cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j447ch4
title: Data from: Trema domingensis rises like a phoenix from the ashes of Trema integerrima: a reassessment of the entire-leaved species of Neotropical Trema (Cannabaceae)

description: We resolve three problems concerning the three entire-leaved species of
 Neotropical Trema. 1) Phylogenetic and morphological results showed that
 T. integerrima (Beurl.) Standl., T. domingensis Urb., and T. laxiflora
 Lundell are a single species; therefore, we combine them under a single
 name. 2) The date of publication gives priority to T. integerrima, as the
 basionym Sponia integerrima Beurl. was published in 1856. However, the
 type specimen, Billberg 308 (S), is not a species of Trema but Pouzolzia
 obliqua (Wedd.) Wedd. (Urticaceae). The next available name for this
 species is T. domingensis, published in 1912. 3) The type of T.
 domingensis, Fuertes 312, is a mixed collection. Specimens of Fuertes 312
 held at B, NY, U, and USD are T. domingensis, while those at P, G, US, and
 Z are Celtis trinervia Lam. We provide a historical review to understand
 how these problems arose and persisted unnoticed for decades.
description: Morphometric data for
 PCA analysisTrema_leaf_morphometric_raw_data_2018.csvSupplementary PCA analysis and figures for manuscriptTrema_leaf_morphometric_supplementary_results_revised_20180906.pdfDNA data file (aligned matrix, nexus format)Trema 5loci combo.nexPhylogenetic tree file output from IQTREE ("best" tree from individual tree search)Trema_5loci_combo_temp.nex.treefile.trePhylogenetic tree file output from IQTREE (trees from bootstrap search)Trema_5loci_combo_temp.nex.boottrees.tre
DOI: 10.5061/dryad.c10q7
title: Data from: Multiple quantitative trait loci influence intra-specific variation in genital morphology between phylogenetically distinct lines of Drosophila montana

description: The evolution of animal genitalia has gained renewed interest, because of
 their potential roles during sexual selection and early stages of species
 formation. Although central to understanding the evolutionary process,
 knowledge of the genetic basis of natural variation in genital morphology
 is limited to a very few species. Using an out-bred cross between
 phylogenetically distinct lines of Drosophila montana, we characterized
 quantitative trait loci (QTLs) affecting the size and shape of the
 distiphallus, a prominent part of the male intromittent organ. Our
 microsatellite-based linkage analysis shows that intra-specific variation
 of the distiphallus involves several QTLs of largely additive effect and
 that a highly significant QTL co-localizes with the same inversion where
 we have earlier localized a large QTL for a sexually selected courtship
 song trait. The latter indicates that inversions can play an important
 role in shaping the evolution of rapidly evolving traits with a potential
 influence on speciation.
description: JEB-2011-00053.R1Contains phenotypic and genotypic data of both parental strains (C13, O66) and the four reciprocal F2 crosses (F2AA, F2AB, F2BA, F2BB). Information on individual microsatellite alleles segregating within strains is also given.
DOI: 10.25934/pr00012539.0
title: Available datapackage for study 'COVID-19 Testing and Linkage to Care with African American Church and Health Agency Partners'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.5061/dryad.gt37j
title: Data from: Open-ocean fish reveal an omnidirectional solution to camouflage in polarized environments

description: Despite appearing featureless to our eyes, the open ocean is a highly
 variable environment for polarization-sensitive viewers. Dynamic visual
 backgrounds coupled with predator encounters from all possible directions
 make this habitat one of the most challenging for camouflage. We tested
 open-ocean crypsis in nature by collecting more than 1500 videopolarimetry
 measurements from live fish from distinct habitats under a variety of
 viewing conditions. Open-ocean fish species exhibited camouflage that was
 superior to that of both nearshore fish and mirrorlike surfaces, with
 significantly higher crypsis at angles associated with predator detection
 and pursuit. Histological measurements revealed that specific arrangements
 of reflective guanine platelets in the fish’s skin produce angle-dependent
 polarization modifications for polarocrypsis in the open ocean, suggesting
 a mechanism for natural selection to shape reflectance properties in this
 complex environment.
description: science data for
 repositoryREAD ME
 FILE
DOI: 10.5061/dryad.c175g
title: Data from: Genetic compatibility underlies benefits of mate choice in an external fertilizer

description: Mate choice is a common feature of sexually-reproducing species. In
 sessile or sedentary external fertilizers however, direct interactions
 between reproductive partners are minimal, and instead mate recognition
 and choice must occur at the level of gametes. It is common for some sperm
 and egg combinations to have higher fertilization success than others, but
 it remains unclear whether differences in fertilization reflect
 gamete-level mate-choice (GMC) for paternal quality or parental
 compatibility. Here, we examine the mechanisms underlying GMC in an
 externally fertilizing ascidian. A manipulative mate-choice assay
 confirmed that offspring viability was greater in clutches where we
 allowed GMC than in clutches where we precluded GMC. Complementary,
 quantitative genetic experiments then revealed that paternal quality
 effects were generally weaker than parental compatibility effects,
 particularly for the trait combination underlying the benefits of GMC.
 Overall, our data suggest that gametes that are more compatible at
 fertilization produce more viable offspring than gametes that are less
 compatible at fertilization. Therefore, although the regalia we typically
 associate with sexual selection are absent in external fertilizers,
 mechanisms that allow females to bias fertilization in favour of some
 males over others produce significant fitness benefits in organisms
 reproducing via the ancestral strategy.
description: Manipulative mate choice
 assay meanData for the
 manipulative mate choice assay analysis of mean offspring
 viabilityManipulative mate choice
 assay overyieldingData for manipulative
 mate choice assay analysis of overyieldingBreeding
 designData for the breeding
 design used to estimate sire and interaction covariance
 matrices
DOI: 10.5061/dryad.nr787
title: Data from: Deep phylogeographic structure and parallel host range evolution in the leaf beetle Agelasa nigriceps

description: To understand the mechanisms behind the diversification of herbivorous
 insects through insect-plant interactions, it is important to know how the
 insects change their diet breadth in response to environmental changes. In
 this study, we investigated the phylogeographic pattern of the leaf beetle
 Agelasa nigriceps to infer the evolutionary history of its host range.
 While this beetle commonly uses Actinidia arguta (Actinidiaceae) as a host
 plant, it has been recorded recently on Pterostyrax hispidus
 (Styracaceae), which is now increasing in abundance at some localities in
 Japan due to the indirect effects of high population size of a mammalian
 herbivore. Considerable variation among populations in the ability of Ag.
 nigriceps to use P. hispidus suggests that P. hispidus is a newly acquired
 host plant for this beetle. Phylogenetic analyses using mitochondrial DNA
 sequences and amplified fragment length polymorphism (AFLP) revealed a
 high degree of phylogeographic structure in Ag. nigriceps throughout
 Japan, which is consistent with the hypothesis that several glacial
 refugia existed in the Japanese archipelago. In contrast, no genetic
 structure associated with the host plants was detected. Both the
 mitochondrial DNA and AFLP analyses showed that populations that can use
 P. hispidus are polyphyletic. These results and geographic variation in
 host use suggest that the host-range expansion to a novel host, P.
 hispidus, is a very recent and possibly ongoing phenomenon, and has
 occurred independently in several regions. Our study illustrates that the
 host range of herbivorous insects can evolve repeatedly in response to
 similar environmental changes.
description: COI
 alignmentAlignment of the
 mitochondrial DNA (COI) sequences of 24 Agelasa nigriceps populations
 collected in JapanCOI_alignment.fasAFLP dataBinary AFLP data matrix (AFLPsurv format) of 8 Agelasa nigriceps populations collected in JapanAFLP_data.txtBayesian consensus tree of COI haplotypesFifty percent majority-rule Bayesian consensus tree of Agelasa nigriceps COI haplotypes.COI_Bayesian_consensus_tree.treNJ tree based on AFLP dataNeighbor-joining tree for eight A. nigriceps populations based on AFLP data.AFLP_NJ_tree.nwkMrBayes input fileImput file for MrBayes analysisMrBayes_input.nexBEAST input filesInput files for BEAST analysisBEAST_input.zip
DOI: 10.5061/dryad.8735
title: Data from: Evolution in extreme environments: replicated phenotypic differentiation in livebearing fish inhabiting sulfidic springs

description: We investigated replicated ecological speciation in the livebearing fishes
 Poecilia mexicana and P. sulphuraria (Poeciliidae), which inhabit
 freshwater habitats and have also colonized multiple sulfidic springs in
 southern Mexico. These springs exhibit extreme hypoxia and high
 concentrations of hydrogen sulfide, which is lethal to most metazoans. We
 used phylogenetic analyses to test whether springs were independently
 colonized, performed phenotypic assessments of body and gill morphology
 variation to identify convergent patterns of trait differentiation, and
 conducted an eco-toxicological experiment to detect differences in sulfide
 tolerances among ecotypes. Our results indicate that sulfidic springs were
 colonized by three different lineages, two within P. mexicana and one
 representing P. sulphuraria. Colonization occurred earlier in P.
 sulphuraria, whereas invasion of sulfidic springs in P. mexicana was more
 recent, such that each population is more closely related to neighboring
 populations from adjacent non-sulfidic habitats. Sulfide spring fish also
 show divergence from non-sulfidic phenotypes and a phenotypic convergence
 towards larger heads, larger gills, and increased tolerance to H2S.
 Together with previous studies that indicated significant reproductive
 isolation between fish from sulfidic and non-sulfidic habitats, this study
 provides evidence for repeated ecological speciation in the independent
 sulfide spring populations of P. mexicana and P. sulphuraria.
description: Tobler_etal_gillmorphometricsGill morphometric data for fish from sulfidic and non-sulfidic habitats, including total gill filament number (TFN), average filament length (AFL), total gill filament length (TGFL), total hemibranch perimeter (THP), total hemibranch area (THA), and body mass (M).Tobler_etal_bodymorphometricsLandmark coordinates for Poecilia mexicana and Poecilia sulphuraria from sulfidic and non-sulfidic habitatsTobler_etal_toleranceSulfide tolerance in Poecilia mexicana and P. sulphuraria from sulfidic and non-sulfidic habitats.
DOI: 10.5061/dryad.h4p8dr30
title: Data from: Biogeography in a continental island: population structure of the relict endemic centipede Craterostigmus tasmanianus (Chilopoda, Craterostigmomorpha) in Tasmania using 16S rRNA and COI

description: We used 16S ribosomal RNA (rRNA) and cytochrome c oxidase subunit I (COI)
 sequence data to investigate the population structure in the centipede
 Craterostigmus tasmanianus Pocock, 1902 (Chilopoda: Craterostigmomorpha:
 Craterostigmidae) and to look for possible barriers to gene flow on the
 island of Tasmania, where C. tasmanianus is a widespread endemic. We first
 confirmed a molecular diagnostic character in 28S rRNA separating
 Tasmanian Craterostigmus from its sister species Craterostigmus crabilli
 (Edgecombe and Giribet 2008) in New Zealand and found no shared
 polymorphism in this marker for the 2 species. In Tasmania, analysis of
 molecular variance analysis showed little variation at the 16S rRNA and
 COI loci within populations (6% and 13%, respectively), but substantial
 variation (56% and 48%, respectively) among populations divided
 geographically into groups. We found no clear evidence of isolation by
 distance using a Mantel test. Bayesian clustering and gene network
 analysis both group the C. tasmanianus populations in patterns which are
 broadly concordant with previously known biogeographical divisions within
 Tasmania, but we did not find that genetic distance varied in a simple way
 across cluster boundaries. The coarse-scale geographical sampling on which
 this study was based should be followed in the future by sampling at a
 finer spatial scale and to investigate genetic structure within clusters
 and across cluster boundaries.
description: SupMat
 SVed09-05-11Supplementary
 materials.
DOI: 10.5061/dryad.6m653
title: Data from: Biological evidence supports an early and complex emergence of the Isthmus of Panama

description: The formation of the Isthmus of Panama, which linked North and South
 America, is key to understanding the biodiversity, oceanography,
 atmosphere, and climate in the region. Despite its importance across
 multiple disciplines, the timing of formation and emergence of the Isthmus
 and the biological patterns it created have been controversial. Here, we
 analyze molecular and fossil data, including terrestrial and marine
 organisms, to show that biotic migrations across the Isthmus of Panama
 began several million years earlier than commonly assumed. An earlier
 evolution of the Isthmus has broad implications for the mechanisms driving
 global climate (e.g., Pleistocene glaciations, thermohaline circulation)
 as well as the rich biodiversity of the Americas.
description: Bacon_Data_ExtantData mined from phylogenies.Bacon_Data_FossilData mined from the Paleobiology Database.
DOI: 10.5061/dryad.qn814
title: Data from: A trait-based trade-off between growth and mortality: evidence from 15 tropical tree species using size-specific RGRs

description: A life-history trade-off between low mortality in the dark and rapid
 growth in the light is one of the most widely accepted mechanisms
 underlying plant ecological strategies in tropical forests. Differences in
 plant functional traits are thought to underlie these distinct ecological
 strategies; however, very few studies have shown relationships between
 functional traits and demographic rates within a functional group. We
 present 8 years of growth and mortality data from saplings of 15 species
 of Dipterocarpaceae planted into logged-over forest in Malaysian Borneo,
 and the relationships between these demographic rates and four key
 functional traits: wood density, specific leaf area (SLA), seed mass, and
 leaf C:N ratio. Species-specific differences in growth rates were
 separated from seedling size effects by fitting nonlinear mixed-effects
 models, to repeated measurements taken on individuals at multiple time
 points. Mortality data were analyzed using binary logistic regressions in
 a mixed-effects models framework. Growth increased and mortality decreased
 with increasing light availability. Species differed in both their growth
 and mortality rates, yet there was little evidence for a statistical
 interaction between species and light for either response. There was a
 positive relationship between growth rate and the predicted probability of
 mortality regardless of light environment, suggesting that this
 relationship may be driven by a general trade-off between traits that
 maximize growth and traits that minimize mortality, rather than through
 differential species responses to light. Our results indicate that wood
 density is an important trait that indicates both the ability of species
 to grow and resistance to mortality, but no other trait was correlated
 with either growth or mortality. Therefore, the growth mortality trade-off
 among species of dipterocarp appears to be general in being independent of
 species crossovers in performance in different light environments.
description: EcologyEvolution_IntensivePlotsData_forDryadGrowth and survival data for seedlings and saplings from six intensively measured plots from the Sabah Biodiversity Experiment. Comma separated, factors indicated with quotation marks "", Species = full name, Seedling_code=unique identifier, co=canopy openness in %, diam=basal diameter in mm, dbh=diameter at 1.3meters in mm, height.apex= height in cm's, day=number of days since planted, survival=(1=alive, 0=dead), problems=(Y=multiple stems confused measures, Q=data point with potential errors), Pl=Plot, Li=Line (20 lines IN each plot), Measure=categorical for each occasion all seedlings where measured.
DOI: 10.34740/kaggle/dsv/14631272
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.2nd8jg3n
title: Data from: AFLP genome scans suggest divergent selection on colour patterning in allopatric colour morphs of a cichlid fish

description: Genome scan-based tests for selection are directly applicable to natural
 populations to study the genetic and evolutionary mechanisms behind
 phenotypic differentiation. We conducted AFLP genome scans in three
 distinct geographic colour morphs of the cichlid fish Tropheus moorii to
 assess whether the extant, allopatric colour pattern differentiation can
 be explained by drift and to identify markers mapping to genomic regions
 possibly involved in colour patterning. The tested morphs occupy adjacent
 shore sections in southern Lake Tanganyika and are separated from each
 other by major habitat barriers. The genome scans revealed significant
 genetic structure between morphs, but a very low proportion of loci fixed
 for alternative AFLP alleles in different morphs. This high level of
 polymorphism within morphs suggested that colour pattern differentiation
 did not result exclusively from neutral processes. Outlier detection
 methods identified six loci with excess differentiation in the comparison
 between a bluish and a yellow-blotch morph and five different outlier loci
 in comparisons of each of these morphs with a red morph. As population
 expansions and the genetic structure of Tropheus make the outlier approach
 prone to false-positive signals of selection, we examined the correlation
 between outlier locus alleles and colour phenotypes in a genetic and
 phenotypic cline between two morphs. Distributions of allele frequencies
 at one outlier locus were indeed consistent with linkage to a colour
 locus. Despite the challenges posed by population structure and
 demography, our results encourage the cautious application of genome scans
 to studies of divergent selection in subdivided and recently expanded
 populations.
description: Tropheus moorii AFLP
 data
DOI: 10.5061/dryad.j477p
title: Data from: Convergences and trends in the evolution of the archosaur pelvis

description: The pelvic structure in non-avian archosaurs plays a key role in
 understanding the evolution of terrestrial locomotor patterns because the
 pelvis contains major attachment sites for proximal hind limb musculature.
 In order to investigate patterns of pelvic evolution in archosaurs, this
 study compiled three pelvic indices, as well as femoral head orientation,
 for 92 archosaur taxa. With the metrics and a reconstructed supertree, we
 examined the correlated evolution of the pelvis and femur, the correlation
 among pelvic components, and temporal trends in the evolution of the
 pelvis. The result shows that archosaurs with medially directed femoral
 heads have more cranially shifted iliac centroids and more posteriorly
 rotated pubes than taxa with anteromedially directed femoral heads. The
 craniad shift of the iliac centroid might be correlated to the posterior
 rotation of pubis. The pelvic structures of pterosaurs, ornithischians,
 sauropods, and avetheropods occupy a different morphospace from basal
 archosaurs, pseudosuchians, basal dinosauromorphs, basal theropods, and
 basal sauropodomorphs in having more cranially expanded ilia, more
 posteriorly rotated pubes, and medially deflected femoral heads. This may
 imply that pterosaurs and those derived dinosaurs independently underwent
 similar shifts in thigh muscles and locomotion. The evolutionary model
 fitting supports the early-burst model for iliac and pubic metrics in more
 inclusive archosaur clades, indicating that larger changes of archosaur
 pelves occurred in early times of the clade's history.
description: Supplementary
 TablesSupplementary Tables
 1-6Supplementary
 Table_2.xlsSupplementary
 FiguresSupplementary Figures
 1-3Spp.
 Figs. 1-3.pdfSupplementary
 Referencesspp.references.docx
DOI: 10.7910/dvn/7dsrur
title: Replication Data for: From ice to fire: A quantitative analysis of violent thawings in non-international frozen conflicts

description: Replication materials for Stracquadanio (2026): Replication Data for: From ice to fire: A quantitative analysis of violent thawings in non-international frozen conflicts
DOI: 10.5061/dryad.1d73qk4
title: Data from: Habitat selection and the value of information in heterogenous landscapes

description: Despite the wide usage of the term information in evolutionary ecology,
 there is no general treatise between fitness (i.e., density-dependent
 population growth) and selection of the environment sensu lato. Here we
 (1) initiate the building of a quantitative framework with which to
 examine the relationship between information use in spatially
 heterogeneous landscapes and density-dependent population growth, and (2)
 illustrate its utility by applying the framework to an existing model of
 breeding habitat selection. We begin by linking information, as a process
 of narrowing choice, to population growth/fitness. Second, we define a
 measure of a population’s penalty of ignorance based on the
 Kullback-Leibler index that combines the contributions of resource
 selection (i.e., biased use of breeding sites) and density-dependent
 depletion. Third, we quantify the extent to which environmental
 heterogeneity (i.e., mean and variance within a landscape) constrains
 sustainable population growth of unbiased agents. We call this the
 heterogeneity-based fitness deficit, and combine this with population
 simulations to quantify the independent contribution of information-use
 strategies to the total population growth rate. We further capitalize on
 this example to highlight the interactive effects of information between
 ecological scales when fear affects individual fitness through phenotypic
 plasticity. Informed breeding habitat selection moderates the demographic
 cost of fear commensurate with density-dependent information use. Thus,
 future work should attempt to differentiate between phenotypic plasticity
 (i.e., acute fear) and demographic responses (i.e., chronic changes in
 population size). We conclude with a broader discussion of information in
 alternative contexts, and explore some evolutionary considerations for
 information use. We note how competition among individuals may constrain
 the information state among individuals, and the implications of this
 constraint under environmental change.
description: Figure
 3Simulated data for
 determining p* for Figure 3Fig 3_p_and
 SK.xlsx