cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.211ck
title: Data from: Single nucleotide polymorphisms reveal genetic structuring of the Carpathian newt and provide evidence of interspecific gene flow in the nuclear genome

description: Genetic variation within species is commonly structured in a hierarchical
 manner which may result from superimposition of processes acting at
 different spatial and temporal scales. In organisms of limited dispersal
 ability, signatures of past subdivision are detectable for a long time.
 Studies of contemporary genetic structure in such taxa inform about the
 history of isolation, range changes and local admixture resulting from
 geographically restricted hybridization with related species. Here we use
 a set of 139 transcriptome-derived, unlinked nuclear single nucleotide
 polymorphisms (SNP) to assess the genetic structure of the Carpathian newt
 (Lissotriton montandoni, Lm) and introgression from its congener, the
 smooth newt (L. vulgaris, Lv). Two substantially differentiated groups of
 Lm populations likely originated from separate refugia, both located in
 the Eastern Carpathians. The colonization of the present range in
 north-western and south-western directions was accompanied by a modest
 loss of variation; admixture between the two groups has occurred in the
 middle of the Eastern Carpathians. Local, apparently recent introgression
 of Lv alleles into several Lm populations was detected, demonstrating
 increased power for admixture detection in comparison to a previous study
 based on a limited number of microsatellite markers. The level of
 introgression was higher in Lm populations classified as admixed than in
 syntopic populations. We discuss the possible causes and propose further
 tests to distinguish between alternatives. Several outlier loci were
 identified in tests of interspecific differentiation, suggesting genomic
 heterogeneity of gene flow between species.
description: SNP
 GenotypesFile containing
 individual SNP genotypes in genepop like format.SNP_mon_vul.xlsx
DOI: 10.5061/dryad.h131s
title: Data from: Gripping during climbing of arboreal snakes may be safe but not economical

description: On the steep surfaces that are common in arboreal environments, many types
 of animals without claws or adhesive structures must use muscular force to
 generate sufficient normal force to prevent slipping and climb
 successfully. Unlike many limbed arboreal animals that have discrete
 gripping regions on the feet, the elongate bodies of snakes allow for
 considerable modulation of both the size and orientation of the gripping
 region. We quantified the gripping forces of snakes climbing a vertical
 cylinder to determine the extent to which their force production favoured
 economy or safety. Our sample included four boid species and one colubrid.
 Nearly all of the gripping forces that we observed for each snake exceeded
 our estimate of the minimum required, and snakes commonly produced more
 than three times the normal force required to support their body weight.
 This suggests that a large safety factor to avoid slipping and falling is
 more important than locomotor economy.
description: SnakeTotalNForceThis file contains all of the Total Normal Force values used in the paper. Each column includes total normal force for 10 locomotor cycles for the snake given by the IDs in line 1.
DOI: 10.5061/dryad.j272c
title: Data from: Landscape models for nuclear genetic diversity and genetic structure in white-footed mice (Peromyscus leucopus)

description: Dramatic changes in the North American landscape over the last 12 000
 years have shaped the genomes of the small mammals, such as the
 white-footed mouse (Peromyscus leucopus), which currently inhabit the
 region. However, very recent interactions of populations with each other
 and the environment are expected to leave the most pronounced signature on
 rapidly evolving nuclear microsatellite loci. We analyzed landscape
 characteristics and microsatellite markers of P. leucopus populations
 along a transect from southern Ohio to northern Michigan, in order to
 evaluate hypotheses about the spatial distribution of genetic
 heterogeneity. Genetic diversity increased to the north and was best
 approximated by a single-variable model based on habitat availability
 within a 0.5-km radius of trapping sites. Interpopulation differentiation
 measured by clustering analysis was highly variable and not significantly
 related to latitude or habitat availability. Interpopulation
 differentiation measured as FST values and chord distance was correlated
 with the proportion of habitat intervening, but was best explained by
 agricultural distance and by latitude. The observed gradients in diversity
 and interpopulation differentiation were consistent with recent habitat
 availability being the major constraint on effective population size in
 this system, and contradicted the predictions of both the postglacial
 expansion and core-periphery hypotheses.
description: Taylor&Hoffman2-Genotypes-afterNullAlleles_GenepopTaylor&Hoffman3-FIG-2-DATATaylor&Hoffman4a-Diversity-Modeling-DATATaylor&Hoffman4b-FIG-3-AB-DATATaylor&Hoffman5a-Distance-MODELS-untransTaylor&Hoffman5b-Distance-MODELS-transTaylor&Hoffman5c-FIG-4A-DATATaylor&Hoffman5d-FIG-4B-DATATaylor&Hoffman1-Genotypes-Original_Genepop-ALL_LOCI
DOI: 10.5061/dryad.22cc7
title: Data from: A population genetic signature of human releases in an invasive ladybeetle

description: Biological invasions have been accelerated by a variety of human
 activities. Propagule pressure, the number of introduced individuals and
 independent introductions, is likely to be influenced by these human
 activities and may be an important factor for successful range expansion
 in new environments. We tested whether the current distribution of the
 predatory ladybeetle Coccinella septempunctata in the introduced range
 (USA) is the result of multiple historical human introductions or natural
 range expansion from the first established populations in the USA. To test
 this hypothesis, we compared historical records of propagule size,
 propagule number, specific introduction locations, and the date of each
 introduction, with estimates of genetic variation in mitochondrial DNA
 (COI). Our results indicated that genetic diversity in the introduced
 range was positively correlated with historical records of propagule size
 and number, and negatively correlated with distance to nearest
 introduction point, suggesting that multiple human releases were
 successful. Higher genetic diversity in populations found near
 introduction points suggest that initial founder effects were limited, but
 lower genetic diversity found farther from introduction points is likely
 the result of serial founder effects during secondary range expansion.
 These results suggest that the current distribution of C. septempunctata
 in the introduced range is the result of a combination of human releases
 and short-range expansion from multiple established populations in
 introduced range.
description: DataSetKajitaHaplotypes in native and introduced rangesdiversityLatitude and longitude, and genetic diversity data set in the introduced rage for beta regressionIntroductionPropagule pressure data setRcode_AIC_selectR codes for AIC, radius selectionRcode_Spational_AnalysesR codes for spatial analysesC7-COI_Nucleotide alignment_Kajita
DOI: 10.5061/dryad.bj287
title: Data from: Sex-biased immunity is driven by relative differences in reproductive investment

description: Sex differences in immunity are often observed, with males generally
 having a weaker immune system than females. However, recent data in a
 sex-role-reversed species in which females compete to mate with males
 suggest that sexually competitive females have a weaker immune response.
 These findings support the hypothesis that sexual dimorphism in immunity
 has evolved in response to sex-specific fitness returns of investment in
 traits such as parental investment and longevity, but the scarcity of data
 in sex-reversed species prevents us from drawing general conclusions.
 Using an insect species in which males make a large but variable parental
 investment in their offspring, we use two indicators of immunocompetence
 to test the hypothesis that sex-biased immunity is determined by
 differences in parental investment. We found that when the value of
 paternal investment was experimentally increased, male immune investment
 became relatively greater than that of females. Thus, in this system, in
 which the direction of sexual competition is plastic, the direction of
 sex-biased immunity is also plastic and appears to track relative parental
 investment.
description: Vincent & Gwynne
 2014 KW
DOI: 10.5061/dryad.tm53q
title: Data from: Climate modifies response of non-native and native species richness to nutrient enrichment

description: Ecosystem eutrophication often increases domination by non-natives and
 causes displacement of native taxa. However, variation in environmental
 conditions may affect the outcome of interactions between native and
 non-native taxa in environments where nutrient supply is elevated. We
 examined the interactive effects of eutrophication, climate variability
 and climate average conditions on the success of native and non-native
 plant species using experimental nutrient manipulations replicated at 32
 grassland sites on four continents. We hypothesized that effects of
 nutrient addition would be greatest where climate was stable and benign,
 owing to reduced niche partitioning. We found that the abundance of
 non-native species increased with nutrient addition independent of
 climate; however, nutrient addition increased non-native species richness
 and decreased native species richness, with these effects dampened in
 warmer or wetter sites. Eutrophication also altered the time scale in
 which grassland invasion responded to climate, decreasing the importance
 of long-term climate and increasing that of annual climate. Thus, climatic
 conditions mediate the responses of native and non-native flora to
 nutrient enrichment. Our results suggest that the negative effect of
 nutrient addition on native abundance is decoupled from its effect on
 richness, and reduces the time scale of the links between climate and
 compositional change.
description: Non-native and native
 species abundance and richness data at the site level for pre-treatment
 year (year 0)This file contains the
 abundance and richness data for non-native and native species for the
 pre-treatment year (year 0) for all Nutnet sites included in our analyses.
 These data was derived at the site level. The description of each variable
 can be found in the ReadMe fileabundance_and_richness_data.csvChange in abundance and richness of non-native and native species after nutrient treatments for sites included in the studyThis file contains data on the change in abundance and richness of non-native and native species after nutrient enrichment (1-3 years) use for analyses. The change in abundance data was derived at the plot level. Metadata can be found in the ReadMe file.change_in_abundance_and_richness_data.csvInformation on sites included in this studyThis file contains information on the name, location, type (experimental or observational) and name of persons in charge of setting and maintaining the NutNet sites which data was used for this study. Information on each of the variables included in this file can be found in the ReadMe file.FloresMoreno-site-PI-table.csv
DOI: 10.5061/dryad.7g2c9
title: Data from: Managing cryptic biodiversity: Fine-scale intralacustrine speciation along a benthic gradient in Alpine whitefish (Coregonus spp.)

description: Whitefish (Coregonus spp.) are an important catch for many freshwater
 fisheries, particularly in Switzerland. In support of this, supplemental
 stocking of whitefish species is carried out, despite lacking complete
 knowledge of the extent, distribution and origin of whitefish diversity in
 these lakes, potentially threatening local endemics via artificial gene
 flow. Here, we investigate phenotypic and genetic differentiation among
 coexisting whitefish species spawning along a depth gradient in a
 subalpine Swiss lake to better delineate intralacustrine whitefish
 biodiversity. We find depth-related clines in adaptive morphology and in
 neutral genetic markers. This individual variation is structured in three
 distinct clusters with spatial overlap. Individual genetic distances
 correlate strongly with differences in growth rate and gill-raker number,
 consistent with predictions of isolation-by-adaptation and ecological
 speciation. Genetic differentiation between species suggests reproductive
 isolation, despite demographic admixture on spawning grounds. Our results
 are consistent with clinal speciation resulting in three species
 coexisting in close ecological parapatry, one (C. sp. “benthic
 intermediate”) being previously unknown. A second unknown species spawning
 in close proximity was found to be of potential allochthonous origin. This
 study highlights the importance of taxonomically unbiased sampling
 strategies to both understand evolutionary mechanisms structuring
 biodiversity and to better inform conservation and fisheries management.
description: Hudson_et_al_Managing_Cryptic_Biodiv_archived_dataRaw data: Sampling event, genotypic, phenotypic (gill-raker, age, standard length) dataHudson_et_al_archived_data.xlsx
DOI: 10.5061/dryad.5t8pq
title: Data from: Multilevel selection in the filamentous ascomycete Neurospora tetrasperma

description: The history of life has been driven by evolutionary transitions in
 individuality, i.e., the aggregation of autonomous individuals to form a
 new, higher-level individual. The fungus Neurospora tetrasperma has
 recently undergone an evolutionary transition in individuality from
 homokaryosis (one single type of nuclei in the same cytoplasm) to
 heterokaryosis (two genetically divergent and free-ranging nuclear types).
 In this species, selection can act at different levels: while nuclei can
 compete in their replication and transmission into short-lived asexual
 spores, at the level of the heterokaryotic individual cooperation between
 nuclear types is required to produce the long-lived sexual spores.
 Conflicts can arise between these two levels of selection if the
 coevolution between nuclear types is disrupted. Here, we investigated the
 extent of multilevel selection in three strains of N. tetrasperma. We
 assessed the ratio between nuclear types under different conditions, and
 measured fitness traits of homo- and heterokaryotic mycelia with varying
 nuclear ratios. We show that the two nuclei have complementary traits,
 consistent with division of labor and cooperation. In one strain, for
 which a recent chromosomal introgression was detected, we observed the
 occurrence of selfish nuclei, enjoying better replication and transmission
 than sister nuclei at the same time as being detrimental to the
 heterokaryon. We hypothesize that introgression has disrupted the
 coevolution between nuclear types in this strain.
description: Meunier_etal_DataThis folder contains all data needed to recreate the main figures and tables of the article. Data concern estimation of genetic nuclear ratios of mating types in N.tetrasperma, under different conditions of medium and duration of growth, by qPCR. Measurements of fitness in heterokaryons under different nuclear ratios and in homokaryons are also provided.Meunieretal_Data.zipMeunieretal_RscriptsThis folder contains all scripts in R used to analyze data from the article. Data files to be used with each script are indicated as comments inside the scripts. See README associated with Data for more information.
DOI: 10.5061/dryad.800pj
title: Data from: An agent-based model of anoikis in the colon crypt displays novel emergent behaviour consistent with biological observations

description: Colorectal cancer (CRC) is a major cause of cancer mortality. Colon crypts
 are multi-cellular flask-shaped invaginations of the colonic epithelium,
 with stem cells at their base which support the continual turnover of the
 epithelium with loss of cells by anoikis from the flat mucosa. Mutations
 in these stem cells can become embedded in the crypts, a process that is
 strongly implicated in CRC initiation. We describe a computational model
 which includes novel features, including an accurate representation of the
 geometry of the crypt mouth. Model simulations yield previously unseen
 emergent phenomena, such as localization of cell death to a small region
 of the crypt mouth which corresponds with that observed in vivo. A
 mechanism emerges in the model for regulation of crypt cellularity in
 response to changes in either cell proliferation rates or membrane
 adhesion strengths. We show that cell shape assumptions influence this
 behaviour, with cylinders recapitulating biology better than spheres.
 Potential applications of the model include determination of roles of
 mutations in neoplasia and exploring factors for altered crypt
 morphodynamics.
description: Cell Centre Crypt
 SimulationCode for simulations
 presented in the paper
DOI: 10.5061/dryad.k514v
title: Data from: Natal dispersers pay a lifetime cost to increased reproductive effort in a wild bird population

description: Natal dispersal is assumed to be costly. Such costs can be difficult to
 detect, and fitness consequences of dispersal are therefore poorly known.
 Because of lower phenotypic quality and/or familiarity with the
 environment, natal dispersers may be less buffered against a sudden
 increase in reproductive effort. Consequently, reproductive costs
 associated with natal dispersal may mostly be detected in harsh breeding
 conditions. We tested this prediction by comparing lifetime reproductive
 success between natal dispersers and non-dispersers in a patchy population
 of collared flycatchers (Ficedula albicollis) when they reared either a
 non-manipulated brood or an experimentally increased or decreased brood.
 Natal dispersers achieved lower lifetime reproductive success than
 non-dispersers only under more stressful breeding conditions (i.e. when
 brood size was experimentally increased). This was mostly due to a lower
 number of recruits produced in the year of the increase. Our results
 suggest a cost associated with natal dispersal paid immediately after an
 increase in reproductive effort and not subsequently compensated for
 through increased survival or future offspring recruitment. Natal
 dispersers adjusted their breeding investment when reproductive effort is
 as predicted but seemed unable to efficiently face a sudden increase in
 effort, which could affect the influence of environmental predictability
 on dispersal evolution.
description: Lifetime reproductive
 successLifetime reproductive
 success for each individualLRS.txtANNUALData about annual recruitment and annual return rate for individuals for which LRS has been estimated (file LRS), as well as breeding year, plot....
DOI: 10.5281/zenodo.18381940
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Jean-Louis Berlandier, http://www.wikidata.org/entity/Q4084961. 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/Q4084961
DOI: 10.15468/dl.awjuq7
title: Occurrence Download

description: A dataset containing 5152 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Tetragonisca angustula, Puma concolor)",
 "HasCoordinate is true",
 "Country is Brazil"
 ]
}

 The dataset includes 5152 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000641-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.8038938
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Jean-Louis Berlandier, http://www.wikidata.org/entity/Q4084961. 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/Q4084961
DOI: 10.5061/dryad.m3t6p5g
title: Data from: The hidden side of a major marine biogeographic boundary: a wide mosaic hybrid zone at the Atlantic–Mediterranean divide reveals the complex interaction between natural and genetic barriers in mussels

description: The Almeria-Oran Front (AOF) is a recognised hotspot of genetic
 differentiation in the sea. It is a barrier to dispersal and an ecological
 boundary, which explain the position of genetic breaks. However, the
 maintenance of genetic differentiation is likely reinforced by genetic
 barriers. A general drawback of previous studies is an insufficient
 density of sampling sites at the transition zone with a conspicuous lack
 of samples from the southern coastline. We analysed the genetic structure
 in the mussel Mytilus galloprovincialis with ancestry-informative loci. We
 discovered a 600 km wide mosaic hybrid zone eastward of the AOF along the
 Algerian coasts. This mosaic zone provides a new twist to our
 understanding of the Atlantic-Mediterranean transition because it
 demonstrates the two lineages can live in sympatry but hardly interbreed.
 This implies some form of reproductive isolation must exist to maintain
 the two genetic backgrounds locally cohesive. The zone ends with an abrupt
 genetic shift at a barrier to dispersal in the Gulf of Bejaia. Simulations
 in models that account for hydrodynamic features of the region support the
 hypothesis that sister hybrid zones could have been differentially trapped
 at two alternative barriers to dispersal or environmental boundaries. A
 preponderantly unidirectional north-south gene flow next to the AOF can
 also maintain a patch of an intrinsically maintained genetic background in
 the south and the mosaic structure. Our results concur with the coupling
 hypothesis that suggests natural barriers mostly explain the position of
 genetic breaks while their maintenance must additionally require genetic
 barriers.
description: Mytilus genbank
 11-GenBank accession
 MK259098 - MK259664