cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p58hb
title: Data from: Genetic distance as an alternative to physical distance for definition of gene units in association studies

description: Background: Some association studies, as the implemented in VEGAS,
 ALIGATOR, i-GSEA4GWAS, GSA-SNP and other software tools, use genes as the
 unit of analysis. These genes include the coding sequence plus flanking
 sequences. Polymorphisms in the flanking sequences are of interest because
 they involve cis-regulatory elements or they inform on untyped genetic
 variants trough linkage disequilibrium. Gene extensions have customarily
 been defined as ± 50 Kb. This approach is not fully satisfactory because
 genetic relationships between neighbouring sequences are a function of
 genetic distances, which are only poorly replaced by physical distances.
 Results: Standardized recombination rates (SRR) from the deCODE
 recombination map were used as units of genetic distances. We searched for
 a SRR producing flanking sequences near the ± 50 Kb offset that has been
 common in previous studies. A SRR ≥ 2 was selected because it led to gene
 extensions with median length = 45.3 Kb and the simplicity of an integer
 value. As expected, boundaries of the genes defined with the ± 50 Kb and
 with the SRR ≥2 rules were rarely concordant. The impact of these
 differences was illustrated with the interpretation of top association
 signals from two large studies including many hits and their detailed
 analysis based in different criteria. The definition based in genetic
 distance was more concordant with the results of these studies than the
 based in physical distance. In the analysis of 18 top disease associated
 loci form the first study, the SRR ≥2 genes led to a fully concordant
 interpretation in 17 loci; the ± 50 Kb genes only in 6. Interpretation of
 the 43 putative functional genes of the second study based in the SRR ≥2
 definition only missed 4 of the genes, whereas the based in the ± 50 Kb
 definition missed 10 genes. Conclusions: A gene definition based on
 genetic distance led to results more concordant with expert detailed
 analyses than the commonly used based in physical distance. The genome
 coordinates for each gene are provided to maintain a simple use of the new
 definitions.
description: Genome coordinates SRR2
 genesGenome coordinates of
 the genes based in the SRR ≥2 definition. Comma separated values (CSV)
 file including one row per gene, and the columns: chromosome, “left”
 boundary, “right” boundary and gene name.Supplementary Table
 1Supplementary table 1:
 Full list of genes in the 18 top loci from the WTCCC GWAS [19] according
 to the authors, the SRR ≥2 or the ± 50 Kb definitions. Excel file
 containing this tableSupp Table
 1.xlsx
DOI: 10.5061/dryad.p3q2rq1
title: Data from: Resource overlap and dilution effects shape host plant use in a myrmecophilous butterfly

description: 1. The effects of consumers on fitness of resource organisms are a complex
 function of the spatio-temporal distribution of the resources, consumer
 functional responses and trait preferences, and availability of other
 resources. 2. The ubiquitous variation in the intensity of species
 interactions has important consequences for the ecological and
 evolutionary dynamics of natural populations. Nevertheless, little is
 known about the processes causing this variation and their operational
 scales. Here, we examine how variation in the intensity of a
 consumer-resource interaction is related to resource timing, resource
 density and abundance of other resources. 3. Using the butterfly consumer
 Phengaris alcon and its two sequential resources, the host plant Gentiana
 pneumonanthe and the host ants Myrmica spp., we investigated how butterfly
 egg-laying depended on focal host plant phenology, density and phenology
 of neighboring host plants and host ant abundance. 4. Butterflies
 preferred plants that simultaneously maximized the availability of both
 larval resources in time and space, i.e., they chose early-flowering
 plants that were of higher nutritional quality for larvae where host ants
 were abundant. Both the probability of oviposition and the number of eggs
 were lower in plant individuals with a high neighbor density than in more
 isolated plants, and this dilution effect was stronger when neighbors
 flowered early. 5. Our results show that plant-herbivore interactions
 simultaneously depend on the spatio-temporal distribution of a focal
 resource, and on the small-scale spatial variation in the abundance of
 other herbivore resources. Given that consumers have negative effects on
 fitness and prefer certain timing of the resource organisms, this implies
 that processes acting at the levels of individuals, populations and
 communities simultaneously contribute to variation in consumer-mediated
 natural selection.
description: Data on Gentiana
 pneumonanthe plant phenology, neighbor density and phenology and number of
 eggs of Phengaris alcondata_plants.txtData on abundances of ants in a meadow occupied by a population of Gentiana pneumonanthedata_ants.txt
DOI: 10.15468/dl.8tdzcd
title: Occurrence Download

description: A dataset containing 84689 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Perca flavescens"
 ]
}

 The dataset includes 84689 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000504-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.31vn6
title: Data from: Stronger spatial genetic structure in recolonized areas than in refugia in the European beech

description: Extant rear-edge populations located in former glacial refugia remain
 understudied despite their high conservation value. These populations
 should have experienced strong genetic drift due to their small size and
 long isolation. Moreover, the prolonged action of isolation-by-distance in
 refugial areas should result in stronger regional spatial genetic
 structure than in recolonized areas, but empirical tests of this
 prediction are scarce. To fill this gap, we first used a set of 16
 microsatellite markers to investigate the genetic structure of European
 beech in France in 65 populations from three refugial areas and one
 control recolonized (non-refugial) area. Then, using the same approach, we
 reanalyzed published isozyme data from 375 populations distributed across
 the entire species range. We found stronger genetic differentiation among
 populations in refugia than in recolonized areas. However, contrary to
 expectations, regional spatial genetic structure was lower within refugia
 than within recolonized areas. Published studies presenting similar
 analyses suggest that our results could have generality across different
 biogeographical settings and types of organisms. Strong and prolonged
 genetic drift in refugial areas could have erased the signature of range
 expansions that is still visible in recolonized areas. Our results
 therefore suggest that Pleistocene population isolation has played a key
 role in increasing the genetic complexity of extant rear-edge populations.
description: SSR Dataset of Fagus
 sylvatica from 65 populations in France and CataloniaSSR Dataset of Fagus
 sylvatica from 65 populations in France and Catalonia.Populations were
 sampled in the field and genotyping was performed at the
 Genome-Transcriptome facility of Bordeaux. Population codes refer to Table
 S1 in supplementary information. Georeferenced locations of populations
 are available in Table S1. SSRs used for this study are described in
 detail in Lefèvre et al (2012), doi:
 10.1111/j.1755-0998.2011.03094.x.SSR
 Dataset.xlsxIsozyme dataset of Fagus
 sylvatica from 375 populations across EuropeIsozyme dataset
 originally published in: Comps B, Gömöry D, Letouzey J, Thiébaut B, Petit
 RJ (2001) Diverging trends between heterozygosity and allelic richness
 during postglacial colonization in the European beech. Genetics, 157,
 389-397.Isozyme
 Dataset.xlsx
DOI: 10.5061/dryad.5pj36
title: Data from: Temperate marine protected area provides recruitment subsidies to local fisheries

description: The utility of marine protected areas (MPAs) as a means of protecting
 exploited species and conserving biodiversity within MPA boundaries is
 supported by strong empirical evidence. However, the potential
 contribution of MPAs to fished populations beyond their boundaries is
 still highly controversial; empirical measures are scarce and modelling
 studies have produced a range of predictions, including both positive and
 negative effects. Using a combination of genetic parentage and relatedness
 analysis, we measured larval subsidies to local fisheries replenishment
 for Australasian snapper (Chrysophrys auratus: Sparidae) from a small (5.2
 km2), well-established, temperate, coastal MPA in northern New Zealand.
 Adult snapper within the MPA contributed an estimated 10.6% (95% CI:
 5.5-18.1%) of newly settled juveniles to surrounding areas (approx. 400
 km2), with no decreasing trend in contributions up to 40 km away.
 Biophysical modelling of larval dispersal matched experimental data,
 showing larvae produced inside the MPA dispersed over a comparable
 distance. These results demonstrate that temperate MPAs have the potential
 to provide recruitment subsidies at magnitudes and spatial scales relevant
 to fisheries management. The validated biophysical model provides a
 cost-efficient opportunity to generalize these findings to other locations
 and climate conditions, and potentially informs the design of MPA networks
 for enhancing fisheries management.
description: Chrysophrys
 auratus_Microsatellite Genotype Data_Sept2017Microsatellite genotype
 data from New Zealand Australasian snapper (Chrysophrys
 auratus)
DOI: 10.5281/zenodo.18380551
title: Inference for Error-Prone Count Data: Estimation under a Binomial Convolution Framework

description: Datasets as well as code snippets used to reproduce the findings of "Inference for Error-Prone Count Data: Estimation under a Binomial Convolution Framework". The analysis code is avaiable at https://github.com/Yuqiu-Yang/binomialConvolution.ORA
DOI: 10.5281/zenodo.15750743
title: Inference for Error-Prone Count Data: Estimation under a Binomial Convolution Framework

description: Datasets as well as code snippets used to reproduce the findings of "Inference for Error-Prone Count Data: Estimation under a Binomial Convolution Framework". The analysis code is avaiable at https://github.com/Yuqiu-Yang/binomialConvolution.ORA
DOI: 10.5061/dryad.1705
title: Data from: Out of the Andes: patterns of diversification in clearwing butterflies

description: Global biodiversity peaks in the tropical forests of the Andes, a striking
 geological feature that has likely been instrumental in generating
 biodiversity by providing opportunities for both vicariant and ecological
 speciation. However, the role of these mountains in the diversification of
 insects, which dominate biodiversity, has been poorly explored using
 phylogenetic methods. Here we study the role of the Andes in the evolution
 of a diverse Neotropical insect group, the clearwing butterflies. We used
 dated species-level phylogenies to investigate the time-course of
 speciation and to infer ancestral elevation ranges for two diverse genera.
 We show that both genera likely originated at middle elevations in the
 Andes in the Middle Miocene, contrasting with most published results in
 vertebrates that point to a lowland origin. Although we detected a
 signature of vicariance caused by the uplift of the Andes at the
 Miocene-Pliocene boundary, most sister species were parapatric without any
 obvious vicariant barrier. Combined with an overall decelerating
 speciation rate, these results suggest an important role for ecological
 speciation and adaptive radiation, rather than simple vicariance.
description: Napeogenesspecies.xmlConcatenated sequences of CoxI, CoxII, EF1a and Tektin genes for all known species of the butterfly Genus Napeogenes (Nymphalidae: Danainae). Format for BEAST.NapeogenesEF1a.nexElongation Factor 1 alpha sequences for specimens of Napeogenes representing all know species and various subspecies.NqpeogenesTektin.nexTektin sequences for specimens of Napeogenes representing all know species and various subspecies.NapeogenesTektin.nexIthomiaspecies.xmlConcatenated sequences of CoxI, CoxII, EF1a, Tektin and wingless genes for all but one known species of the butterfly Genus Ithomia(Nymphalidae: Danainae). Format for BEAST.
DOI: 10.5061/dryad.k5904
title: Data from: Characterization of puma-livestock conflicts in rangelands of central Argentina

description: Livestock predation is one of the major causes of conflicts between humans
 and pumas (Puma concolor). Using data from interviews to ranchers and
 kill-site inspections, we characterized puma-livestock conflicts in
 Villarino and Patagones counties of central Argentinean rangelands.
 Depredation was considered the major cause of livestock losses, and puma
 attacks were reported in 46.6% and 35.4% of ranches in Villarino and
 Patagones, respectively. The majority of ranches underwent losses smaller
 than 1000 USD. The proportion of livestock lost to predation (0.1-10.4%)
 and financial losses (5.3-1560.4 USD) per ranch/year varied across ranches
 and small sheep ranches in Villarino were affected the most. Depredation
 was recorded only at night and preferentially in grassland with shrubs and
 cropland habitats. Although nocturnal enclosures appeared to decrease
 sheep losses, puma hunting was considered the most effective form of
 reducing depredation and was implemented by most ranchers. Mortality rates
 were 3.7 and 1.1-1.56 individuals/year x 100km2 for sheep and pumas,
 respectively. Nocturnal fencing, shepherding and spatial separation from
 predators may efficiently reduce sheep losses. However, the poor
 association between the intensity of puma persecution and puma-related
 livestock losses suggests that conflict mitigation in central Argentina is
 not only about reducing damage but also about increasing tolerance.
description: Data sheets and
 databaseKill site data
 base15- kill
 site data base.xlsx
DOI: 10.5061/dryad.sd5m9
title: Data from: Molecular data and ecological niche modeling reveal the Pleistocene history of a semi-aquatic bug (Microvelia douglasi douglasi) in East Asia

description: This study investigated the Pleistocene history of a semi-aquatic bug,
 Microvelia douglasi douglasi Scott, 1874 (Hemiptera: Veliidae) in East
 Asia. We used M. douglasi douglasi as a model species to explore the
 effects of historical climatic fluctuations on montane semi-aquatic
 invertebrate species. Two hypotheses were developed using ecological niche
 models (ENM). First, we hypothesized that M. douglasi douglasi persisted
 in suitable habitats in southern Guizhou, southern Yunnan, Hainan, Taiwan
 and southeast China during the LIG. After that, the populations expanded
 (Hypothesis 1). Since the spatial prediction in the LGM was significantly
 larger than in the LIG, we then hypothesized that the population expanded
 during the LIG to LGM transition (Hypothesis 2). We tested these
 hypotheses using mitochondrial data (COI+COII) and nuclear data
 (ITS1+5.8S+ITS2). Young lineages, relatively deep splits, lineage
 differentiation among mountain ranges in central, south and southwest
 China and high genetic diversities were observed in these suitable
 habitats. Evidence of mismatch distributions and neutrality tests indicate
 that a population expansion occurred in the late Pleistocene. The Bayesian
 skyline plot (BSP) revealed an unusual population expansion that likely
 happened during the cooling transition between LIG and LGM. The results of
 genetic data were mostly consistent with the spatial predictions from ENM,
 a finding that can profoundly improve phylogeographic research. The
 ecological requirements of M. douglasi douglasi, together with the
 geographical heterogeneity and climatic fluctuations of Pleistocene in
 East Asia, could have shaped this unusual demographic history. Our study
 contributes to our knowledge of semi-aquatic bug/invertebrate responses to
 Pleistocene climatic fluctuations in East Asia.
description: Maxent Input files and
 Bioclimate dataMaxent Input files and
 Bioclimate dataMaxent INPUT DATA and
 Bioclimate data.docxIndividual samples and
 accession numbersIndividual samples and
 accession numbersDNA sequence
 alignments(COI+COII)DNA sequence
 alignments(COI+COII)DNA sequence
 alignments(ITS1+5.8S+ITS2)DNA sequence
 alignments(ITS1+5.8S+ITS2)
DOI: 10.5061/dryad.n5d23
title: Data from: Jaw biodynamic data for 24 patients with chronic unilateral temporomandibular disorder

description: This study assessed 24 adult patients, suffering from severe chronic
 unilateral pain diagnosed as temporomandibular joint (TMJ) disorder (TMD).
 The full dentate patients had normal occlusion and had never received an
 occlusal therapy, i.e., were with natural dental evolution/maturation. The
 following functional and dynamic factors were assessed: (1) chewing
 function; (2) TMJ remodeling or the condylar path (CP); and (3) lateral
 jaw motion or lateral guidance (LG). CPs were assessed using conventional
 axiography, and LG was assessed by K7 jaw tracking. Seventeen (71%) of the
 24 (100%) patients consistently showed a habitual chewing side. The mean
 (standard deviation [SD]) of the CP angles was 47.90 (9.24) degrees. The
 mean (SD) of the LG angles was 42.95 (11.78) degrees. Data collection
 emerged from the conception of a new TMD paradigm where the affected side
 could be the habitual chewing side, the side with flatter lateral jaw
 motion or the side with an increased CP angle. These data may lead to
 improved diagnosis, therapy plans and evolution in TMD patients.
description: Data Table 1. Main
 biologic characteristics of the randomly selected 24 patients suffering
 from chronic (over 6-Months) tempormandibular joint disorders (TMD) with
 substantial selfreported unilateral painBiological
 characteristics of patientsTable 1. Biological
 Characteristics.xlsxData Table 2. Condylar
 PathTable 2 shows mean (from
 2 independent assessor’s measurements) values of Condylar Path angles on
 each side of patients. Measurement units: degrees.Table 2. Condylar
 Path.xlsxData Table 3. Lateral
 GuidanceLateral anterior
 guidance (LG) angles of patients suffering from susbstantial chronic
 unilateral TMD pain.Table 3. Lateral
 Guidance.xlsxData Table 4. Asymmetry
 and Equation indexes of condylar path and lateral guidance
 anglesAsymmetry indexes
 (quotient between differences and sums of a particular outcome) of
 condylar path (CP) and lateral guidance (LG) angles. The algorithm
 “Equation” correlates both CP and LG outcomes: (Right CP × left LG) /
 (left CP × right LG)Table 4. Asymmetry
 Indexes.xlsxData Table 5. CP and LG
 outcomes reliabilityRaw measurements of
 condylar path (CP), and lateral anterior guidances (LG) from two
 independent assessorsTable 5. CP and LG outcomes
 reliability.xlsx
DOI: 10.5061/dryad.473b6
title: Data from: Population structure of mtDNA variation due to Pleistocene fluctuations in the South American maned wolf (Chrysocyon brachyurus, Illiger, 1815): management units for conservation

description: The maned wolf (Chrysocyon brachyurus) is one of the largest South
 American canids, and conservation across this charismatic carnivore’s
 large range is presently hampered by a lack of knowledge about possible
 natural subdivisions which could influence the population’s viability. To
 elucidate the phylogeographic patterns and demographic history of the
 species, we used 2 mtDNA markers (D-loop and cytochrome b) from 87
 individuals collected throughout their range, in Argentina, Bolivia,
 Brazil, and Uruguay. We found moderate levels of haplotype and nucleotide
 diversity, and the 14 D-loop haplotypes were closely related. Genetic
 structure results revealed 4 groups, and when coupled with model
 inferences from a coalescent analysis, suggested that maned wolves have
 undergone demographic fluctuations due to changes in climate and habitat
 during the Pleistocene glaciation period approximately 24000 years before
 present (YBP). This genetic signature points to an event that occurred
 within the timing estimated for the start of the contraction of the
 Cerrado around 50000 YBP. Our results reveal a genetic signature of
 population size expansion followed by contraction during Pleistocene
 interglaciations, which had similar impacts on other South American
 mammals. The 4 groups should for now be considered management units,
 within which future monitoring efforts should be conducted independently.
description: KM406516- KM406517 and
 KM406502- KM406515Maned wolves mtDNA
 haplotypes. Two haplotypes of Cytochrome b fragment and 14 haplotypes of
 hypervariable Dloop fragmentGonzalez et al 2
 reviewsupplementary materialsJOH-2014-154review2
DOI: 10.5061/dryad.41m4d
title: Data from: The forgotten flies: the importance of non-syrphid Diptera as pollinators

description: Bees, hoverflies and butterflies are taxa frequently studied as
 pollinators in agricultural and conservation contexts. Although there are
 many records of non-syrphid Diptera visiting flowers, they are generally
 not regarded as important pollinators. We use data from 30
 pollen-transport networks and 71 pollinator-visitation networks to compare
 the importance of various flower-visiting taxa as pollen-vectors. We
 specifically compare non-syrphid Diptera and Syrphidae to determine
 whether neglect of the former in the literature is justified. We found no
 significant difference in pollen-loads between the syrphid and non-syrphid
 Diptera. Moreover, there was no significant difference in the level of
 specialization between the two groups in the pollen-transport networks,
 though the Syrphidae had significantly greater visitation evenness. Flower
 visitation data from 33 farms showed that non-syrphid Diptera made up the
 majority of the flower-visiting Diptera in the agricultural studies (on
 average 82% abundance and 73% species richness), and we estimate that
 non-syrphid Diptera carry 84% of total pollen carried by farmland Diptera.
 As important pollinators, such as bees, have suffered serious declines, it
 would be prudent to improve our understanding of the role of non-syrphid
 Diptera as pollinators.
description: Visitation network and
 pollen transport data of the studies used in the
 analysisPlant-pollinator
 visitation network data and pollen transport data (including number of
 pollen grains found on the insects' bodies when swabbed) of the
 studies used in the analysis. The tabs along the bottom are for each of
 the 11 studies. Latin names are given. The habitat, sampling design
 (transect or plot design) and location are given at the top of each
 spreadsheet.DRYAD Orford et
 al..xlsx