cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8q3m5r0
title: Data from: A dark scenario for Cerrado plant species: effects of future climate, land use and protected areas ineffectiveness

description: Aim: The anthropogenic climate change and land-use change are considered
 two of the main factors that are altering biodiversity at the global
 scale. An evaluation that combined both factors can be relevant to detect
 which species could be the most vulnerable and reveal the regions of
 highest stability or susceptibility to biodiversity. We aimed to (i)
 assess the effect of climate change and land-use on the distribution of
 Cerrado plant species for different countries where they occur, (ii)
 evaluate the effectiveness of the current network of protected areas (PAs)
 to safeguards species under different greenhouse-gas (GHG) emissions and
 land-use scenarios and (iii) estimate the vulnerability of species based
 on protection effectiveness and habitat loss. Location: Bolivia, Brazil,
 and Paraguay. Methods: We modeled the distribution of 1,553 plant species
 of Cerrado and evaluated species range loss caused by present and future
 land-use and two GHG for 2050 and 2080. We assessed species vulnerability
 combining the representativeness of species within conservation units with
 the loss of species’ ranges outside PAs. Results: We found that climate
 change and land-use will cause great damage to Cerrado flora by 2050 and
 2080, even under optimistic conditions. The greatest impacts of land-use
 will occur in the regions where the greatest richness will be harbored.
 The conservation of the species will be seriously affected since the PA
 network is not as effective in safeguarding them under current or future
 conditions. Main conclusions: The low level of protection together with
 the losses caused by the advance of agricultural lands will lead most
 species being highly vulnerable. Due to the distinct impacts of climate
 and land-use over the three countries, conservation strategies should be
 implemented at transboundary and national levels.
description: Plant species records of
 Cerrado ecoregionThe
 “species_records.txt” is a tab-delimited text file that includes cleaned
 occurrence records of plants species from different sources (e.g.
 speciesLinks, Tropicos, GBIF, etc) used to create ecological niches models
 of the research "A dark scenario for Cerrado plant species: effects
 of future climate, land-use and, protected areas
 ineffectiveness".species_records.txt
DOI: 10.5061/dryad.7jf48t0
title: Data from: Characterization of the bacterial microbiota in wild-caught Ixodes ventalloi

description: Exploring the microbial diversity of ticks is crucial to understand
 geographical dispersion and pathogen transmission. Tick microbes
 participate in many biological processes implicated in the acquisition,
 maintenance, and transmission of pathogens, and actively promote host
 phenotypic changes, and adaptation to new environments. The microbial
 community of Ixodes ventalloi still remains unexplored. In this study, the
 bacterial microbiota of wild-caught I. ventalloi was characterized using
 shotgun-metagenomic sequencing in samples from unfed adults collected
 during December 2013-January 2014 in two locations from Sicily, Italy. The
 microbiota identified in I. ventalloi was mainly composed of symbiotic,
 commensal, and environmental bacteria. Interestingly, we identified the
 genera Anaplasma and Borrelia as members of the microbiota of I.
 ventalloi. These results advance our information on I. ventalloi
 microbiota composition, with potential implications in tick-host
 adaptation, geographic expansion, and vector competence.
description: BAM_mappedReadsBAM file corresponding to the reads of Location1 and Location2 samples of I. ventalloi mapping to the bacterial genome reference list.
DOI: 10.5061/dryad.nn75v55
title: Data from: Moderate heritability and low evolvability of sperm morphology in a species with high risk of sperm competition, the collared flycatcher Ficedula albicollis

description: Spermatozoa represent the morphologically most diverse type of animal
 cells and show remarkable variation in size across and also within
 species. To understand the evolution of this diversity, it is important to
 reveal to what degree this variation is genetic or environmental in origin
 and whether this depends on species’ life‐histories. Here we applied
 quantitative genetic methods to a pedigreed multigenerational data set of
 the collared flycatcher Ficedula albicollis, a passerine bird with high
 levels of extra‐pair paternity, to partition genetic and environmental
 sources of phenotypic variation in sperm dimensions for the first time in
 a natural population. Narrow‐sense heritability (h2) of total sperm length
 amounted to 0.44±0.14 SE while the corresponding figure for evolvability
 (estimated as coefficient of additive genetic variation, CVa) was
 0.02±0.003 SE. We also found an increase in total sperm length within
 individual males between the arrival and nestling period. This seasonal
 variation may reflect constraints in the production of fully elongated
 spermatozoa shortly after arrival at the breeding grounds. There was no
 evidence of an effect of male age on sperm dimensions. In many previous
 studies on laboratory populations of several insect, mammal and avian
 species, heritabilities of sperm morphology were higher while
 evolvabilities were similar. Explanations for the differences in
 heritability may include variation in the environment (laboratory vs.
 wild), intensity of sexual selection via sperm competition (high vs. low)
 and genetic architecture that involves unusual linkage disequilibrium
 coupled with overdominance in one of the studied species.
description: 12000sperms
 Measurements of
 individual spermatozoa   
 600samples
 Datafile
 containing other variables   
 measurement_errors A file for calculation of repeatability of measurements (based on 600 spermatozoa from 30 samples measured twice)   vc Variance components from Asreml-R (to draw Figure 1)   pedigree   R-script
DOI: 10.5061/dryad.f7k2333
title: Data from: The evolution of the dicynodont sacrum: constraint and innovation in the synapsid axial column

description: Constraint is a universal feature of morphological evolution. The
 vertebral column of synapsids (mammals and their close relatives) is a
 classic example of this phenotypic restriction, with greatly reduced
 variation in the number of vertebrae compared to the sauropsid lineage.
 Synapsids generally possess only three sacral vertebrae, which articulate
 with the ilium and play a key role in locomotion. Dicynodont anomodonts
 are the exception to this rule, possessing seven or more sacral vertebrae
 while reaching a range of body sizes rivaled among synapsids only by
 therian mammals. Here we explore the evolution of this unusual sacral
 morphology in dicynodonts by 1) hypothesizing homologies of the additional
 sacral vertebrae, 2) using ancestral state reconstruction and phylogenetic
 regressions (e.g., logistic regression, Poisson regression) to track the
 coevolution of sacral count and body size, and 3) proposing mechanisms by
 which additional sacral vertebrae were incorporated during dicynodont
 evolution. We find that sacral vertebra morphology covaries with sacral
 count in consistent ways across dicynodonts, implying that sacra with a
 given number of vertebrae are composed of homologous elements. There is a
 correlation between increased sacral count and larger body size,
 especially at the shift from four to five sacrals near the origin of
 Bidentalia. Based on position, morphology, and the consistent number of
 presacral vertebrae among dicynodonts, we hypothesize that the additional
 sacrals anterior to the plesiomorphic three are duplications of the first
 sacral, and that a single caudosacral was incorporated by a shift in the
 identity of the anteriormost caudal vertebra. Although changes in sacral
 count appear to be correlated with shifts in body size in dicynodonts, the
 evolution of general morphological conservativism in the synapsid sacrum
 remains to be further explored.
description: Griffin and
 Angielczyk_Supplementary InformationA PDF with supplementary
 figures 1–10, supplementary table 1, and captions for other supplementary
 filesGriffinandAngielczyk R
 codeR
 code used for this study's analysesGriffinandAngielczyk_Rcode.ROlroydetal_2018_timecalibratedTime-calibrated phylogenetic tree file of the relationships of dicynodonts and other anomodonts used in our analyses. This .tre file, with filename, is used in the R code.dicynodont_sizesA .csv file containing all anomodont taxa used in our analyses involving basal skull length, with corresponding basal skull lengths (“bsl”) for each taxon. This .csv file, with filename, is used in the R code.dicynodont_sacrum_statesA .csv file containing all anomodont taxa used in our analyses involving sacral counts, with corresponding sacrum count state for each taxon. Coding of states described in the main text. This .csv file, with filename, is used in the R code.
DOI: 10.5061/dryad.td54031
title: Data from: Spatio-temporal dynamics of density-dependent dispersal during a population colonisation

description: Predicting population colonisations requires understanding how
 spatio-temporal changes in density affect dispersal. Density can inform on
 fitness prospects, acting as a cue for either habitat quality, or
 competition over resources. However, when escaping competition, high local
 density should only increase emigration if lower-density patches are
 available elsewhere. Few empirical studies on dispersal have considered
 the effects of density at the local and landscape scale simultaneously. To
 explore this, we analyze 5 years of individual-based data from an
 experimental introduction of wild guppies Poecilia reticulata. Natal
 dispersal showed a decrease in local density dependence as density at the
 landscape level increased. Landscape density did not affect dispersal
 among adults, but local density-dependent dispersal switched from negative
 (conspecific attraction) to positive (conspecific avoidance), as the
 colonisation progressed. This study demonstrates that densities at various
 scales interact to determine dispersal, and suggests that dispersal
 trade-offs differ across life stages.
description: guppy dispersal
 datadata file created in R,
 subset of a larger dataset containing individual based data throughout 10
 years of monitoring of four guppy populationsdata.csvdensity-dependent-dispersal analysesCompressed folder containing a documented R package (DDDEvo) with the necessary scripts and instructions to reproduce the analyses contained in the paper.density-dependent-dispersal.zip
DOI: 10.5061/dryad.kb401ch
title: Data from: Local and regional scale habitat heterogeneity contribute to genetic adaptation in a commercially important marine mollusc (Haliotis rubra) from southeastern Australia

description: Characterising adaptive genetic divergence among conspecific populations
 is often achieved by studying genetic variation across defined
 environmental gradients. In marine systems this is challenging due to a
 paucity of information on habitat heterogeneity at local and regional
 scales and a dependency on sampling regimes that are typically limited to
 broad longitudinal and latitudinal environmental gradients. As a result,
 the spatial scales at which selection processes operate and the
 environmental factors that contribute to genetic adaptation in marine
 systems are likely to be unclear. In this study we explore patterns of
 adaptive genetic structuring in a commercially- harvested abalone species
 (Haliotis rubra) from south-eastern Australia, using a panel of
 genome-wide SNP markers (5,239 SNPs), and a sampling regime informed by
 marine LiDAR bathymetric imagery and 20-year hindcasted oceanographic
 models. Despite a lack of overall genetic structure across the sampling
 distribution, significant genotype associations with heterogeneous habitat
 features were observed at local and regional spatial scales, including
 associations with wave energy, ocean current, sea surface temperature, and
 geology. These findings provide insights into the potential resilience of
 the species to changing marine climates and the role of migration and
 selection on recruitment processes, with implications for conservation and
 fisheries management. This study points to the spatial scales at which
 selection processes operate in marine systems and highlights the benefits
 of geospatially-informed sampling regimes for overcoming limitations
 associated with marine population genomic research.
description: Hrubra total SNP
 datasetTotal genomic dataset
 consisting of 5,239 SNP loci. Individual and population codes correspond
 with those provided in Table 1 of the manuscriptAbaloneSites_Final_EnvironmentalData.xlsx
DOI: 10.5061/dryad.0kf782p
title: Data from: Ancient and contingent body shape diversification in a hyperdiverse fish radiation

description: [No abstract entered]
description: Landmark
 DataTPS file containing
 landmark dataChapter 1_Disparity
 Data.TPSPhylogenetic
 TreeA
 nexus file containing the phylogenetic tree used in the phylogenetic
 comparative methods.Chapter
 1_trees_final.nexusPrincipal Component
 scoresPrincipal Component
 scores used to construct the morphospace and also used in the mvMORPH
 analysis.Chapter 1_data_all
 PCs.csvPhylogeneticEM
 dataData used for
 PhylogeneticEM analysisChapter
 1_PhylogeneticEM_data.csvConevol
 scriptScript used to run
 Conevol analysis in RChapter
 1_Conevol.txtMVmorph
 scriptScript used to perform
 MVmorph analysis in RChapter
 1_MVmorph.txtMVmorph_uncertainty
 scriptScript used to perform
 MVmorph analysis while accounting for uncertainty in the trophic
 ecologyChapter 1_MVmorph_uncertainty
 code.txtPhylogeneticEM
 scriptScript used to perform
 PhylogeneticEM analysis in RChapter
 1_PhylogeneticEM.RSurface
 scriptScript used to perform
 SURFACE analysis in RChapter 1_Phylomorpospace and
 Surface.txtCo-occurrence
 scriptCalculate the
 probability of at least c of m shifts in morphological regime falling on
 the same branches of a phylogeny as e shifts in ecologyCo-occurrence.R
DOI: 10.5061/dryad.j1m1t3t
title: Data from: Hierarchical distance sampling to estimate population sizes of common lizards across a desert ecoregion

description: 1) Multi-species wildlife monitoring across large geographical regions is
 important for effective conservation planning in response to expected
 impacts from climate change and land use. Unlike many species of birds,
 mammals, and amphibians which can be efficiently sampled using automated
 sensors including cameras and sound recorders, reptiles are often much
 more challenging to detect, in part because of their typically cryptic
 behavior and generally small body sizes. Although many lizard species are
 more active during the day which makes them easier to detect using visual
 encounter surveys, they may be unavailable for sampling during certain
 periods of the day or year due to their sensitivity to temperature. 2) In
 recognition of these sampling challenges, we demonstrate application of a
 recent innovation in distance sampling that adjusts for temporary
 emigration between repeat survey visits. We used transect surveys to
 survey lizards at 229 sites throughout the Mojave Desert in California,
 USA, 2016. 3) We estimated a total population size of 80 million (90% CI:
 64–97 million) for the three most common species of lizards across this
 66,830 km2 ecoregion. We mapped how density at the 1-km2 scale was
 predicted to vary with vegetation cover and human development. We
 validated these results against independent surveys from the southern
 portion of our study area. 4) Our methods and results demonstrate how
 multi-species monitoring programs spanning arid ecoregions can better
 incorporate information about reptiles.
description: R code used in
 modelingR code used in modeling;
 use in combination with attached RData objectlizard_model.Rlizard_dataRData object used in modeling; use in combination with attached R code
DOI: 10.5061/dryad.r2d5451
title: Data from: The Sarracenia alata pitcher plant system and obligate arthropod inquilines should be considered an evolutionary community

description: Aim: The Sarracenia alata pitcher plant and inquiline species comprise an
 ecological community. These inquilines span the continuum in their
 ecological association with the host pitcher plant, from species that
 contain little-to-no interaction with the plant to species that are
 completely dependent on the plant for their entire life cycle. We are
 interested in testing if degree of ecological dependence is positively
 correlated with a shared evolutionary history, and in identifying members
 of this community that display concordant phylogeographic structure.
 Location: Southeastern United States Methods: We collected genome-wide
 sequence data from a set of arthropods that are ecologically-associated
 with the plant to estimate comparative phylogeographic patterns among the
 species. We estimated species tree distributions from biallelic unlinked
 SNP data and used phylogeographic concordance factors (PCFs) to test
 degree of phylogeographic concordance among community members. In
 addition, we calculated AMOVAs and FST values to identify population
 genetic structure across the landscape, and compared these traditional
 values to the tree-based approach. Results: Obligate members of the
 pitcher plant community display concordant phylogeographic patterns,
 suggesting their ecological dependence has manifested itself into a shared
 evolutionary history. In contrast, two spider species do not contain
 significant population genetic structure or similar phylogeographic
 histories, highlighting their loose association with the host pitcher
 plant. Main conclusion: The Sarracenia alata pitcher plant system should
 be considered an evolutionary community, where multiple members sharing
 strong ecological interactions also display concordant phylogeographic
 structure. This work demonstrates that PCFs provide an important
 quantitative measure into assessing community structure and illustrate how
 simulations can be used to assess significance of shared patterns of
 phylogeographic structure across the landscape.
description: Data
 filesData and output files
 produced by pyrad.data.tar.gzAMOVA and Fst analysesData and script for AMOVA and Fst analyses.amova_fst.tar.gzSNAPP analysesData and script for converting snp files into snapp input files.snapp.tar.gzPopulation genetic summary statisticsScript for calculating population genetic summary statistics.summarystats.tar.gzPhylogeographic concordance factor analysisData and scripts for running Phylogeographic Concordance Factors (PCFs) and testing for significance with the analysis.pcfs.tar.gz
DOI: 10.5061/dryad.tj3bd3n
title: Data from: Rarity does not limit genetic variation or preclude subpopulation structure in the geographically restricted desert forb Astragalus lentiginosus var. piscinensis

description: Premise of the study: Characteristics of rare taxa include small
 population sizes and limited geographical ranges. The genetic consequences
 of rarity are poorly understood for most taxa. A small geographical range
 could result in reduced opportunity for isolation by distance or
 environment, thereby limiting genetic structure and variation, but few
 studies explore genetic structure at small spatial scales with sufficient
 resolution to test this hypothesis. Moreover, few comparative genetic
 studies exist among infrataxa differing in rarity. Here, we compare
 genetic variation among varieties of Astragalus lentiginosus differing in
 range size. Additionally, we ask if genetic structure exists in A. l. var.
 piscinensis, a rare taxon consisting of several thousand individuals that
 persist on ~8 km2 of alkaline soil. Methods: We compared genetic variation
 among 11 varieties of A. lentiginosus differing in range size using a
 genotyping by sequencing (GBS) approach, which generated 11,475 single
 nucleotide polymorphisms (SNPs). We characterized genetic structure among
 subpopulations of A. l. var. piscinensis using a second GBS dataset of
 7,274 SNPs and explored associations between genetic structure and
 environmental variation. Key results: We found no association between
 genetic variation and range size among varieties of A. lentiginosus.
 Additionally, despite the extremely small range of A. l. var. piscinensis,
 we report a well-defined genetic structure among subpopulations associated
 with microhabitat variation in soil composition. Conclusion: Our results
 suggest that fine scale genetic structure may exist within other rare
 Astragalus taxa and that rarity does not preclude the maintenance of
 genetic diversity in this genus. In compliance with data protection
 regulations, please contact the publication office if you would like to
 have your personal information removed from the database.
description: RangeMapsKMZ files of range polygons used in the study along with SEINet records used to generate those polygons. Outline of Fish Slough, CA, USA also included.genotypeEstimatesGenotype estimates for all SNPs for all individuals.abioticDataAbiotic data corresponding to each individual sampled. Sample names correspond to those in the genotype estimate file.
DOI: 10.5061/dryad.0j18k00
title: Data from: Pliocene and Eocene provide best analogs for near-future climates

description: As the world warms due to rising greenhouse gas concentrations, the Earth
 system moves toward climate states without societal precedent, challenging
 adaptation. Past Earth system states offer possible model systems for the
 warming world of the coming decades. These include the climate states of
 the Early Eocene (ca. 50 Ma), the Mid-Pliocene (3.3–3.0 Ma), the Last
 Interglacial (129–116 ka), the Mid-Holocene (6 ka), preindustrial (ca.
 1850 CE), and the 20th century. Here, we quantitatively assess the
 similarity of future projected climate states to these six geohistorical
 benchmarks using simulations from the Hadley Centre Coupled Model Version
 3 (HadCM3), the Goddard Institute for Space Studies Model E2-R (GISS), and
 the Community Climate System Model, Versions 3 and 4 (CCSM) Earth system
 models. Under the Representative Concentration Pathway 8.5 (RCP8.5)
 emission scenario, by 2030 CE, future climates most closely resemble
 Mid-Pliocene climates, and by 2150 CE, they most closely resemble the
 Eocene climates. Under RCP4.5, climate stabilizes at Pliocene-like
 conditions by 2040 CE. Pliocene-like and Eocene-like climates emerge first
 in continental interiors and then, expand outward. Geologically novel
 climates are uncommon in RCP4.5 (&lt;1%) but reach 8.7% of the globe
 under RCP8.5, characterized by high temperatures and precipitation. Hence,
 RCP4.5 is roughly equivalent to stabilizing at Pliocene-like climates,
 while unmitigated emission trajectories, such as RCP8.5, are similar to
 reversing millions of years of long-term cooling on the scale of a few
 human generations. Both the emergence of geologically novel climates and
 the rapid reversion to Eocene-like climates may be outside the range of
 evolutionary adaptive capacity.
description: Projected future climate
 analogs of 2020-2280 CE, using a baseline of geohistorical climates back
 to the EoceneThis dataset contains
 Matlab code to calculate multivariate distances. It compares future time
 periods (target) to a reference baseline (reference). Considering these
 one-to-many comparisons, the minimum multivariate distance for a focal
 location is defined as the closest analog. The input climate data, as well
 as output analog data, are included as well.analog_fast.zip