cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7h8q2
title: Data from: Naturally rare versus newly rare: demographic inferences on two timescales inform conservation of Galápagos giant tortoises

description: Long-term population history can influence the genetic effects of recent
 bottlenecks. Therefore, for threatened or endangered species, an
 understanding of the past is relevant when formulating conservation
 strategies. Levels of variation at neutral markers have been useful for
 estimating local effective population sizes (Ne) and inferring whether
 population sizes increased or decreased over time. Furthermore, analyses
 of genotypic, allelic frequency, and phylogenetic information can
 potentially be used to separate historical from recent demographic
 changes. For 15 populations of Galápagos giant tortoises (Chelonoidis
 sp.), we used 12 microsatellite loci and DNA sequences from the
 mitochondrial control region and a nuclear intron, to reconstruct
 demographic history on shallow (past ~100 generations, ~2500 years) and
 deep (pre-Holocene, &gt;10 thousand years ago) timescales. At the deep
 timescale, three populations showed strong signals of growth, but with
 different magnitudes and timing, indicating different underlying causes.
 Furthermore, estimated historical Ne of populations across the archipelago
 showed no correlation with island age or size, underscoring the complexity
 of predicting demographic history a priori. At the shallow timescale, all
 populations carried some signature of a genetic bottleneck, and for 12
 populations, point estimates of contemporary Ne were very small (i.e.,
 &lt; 50). On the basis of the comparison of these genetic estimates
 with published census size data, Ne generally represented ~0.16 of the
 census size. However, the variance in this ratio across populations was
 considerable. Overall, our data suggest that idiosyncratic and
 geographically localized forces shaped the demographic history of tortoise
 populations. Furthermore, from a conservation perspective, the separation
 of demographic events occurring on shallow versus deep timescales permits
 the identification of naturally rare versus newly rare populations; this
 distinction should facilitate prioritization of management action.
description: Garrick_etal_2014_ECE_Dryad_data
DOI: 10.5061/dryad.h22c122
title: Data from: Predation-mediated ecosystem services and disservices in agricultural landscapes

description: Ecological intensification may reduce environmental externalities of
 agriculture by harnessing biodiversity to benefit regulating ecosystem
 services. However, to propose management options for the production of
 such services, there is a need to understand the spatio-temporal dynamics
 of net effects between ecosystem services and disservices provided by wild
 organisms across taxonomic groups in relation to habitat and landscape
 management. We studied the contribution of predatory vertebrates and
 invertebrates (including both carnivores and seed herbivores) to
 regulating ecosystem services and disservices in 16 cereal fields in
 response to a local habitat contrast and a landscape complexity gradient.
 From May to November 2016 we provided weed (predation reflects an
 ecosystem service) and crop (predation reflects a disservice) seeds, as
 well as pest (predation reflects an ecosystem service) and beneficial
 (predation reflects a disservice) invertebrate prey to predators. Seed
 predation was dominated by vertebrates, while vertebrates and
 invertebrates contributed equally to predation of animal prey. Before
 harvest, predation steadily increased from very low levels in May to high
 levels in July independent of the resource type. After harvest, ecosystem
 services declined more rapidly than disservices. The presence of adjacent
 semi-natural grasslands promoted crop seed predation, but reduced pest
 prey predation. Predation on beneficial prey decreased with increasing
 proportions of semi-natural grassland in the landscape. Predatory
 vertebrates and invertebrates provide important ecosystem services due to
 the consumption of pests. However, beneficial invertebrates and crop seeds
 were often consumed to a similar or even higher extent than harmful
 invertebrates or weed seeds. Our results therefore raise concerns that
 management options aimed at enhancing service providers may simultaneously
 increase levels of disservices. By considering positive and negative
 effects simultaneously, this study addresses an important knowledge gap
 and highlights the importance of interactions between local management,
 landscape composition and service and disservice provision across taxa and
 over time. Considering trade-offs between ecosystem services and
 disservices when evaluating the net effects of biodiversity conservation
 measures on ecosystem service provision is crucial. Future
 agri-environment schemes that offer payments for semi-natural habitats may
 need to provide higher compensation for farmers in cases where net effects
 are likely to be negative.
description: Data from
 Predation-mediated ecosystem services and disservices in agricultural
 landscapesDataTschumi2018EcolApplDryad.xlsx
DOI: 10.15468/dl.43e4bs
title: Occurrence Download

description: A dataset containing 314 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Nyctereutes procyonoides records in Chornobyl Radiation and Ecological Biosphere Reserve, Ukraine, ELP project"
 ]
}

 The dataset includes 314 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000797-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mj5m8
title: Data from: The phenotypic effects of spontaneous mutations in different environments

description: Understanding the context-dependence of mutation represents the current
 frontier of mutation research. In particular, understanding how traits
 vary in their abilities to accrue mutational variation and how the
 environment influences expression of mutant phenotypes yields insight into
 evolutionary processes. We conducted phenotypic assays in four
 environments using a set of Daphnia pulex mutation accumulation lines to
 examine the context-dependence of mutation. Life-history traits accrued
 mutational variance faster than morphological traits when considered in
 individual environments. Across environments, the mutational variance in
 plasticity was also greater for life-history than morphological traits
 although this pattern was less robust. In addition, the expression of
 mutational variance depended on the environment, which resulted in changes
 in the rank order of genotype performance across environments in some
 cases. Such cryptic genetic variation resulting from mutation may maintain
 genetic diversity and allow for rapid adaptation in spatially or
 temporally variable environments.
description: DryadThis excel workbook
 contains all the data used for analyses in the manuscript. The first
 worksheet "All" was used for estimating variance components and
 subsequent analyses involving these metrics. The remaining worksheets were
 used for the pairwise environment fixed effects ANOVAs. Raw data is
 indicated by a lower case "o" after the trait
 abbreviation.
DOI: 10.5061/dryad.51n8n
title: Data from: Carbon assimilation and habitat segregation in resurrection plants: a comparison between desiccation- and non-desiccation-tolerant species of Neotropical Velloziaceae (Pandanales)

description: Desiccation tolerance is the ability that some organisms show to
 equilibrate their water content with that of dry air and recover when
 water supplies are re-established. This is a widespread although rare
 strategy in angiosperms, and most desiccation-tolerant (DT) species are
 restricted to tropical rock outcrops. Such restricted ecological range is
 attributed to weak competitive potential caused by low productivity, due
 to the temporal limitation in carbon assimilation that occurs when plants
 desiccate. However, few studies addressing this question in angiosperms
 have been conducted. We investigate 20 species of Velloziaceae of campos
 rupestres that differ in their desiccation tolerance. Campos rupestres is
 an ecoregion characterized by particular vegetation growing on rocky
 substrates that occurs along mountains in central/south-eastern Brazil,
 above 900 m a.s.l. It is considered a Neotropical hotspot and the main
 centre of diversity for DT vascular plants and the Velloziaceae. Here, we
 tested whether carbon assimilation rates, functional traits and species
 habitats corroborate the hypothesized trade-off between productivity and
 desiccation tolerance. All species showed similar photosynthetic rates
 during the wet season; in the dry season, only DT species showed drastic
 decrease in their metabolism. Non-desiccation-tolerant (NT) species are
 larger than DT ones (i.e. greater maximum plant height; stem volume).
 Relative canopy area and stem dry-matter content were lower in DT compared
 to NT, while leaf phosphorous concentration was higher in DT. The
 remaining morphofunctional traits evaluated did not vary between these
 groups. DT species occupied mainly exposed rock soils, while NT species
 occurred in deep, sandy soil habitats. Our results support the hypothesis
 of a trade-off between desiccation tolerance and productivity in
 angiosperms and suggest that DT strategy may only evolve and persist in
 habitats where severe growth limitations due to drought limit competition
 from more productive species.
description: FE-2014-00400-RawDataWorksheets providing the raw data of Amax, gs, water potential, and morphofunctional traits measured in the field for individuals of the 20 species of Velloziaceae studied in the companion paper.
DOI: 10.5061/dryad.p3g8r54
title: Data from: Host genotype and environment affect the trade-off between horizontal and vertical transmission of the parasite Edhazardia aedis

description: Background: If a parasite is able to transmit horizontally or vertically,
 which transmission mode will it choose? We investigated how the growth
 conditions and the genotype of the mosquito Aedes aegypti affect the
 transmission mode of the parasite Edhazardia aedis. Results: In poor
 conditions the parasites were more likely to be transmitted horizontally,
 whereas in favourable conditions they were more likely to be transmitted
 vertically. This plasticity appears to be adaptive. Unfavourable
 conditions delayed emergence, giving the parasite more time to produce its
 horizontally transmitted stage; in more favourable conditions mosquitoes
 have greater reproductive success, increasing the effectiveness of
 vertical transmission. In addition, the parasite's ability to
 transmit vertically was influenced by the genetic background of the host
 (i.e., its full-sib family), giving a genetic correlation between the
 host's life-history and which of the parasite's transmission
 mode it enables. In particular, genotypes with large bodies (and therefore
 high fecundity) were more likely to enable vertical transmission than
 genotypes with small bodies. This led to a trade-off among the host's
 families (which can be interpreted as a genetic correlation) for the
 parasite's transmission mode. Conclusions: Since horizontal
 transmission is linked to higher virulence than vertical transmission, the
 host's contribution to transmission mode has important consequences
 for the evolution of parasites with mixed-mode transmission.
description: BMC_dataset_ParasiteTransmissionBMC_dataset.xlsx
DOI: 10.5061/dryad.jg385
title: Data from: Within-season variation in sexual selection in a fish with dynamic sex roles

description: The strength of sexual selection may vary between species, among
 populations, and within populations over time. While there is growing
 evidence that sexual selection may vary between years, less is known about
 variation in sexual selection within a season. Here, we investigate
 within-season variation in sexual selection in male two-spotted gobies
 (Gobiusculus flavescens). This marine fish experiences a seasonal change
 in the operational sex ratio from male- to female-biased, resulting in a
 dramatic decrease in male mating competition over the breeding season. We
 therefore expected stronger sexual selection on males early in the season.
 We sampled nests and nest-holding males early and late in the breeding
 season and used microsatellite markers to determine male mating and
 reproductive success. We first analysed sexual selection associated with
 the acquisition of nests by comparing nest-holding males to population
 samples. Among nest-holders, we calculated the potential strength of
 sexual selection and selection on phenotypic traits. We found remarkable
 within-season variation in sexual selection. Selection on male body size
 related to nest acquisition changed from positive to negative over the
 season. The opportunity for sexual selection among nest-holders was
 significantly greater early in the season rather than late in the season,
 partly due to more unmated males. Overall, our study documents a
 within-season change in sexual selection that corresponds with a
 predictable change in the operational sex ratio. We suggest that many
 species may experience within-season changes in sexual selection and that
 such dynamics are important for understanding how sexual selection
 operates in the wild.
description: Male mating and
 reproductive success and phenotypic traitsMales_Gaasevik2008.txtAdditional datasets on male sizesadditional_samples.txtRaw microsatellite datamicrosatellites.txt
DOI: 10.5061/dryad.4m83g
title: Data from: History of the fragmentation of the African rain forest in the Dahomey Gap: insight from the demographic history of Terminalia superba

description: Paleo-environmental reconstructions show that the distribution of tropical
 African rain forests was affected by Quaternary climate changes. They
 suggest that the Dahomey Gap (DG) - the savanna corridor that currently
 separates Upper Guinean (UG, West Africa) and Lower Guinean (LG, western
 Central Africa) rain forest blocks – was forested during the African Humid
 Holocene period (from at least 9 ka till 4.5 ka), and possibly during
 other interglacial periods, while an open vegetation developed in the DG
 under drier conditions, notably during glacial maxima. Nowadays, relics of
 semi-deciduous forests containing UG and LG forest species are still
 present within the DG. We used one of these species, the pioneer tree
 Terminalia superba (Combretaceae), to study past forest fragmentation in
 the DG and its impact on infraspecific biodiversity. A Bayesian clustering
 analysis of 299 individuals genotyped at 14 nuclear microsatellites
 revealed five parapatric genetic clusters (UG, DG, and three in LG) with
 low to moderate genetic differentiation (Fst from 0.02 to 0.24).
 Approximate Bayesian Computation analyses inferred a demographic
 bottleneck around the penultimate glacial period in all populations. They
 also supported an origin of the DG population by admixture of UG and LG
 populations around 54 000 (27 600 - 161 000) years B.P., thus before the
 Last Glacial Maximum. These results contrast with those obtained on
 Distemonanthus benthamianus where the DG population seems to originate
 from the Humid Holocene period. We discuss these differences in light of
 the ecology of each species. Our results challenge the simplistic view
 linking population fragmentation/expansion with glacial/interglacial
 periods in African forest species.
description: Demenou-et-al.accepted_DryadColumn A: Individual ID; Column B: Country of origin; Column C: Location of origin; Column D: Code of Country of origin; Columns E and F: Spatial coordinates of the individuals (degree decimals); Column G: Individuals used for Spatial Genetic Structure, Pswc and Psec (with * individuals not used for STRUCTURE analysis) Columns H to AI: Genotypes of the individuals at the 14 nuclear SSR (P37, P8, P30, P25, P17, P28, P5, P42, P12, P32, P22, P44, P34, P24)Demenou-et-al.2017_Dryad.xls
DOI: 10.5061/dryad.v3c31
title: Data from: Genetic structure of Daphnia galeata populations in Eastern China

description: This study presents the first examination of the genetic structure of
 Daphnia longispina complex populations in Eastern China. Only one species,
 D. galeata, was present across the eight investigated lakes; as identified
 by taxon assignment using allelic variation at 15 microsatellite loci.
 Three genetically differentiated D. galeata subgroups emerged independent
 of the type of statistical analysis applied. Thus, Bayesian clustering,
 discriminant analysis based on results from factorial correspondence
 analysis, and UPGMA clustering consistently showed that populations from
 two neighbouring lakes were genetically separated from a mixture of
 genotypes found in other lakes, which formed another two subgroups. Clonal
 diversity was high in all D. galeata populations, and most samples showed
 no deviation from Hardy-Weinberg equilibrium, indicating that clonal
 selection had little effect on the genetic diversity. Overall, populations
 did not cluster by geographical origin. Further studies will show if the
 observed pattern can be explained by natural colonization processes or by
 recent anthropogenic impact on predominantly artificial lakes.
description: Daphnia galeata
 microsats data
DOI: 10.15468/dl.5mhh6s
title: Occurrence Download

description: A dataset containing 2798 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hydrolea spinosa",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2798 records from 205 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000798-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.420b8vn
title: Data from: Plant–insect interactions: double-dating associated insect and plant lineages reveals asynchronous radiations

description: An increasing number of plant-insect studies using phylogenetic analysis
 suggest that cospeciation events are rare in plant–insect systems.
 Instead, nonrandom patterns of phylogenetic congruence are produced by
 phylogenetically conserved host switching (to related plants) or tracking
 of particular resources or traits (e.g., chemical). The dominance of host
 switching in many phytophagous insect groups may make the detection of
 genuine cospeciation events difficult. One important test of putative
 cospeciation events is to verify whether reciprocal speciation is
 temporally plausible. We explored techniques for double-dating of both
 plant and insect phylogenies. We use dated molecular phylogenies of a
 psyllid (Hemiptera)–Genisteae (Fabaceae) system, a predominantly
 monophagous insect–plant association widespread on the Atlantic
 Macaronesian islands. Phylogenetic reconciliation analysis suggests high
 levels of parallel cladogenesis between legumes and psyllids. However,
 dating using molecular clocks calibrated on known geological ages of the
 Macaronesian islands revealed that the legume and psyllid radiations were
 not contemporaneous but sequential. Whereas the main plant radiation
 occurred some 8 million years ago, the insect radiation occurred about 3
 million years ago. We estimated that &gt;60% of the psyllid speciation
 has resulted from host switching between related hosts. The only evidence
 for true cospeciation is in the much more recent and localized radiation
 of genistoid legumes in the Canary Islands, where the psyllid and legume
 radiations have been partially contemporaneous. The identification of
 specific cospeciation events over this time period, however, is hindered
 by the phylogenetic uncertainty in both legume and psyllid phylogenies due
 to the apparent rapidity of the species radiations.
description: Insect
 data12S+COmatrix+Tre+GenBank.nexPlant dataLegumeMatrix+Tre+GenBank.nexTreeBASE Study 1073
DOI: 10.5061/dryad.2tg68
title: Data from: Genetic population structure of the blister beetle Gnathium minimum: core and peripheral populations

description: Populations on the periphery of a species’ range tend to contain lower
 genetic variation and increased genetic differentiation compared to
 populations at the core of a species range, although some exceptions to
 this generalization occur. The blister beetle Gnathium minimum (Say)
 exhibits a wide-ranging distribution in the western United States but has
 peripheral or disjunct populations in Mexico, Florida, and Wisconsin. We
 used amplified fragment length polymorphism (AFLP) to compare the genetic
 variation and magnitude of genetic differentiation of the Wisconsin
 peripheral population to western core populations (Colorado, Kansas, New
 Mexico, and Texas). The proportion of polymorphic loci was 53.6 and 54.3,
 and expected heterozygosity 0.1864 and 0.1933 for the Kansas/Colorado (n =
 87) and New Mexico/Texas (n = 35) regions, respectively. Specimens from
 Wisconsin (n = 121) had a lower proportion of polymorphic loci (38.4) and
 expected heterozygosity (0.1475). Genetic cluster estimation with GENELAND
 and F ST values showed greater genetic differentiation among the sampling
 locations within Wisconsin compared to core regions. Significant
 isolation-by-distance (IBD) was also observed in Wisconsin but not within
 the core regions. Lower genetic variation and increased isolation may
 reduce the Wisconsin population’s ability to respond to change, thereby
 increasing their susceptibility to extinction.
description: MarschalekBerres_JHered_DataAFLP data
DOI: 10.5061/dryad.241d1fs
title: Data from: Tau imaging detects distinctive distribution of tau pathology in ALS/PDC on the Kii Peninsula

description: OBJECTIVE: To characterize the distribution of tau pathology in patients
 with amyotrophic lateral sclerosis/parkinsonism-dementia complex on the
 Kii Peninsula (Kii ALS/PDC) by tau PET using [11C]PBB3 as ligand. METHODS:
 This is a cross-sectional study of five patients with ALS/PDC and one
 asymptomatic participant with a dense family history of ALS/PDC from the
 Kii Peninsula who took part in this study. All were men, and their age was
 76 ± 8 (mean ± SD) years. Thirteen healthy men (69 ± 6 years) participated
 as healthy controls (HCs). Dynamic PET scans were performed following
 injection of [11C]PBB3, and parametric PET images were generated by
 voxel-by-voxel calculation of binding potential (BPND) using a multilinear
 reference tissue model. [11C]PiB PET, MRI, and cognitive tests were also
 performed. RESULTS: A voxel-based comparison of [11C]PBB3 BPND illustrated
 PET-detectable tau deposition in the cerebral cortex and white matter, and
 pontine basis including the corticospinal tract in Kii ALS/PDC patients
 compared with HCs (uncorrected p &lt; 0.05). Group-wise VOI analysis
 of [11C]PBB3 BPND images showed increased BPND in the hippocampus and in
 frontal and parietal white matters of Kii ALS/PDC patients relative to HCs
 (p &lt; 0.05, Holm-Sidak multiple comparisons test). BPND in frontal,
 temporal, and parietal gray matters correlated with Mini-Mental State
 Examination scores in Kii ALS/PDC subjects (p &lt; 0.05). All Kii
 ALS/PDC patients were negative for [11C]PiB (amyloid β) except one with
 marginal positivity. CONCLUSION: [11C]PBB3 PET visualized the
 characteristic topography of tau pathology in Kii ALS/PDC, corresponding
 to clinical phenotypes of this disease.
description: Shinotoh_e-Fig.1a,bReference voxels were extracted by intersecting voxels with BP*ND values above mean -2SD for a range of 0.36 and cortical and cerebellar cortical gray matter on MRI in each participant.