cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1st98
title: Data from: Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous character data: A case study with the lizard Anolis roosevelti

description: In recent years, enormous effort and investment has been put into
 assembling the tree of life: a phylogenetic history for all species on
 Earth. Overwhelmingly, this progress toward building an ever increasingly
 complete phylogeny of living things has been accomplished through
 sophisticated analysis of molecular data. In the modern genomic age,
 molecular genetic data have become very easy and inexpensive to obtain for
 many species. However, some lineages are poorly represented in or absent
 from tissue collections, or are unavailable for molecular analysis for
 other reasons such as restrictive biological sample export laws. Other
 species went extinct recently and are only available in formalin museum
 preparations or perhaps even as sub-fossils. In this brief communication
 we present a new method for placing cryptic, recently extinct, or
 hypothesized taxa into an ultrametric phylogeny of extant taxa using
 continuous character data. This method is based on a relatively simple
 modification of an established Maximum Likelihood (ML) method for
 phylogeny inference from continuous traits. We show that the method works
 well on simulated trees and data. We then apply it to the case of placing
 the Culebra Island Giant Anole (Anolis roosevelti) into a phylogeny of
 Caribbean anoles. Anolis roosevelti is a ‘crown-giant’ ecomorph anole
 hypothesized to have once been found throughout the Spanish, U.S., and
 British Virgin Islands, but that has not been encountered or collected
 since the 1930s. Although this species is widely thought to be closely
 related to the Puerto Rican giant anole, A. cuvieri, our ML method
 actually places A. roosevelti in a different part of the tree and closely
 related to a clade of morphologically similar species. We are unable,
 however, to reject a phylogenetic position for A. roosevelti that places
 it as sister taxon to A. cuvieri; although close relationship with the
 remainder of Puerto Rican anole species is strongly rejected by our
 method.
description: Reproducible analysis R
 markdown (.Rmd) fileThis file contains
 original code for all the analyses of the paper. It can be run (after
 installing knitr and required software) with the command:
 knit2html("Revell-etal-2015.dryad-code.Rmd"), for
 instance.Revell-etal-2015.dryad-code.RmdHTML output of R markdown fileRevell-etal-2015.dryad-entry.htmlCaribbean Anolis tree used in analysisRevell-etal.tree.treMorphological data file used for analysisRevell-etal.data.csv
DOI: 10.5061/dryad.30h0n
title: Data from: Abiotic and biotic predictors of macroecological patterns in bird and butterfly coloration

description: Animal color phenotypes are invariably influenced by both their biotic
 community and the abiotic environments. A host of hypotheses have been
 proposed for how variables such as solar radiation, habitat shadiness,
 primary productivity, temperature, rainfall and community diversity might
 affect animal color traits. However, while individual factors have been
 linked to coloration in specific contexts, little is known about which
 factors are most important across broad taxonomic and geographic scales.
 Using data collected from 570 species of birds and 424 species of
 butterflies from Australia which inhabit an area spanning a latitudinal
 range of 35 degrees and covering deserts, tropical and temperate forests,
 savannas and heathlands, we test multiple hypotheses from the coloration
 literature and assess their relative importance. We show that bird and
 butterfly species exhibit more reflective and less saturated colors in
 better-lit environments, a pattern that is robust across an array of
 variables expected to influence the intensity or quality of ambient light
 in an environment. Both taxa display more diverse colors in regions with
 greater net primary production and longer growing seasons. Models that
 included variables related to energy inputs and resources in ecosystems
 have better explanatory power for bird and butterfly coloration overall
 than do models that included community diversity metrics. However, the
 diversity of the bird community in an environment was the single most
 powerful predictor of color pattern variation in both birds and
 butterflies. We observed strong similarities across taxa in the covariance
 between color and environmental factors, suggesting the presence of
 fundamental macro-ecological drivers of visual appearance across disparate
 taxa.
description: Dalrymple_etal_EM2018Data from Dalrymple. et al. Abiotic and biotic predictors of macroecological patterns in bird and butterfly coloration. Ecological Monographs Data for each grid cell in the study range is presented, including bird and butterfly colour (response) variables and environmental (predictor) variables. Predictor variables relate to the community diversity and averages of the data available for the energy and resources in the environment and the habitat conditions in the grid cells. See manuscript for details on data sourcing and units on environmental variables. see Dalrymple et al 2015 Birds, butterflies and flowers in the tropics are not more colourful than those at higher latitudes. Global Ecology and Biogeography, 24(12), 1424-1432. DOI: 10.1111/geb.12368 for information on bird and butterfly color data and methodology. .csv fileDalrymple_etal_EM2018_scriptforanalysesR script for application to Dalrymple_etal_EM2018.CSV data file - produces analyses and some figures. .txt fileDalrymple_etal_EM2018_Rcode.txt
DOI: 10.5061/dryad.ms75s
title: Data from: Humpback whales feed on hatchery-released juvenile salmon

description: Humpback whales are remarkable for the behavioural plasticity of their
 feeding tactics and the diversity of their diets. Within the last decade
 at hatchery release sites in Southeast Alaska, humpback whales have begun
 exploiting juvenile salmon, a previously undocumented prey. The
 anthropogenic source of these salmon and their important contribution to
 local fisheries makes the emergence of humpback whale predation a concern
 for the Southeast Alaska economy. Here, we describe the frequency of
 observing humpback whales, examine the role of temporal and spatial
 variables affecting the probability of sighting humpback whales and
 describe prey capture behaviours at five hatchery release sites. We
 coordinated twice-daily 15 min observations during the spring release
 seasons 2010–2015. Using logistic regression, we determined that the
 probability of occurrence of humpback whales increased after releases
 began and decreased after releases concluded. The probability of whale
 occurrence varied among release sites but did not increase significantly
 over the 6 year study period. Whales were reported to be feeding on
 juvenile chum, Chinook and coho salmon, with photographic and video
 records of whales feeding on coho salmon. The ability to adapt to new prey
 sources may be key to sustaining their population in a changing ocean.
description: Chenoweth et al 2017.
 Roy_Soc_Open_Science.RR Code for the
 calculation of most in-text results, Tables 1 and 2 and the production of
 Figure 3.Chenoweth et al 2017.
 Roy_Soc_Open_Science.RBehaveNewData2This dataframe includes the combinations of predictors necessary for creation of Figure 3. The models created by Chenoweth_et_al_2017_Roy_Soc_Open_Sci.R provides the predicted probabilities of humpback whale sighting based on these predictors.HatcheryObsThis dataframe provides observations from all five hatchery release sites over six years. The raw data has been filtered as described in the methods section of the manuscript.Releases.SumThis dataframe provides the Julian Day of the first and last releases from all five hatchery release site in all six years. This dataframe is required by Chenoweth et al 2017. Roy_Soc_Open_Science.R
DOI: 10.15468/dl.xvxzpp
title: Occurrence Download

description: A dataset containing 158 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Myristica fragrans",
 "HasCoordinate is true",
 "BasisOfRecord is Human Observation"
 ]
}

 The dataset includes 158 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000645-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5j2h4
title: Data from: Multiple origins of sex chromosome fusions correlated with chiasma localization in Habronattus jumping spiders (Araneae: Salticidae)

description: Entelegyne spiders rarely show fusions yielding neo-Y chromosomes, which
 M. J. D. White attributed to a constraint in spiders, namely their
 proximal chiasma localization acting to upset meiotic segregation in males
 with fusions. Of the 75 taxa of Habronattus and outgroups studied, 47 have
 X1X20 sex chromosomes in males, 10 have X1X2Y, 15 have X1X2X3Y, 2 have X0,
 and one has both X1X20 and X1X2X3Y. Chromosome numbers and behavior
 suggest neo-Ys formed by an autosome-X fusion to make X1X2Y, with a second
 fusion to an autosome to make X1X2X3Y. Phylogeny shows at least 8-15 gains
 (or possibly some losses) of neo-Y (i.e. X-autosome fusions), a remarkable
 number for such a small clade. In contrast to the many X-autosome fusions,
 at most one autosome-autosome fusion is indicated. Origins of neo-Y are
 correlated significantly with distal localization of chiasmata, supporting
 White’s hypothesis that evolution of neo-Y systems is facilitated by
 looser pairing (distal chiasmata) at meiosis. However, an alternative (or
 contributing) explanation for the correlation is that X-autosome fusions
 were selected to permit isolation of male-favored alleles to the neo-Y
 chromosome, aided by distal chiasmata limiting recombination. This
 intralocus sexual conflict hypothesis could explain both the many
 X-autosome fusions, and the stunning complexity of male Habronattus
 courtship displays.
description: HabronattusChromosomes2013-MaddisonLeducRobertDNA sequences from Maddison & Hedin (2003), realigned, plus original observations on sex chromosomes and chiasma localization. Phylogenies from BEAST analysis and Maddison & Hedin 2003.
DOI: 10.5281/zenodo.18381941
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Arthur Whistler, http://www.wikidata.org/entity/Q16647536. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q16647536
DOI: 10.5281/zenodo.8035550
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Arthur Whistler, http://www.wikidata.org/entity/Q16647536. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q16647536
DOI: 10.5061/dryad.vr2ns
title: Data from: Angelfishes, paper tigers and the devilish taxonomy of the Centropyge flavissima complex

description: The pygmy angelfishes (genus Centropyge) provide numerous examples of
 discordance between color morphology, taxonomy and evolutionary genetic
 lineages. This discordance is especially evident in the Centropyge
 flavissima complex, which includes three primary color morphs, three
 previously recognized species (C. flavissima, C. eibli and C. vrolikii)
 and three distinct mitochondrial (mtDNA) lineages that do not align with
 species designations. Our previous research showed that the putative C.
 flavissima arose independently in the Indian and Pacific Oceans, and the
 three mtDNA lineages align with geography rather than species assignments.
 Here we add 157 specimens to the previous dataset of 291 specimens, spread
 across a greater geographic range, to pinpoint the distribution of mtDNA
 lineages and color morphs. We found that the mtDNA lineages show
 remarkably strong geographic boundaries corresponding to the Indian Ocean,
 Central-West Pacific and Central-South Pacific. We also test the validity
 of the ‘Black Tiger Centropyge’ in the C. flavissima species complex, a
 taxonomic oddity that is restricted to shoals and atolls off the coast of
 northwestern Australia, and the newly named C. cocosensis (Shen et al. sp.
 nov. 2016) assigned to the C. flavissima lineage in the Indian Ocean. We
 conclude that the Black Tiger Centropyge is not a valid species but an
 intermediate between sympatric color morphs that correspond to the
 putative species C. eibli and C. vrolikii. Our greater sampling effort
 also do not support the genetic distinctiveness of C. cocosensis given
 shared mtDNA haplotypes with the sympatric C. eibli and C. vrolikii, but
 instead we find conflicting lines of evidence concerning the taxonomy of
 this group. We urge caution and taxonomic restraint until the true nature
 of this species complex can be revealed.
description: Trimmed and aligned
 cytochrome b sequences, formated as .fasta, from the Centropyge J Hered
 BriefJ Hered
 Brief, Trimmed Nucleotide Alignment,
 formatted.fasta
DOI: 10.18112/openneuro.ds006803.v1.1.1
title: NeuroTechs Dataset for Stem Skills
DOI: 10.5061/dryad.1292
title: Data from: Inter-population variation in mating system and late-stage inbreeding depression in Magnolia stellata

description: Inbreeding has the potential to cause evolutionary changes in populations,
 although these changes are likely to drive populations to extinction
 through inbreeding depression and reductions in genetic diversity. We
 investigated the mating system and late-stage inbreeding depression (δ) in
 10 populations of Magnolia stellata using nine microsatellite markers and
 evaluated the effects of population size and the degree of population
 isolation through inbreeding and inbreeding depression on the persistence
 of populations. The outcrossing rates were very similar (~0.7) among
 populations, but the correlations of paternity, fractions of biparental
 inbreeding and inbreeding coefficients at the seed stage (FS) varied among
 populations, suggesting that the level of outcrossing was similar among
 populations, while the quality of it was not. A significant negative
 correlation was detected between FS and population size. The average value
 of δ was 0.709, and the values in six of the 10 populations were
 significant. The values of δ differed among populations, although clear
 relationships with population size and the degree of population isolation
 were not detected. However, in one population, which was very small and
 located in the edge of the species' range, we obtained a very low
 value of δ (-0.096), which may be indicative of purging or the fixation of
 deleterious alleles. Existing M. stellata populations that are small (and
 thus might be expected to have higher frequencies of inbreeding) and have
 large values of δ may be in danger of declining, even if the populations
 are located within the central region of the species range.
description: GenotypeData100304.txtThis data is simple tab delimited text and its line break style is UNIX. It contains 9 microsatellite genotypes of 142 maternal trees and 1216 their seeds. In column headings, pop, family, fruit indicates population code, family and fruit ID, respectively. Fruit ID, whose value is 0, indicates that the individual is the maternal tree of seeds that has the same family ID of it. Lia and Lib indicates first and second alleles of the loci, respectively. Li_oc and Lall_oc indicates the outcrossing status of ith locus and over all loci. For example, if the value of L1_oc is 0 or 1, the status of first locus is selfed or outcrossed, respectively. NA indicates no data.seed_data_of_10_pop100304.txt
DOI: 10.5061/dryad.85s4m
title: Data from: Multi-scale and antagonist selection on life-history traits in parasitoids: a community ecology perspective

description: 1) Life-history traits within ecological communities can be influenced by
 regional environmental conditions (external filters) and community-wide
 density-dependent processes (internal filters). While traits in a regional
 context may converge to a narrow range of values because of environmental
 filtering, species belonging to a guild may present contrasting traits as
 a means of niche differentiation, allowing coexistence whilst exploiting
 the same resources. 2) To disentangle the role of external and internal
 filters on phenotypic diversity within ecological communities, we examined
 the patterns of life-history trait variation within a guild of insect
 parasitoids during two successive years across three contrasted regions in
 relation to several ecological factors. 3) By combining a mean-field
 approach and an analysis of phenotypic variance across organizational
 levels (from individual to guild), we showed that the patterns of
 life-history trait variation across regions are consistent with local
 adaptation or adaptive phenotypic plasticity while the patterns of
 phenotypic variation within regions suggested how coexistence modulates
 life-history traits expression through niche differentiation. 4) Within a
 given region, phenotypic pattern of parasitoid life-history traits may
 also arise from bottom-up effects of trophic webs: insect host species
 could also control parasitoid life-history traits in nature. Our results
 also showed that parasitoid life-history traits presented contrasting
 variation patterns according to the sampling year, suggesting temporal
 variations in evolutionary and ecological dynamics of parasitoid species.
 5) The application of such trait-based studies to insect parasitoids has
 the potential to provide further insight on how agricultural environments
 contribute to differential diversification among natural enemies guilds,
 highlighting the main role of agricultural landscape management for
 organisms' responses.
description: Datasets for the MS FE
 2017 00585 R1This Excel file contains
 all the data used in the study published in Functional Ecology present
 paper. This file has three Excel spreadsheet : 1) Data used for the linear
 models (part 1 of the paper) ; 2) Data used for the T-statistics (part 2
 of the paper) ; 3) Data used for the Hypervolume calculus (part 3 of the
 paper).Data
 for Dryad FE 2017 00585 R1.xlsx
DOI: 10.5061/dryad.355
title: Data from: The ecological dynamics of clade diversification and community assembly

description: Clades diversify in an ecological context, but most macroevolutionary
 models do not directly encapsulate ecological mechanisms that influence
 speciation and extinction. A data set of 245 chordate, arthropod, mollusk,
 and magnoliophyte phylogenies had a majority of clades that showed rapid
 lineage accumulation early with a slowing more recently, whereas a small
 but significantminority showed accelerated lineage accumulation in their
 recent histories. Previous analyses have demonstrated that
 macroevolutionary birthdeath models can replicate the pattern of slowing
 lineage accumulation only by a strong decrease in speciation rate with
 increasing species richness and extinction rate held extremely low or
 absent. In contrast, the metacommunity model presented here could generate
 the full range of patterns seen in the real phylogenies by simply
 manipulating the degree of ecological differentiation of new species at
 the time of speciation. Specifically, the metacommunity model predicts
 that clades showing decelerating lineage accumulation rates are those that
 have diversified by ecological modes of speciation, whereas clades showing
 accelerating lineage accumulation rates are those that have diversified
 primarily by modes of speciation that generate little or no ecological
 diversification. A number of testable predictions that integrate data from
 molecular systematics, community ecology, and biogeography are also
 discussed.
description: Electronic Supplement of
 Data.xls
DOI: 10.15468/dl.ej78gm
title: Occurrence Download

description: A dataset containing 292019 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-86.791 34.448,-75.904 34.448,-75.904 38.67,-86.791 38.67,-86.791 34.448))",
 "OccurrenceStatus is Present",
 "TaxonKey is Caudata"
 ]
}

 The dataset includes 292019 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000616-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sd116
title: Data from: Epidemiology of Hepatitis E Virus in China: results from the Third National Viral Hepatitis Prevalence Survey, 2005-2006

description: In China, hepatitis E virus (HEV) is prevalent and causes disease, but its
 epidemiological profile is not well understood. We used a commercial
 enzyme-linked immunosorbent assay to detect total antibodies to hepatitis
 E virus in 15,862 serum samples collected during the Third National Viral
 Hepatitis Prevalence Survey. The results were analyzed to calculate
 estimates of HEV seroprevalence and to examine the effects of some
 putative risk factors. The seroprevalence of HEV in the general Chinese
 population during the period from 2005 through 2006 was 23.46% (95%
 confidence interval [CI], 18.41%–28.50%). The farming population, the age
 group of 15–60 year olds, and those living in the Midwest or Mideast
 region and in Xinjiang province had the highest seroprevalence estimates.
 The prevalence of HEV is high in China. The seroprevalence rate of HEV
 shows an unbalanced distribution among areas with different geographic
 location and economic development levels. The characteristics of the
 distribution associated may be due to the route of HEV transmission (via
 contaminated water or animal reservoirs). Within the same region, the
 seroprevalence of HEV is generally increased with age.
description: dataall the tables and
 figuresEpidemiology_of_Hepatitis_E_Virus_in_China_figure_for-Plosone-09.doc
DOI: 10.5061/dryad.8887
title: Data from: Characterization of microsatellite loci and reliable genotyping in a polyploid plant, Mercurialis perennis (Euphorbiaceae)

description: For many applications in population genetics, codominant simple sequence
 repeats (SSRs) may have substantial advantages over dominant anonymous
 markers such as AFLPs. In high polyploids, however, allele dosage of SSRs
 cannot easily be determined and alleles are not easily attributable to
 potentially diploidized loci. Here, we argue that SSRs may nonetheless be
 better than AFLPs for polyploid taxa if they are analyzed as effectively
 dominant markers, because they are more reliable and more precise. We
 describe the transfer of SSRs developed for diploid Mercurialis huetii to
 the clonal dioecious M. perennis. Primers were tested on a set of 54 male
 and female plants from natural decaploid populations. Eight of 65 tested
 loci produced polymorphic fragments. Binary profiles from four different
 scoring routines were used to define multilocus lineages (MLLs). Allowing
 for fragment differences within one MLL, all analyses revealed the same 14
 MLLs, without conflicting with merigenet, sex or plot assignment. For
 semiautomatic scoring, a combination of as few as two of the four most
 polymorphic loci resulted in unambiguous discrimination of clones. Our
 study demonstrates that microsatellite fingerprinting of polyploid plants
 is a cost-efficient and reliable alternative to AFLPs, not least because
 fewer loci are required than for diploids.
description: Pfeiffer et
 al_JOH-2010-168.R1_Mercurialis_01matricesPrimary data: 01
 matrices (3 scoring routines) for the SSR fingerprinting (8 loci) in
 polyploid Mercurialis perennis; see sheet "Description" for
 further details