cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k37q7
title: Data from: Recent Warming, Rather than Industrial Emissions of Bioavailable Nutrients, is the Dominant Driver of Lake Primary Production Shifts across the Athabasca Oil Sands Region

description: Freshwaters in the Athabasca Oil Sands Region (AOSR) are vulnerable to the
 atmospheric emissions and land disturbances caused by the local oil sands
 industry; however, they are also affected by climate change. Recent
 observations of increases in aquatic primary production near the main
 development area have prompted questions about the principal drivers of
 these limnological changes. Is the enhanced primary production due to
 deposition of nutrients (nitrogen and phosphorus) from local industry or
 from recent climatic changes? Here, we use downcore, spectrally-inferred
 chlorophyll-a (VRS-chla) profiles (including diagenetic products) from 23
 limnologically-diverse lakes with undisturbed catchments to characterize
 the pattern of primary production increases in the AOSR. Our aim is to
 better understand the relative roles of the local oil sands industry
 versus climate change in driving aquatic primary production trends.
 Nutrient deposition maps, generated using geostatistical interpolations of
 spring-time snowpack measurements from a grid pattern across the AOSR,
 demonstrate patterns of elevated total phosphorus, total nitrogen, and
 bioavailable nitrogen deposition around the main area of industrial
 activity. However, this pattern is not observed for bioavailable
 phosphorus. Our paleolimnological findings demonstrate consistently
 greater VRS-chla concentrations compared to pre-oil sands development
 levels, regardless of morphological and limnological characteristics,
 landscape position, bioavailable nutrient deposition, and dibenzothiophene
 (DBT)-inferred industrial impacts. Furthermore, breakpoint analyses on
 VRS-chla concentrations across a gradient of DBT-inferred industrial
 impact show limited evidence of a contemporaneous change among lakes.
 Despite the contribution of bioavailable nitrogen to the landscape from
 industrial activities, we find no consistency in the spatial pattern and
 timing of VRS-chla shifts with an industrial fertilizing signal. Instead,
 significant positive correlations were observed between VRS-chla and
 annual and seasonal temperatures. Our findings suggest warmer air
 temperatures and likely decreased ice covers are important drivers of
 enhanced aquatic primary production across the AOSR.
description: VRS-chlorophyll-a data
 from 23 sediment cores from study lakes in the Athabasca Oil Sands Region,
 Alberta, CanadaSummersEtAl_PlosONE_Dryad_ChlaData.xlsxNutrient (TN, DIN, TP, TDP, SRP) data from snowpack samples in the Athabasca Oil Sands Region, Alberta, CanadaSummersEtAl_PlosONE_Dryad_NutrientsData.xlsx
DOI: 10.5061/dryad.62s00
title: Data from: A multilocus sequencing approach reveals the cryptic phylogeographical history of Phyllodoce nipponica Makino (Ericaceae)

description: Discordant phylogeographical patterns among species with similar
 distributions may not only denote specific biogeographical histories of
 different species, but also could represent stochastic variance of
 genealogies in applied genetic markers. A multilocus investigation
 representing different genomes can be used to address the latter concern,
 allowing robust inference to biogeographical history. In the present
 study, we conducted a multilocus phylogeographical analysis to re-examine
 the genetic structuring of Phyllodoce nipponica, in which chloroplast
 (cp)DNA markers exhibited a discordant pattern compared to those of other
 alpine plants. The geographical structure of sequence variation at five
 nuclear loci was not consistent with that of cpDNA and showed
 differentiation between the northern and southern parts of the range of
 this species. Its demographic history inferred from the
 isolation-with-migration model suggests that the north–south divergence
 originated from Pleistocene vicariance. In addition, the demographic
 parameters showed a lack of chloroplast-specific gene flow, suggesting
 that stochastic variance in genealogy resulted in the discordant
 geographical structure. Thus, P. nipponica probably experienced
 Pleistocene vicariance between its southern and northern range parts in
 concordance with other alpine plants in the Japanese archipelago. The
 findings of the present study demonstrates the importance of using a
 multilocus approach for inferring population dynamics, as well as for
 reconciling discordant phylogeographical patterns among species.
description: input_for_IM_analysisSequences of all samples used in IM analysis.12loci+cp.txtInput_for_STRUCTURE_analysis5loci_Pn.str
DOI: 10.5061/dryad.gr7026q
title: Data from: Changes in desert avifauna associated with the functional extinction of a terrestrial top predator

description: We investigated how long-term suppression of populations of a top
 predator, the dingo Canis dingo, affected composition of sympatric
 avifauna in Australian deserts, by surveying bird assemblages across ~80
 000 km2 of arid dunefields on either side of the Dingo Barrier Fence (DBF;
 a 5,614 km-long fence separating ecosystems in which dingoes are abundant
 from ecosystems in which dingoes are functionally extinct). Using
 fourth-corner modelling, incorporating species’ traits, we identified
 apparent declines of sedentary birds that nest in low vegetation and small
 birds that feed primarily on grass seed, and increases in scavenging birds
 associated with the functional extinction of dingoes. Occupancy differed
 between sites inside and outside the DBF in 13 bird species. We
 hypothesise that these differences in bird assemblages across the DBF
 result, in part, from increases in kangaroos (Macropus spp.) and red foxes
 (Vulpes vulpes) in arid landscapes where dingoes have been removed. Our
 study provides evidence that the functional extinction of a large
 terrestrial predator has had pervasive ecosystem effects, including shifts
 in composition of avian assemblages.
description: Bird survey data for
 dryad
DOI: 10.6084/m9.figshare.31077610
title: landslide data-CLP

description: landslide distribution in CLP, open it useing ARCGIS.
DOI: 10.6084/m9.figshare.31077610.v1
title: landslide data-CLP

description: landslide distribution in CLP, open it useing ARCGIS.
DOI: 10.5061/dryad.s6h18
title: Data from: Multiple evolutionary pathways to decreased lateral plate coverage in freshwater threespine sticklebacks

description: Adaptation to novel environments can be based either on standing genetic
 variation or variation attributable to new mutations. When standing
 genetic variation for a functional adaptation is lacking, and variation
 due to new mutations is not yet available, adaptation is possible only
 through alternative functional solutions. Reduction in the number of bony
 lateral plates as an adaptation to freshwater colonization by marine
 threespine sticklebacks (Gasterosteus aculeatus) has occurred in numerous
 independent cases through allelic substitution in the ectodysplasin-a
 (Eda) gene. Studying the phenotypic and genetic variation in plate number
 and size in five marine and six freshwater threespine stickleback
 populations, we found that when variation in Eda was limiting (i.e.
 alleles associated with the low-plate morph were missing or in extremely
 low frequency), plate number reduction did not take place in freshwater
 populations, but reduced lateral plate coverage was achieved by a
 reduction in the size of lateral plates. Our results suggest that this
 phenotypically and genetically discrete “small-plated” threespine
 stickleback – which is the dominant form in three northern European
 freshwater populations – may be functionally equivalent to the low-plated
 morph and hence, serve as an example of convergent evolution towards
 functional similarity in the face of genetic constraints.
description: dryad_polymorphic_lociGenepop file format of polymorphic loci used to test for bottlenecks and demographic expansion. For details see Methods.QTL_lateralplatesGenotype data for the putative lateral plate QTL including individuals not phenotyped. Ind - individual, Pop - population, alleles one and two for each locus are provided as separate columns, e.g. Stn380.1 for locus 1 of Stn380 and Stn380.2 for locus 2 of Stn380.dryad.QTL.csvlateral_plate_morphologyLateral plate size and genotypes for putative lateral plate QTL and Eda. Hab-habitat, Morph-lateral plate morph (see Methods for morph classification), body.d-body depth, rat.4-ratio of lateral plate height at fourth myomere and body depth.dryad.morph.csv
DOI: 10.5061/dryad.5nt3045
title: Data from: Linking locomotor performance to morphological shifts in urban lizards

description: Urban habitats are drastically modified from their natural state, creating
 unique challenges and selection pressures for organisms that reside in
 them. We compared locomotor performance of Anolis lizards from urban and
 forest habitats on tracks differing in angle and substrate, and found that
 using artificial substrates came at a cost: lizards ran substantially
 slower and frequently lost traction on man-made surfaces compared to bark.
 We found that various morphological traits were positively correlated with
 sprint speed and that these same traits were significantly larger in urban
 compared to forest lizards. We found that urban lizards ran faster on both
 man-made and natural surfaces, suggesting similar mechanisms improve
 locomotor performance on both classes of substrate. Thus, lizards in urban
 areas may be under selection to run faster on all flat surfaces, while
 forest lizards face competing demands of running, jumping, and clinging to
 narrow perches. Novel locomotor challenges posed by urban habitats likely
 have fitness consequences for lizards that cannot effectively use man-made
 surfaces, providing a mechanistic basis for observed phenotypic shifts in
 urban populations of this species.
description: Winchell_urbansprints_datasprint speed, morphology, and habitat data for Winchell et al. "Linking Locomotor Performance to Morphological Shifts in Urban Lizards"
DOI: 10.5061/dryad.m248h
title: Data from: Evolution of genetic variance during adaptive radiation

description: Genetic correlations between traits can concentrate genetic variance into
 fewer phenotypic dimensions that can bias evolutionary trajectories along
 the axis of greatest genetic variance and away from optimal phenotypes,
 constraining the rate of evolution. If genetic correlations limit
 adaptation, rapid adaptive divergence between multiple contrasting
 environments may be difficult. However, if natural selection increases the
 frequency of rare alleles after colonisation of new environments, an
 increase in genetic variance in the direction of selection can accelerate
 adaptive divergence. Here, we explored adaptive divergence of an
 Australian native wildflower by examining the alignment between divergence
 in phenotype mean and divergence in genetic variance among four
 contrasting ecotypes. We found divergence in mean multivariate phenotype
 along two major axes represented by different combinations of plant
 architecture and leaf traits. Ecotypes also showed divergence in the level
 of genetic variance in individual traits, and the multivariate
 distribution of genetic variance among traits. Divergence in multivariate
 phenotypic mean aligned with divergence in genetic variance, with much of
 the divergence in phenotype among ecotypes associated with changes in
 trait combinations containing substantial levels of genetic variance.
 Overall, our results suggest that natural selection can alter the
 distribution of genetic variance underlying phenotypic traits, increasing
 the amount of genetic variance in the direction of natural selection and
 potentially facilitating rapid adaptive divergence during an adaptive
 radiation.
description: Phenotype data to
 estimate divergence in meanTen phenotypic traits
 with ecotype and population identifiers.Data_Exp1_Dmatrix.csvPhenotype data to estimate genetic varianceTen phenotypic traits with ecotype, population (block), sire and dam identifiers.Data_Exp2_Gvariance.csv
DOI: 10.5061/dryad.dv6j84kt
title: Data from: Discrimination of hybrid classes using cross-species amplification of microsatellite loci: methodological challenges and solutions in Daphnia

description: Microsatellite markers are important tools in population, conservation and
 forensic studies and are frequently used for species delineation, the
 detection of hybridization and introgression. Therefore, marker sets that
 amplify variable DNA regions in two species are required; however,
 cross-species amplification is often difficult, as genotyping errors such
 as null alleles may occur. In order to estimate the level of potential
 misidentifications based on genotyping errors, we compared the occurrence
 of parental alleles in laboratory and natural Daphnia hybrids (Daphnia
 longispina group). We tested a set of twelve microsatellite loci with
 regard to their suitability for unambiguous species and hybrid class
 identification using F1 hybrids bred in the laboratory. Further, a large
 set of 44 natural populations of D. cucullata, D. galeata and D.
 longispina (1715 individuals) as well as their interspecific hybrids were
 genotyped to validate the discriminatory power of different marker
 combinations. Species delineation using microsatellite multi-locus
 genotypes produced reliable results for all three studied species using
 assignment tests. D. galeata x cucullata hybrid detection was limited due
 to three loci exhibiting D. cucullata specific null alleles which most
 likely are caused by differences in primer binding sites of parental
 species. Overall discriminatory power in hybrid detection was improved
 when a subset of markers was identified that amplifies equally well in
 both species.
description: Thielsch et al. MER
 Discrimination of hybrid classes in DaphniaZipped archive contains
 text files including genotyping data, locality information, infiles for
 NewHybrids, Structure, Genetix, and Micro-Checker (xls) as well as an
 information file about the data package
DOI: 10.5061/dryad.t4s0c
title: Data from: Evolutionary epidemiology of schistosomiasis: linking parasite genetics with disease phenotype in humans

description: Here we assess the role of parasite genetic variation in host disease
 phenotype in human schistosomiasis by implementing concepts and techniques
 from environmental association analysis in evolutionary epidemiology.
 Schistosomiasis is a tropical disease that affects more than 200 million
 people worldwide and is caused by parasitic flatworms belonging to the
 genus Schistosoma. While the role of host genetics has been extensively
 studied and demonstrated, nothing is yet known on the contribution of
 parasite genetic variation to host disease phenotype in human
 schistosomiasis. In this study microsatellite genotypes of 1561
 Schistosoma mansoni larvae collected from 44 human hosts in Senegal were
 linked to host characteristics such as age, gender, infection intensity,
 liver and bladder morbidity by means of multivariate regression methods
 (on each parasite locus separately). This revealed a highly significant
 association between allelic variation at the parasite locus L46951 and
 host infection intensity and bladder morbidity. Locus L46951 is located in
 the 3’ untranslated region of the cGMP-dependent protein kinase gene that
 is expressed in reproductive organs of adult schistosome worms and appears
 to be linked to egg production. This putative link between parasite
 genetic variation and schistosomiasis disease phenotype sets the stage for
 further functional research.
description: Microsatellite genotypes
 and host phenotypesThe worksheet
 “microsatellite genotypes” contains data from individual parasites (S.
 mansoni larvae) collected in Senegal, genotyped with nine microsatellite
 loci combined in a single multiplex: L46951, smd25, smd28 and smd89
 (Durand et al., 2000); CA11-1 and S9-1 (Blair et al., 2001); smd11, smd43
 and sdma28 (Curtis et al., 2001). This dataset represents 1692 parasites
 from 63 human hosts with at least five out of the nine loci successfully
 amplified. The worksheet “host phenotypes” contains host phenotypic data
 from the 63 human hosts. The host variables include gender, village*,
 liver morbidity (IP score), bladder morbidity (UBS score), Schistosoma
 mansoni infection intensity (epg**), Schistosoma haematobium infection
 intensity (ep 10ml**) and circulating anodic antigen (CAA) concentrations
 (picogram of CAA per mL). village* : Pakh (code 200), Ndieumeul (code
 501), Diokhor Takh (code 502) epg**: number of eggs per gram of faeces;
 ep10ml**: number of eggs per 10 ml of urine.
DOI: 10.15468/dl.htt468
title: Occurrence Download

description: A dataset containing 54177 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Geometry POLYGON((-101.26 41.05,-68.37 41.05,-68.37 57.29,-101.26 57.29,-101.26 41.05))",
 "HasCoordinate is true",
 "License is one of (CC-BY-NC 4.0, CC-BY 4.0, CC0 1.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Ochrophyta"
 ]
}

 The dataset includes 54177 records from 84 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000749-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.r0881
title: Data from: Completeness of the eutherian mammal fossil record and implications for reconstructing mammal evolution through the Cretaceous/Paleogene mass extinction

description: There is a well-established discrepancy between paleontological and
 molecular data regarding the timing of the origin and diversification of
 placental mammals. Molecular estimates place interordinal diversification
 dates in the Cretaceous, whilst no unambiguous crown placental fossils
 have been found prior to the end-Cretaceous mass extinction. Here, the
 completeness of the eutherian fossil record through geological time is
 evaluated in order to assess the suggestion that a poor fossil record is
 largely responsible for the difference in estimates of placental origins.
 The completeness of fossil specimens was measured using the Character
 Completeness Metric, a metric that quantifies the completeness of fossil
 taxa as the percentage of phylogenetic characters that are available to be
 scored for any given taxon. Our dataset was comprised of 33 published
 cladistic matrices representing 445 genera, of which 333 were coded at the
 species-level. There was no significant difference in eutherian
 completeness across the Cretaceous/Palaeogene boundary. This suggests that
 the lack of placental mammal fossils in the Cretaceous is not due to a
 poor fossil record, but more likely represents a genuine absence of
 placental mammals in the Cretaceous. This result supports the ‘explosive
 model’ of early placental evolution, whereby placental mammals originated
 around the time of the Cretaceous/Palaeogene boundary and diversified soon
 after the event. No correlation was found between the completeness pattern
 observed in this study and those of previous completeness studies on birds
 and sauropodomorph dinosaurs, suggesting that different factors affect the
 preservation of these groups. No correlations were found with various
 isotope proxy measures, but Akaike Information Criterion analysis found
 that eutherian Character Completeness Metric scores were best explained by
 models involving the marine carbonate strontium isotope ratios
 (87Sr/86Sr), suggesting that the tectonic activity might play a role in
 controlling the completeness of the eutherian fossil record.
description: Davies et al.
 Supplementary materialSupplementary material -
 7 supplementary tables, and 1 supplementary figure. Includes table of all
 genus level taxa and their CCM values, as well as extended species and
 genus level resultsDaviesetal_supplementary.docx
DOI: 10.5061/dryad.df878
title: Data from: From resource to female defence: the impact of roosting ecology on a bat's mating strategy

description: With their extraordinary species richness and diversity in ecological
 traits and social systems, bats are a promising taxon for testing
 socio-ecological hypotheses in order to get new insights into the
 evolution of animal social systems. Regarding its roosting habits,
 proboscis bats form an extreme by occupying sites which are usually
 completely exposed to daylight (e.g. tree trunks, vines or rocks). This is
 accompanied by morphological and behavioural adaptations to remain cryptic
 in exposed day roosts. With long-term behavioural observations and genetic
 parentage analyses of individually marked proboscis bats, we assessed its
 social dispersion and male mating strategy during day and night. Our
 results reveal nocturnal male territoriality—a strategy which most closely
 resembles a resource-defence polygyny that is frequent also in other
 tropical bats. Its contrasting clumped social dispersion during the day is
 likely to be the result of strong selection for crypsis in exposed roosts
 and is accompanied by direct female defence in addition to male
 territoriality. To the best of our knowledge, such contrasting male mating
 strategies within a single day–night cycle have not been described in a
 vertebrate species so far and illustrate a possible evolutionary
 trajectory from resource-defence to female-defence strategy by small
 ecologically driven evolutionary steps.
description: Günther et al.
 RSOS-160503_Microsatellite_GenotypesDataset of 510
 individual bats with allele lengths at ten different microsatellite loci.
 Each row represents an individual bat with its ID, age at capture, sex,
 colony of capture, date of capture, and both the lengths of both alleles
 at the ten different microsatellite loci. Details on each loci (Rn01,
 Rn04, Rn09, Rn10, Rn11, Rn13, Rn16, Rn18, Sb84, Sb85) can be found in the
 supplementary material of the manuscript RSOS-160503 by Günther et al.
 2016 (Royal Society Open Science).Günther et al.
 RSOS-160503_Genotypes.xlsx