cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m80f888
title: Data from: Costs and drivers of helminth parasite infection in wild female baboons

description: 1. Helminth parasites can have wide ranging, detrimental effects on host
 reproduction and survival. These effects are best documented in humans and
 domestic animals, while only a few studies in wild mammals have identified
 both the forces that drive helminth infection risk and their costs to
 individual fitness. 2. Working in a well-studied population of wild
 baboons (Papio cynocephalus) in the Amboseli ecosystem in Kenya, we
 pursued two goals, to: (i) examine the costs of helminth infections in
 terms of female fertility and glucocorticoid hormone levels, and (ii) test
 how processes operating at multiple scales—from individual hosts to social
 groups and the population at large—work together to predict variation in
 female infection risk. 3. To accomplish these goals, we measured helminth
 parasite burdens in 745 fecal samples collected over 5 years from 122
 female baboons. We combine these data with detailed observations of host
 environments, social behaviors, hormone levels, and interbirth intervals.
 4. We found that helminths are costly to female fertility: females
 infected with more diverse parasite communities (i.e. higher parasite
 richness), exhibited longer interbirth intervals than females infected by
 fewer parasite taxa. We also found that females exhibiting high Trichuris
 trichiura egg counts also had high glucocorticoid levels. Female infection
 risk was best predicted by factors at the host-, social group-, and
 population level: females facing the highest risk were old, socially
 isolated, living in dry conditions, and infected with other helminths. 5.
 Our results provide an unusually holistic understanding of the factors
 that contribute to inter-individual differences in parasite infection, and
 they contribute to just a handful of studies linking helminths to host
 fitness in wild mammals.
description: Akinyi et al_helminth
 costs and driversThe file contains data
 on samples collected from female baboons to test the costs and drivers of
 helminth infection.Akinyi et
 al_helminth_costs_and_drivers.zip
DOI: 10.5061/dryad.78276h1
title: Data from: A multiple peak adaptive landscape based on feeding strategies and roosting ecology shaped the evolution of cranial covariance structure and morphological differentiation in phyllostomid bats

description: We explored the evolution of morphological integration in the most
 noteworthy example of adaptive radiation in mammals, the New World
 leaf-nosed bats, using a massive dataset and by combining phylogenetic
 comparative methods and quantitative genetic approaches. We demonstrated
 that the phenotypic covariance structure remained conserved on a broader
 phylogenetic scale but also showed a substantial divergence between
 inter-clade comparisons. Most of the phylogenetic structure in the
 integration space can be explained by splits at the beginning of the
 diversification of major clades. Our results provide evidence for a
 multiple peak adaptive landscape in the evolution of cranial covariance
 structure and morphological differentiation, based upon diet and roosting
 ecology. In this scenario, the successful radiation of phyllostomid bats
 was triggered by the diversification of dietary and roosting strategies,
 and the invasion of these new adaptive zones lead to changes in phenotypic
 covariance structure and average morphology. Our results suggest that
 intense natural selection preceded the invasion of these new adaptive
 zones and played a fundamental role in shaping cranial covariance
 structure and morphological differentiation in this hyper-diverse clade of
 mammals. Finally, our study demonstrates the power of combining
 comparative methods and quantitative genetic approaches when investigating
 the evolution of complex morphologies.
description: Table S4 - Estimated
 repeatabilities for 35 linear distances in the skull of phyllostomid
 bats.Supplementary Table
 S4.xlsxTable S5 - Similarity
 patterns in covariance matrix for 48 phyllostomid species estimated by
 Random Skewers. The diagonal contains the matrix repeatability for each
 species.Supplementary Table
 S5.xlsTable S6 - Magnitude of
 integration distance matrix.Supplementary Table
 S6.xlsTable S7 - Phylogenetic
 distance matrix.Supplementary Table
 S7.xlsTable S8 - Morphological
 distance matrix.Supplementary Table
 S8.xlsTable S9 - Dietary
 matrix.Supplementary Table
 S9.xlsTable S10 - Roosting
 matrix.Supplementary Table
 S10.xlsTable S11 - Similarity
 patterns in covariance matrix for 48 phyllostomid species and 47 internal
 nodes estimated by Random Skewers. The diagonal contains the matrix
 repeatability for each species.Supplementary Table
 S11.xlsTable S15 - Similarity
 patterns in covariance matrix for 48 phyllostomid species and 47 internal
 nodes estimated by Krzanowski. The diagonal contains the matrix
 repeatability for each species.Supplementary Table
 S15.xlsxTable S16 - Similarity
 patterns in correlation matrix for 48 phyllostomid species and 47 internal
 nodes estimated by Krzanowski. The diagonal contains the matrix
 repeatability for each species.Supplementary Table
 S16.xlsx
DOI: 10.5061/dryad.rt2vs67
title: Data from: Time to monitor livestock carcasses for biodiversity conservation and public health

description: Law enforcement and integration of environmental issues into other
 policies able to affect species and ecosystems are cornerstones for the
 effective protection of biodiversity. We illustrate the necessity of
 monitoring and improving such enforcement and integration through the
 example of the European sanitary policies for managing livestock carcasses
 after the “mad cow disease” outbreak while supporting scavengers’
 conservation. Continuous updates of EU sanitary regulations for
 reconciling scavenger conservation and public health have led to actions
 whose implementation and monitoring rely on delineating scavenger feeding
 zones (SFZs) and estimating livestock mortality and scavenger feeding
 requirements (SFRs). However, the lack of clear and homogeneous criteria
 to calculate SFRs results in remarkable variations (e.g. of up to
 &gt;450% in some regions). Though we offer a prospective approach to
 improve SFR calculations, we show here the high levels of uncertainty in
 these estimates based on the imperfect information available regarding
 scavengers’ ecology. Synthesis and applications. The multiple
 socioeconomic and ecological impacts of sanitary crises such as “mad cow
 disease” underpin the need for high‐level political commitments to
 guarantee public health, food security and biodiversity conservation. To
 effectively integrate scavenger conservation into sanitary policies, the
 shortfalls here detected when estimating scavenger feeding requirements
 should be addressed. We recommend policymakers establish systematic
 on‐ground carcass monitoring for detecting implementation gaps (e.g. food
 shortages compromising scavenger conservation, potential risks of disease
 transmission), and to modify EU sanitary regulations accordingly. This
 monitoring would increase knowledge on scavenging ecology and
 epidemiological surveillance while enhancing cross‐compliance. Lessons
 learned in Europe may help to integrate conservation issues into other
 sectorial policies worldwide.
description: Data from Mateo-Tomás et
 al in J Appl EcolData from "Time to
 monitor livestock carcasses for biodiversity conservation and public
 health" to estimate annual scavenger feeding requirements (SFRs) for
 griffon vulture, brown bear and Iberian wolf in Spain. Published by P.
 Mateo-Tomás, P.P. Olea and J.V. López-Bao in Journal of Applied
 Ecology.Data from Mateo-Tomás et al J
 Appl Ecol .docx
DOI: 10.5061/dryad.16d29d6
title: Data from: How has the environment shaped geographical patterns of insect body sizes? A test of hypotheses using sphingid moths

description: Aim: We mapped the geographical pattern of body sizes in sphingid moths
 and investigated latitudinal clines. We tested hypotheses concerning their
 possible environmental control, i.e., effects of temperature (negative:
 temperature size rule or Bergmann’s rule; positive: converse Bergmann
 rule), food availability, robustness to starvation during extreme weather,
 and seasonality. Location: Old World and Australia/Pacific region Methods:
 Body size data of 950 sphingid species were compiled and related to their
 distribution maps. Focusing on body length, we mapped the median and
 maximum size of all species occurring in 100 km grid cells. In a
 comparative approach we tested the predictions from explanatory hypotheses
 by correlating species’ size to the average environmental conditions
 encountered throughout their range, under univariate and multivariate
 models. We accounted for phylogeny by stepwise inclusion of
 phylogenetically informed taxonomic classifications into hierarchical
 random-intercept mixed models. Results: Median body sizes showed a
 distinctive geographical pattern, with large species in the Middle East
 and the Asian tropics, and smaller species in temperate regions and the
 Afrotropics. Absolute latitude explained very little body size variation,
 but there was a latitudinal cline of maximum size. Species’ median size
 was correlated to net primary productivity, supporting the food
 availability hypothesis, whereas support for other hypotheses was weak.
 Environmental correlations contributed much less (i.e., &lt;10%) to
 explaining overall size variation than phylogeny (inclusion of which led
 to models explaining &gt;70% of variability). Main conclusion: The
 intuitive impression of larger species in the tropics is shaped by larger
 size maxima. Median body sizes are only very weakly related to latitude.
 Most of the geographic variation in body size in sphingid moths is
 explained by their phylogenetic past. NPP and forest cover correlate
 positively with the body size, which supports the idea that food
 availability allowed the evolution of larger sizes.
description: Sphingid body
 sizeBody size measures (body
 length, forewing length, thorax width) as used and described in Beerli et
 al. Nomenclature and taxonomic placement are consistent with our range map
 data (available on mol.org), but they may differ from nomenclature used in
 referenced sources as well as current taxonomic placements. Measures are
 for n = 1 individual per species. See the publication for an explanation
 of the "set_scan"-columns. The datafile is identical to Appendix
 ES1 published through the journal's website.Beerli_etal_ES1.csv
DOI: 10.5061/dryad.8h350
title: Data from: A parametric method for assessing diversification rate variation in phylogenetic trees

description: Phylogenetic hypotheses are frequently used to examine variation in rates
 of diversification across the history of a group. Patterns of
 diversification-rate variation can be used to infer underlying ecological
 and evolutionary processes responsible for patterns of cladogenesis. Most
 existing methods examine rate variation through time. Methods for
 examining differences in diversification among groups are more limited.
 Here we present a new method, parametric rate comparison (PRC), that
 explicitly compares diversification rates among lineages in a tree using a
 variety of standard statistical distributions. PRC can identify subclades
 of the tree where diversification-rates are at variance with the remainder
 of the tree. A randomization test can be used to evaluate how often such
 variance would appear by chance alone. The method also allows for
 comparison of diversification-rate among a priori defined groups. Further,
 the application of the PRC method is not restricted to monophyletic
 groups. We examined the performance of PRC using simulated data which
 showed that PRC has acceptable false positive rates and statistical power
 to detect rate variation. We apply the PRC method to the well-studied
 radiation of North American Plethodon salamanders, and support the
 inference that the large-bodied P. glutinosus clade has a higher
 historical rate of diversification compared to other Plethodon
 salamanders.
description: PRC_archive
DOI: 10.5061/dryad.d48hq
title: Data from: Looking at cerebellar malformations through text-mined interactomes of mice and humans

description: We have generated and made publicly available two very large networks of
 molecular interactions: 49,493 mouse-specific and 52,518 human-specific
 interactions. These networks were generated through automated analysis of
 368,331 full-text research articles and 8,039,972 article abstracts from
 the PubMed database, using the GeneWays system. Our networks cover a wide
 spectrum of molecular interactions, such as bind, phosphorylate,
 glycosylate, and activate; 207 of these interaction types occur more than
 1,000 times in our unfiltered, multi-species data set. Because mouse and
 human genes are linked through an orthological relationship, human and
 mouse networks are amenable to straightforward, joint computational
 analysis. Using our newly generated networks and known associations
 between mouse genes and cerebellar malformation phenotypes, we predicted a
 number of new associations between genes and five cerebellar phenotypes
 (small cerebellum, absent cerebellum, cerebellar degeneration, abnormal
 foliation, and abnormal vermis). Using a battery of statistical tests, we
 showed that genes that are associated with cerebellar phenotypes tend to
 form compact network clusters. Further, we observed that cerebellar
 malformation phenotypes tend to be associated with highly connected genes.
 This tendency was stronger for developmental phenotypes and weaker for
 cerebellar degeneration.
description: Data from: Looking at
 Cerebellar Malformations through Text-Mined Interactomes of Mice and
 HumansSee original publication
 and documentation files included in this archive. Archive format is POSIX
 'tar' archive compressed using GNU zip (gzip). The included data
 files are tab-separated ASCII. Some Matlab scripts are
 provided.iossifov-2009.tgz
DOI: 10.5061/dryad.2jd88
title: Data from: A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation

description: The Neotropical evaniid genus Evaniscus Szépligeti currently includes six
 species. Two new species are described, Evaniscus lansdownei Mullins, sp.
 n. from Colombia and Brazil and Evaniscus rafaeli Kawada, sp. n. from
 Brazil. Evaniscus sulcigenis Roman, syn. n., is synonymized under
 Evaniscus rufithorax Enderlein. An identification key to species of
 Evaniscus is provided. Thirty-five parsimony informative morphological
 characters are analyzed for six ingroup and four outgroup taxa. A topology
 resulting in a monophyletic Evaniscus is presented with Evaniscus tibialis
 and Evaniscus rafaeli as sister to the remaining Evaniscus species. The
 Hymenoptera Anatomy Ontology and other relevant biomedical ontologies are
 employed to create semantic phenotype statements in Entity-Quality (EQ)
 format for species descriptions. This approach is an early effort to
 formalize species descriptions and to make descriptive data available to
 other domains.
description: evaniscus_merged_owlWeb Ontology Language (OWL) representation of descriptive character matrix from [Mullins et al. 2012] using the Comparative Data Analysis Ontology (CDAO). Character states are annotated with Entity–Quality phenotype descriptions using the Hymenoptera Anatomy Ontology (HAO), Phenotype and Trait Ontology (PATO), and the Biospatial Ontology (BSPO).evaniscus_merged.owl
DOI: 10.5061/dryad.fc57r
title: Data from: Species of Adialytus Förster, 1862 (Hymenoptera, Braconidae, Aphidiinae) in Iran: taxonomic notes and tritrophic associations

description: The species of Adialytus Förster in Iran are taxonomically studied and new
 data on distribution and host associations are presented. The existence of
 a species complex, in the case of Adialytus ambiguus (Haliday), and the
 morphological variability in commonly used taxonomic characters has been
 discussed. In total, four valid species belonging to the genus Adialytus
 including Adialytus ambiguus (Haliday), Adialytus salicaphis (Fitch),
 Adialytus thelaxis (Starý) and Adialytus veronicaecola (Starý) have been
 identified and recorded from Iran. Also, we recognized two additional
 phenotypes: “Adialytus arvicola” (Starý) and “Adialytus cf. ambiguus”
 (Haliday). These phenotypes and Adialytus veronicaecola are newly recorded
 from Iran in association with Sipha and Aphis species, respectively. An
 illustrated key for identification of the species and two variable
 phenotypes is presented.
description: The morphometric and
 meristic data for different characters of Adialytus species (Female) in
 IranMeasurement of the
 length and aspect ratio of diagnostic characters for separation of
 Adialytus specesDataFile_Adialytus.docFigure 02 AntennaeFigure 2. Antenna of Adialytus species A Adialytus ambiguus B Adialytus cf. ambiguus C Adialytus arvicola D Adialytus salicaphis E Adialytus thelaxis F Adialytus veronicaecola.Figure 03 ForewingsFigure 3. Fore wing of Adialytus species A Adialytus ambiguus B Adialytus cf. ambiguus C Adialytus arvicola D Adialytus salicaphis E Adialytus thelaxis F Adialytus veronicaecola.Figure 03 Foreiwngs.jpgFigure 04 Hind LegsFigure 4. Hind leg of Adialytus species, excluding tarsomeres A Adialytus ambiguus B Adialytus cf. ambiguus C Adialytus arvicola D Adialytus salicaphis E Adialytus thelaxis F Adialytus veronicaecola.Figure 04 Legs-Plate.jpgFigure 05 PetiolFigure 5. Petiole or first metasomal tergite of Adialytus species A Adialytus ambiguus B Adialytus cf. ambiguus C Adialytus arvicola D Adialytus salicaphis E Adialytus thelaxis F Adialytus veronicaecola.Figure 06 Female genitaliaFigure 6. Female genitalia of Adialytus species A Adialytus ambiguus B Adialytus cf. ambiguus C Adialytus arvicola D Adialytus salicaphis E Adialytus thelaxis F Adialytus veronicaecola.Figure 06 Female Genitalia.jpg
DOI: 10.5281/zenodo.18390471
title: LINF_320010700

description: TauE-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.5281/zenodo.18390472
title: LINF_320010700

description: TauE-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.5061/dryad.b6k41
title: Data from: Avian predation pressure as a potential driver of periodical cicada cycle length

description: The extraordinarily long life cycles, synchronous emergences at 13- or
 17-year intervals, and complex geographic distribution of periodical
 cicadas (Magicicada spp.) in eastern North America are an evolutionary
 enigma. Although a variety of factors, including satiation of above-ground
 predators and avoidance of interbrood hybridization, have been
 hypothesized to shape the evolution of this system, no empirical support
 for these mechanisms has previously been reported beyond the observation
 that bird predation can extirpate small, experimentally mistimed
 emergences. Here we show that periodical cicada emergences appear to set
 populations of potential avian predators on numerical trajectories that
 result in significantly lower potential predation pressure during the
 subsequent emergence. This result provides new support for the importance
 of predators in shaping periodical cicada life history, offers an
 ecological rationale for why emergences are synchronized at the observed
 multi-year intervals, and may explain some of the developmental plasticity
 observed in these unique insects.
description: cicada_finalContains the data used in the final repeated-measures analyses. Data include the BBS route information (STATE, ROUTE, RTCODE, LAT, LONG), the number of years of data (NYEARS), whether the site includes data for all (cicada) years or not (EMALL), the type of cicada (13 or 17 year; TYPE) and brood number (BROOD), and the mean standardized bird data for each year vis-a-vis the cicada cycle from emergence - 4 (YM4) through year 12 after emergence (Y12) for sites within the range of 13-year broods or year 16 after emergence (Y16) for sites within the range of 17-year broods. Missing values are listed as -9.bbs_cicada_dataThis file contains the original BBS data for the 15 bird species used in the analyses along with the associated cicada brood data. Each line contains the following data: SPECIES (AOU number), STATE, ROUTE, OBSNUM {observer number), LATitude, LONGitude, YEAR, BIRDS (N birds observed), log-transformed N birds, N birds standardized to mean of 0 and SD=1, YRSFRMEM (years from the last emergence), TYPE (13-year or 17-year), BROOD number, NYEARS (of data for that site overall), EMEVENT (whether the data for that site includes an emergence year or not), EMALL (whether the data for that site includes values for all years of the relevant cicada cycle), XMASS (mass of the bird species).
DOI: 10.15468/dl.5vb944
title: Occurrence Download

description: A dataset containing 3015 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "TaxonKey is Coenonympha glycerion"
 ]
}

 The dataset includes 3015 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001589-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.v74b8
title: Data from: Signatures of natural selection among lineages and habitats in Oncorhynchus mykiss

description: Recent advances in molecular interrogation techniques now allow
 unprecedented genomic inference about the role of adaptive genetic
 divergence in wild populations. We used high-throughput genotyping to
 screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs)
 for the economically and culturally important salmonid Oncorhynchus
 mykiss. Samples included 805 individuals from 11 anadromous and resident
 populations from the northwestern United States and British Columbia, and
 represented two major lineages including paired populations of each life
 history within single drainages of each lineage. Overall patterns of
 variation affirmed clear distinctions between lineages and in most
 instances, isolation by distance within them. Evidence for divergent
 selection at eight candidate loci included significant landscape
 correlations, particularly with temperature. High diversity of two
 nonsynonymous mutations within the peptide-binding region of the major
 histocompatibility complex (MHC) class II (DAB) gene provided signatures
 of balancing selection. Weak signals for potential selection between
 sympatric resident and anadromous populations were revealed from genome
 scans and allele frequency comparisons. Our results suggest an important
 adaptive role for immune-related functions and present a large genomic
 resource for future studies.
description: DRYAD SNP data for
 Limborg et al. 2012This file contains the
 SNP genotype data used for the associated publication. Genotypes are
 presented in a 3 digit genepop format with alternate alleles scored as 100
 and 200 respectively.Limborg et al. 2012_Oncorhyncus
 mykiss_SNP data.xlsx