cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s2df3
title: Data from: Evolutionary prediction of medicinal properties in the genus Euphorbia L.

description: The current decrease of new drugs brought to the market has fostered
 renewed interest in plant-based drug discovery. Given the alarming rate of
 biodiversity loss, systematic methodologies in finding new plant-derived
 drugs are urgently needed. Medicinal uses of plants were proposed as proxy
 for bioactivity, and phylogenetic patterns in medicinal plant uses have
 suggested that phylogeny can be used as predictive tool. However, the
 common practice of grouping medicinal plant uses into standardised
 categories may restrict the relevance of phylogenetic predictions.
 Standardised categories are mostly associated to systems of the human body
 and only poorly reflect biological responses to the treatment. Here we
 show that medicinal plant uses interpreted from a perspective of a
 biological response can reveal different phylogenetic patterns of presumed
 underlying bioactivity compared to standardised methods of medicinal plant
 use classification. In the cosmopolitan and pharmaceutically highly
 relevant genus Euphorbia L., identifying plant uses modulating the
 inflammatory response highlighted a greater phylogenetic diversity and
 number of potentially promising species than standardised categories. Our
 interpretation of medicinal plant uses may therefore allow for a more
 targeted approach for future phylogeny-guided drug discovery at an early
 screening stage, which will likely result in higher discovery rates of
 novel chemistry with functional biological activity.
description: Alignment
 fileAligned DNA sequence
 from plastid marker ndhF. The matrix includes sequences (1789 base pairs)
 of 560 Euphorbia species retrieved from GenBank.ndhF_FINALnodups_560spBayesSimple.nexSet of 1000 Bayesian treesRandomly selected subset of 1000 trees within the 95% credible set.posteriorsample3.nexR scriptRscript.txt
DOI: 10.5061/dryad.2g75hp3
title: Data from: Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

description: The idea that noncrop habitat enhances pest control and represents a
 win–win opportunity to conserve biodiversity and bolster yields has
 emerged as an agroecological paradigm. However, while noncrop habitat in
 landscapes surrounding farms sometimes benefits pest predators, natural
 enemy responses remain heterogeneous across studies and effects on pests
 are inconclusive. The observed heterogeneity in species responses to
 noncrop habitat may be biological in origin or could result from variation
 in how habitat and biocontrol are measured. Here, we use a pest-control
 database encompassing 132 studies and 6,759 sites worldwide to model
 natural enemy and pest abundances, predation rates, and crop damage as a
 function of landscape composition. Our results showed that although
 landscape composition explained significant variation within studies, pest
 and enemy abundances, predation rates, crop damage, and yields each
 exhibited different responses across studies, sometimes increasing and
 sometimes decreasing in landscapes with more noncrop habitat but overall
 showing no consistent trend. Thus, models that used landscape-composition
 variables to predict pest-control dynamics demonstrated little potential
 to explain variation across studies, though prediction did improve when
 comparing studies with similar crop and landscape features. Overall, our
 work shows that surrounding noncrop habitat does not consistently improve
 pest management, meaning habitat conservation may bolster production in
 some systems and depress yields in others. Future efforts to develop tools
 that inform farmers when habitat conservation truly represents a win–win
 would benefit from increased understanding of how landscape effects are
 modulated by local farm management and the biology of pests and their
 enemies.
description: BioControlDatabaseThis pest-control database encompasses 132 studies and 6,759 sites worldwide. Data discussed and interpreted in Karp et al. (2018) Crop pests and predators exhibit inconsistent responses to surrounding landscape composition. PNAS.
DOI: 10.15468/dl.udrv3p
title: Occurrence Download

description: A dataset containing 657771 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((3.04426 47.0406,2.94896 46.84848,3.09197 46.64322,3.20802 46.40115,3.31024 45.97768,3.38967 45.96113,3.55985 45.95071,3.56158 45.99412,3.51582 46.0741,3.50907 46.13656,3.3732 46.51107,3.35452 46.57261,3.27133 46.67653,3.22157 46.70263,3.17833 46.74423,3.12381 46.8071,3.09943 46.85329,3.10071 46.93155,3.20656 46.96683,3.16486 47.01815,3.08211 47.06433,3.04426 47.0406))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 657771 records from 738 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001705-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kc7h9
title: Data from: Evaluating the impact of domestication and captivity on the horse gut microbiome

description: The mammal gut microbiome, which includes host microbes and their
 respective genes, is now recognized as an essential second genome that
 provides critical functions to the host. In humans, studies have revealed
 that lifestyle strongly influences the composition and diversity of the
 gastrointestinal microbiome. We hypothesized that these trends in humans
 may be paralleled in mammals subjected to anthropogenic forces such as
 domestication and captivity, in which diets and natural life histories are
 often greatly modified. We investigated fecal microbiomes of Przewalski’s
 horse (PH; Equus ferus przewalskii), the only horses alive today not
 successfully domesticated by humans, and herded, domestic horse (E. f.
 caballus) living in adjacent natural grasslands. We discovered PH fecal
 microbiomes hosted a distinct and more diverse community of bacteria
 compared to domestic horses, which is likely partly explained by different
 plant diets as revealed by trnL maker data. Within the PH population, four
 individuals were born in captivity in European zoos and hosted a
 strikingly low diversity of fecal microbiota compared to individuals born
 in natural reserves in France and Mongolia. These results suggest that
 anthropogenic forces can dramatically reshape equid gastrointestinal
 microbiomes, which has broader implications for the conservation
 management of endangered mammals.
description: trnL data
 setThis file contains trnL
 data with metadata. The trnL data have been processed as described in
 Metcalf et al. 2017.Diet.Matrix-final.txtDiet.Matrix.taxonomyTaxonomy strings assigned to trnL sequences. Taxonomy could not be assigned to most sequences.Sample metadata, Supplementary Table 3TableS3_CORRECTED_2018.xlsx
DOI: 10.5061/dryad.g94676pg
title: Data from: Islands and streams: clusters and gene flow in wild barley populations from the Levant

description: The domestication of plants frequently results in a high level of genetic
 differentiation between domesticated plants and their wild progenitors.
 This process is counteracted by gene flow between wild and domesticated
 plants because they are usually able to inter-mate and to exchange genes.
 We investigated the extent of gene flow between wild barley Hordeum
 spontaneum and cultivated barley Hordeum vulgare, and its effect on
 population structure in wild barley by analyzing a collection of 896 wild
 barley accessions (Barley1K) from Israel and all available Israeli H.
 vulgare accessions from the Israeli gene bank. We compared the performance
 of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP)
 marker data genotyped over a core collection in estimating population
 parameters. Estimates of gene flow rates with SSR markers indicated a high
 level of introgression from cultivated barley into wild barley. After
 removing accessions from the wild barley sample that were recently admixed
 with cultivated barley, the inference of population structure improved
 significantly. Both SSR and SNP markers showed that the genetic population
 structure of wild barley in Israel corresponds to the three major
 ecogeographic regions: the coast, the Mediterranean north, and the deserts
 in the Jordan valley and the South. Gene flow rates were estimated to be
 higher from north to south than in the opposite direction. As has been
 observed in other crop species, there is a significant exchange of alleles
 between the wild species and domesticated varieties that needs to be
 accounted for in the population genetic analysis of domestication.
description: Barley1K_microsatellitesB1K illuminaBarley1k locationMS Excel spreadsheet showing Barley1k locations.Barley1k_location.xls
DOI: 10.5683/sp3/sn7g7x
title: Replication data for: Comparative evaluation of otolith and fin ray as tools for assessing population differentiation in Atlantic sturgeon (Acipenser oxyrinchus)

description: This data repository compile the raw dataset used in the article titled "Comparative evaluation of otolith and fin ray as tools for assessing population differentiation in Atlantic sturgeon (Acipenser oxyrinchus)" published in PlosONE. Data are trace element chemistry transects in both fin rays and otoliths, for both sampling sites.
DOI: 10.5061/dryad.t5sd8c8
title: Data from: Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set

description: The Neotropical moth-like butterflies (Hedylidae) are perhaps the most
 unusual butterfly family. In addition to being species-poor, this family
 is predominantly nocturnal and has anti-bat ultrasound hearing organs.
 Evolutionary relationships among the 36 described species are largely
 unexplored. A 13-gene anchored hybrid enrichment probe set
 (‘BUTTERFLY2.0’), that includes standard markers used in butterfly
 phylogenetics, captured sequences from decades-old museum specimens, and
 appears to be a cost-effective technique to infer phylogenetic
 relationships of the butterfly tree of life. Our dataset comprises up to
 10,898 aligned base pairs from each of the 22 species of Hedylidae and 19
 outgroups. Eleven of the thirteen loci were captured from 100% of the
 taxa, and the remaining loci were captured from ≥94% of taxa. The inferred
 phylogeny had robust support at 80% of nodes. Our results are consistent
 with morphological work, with Macrosoma tipulata sister to all remaining
 hedylids, followed by M. semiermis sister to the remaining species in the
 genus. We tested the hypothesis that nocturnality evolved only once from
 diurnality in Hedylidae, and showed that the ancestral condition was
 likely diurnal, with a shift to nocturnality early in the diversification
 of this family.
description: READMEAll supplemental files
 and figures referenced in publicationFolder contains the
 following supplemental files: SuppFile1.Catalog.pdf
 Fig.S6.ASR_Diel_parsimony.pdf Fig.S5.ASR_Diel_Phytools.pdf
 Table.S2.Extraction_loci.xlsx Table.S1.Sample_localities.xlsx
 Table.S3.Quantification.xlsx Fig.S3.ML_supports.pdf
 Fig.S4.Astral_probeonly.pdf Table.S4.PartModels.xlsx
 Fig.S1.MLbest_probe+flank.pdf
 Fig.S2.MLbest_probeonly.pdfKawahara_etal_2018_All_supplements_final.zipConcatenated supermatrix of probe and flanking sequences for all loci and specimensConcatenated supermatrix of probe and flanking sequences for all loci and specimens. This matrix was use to build the phylogeny in the paper.Concatenated_supermatrix_combined_probe+flank_FINAL.fastaBUTTERFLY2.0_kitSpecification file for the BUTTERFLY2.0 probe set used to order probes from Agilent Technologies (http://www.agilent.com/)Hedylid_tree_combined_probe+flank_FINALTree file for the final Fig. 1 tree built from using probe and flanking sequences. This tree was uploaded to the Open Tree of Life https://tree.opentreeoflife.org/Hedylid_tree_UFboot_combined_probe+flank_FINALSame tree file as Hedylid_tree_combined_probe+flank_FINAL.tre, but with UltraFast bootstrap support values
DOI: 10.15468/dl.2kjmwd
title: Occurrence Download

description: A dataset containing 2388 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "PublishingOrg is ccd1ddc0-6c21-11de-8224-b8a03c50a862",
 "TaxonKey is Synallaxis"
 ]
}

 The dataset includes 2388 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001738-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3680n0c
title: Data from: Using historical biogeography models to study color pattern evolution

description: Color is among the most striking features of organisms, varying not only
 in spectral properties like hue and brightness, but also in where and how
 it is produced on the body. Different combinations of colors on a bird’s
 body are important in both environmental and social contexts. Previous
 comparative studies have treated plumage patches individually or derived
 plumage complexity scores from color measurements across a bird’s body.
 However, these approaches do not consider the multivariate nature of
 plumages (allowing for plumage to evolve as a whole) or account for
 interpatch distances. Here, we leverage a rich toolkit used in historical
 biogeography to assess color pattern evolution in a cosmopolitan radiation
 of birds, kingfishers (Aves: Alcedinidae). We demonstrate the utility of
 this approach and test hypotheses about the tempo and mode of color
 evolution in kingfishers. Our results highlight the importance of
 considering interpatch distances in understanding macroevolutionary trends
 in color diversity and demonstrate how historical biogeography models are
 a useful way to model plumage color pattern evolution. Furthermore, they
 show that distinct color mechanisms (pigments or structural colors) spread
 across the body in different ways and at different rates. Specifically,
 net rates are higher for structural colors than pigment-based colors.
 Together, our study suggests a role for both development and selection in
 driving extraordinary color pattern diversity in kingfishers. We
 anticipate this approach will be useful for modeling other complex
 phenotypes besides color, such as parasite evolution across the body.
description: Plumage complexity
 metricsMean interpatch
 distances from spectral data and mechanistic complexity scores calculated
 from RevBayes analysesinterpatch_dist.csvCarotenoid scoresking_co.nexEumelanin scoresking_e.nexPhaeomelanin scoresking_p.nexStructural barbules scoresking_sb.nexStructural ramus scoresking_sr.nexStructural white scoresking_w.nexPlumage patch distances for folded-wing configurationatlas_folded.txtPhaeomelanin analysis scriptRevbayes formatp_dec_dist_noclado_folded.revUtility functions in RUtility functions for analyzing plumage complexityutility_functions.RBird network plotCode to produce figure 3plotBird.RVideo S1Video of color changes in the plumage of a hook-billed kingfisher (Melidora macrorrhina, FMNH 280141).plumage_supp_video1.mp4Specimen listScientific name and catalog numbers for specimens assessed at the Field Museum of Natural History (FMNH).catnums.csvSupplementary tables and figuresEliason_plumage_supp_accepted_r1.pdfAncestral state reconstructionsAncestral state reconstructions (shown as bird cartoons at nodes and tips) from RevBayes analysis for different plumage color mechanisms and wing configurations. Lightness of color reflects certainty in ancestral state reconstruction at a given node.ancestral_reconstructions.zip
DOI: 10.5061/dryad.h517t14
title: Data from: The evolution of traits and functions in herbivorous coral reef fishes through space and time

description: Herbivory by fishes has been identified as a key ecological process
 shaping coral reefs through time. Although taxonomically limited,
 herbivorous reef fishes display a wide range of traits, which results in
 varied ecosystem functions on reefs around the world. Yet, we understand
 little about how these trait combinations and functions in ecosystems
 changed through time and across biogeographic realms. Here we used fossils
 and phylogenies in a functional ecological framework to reveal temporal
 changes in nominally herbivorous fish assemblages among oceanic basins in
 both trait space and lineage richness among functions. We show that the
 trait space occupied by extant herbivorous fishes in the Indo-Pacific
 resulted from an expansion of traits from the ancestral Tethyan
 assemblages. By contrast, trait space in the Atlantic is the result of
 lineage turnover, with relatively recent colonization by lineages that
 arose in the east Tethys/Indo-Pacific. From an ecosystem function
 perspective, the Atlantic supports a depauperate fauna, with few extant
 herbivorous reef fish lineages performing each function. Indo-Pacific
 fishes support both more functions and more lineages within each function,
 with a marked Miocene to Pleistocene expansion. These disparities
 highlight the importance of history in explaining global variation in fish
 functional composition on coral reefs.
description: Main
 dataData.zipR ScriptsScripts.zipPhylogenetic treesTrees.zipResults from the BayesTraits analysisResults_BayesTraits.zip
DOI: 10.5061/dryad.vr184
title: Data from: Landscape connectivity for wildlife: development and validation of multi-species linkage maps

description: The ability to identify regions of high functional connectivity for
 multiple wildlife species is of conservation interest with respect to
 forest management and corridor planning. We present a method that does not
 require independent, field-collected data, is insensitive to the placement
 of source and destination sites (nodes) for modeling connectivity, and
 does not require the selection of a focal species. In the first step of
 our approach, we created a cost surface that represented permeability of
 the landscape to movement for a suite of species. We randomly selected
 nodes around the perimeter of the buffered study area and used circuit
 theory to connect pairs of nodes. When the buffer was removed, the
 resulting current density map represented, for each grid cell, the
 probability of use by moving animals. We found that using nodes that were
 randomly located around the perimeter of the buffered study area was less
 biased by node placement than randomly selecting nodes within the study
 area. We also found that a buffer of ≥ 20% of the study area width was
 sufficient to remove the effects of node placement on current density. We
 tested our method by creating a map of connectivity in the Algonquin to
 Adirondack region in eastern North America, and we validated the map with
 independently collected data. We found that amphibians and reptiles were
 more likely to cross roads in areas of high current density, and fishers
 (Pekania [Martes] pennanti) used areas with high current density within
 their home ranges. Our approach provides an efficient and cost-effective
 method of predicting areas with relatively high functional connectivity.
description: current_map_rasterA current density map, produced by software Circuitscape. The cost surface was meant to represent permeability of the landscape to movement of forest- and wetland-dwelling species (high cost (1000) to impermeable land (major roads, development, large water bodies); medium cost (100) to semi-permeable land (minor roads, agriculture); and low cost (10) to natural cover (forest, wetland, etc.)). We selected 50 nodes at random locations around the perimeter of the buffered study area and connected them with current using software Circuitscape to produce the current density map.Shapefile of eastern Ontario study areaA shapefile depicting our eastern Ontario study areastudyarea_shapefile.zip
DOI: 10.5061/dryad.j17pm
title: Data from: A continuous morphological approach to study the evolution of pollen in a phylogenetic context: an example with the order Myrtales

description: The study of pollen morphology has historically allowed evolutionary
 biologists to assess phylogenetic relationships among Angiosperms, as well
 as to better understand the fossil record. During this process, pollen has
 mainly been studied by discretizing some of its main characteristics such
 as size, shape, and exine ornamentation. One large plant clade in which
 pollen has been used this way for phylogenetic inference and character
 mapping is the order Myrtales, composed by the small families Alzateaceae,
 Crypteroniaceae, and Penaeaceae (collectively the “CAP clade”), as well as
 the large families Combretaceae, Lythraceae, Melastomataceae, Myrtaceae,
 Onagraceae and Vochysiaceae. In this study, we present a novel way to
 study pollen evolution by using quantitative size and shape variables. We
 use morphometric and morphospace methods to evaluate pollen change in the
 order Myrtales using a time-calibrated, supermatrix phylogeny. We then
 test for conservatism, divergence, and morphological convergence of pollen
 and for correlation between the latitudinal gradient and pollen size and
 shape. To obtain an estimate of shape, Myrtales pollen images were
 extracted from the literature, and their outlines analyzed using elliptic
 Fourier methods. Shape and size variables were then analyzed in a
 phylogenetic framework under an Ornstein-Uhlenbeck process to test for
 shifts in size and shape during the evolutionary history of Myrtales. Few
 shifts in Myrtales pollen morphology were found which indicates
 morphological conservatism. Heterocolpate, small pollen is ancestral with
 largest pollen in Onagraceae. Convergent shifts in shape but not size
 occurred in Myrtaceae and Onagraceae and are correlated to shifts in
 latitude and biogeography. A quantitative approach was applied for the
 first time to examine pollen evolution across a large time scale. Using
 phylogenetic based morphometrics and an OU process, hypotheses of pollen
 size and shape were tested across Myrtales. Convergent pollen shifts and
 position in the latitudinal gradient support the selective role of
 harmomegathy, the mechanism by which pollen grains accommodate their
 volume in response to water loss.
description: Kriebel_Khabbazian_Sytsma_2017This data package includes the files needed to reproduce the analyses of the following paper: Kriebel, R., Khabbazian, M., and K. J. Sytsma. A continuous morphological approach to study the evolution of pollen in a phylogenetic context: an example with the order Myrtales