealand endemic scallop Pecten novaezelandiae"Geographic data Input GenelandInput file Structure analysisInput file used for Structure analysis in the manuscript "Emerging patterns of genetic variation in the New Zealand endemic scallop Pecten novaezelandiae"Input file Structure
DOI: 10.5061/dryad.57rr4
title: Data from: Habitat-driven population structure of bottlenose dolphins, Tursiops truncatus, in the North-East Atlantic

description: Despite no obvious barrier to gene flow, historical environmental
 processes and ecological specializations can lead to genetic
 differentiation in highly mobile animals. Ecotypes emerged in several
 large mammal species as a result of niche specializations and/or social
 organization. In the North-West Atlantic, two distinct bottlenose dolphin
 (Tursiops truncatus) ecotypes (i.e. ‘coastal’ and ‘pelagic’) have been
 identified. Here, we investigated the genetic population structure of
 North-East Atlantic (NEA) bottlenose dolphins on a large scale through the
 analysis of 381 biopsy-sampled or stranded animals using 25
 microsatellites and a 682-bp portion of the mitochondrial control region.
 We shed light on the likely origin of stranded animals using a carcass
 drift prediction model. We showed, for the first time, that coastal and
 pelagic bottlenose dolphins were highly differentiated in the NEA.
 Finer-scale population structure was found within the two groups. We
 suggest that distinct founding events followed by parallel adaptation may
 have occurred independently from a large Atlantic pelagic population in
 the two sides of the basin. Divergence could be maintained by philopatry
 possibly as a result of foraging specializations and social organization.
 As coastal environments are under increasing anthropogenic pressures,
 small and isolated populations might be at risk and require appropriate
 conservation policies to preserve their habitats. While genetics can be a
 powerful first step to delineate ecotypes in protected and difficult to
 access taxa, ecotype distinction should be further documented through diet
 studies and the examination of cranial skull features associated with
 feeding.
description: Data from Louis et al.
 Mol EcolLouis_etal_data.zip