cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t749b
title: Data from: Are flatfishes (Pleuronectiformes) monophyletic?

description: All extant species of flatfish (order Pleuronectiformes) are thought to
 descend from a common ancestor, and therefore to represent a monophyletic
 group. This hypothesis is based largely on the dramatic bilateral
 asymmetry and associated ocular migration characteristics of all flatfish.
 Yet, molecular-based phylogenetic studies have been inconclusive on this
 premise. Support for flatfish monophyly has varied with differences in
 taxonomic and gene region sampling schemes. Notably, the genus Psettodes
 has been found to be more related to non-flatfishes than to other
 flatfishes in many recent studies. The polyphyletic nature of the
 Pleuronectiformes is often inferred to be the result of weak historical
 signal and/or artifact of phylogenetic inference due to a bias in the
 data. In this study, we address the question of pleuronectiform monophyly
 with a broad set of markers (from six phylogenetically informative nuclear
 loci) and inference methods designed to limit the influence of
 phylogenetic artifacts. Concomitant with a character-rich analytical
 strategy, an extensive taxonomic sampling of flatfish and potential close
 relatives is used to increase power and resolution. Results of our
 analyses are most consistent with a non-monophyletic Pleuronectiformes
 with Psettodes always being excluded. A fossil-calibrated Bayesian relaxed
 clock analysis estimates the age of Pleuronectoidei to be 73 Ma, and the
 time to most recent common ancestor of Pleuronectoidei, Psettodes, and
 other relative taxa to be 77 Ma. The ages are much older than the records
 of any fossil pleuronectiform currently recognized. We discuss our
 findings in the context of the available morphological evidence and
 discuss the compatibility of our molecular hypothesis with morphological
 data regarding extinct and extant flatfish forms.
description: pleuroProtGenes.123Nexus alignment file with character sets and export block. Includes sequences generate for this study and those retrieved from GenBank.
DOI: 10.5061/dryad.k0q1n
title: Data from: Plant-pollinator networks in semi-natural grasslands are resistant to the loss of pollinators during blooming of mass-flowering crops

description: Mass-flowering crops lead to spatial redistributions of pollinators and to
 transient shortages within nearby semi-natural grasslands, but the impacts
 on plant-pollinator interactions remain largely unexplored. Here, we
 characterised which pollinator species are attracted by oilseed rape and
 how this affected the structure of plant-pollinator networks in nearby
 grasslands. We surveyed 177 networks from three countries (Germany, Sweden
 and United Kingdom) in 24 landscapes with high crop cover, and compared
 them to 24 landscapes with low or no oilseed rape during and after crop
 blooming. On average 55% of grassland pollinator species were found on the
 crop, which attracted 8-35% of individuals away from grasslands. However,
 networks in the grasslands were resistant to these reductions, since
 mainly abundant and highly mobile species were attracted. Nonetheless,
 simulations indicated that network structural changes could be triggered
 if &gt;50% of individuals were attracted to the crop (a value
 well-above that found in our study system), which could affect community
 stability and resilience to further disturbance.
description: Raw data on
 plant-pollinator interactionsFile showing all sites
 and every individual pollinator surveyed and the plant it interacted
 with.Magrach et al data for
 DRYAD.csv
DOI: 10.5061/dryad.t5606
title: Data from: Downsizing a giant: re-evaluating Dreadnoughtus body mass

description: Estimates of body mass often represent the founding assumption on which
 biomechanical and macroevolutionary hypotheses are based. Recently, a
 scaling equation was applied to a newly discovered titanosaurian sauropod
 dinosaur (Dreadnoughtus), yielding a 59 300 kg body mass estimate for this
 animal. Herein, we use a modelling approach to examine the plausibility of
 this mass estimate for Dreadnoughtus. We find that 59 300 kg for
 Dreadnoughtus is highly implausible and demonstrate that masses above 40
 000 kg require high body densities and expansions of soft tissue volume
 outside the skeleton several times greater than found in living
 quadrupedal mammals. Similar results from a small sample of other
 archosaurs suggests that lower-end mass estimates derived from scaling
 equations are most plausible for Dreadnoughtus, based on existing
 volumetric and density data from extant animals. Although volumetric
 models appear to more tightly constrain dinosaur body mass, there remains
 a clear need to further support these models with more exhaustive data
 from living animals. The relative and absolute discrepancies in mass
 predictions between volumetric models and scaling equations also indicate
 a need to systematically compare predictions across a wide size and
 taxonomic range to better inform studies of dinosaur body size.
description: ConvexHullsMinimum convex hull volumes for individual body segments of the Dreadnoughtus, Apatosaurus and Giraffatitan models.
DOI: 10.5061/dryad.56p0f
title: Data from: Historical climatic variability and geographical barriers as drivers of community composition in a biodiversity hotspot

description: Aim: To evaluate the roles of Quaternary (&lt; 2.6 Ma) climatic
 stability and geologic barriers (i.e. the Andes Mountains) in shaping the
 modern community composition and patterns of endemism in Neotropical dry
 forest bird communities. Location: Marañón Valley and Tumbes,
 north-western Peru. Methods: We recorded presence and abundance of species
 in six dry forest bird communities on either side of the Andes Mountains.
 We used the data to calculate the beta diversity and phylogenetic beta
 diversity across regional and local scales. We compared the observed
 results to randomly permuted communities to determine if the communities
 were significantly more or less similar than we would expect by chance.
 Mantel tests evaluated whether beta diversity and phylogenetic beta
 diversity measures were correlated and whether there was a correlation
 between spatial distance and community diversity. Results: Bird community
 composition, including abundance, is highly heterogeneous in north-western
 Peru, even at relatively local scales. Communities on either side of the
 Andes are significantly different based on beta diversity and phylogenetic
 beta diversity. Communities subjected to more historical climatic
 fluctuations share a more similar species composition than communities
 that are relatively buffered from climatic change. Main conclusions: The
 Andes structure dry forest bird communities in north-western Peru. Greater
 community similarity in climatically unstable areas may be the product of
 formerly more continuous forest and/or movement of species among
 communities. In climatically stable regions, species turnover is not
 different from random expectations, which may reflect habitat loss and
 increased homogenization from anthropogenic landscape changes. Both the
 Andes and the historical (Quaternary) climatic regimes of north-western
 Peru are likely responsible for the high endemism and distributions of its
 dry forest bird communities.
description: Oswald et al 2015 NW
 Peru dry forest bird census dataDry forest bird census
 data from northwest Peru. Locality name, date, latitude, longitude,
 elevation, species, number of individuals, and habitat (some missing data)
 are included in the spreadsheet.Oswald_et_al_2015_dryad.56p0f.xlsx
DOI: 10.5061/dryad.36d35
title: Data from: Functional characterization of the TAS2R38 bitter taste receptor for phenylthiocarbamide in colobine monkeys

description: Bitterness perception in mammals is mostly directed at natural toxins that
 induce innate avoidance behaviours. Bitter taste is mediated by the G
 protein-coupled receptor TAS2R, which is located in taste cell membranes.
 One of the best-studied bitter taste receptors is TAS2R38, which
 recognizes phenylthiocarbamide (PTC). Here we investigate the
 sensitivities of TAS2R38 receptors to PTC in four species of leaf-eating
 monkeys (subfamily Colobinae). Compared with macaque monkeys (subfamily
 Cercopithecinae), colobines have lower sensitivities to PTC in behavioural
 and in vitro functional analyses. We identified four non-synonymous
 mutations in colobine TAS2R38 that are responsible for the decreased
 sensitivity of the TAS2R38 receptor to PTC observed in colobines compared
 with macaques. These results suggest that tolerance to bitterness in
 colobines evolved from an ancestor that was sensitive to bitterness as an
 adaptation to eating leaves.
description: Macaque mutants
 mimicking colobineFunctional data for the
 Macaque mutants mimicking colobineコピー201607-Macaque mutants
 mimicking colobine (002).xlsxColobine functional
 analysisFunctional data for
 colobines150624-Colobine.Raw-Data.xlsxColobine mutants mimicking macaqueFunctional data for colobine mutants mimicking macaque150624-Colobine mutants mimicking macaque.xlsxBehavior dataBehavior dataBehavior_Fisher exact_Binomial.xlsx
DOI: 10.5061/dryad.6180s6f
title: Data from: Phylogenetic and morphological investigation of the Mochlus afer-sundevallii Species Complex (Squamata: Scincidae) across the arid corridor of sub-Saharan Africa

description: The aridification of Africa resulted in the fragmentation of forests and
 the expansion of an arid corridor stretching from the northeast to
 southwest portion of sub-Saharan Africa, but the role this corridor has
 had in species-level diversification of southern African vertebrates is
 poorly understood. The, skink species Mochlus afer and M. sundevallii
 inhabit wide areas of the arid corridor and are therefore an ideal species
 pair for studying patterns of genetic and phenotypic diversity associated
 with this landscape. However, species boundaries between these taxa have
 been controversial. Using multi-locus molecular and morphological
 datasets, we investigate diversification patterns of the M.
 afer-sundevallii Species Complex across the arid corridor. Although
 analysis of genetic data reveals some genetic structure among geographic
 populations, results of phylogenetic and morphological analyses provide
 little support for two distinct evolutionary lineages, suggesting that
 populations previously referred to as M. afer and M. sundevallii represent
 a single species, Mochlus sundevallii. Genetic diversity is unequally
 distributed across the arid corridor, with observed patterns consistent
 with aridification-facilitated diversification southward across southern
 Africa. Additional geographic and population-level sampling is necessary
 before more conclusive inferences can be drawn about the role historical
 climate transitions has played in skink diversification patterns across
 southern Africa.
description: Mochlus Concatenated
 AlignmentMochlus_Concatenated_FINAL.nexTopologiesMochlus_Topologies.pdfMeasurementsMochlus_Measurements.xlsx
DOI: 10.5061/dryad.2qf2f
title: Data from: The maintenance of obligate sex in finite, structured populations subject to recurrent beneficial and deleterious mutation

description: Although there is no known general explanation as to why sexual
 populations resist asexual invasion, previous work has shown that sexuals
 can outcompete asexuals in structured populations. However, it is
 currently unknown whether costly sex can be maintained with the weak
 structure that is commonly observed in nature. We investigate the
 conditions under which obligate sexuals resist asexual invasion in
 structured populations subject to recurrent mutation. We determine the
 level of population structure needed to disfavour asexuals, as calculated
 using the average Fst between all pairs of demes. We show that the
 critical Fst needed to maintain sex decreases as the population size
 increases, and approaches modest levels as observed in many natural
 populations. Sex is maintained with lower Fst if there are both
 advantageous and deleterious mutation, if mutation rates are sufficiently
 high, and if deleterious mutants have intermediate selective strengths,
 which maximises the effect of Muller's Ratchet. Additionally, the
 critical Fst needed to maintain sex is lower when there are a large number
 of subpopulations. Lower Fst values are needed to maintain sex when demes
 vary substantially in their pairwise distances (e.g., when arrayed along
 one dimension), although this effect is often modest, especially if some
 long-distance dispersal is present.
description: Simulation files as used
 in paperREADME.TXT FOR
 SIMULATION FILES: These files are the source code for the one-dimensional
 and two-dimensional population simulations used in the Hartfield et al
 2012 paper "The maintenance of obligate sex in finite, structured
 populations subject to recurrent beneficial and deleterious
 mutation". Simulations are written in C and need to be compiled prior
 to execution. See blurb at start of each program for description and how
 to execute. Please also note that simulations use routines that are part
 of the GNU Scientific Library (GSL). Since GSL is distributed under the
 GNU General Public License(http://www.gnu.org/copyleft/gpl.html), you must
 download it separately from these files. Note that we have also uploaded a
 Mathematica file, outlining the study into obtaining confidence intervals,
 as described in the manuscript. Comments should be sent to Matthew
 Hartfield (matthew.hartfield@ird.fr)Hartfield_etal_2012_sims.zip
DOI: 10.5061/dryad.15pg4g4
title: Data from: Phylogeography of African locust bean (Parkia biglobosa) reveals genetic divergence and spatially structured populations in West and Central Africa

description: The evolutionary history of African savannah tree species is crucial for
 the management of their genetic resources. In this study, we investigated
 the phylogeography of Parkia biglobosa and its modelled distribution under
 past and present climate conditions. This tree species is very valued and
 widespread in West Africa, providing edible and medicinal products. A
 large sample of 1 610 individuals from 84 populations, distributed across
 12 countries in Western and Central Africa, were genotyped using eight
 nuclear microsatellites. Individual-based assignments clearly
 distinguished three genetic clusters, extreme West Africa (EWA), centre of
 West Africa CWA), and Central Africa (CA). Overall, estimates of genetic
 diversity were moderate to high, with lower values for populations in EWA
 (AR=6.4, HE=0.78 and HO=0.7) and CA (AR=5.9, HE=0.67 and HO=0.61) compared
 to populations in CWA (AR=7.3, HE=0.79 and HO=0.75). The overall
 population differentiation was found to be moderate (FST=0.09). A highly
 significant isolation-by-distance pattern was detected, with a marked
 phylogeographic signature suggesting possible effects of past climate and
 geographic barriers to migration. Modelling the potential distribution of
 the species showed a contraction during the last glaciations followed by
 expansion events. The exploratory Approximate Bayesian Computation
 conducted suggests a best-supported scenario in which the cluster CWA
 traced back to the ancestral populations and a first split between EWA and
 CWA took place about 160 000 years BP, then a second split divided CA and
 CWA, about 100 000 years BP. However, our genetic data do not enable to
 conclusively distinguish among a few alternative possible scenarios.
description: Microsatellite
 GenotypesData file contains
 microsatellite genotypes for the 8 SSRs studied in 1610 individuals from
 84 populations - format is Genalex - coordinates of populations are in
 columns 21 and 22.84-Pops-data-20160630_DRYAD.xlsx
DOI: 10.15468/dl.pcymkr
title: Occurrence Download

description: A dataset containing 328128 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Turdus",
 "Year 2000-2025"
 ]
}

 The dataset includes 328128 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000524-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8m6j3
title: Data from: Phylogeographic model selection leads to insight into the evolutionary history of four-eyed frogs

description: Phylogeographic research investigates biodiversity at the interface
 between populations and species, in a temporal and geographic context.
 Phylogeography has benefited from analytical approaches that allow
 empiricists to estimate parameters of interest from the genetic data
 (e.g., θ = 4Neμ, population divergence, gene flow), and the widespread
 availability of genomic data allow such parameters to be estimated with
 greater precision. However, the actual inferences made by phylogeographers
 remain dependent on qualitative interpretations derived from these
 parameters’ values and as such may be subject to overinterpretation and
 confirmation bias. Here we argue in favor of using an objective approach
 to phylogeographic inference that proceeds by calculating the probability
 of multiple demographic models given the data and the subsequent ranking
 of these models using information theory. We illustrate this approach by
 investigating the diversification of two sister species of four-eyed frogs
 of northeastern Brazil using single nucleotide polymorphisms obtained via
 restriction-associated digest sequencing. We estimate the composite
 likelihood of the observed data given nine demographic models and then
 rank these models using Akaike information criterion. We demonstrate that
 estimating parameters under a model that is a poor fit to the data is
 likely to produce values that lead to spurious phylogeographic inferences.
 Our results strongly imply that identifying which parameters to estimate
 from a given system is a key step in the process of phylogeographic
 inference and is at least as important as being able to generate precise
 estimates of these parameters. They also illustrate that the incorporation
 of model uncertainty should be a component of phylogeographic hypothesis
 tests.
description: Thome.fscGenetic data analysis files.
DOI: 10.5061/dryad.r5nj3
title: Data from: Characterizing selection in black-throated blue warblers using a sexual network approach

description: Our understanding of trait evolution is built upon studies that examine
 the correlation between traits and fitness, most of which implicitly
 assume all individuals experience similar selective environments. However,
 accounting for differences in selective pressures, such as variation in
 the social environment, can advance our understanding of how selection
 shapes individual traits and subsequent fitness. In this study, we test
 whether variation in the social environment affects selection on
 individual phenotype. We apply a new sexual network framework to quantify
 each male's social environment as the mean body size of his primary
 competitors. We test for direct and social selection on male body size
 using a 10-year dataset on black-throated blue warblers (Setophaga
 caerulescens), a territorial species for which body size is hypothesized
 to mediate competition for mates. We found that direct selection on body
 size was weak and non-significant, as was social selection via the body
 size of the males’ competitors. Analyzing both types of selection
 simultaneously allows us to firmly reject a role for body size in
 competitive interactions between males and subsequent male fitness in this
 population. We evaluate the application of the sexual network approach to
 empirical data, and suggest that other phenotypic traits such as song
 characteristics and plumage may be more relevant than body size for
 male-male competition in this small passerine bird.
description: Data for selection
 analysis on male black-throated blue warblersThe data file includes
 morphological measurements and reproductive success data for individual
 males, as well as average morphological measurements for individual
 males' competitors. We include standardized and unstandardized
 variables, as well as weighted and unweighted values for the morphology of
 the competitors. Full details are in the ReadMe file, as is R code to
 assist with re-creating analyses from the article.BTBW_dryad.csv
DOI: 10.5061/dryad.2538d
title: Data from: Metabolic costs imposed by hydrostatic pressure constrain bathymetric range in the lithodid crab Lithodes maja

description: Changing climate is shifting the distributions of marine species, yet the
 potential for shifts in depth distributions is virtually unexplored.
 Hydrostatic pressure is proposed to contribute to a physiological
 bottleneck constraining depth range extension in shallow-water taxa.
 However, bathymetric limitation by hydrostatic pressure remains
 undemonstrated, and the mechanism limiting hyperbaric tolerance remains
 hypothetical. Here, we assess the effects of hydrostatic pressure in the
 lithodid crab Lithodes maja (bathymetric range 4-790 m depth,
 approximately equivalent to 0.1 to 7.9 MPa hydrostatic pressure). Heart
 rate decreased with increasing hydrostatic pressure, and was significantly
 lower at ≥10.0 MPa than at 0.1 MPa. Oxygen consumption increased with
 increasing hydrostatic pressure to 12.5 MPa, before decreasing as
 hydrostatic pressure increased to 20.0 MPa: oxygen consumption was
 significantly higher at 7.5-17.5 MPa than at 0.1 MPa. Increases in
 expression of genes associated with neurotransmission, metabolism and
 stress were observed between 7.5 and 12.5 MPa. We suggest that hyperbaric
 tolerance in L. maja may be oxygen-limited by hyperbaric effects on heart
 rate and metabolic rate, but that L. maja’s bathymetric range is limited
 by metabolic costs imposed by the effects of high hydrostatic pressure.
 These results advocate including hydrostatic pressure in a complex model
 of environmental tolerance, where energy-limitation constrains
 biogeographic range, and facilitate incorporating hydrostatic pressure
 into the broader metabolic framework for ecology and evolution. Such an
 approach is crucial for accurately projecting biogeographic responses to
 changing climate, and for understanding the ecology and evolution of life
 at depth.
description: Acute hyperbaric
 tolerance heart rate and molar oxygen consumption dataAcute hyperbaric
 tolerance mass-normalised heart rate and mass-normalised mass-specific
 molar oxygen consumption.Brown&al._J_Exp_Biol_17_acute_hyperbaric_tolerance.xlsxSustained hyperbaric tolerance heart rate and molar oxygen consumption dataSustained hyperbaric tolerance mass-normalised heart rate and mass-normalised mass-specific molar oxygen consumption.Brown&al._J_Exp_Biol_17_sustained_hyperbaric_tolerance.xlsx