cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.62h5m
title: Data from: Seed dispersers help plants to escape global warming

description: Plants are shifting their ranges towards higher elevations in response to
 global warming, yet such shifts are occurring at a rate slower than is
 needed to keep pace with a rapidly changing climate. There is, however, an
 almost complete lack of knowledge on seed dispersal across altitude, a key
 process to understand what constrains climate-driven range shifts. Here,
 we report the first direct empirical evidence on altitudinal seed
 dispersal mediated by two common frugivorous mammals: the red fox Vulpes
 vulpes and the pine marten Martes martes. We conducted a three-year
 (bait-marking) experiment in a mountainous region of Spain. We offered
 experimental fruits containing colour-coded seed mimics at feeding
 stations that simulated source trees. The colour codes allowed us to
 identify the exact origin of seed mimics found later in mammal scats.
 Nearly half (47%) of the dispersal events occurred towards higher
 elevations, despite only ca 25% of the study area being above the average
 altitude of the feeding stations (1344 m). Seeds dispersed uphill gained
 an average of 106 m (median = 111 m) and a maximum of 288 m, greatly
 exceeding the estimated requirements to escape warming (35.4 m per
 decade). Yet, foxes mediated much more uphill seed dispersal than martens
 (57% and 26% of dispersal events, respectively), which can be explained by
 between-disperser differences in home range size and habitat specificity.
 Dispersers with larger home ranges move farther and potentially disperse
 more seeds to higher altitudes, while habitat generalism is necessary to
 transport seeds above vegetation belts delimiting contrasting habitat
 types. We discuss how both traits (home range size and habitat
 specificity) can be used to infer altitudinal seed dispersal across
 disperser species and mountainous landscapes.
description: Gonzalez-Varo et al.
 (2017) Altitudinal Seed Dispersal EventsData on seed dispersal
 events obtained by a 3-year (bait-marking) experiment in which we offered
 experimental fruits containing colour-coded seed mimics at feeding
 stations that simulated source trees. The colour codes allowed us to
 identify the exact origin of seed mimics found later in fox and marten
 scats. See ReadMe file for details.Gonzalez-Varo_et_al_2017_seed_dispersal_events.csv
DOI: 10.5061/dryad.95h17
title: Data from: A Poissonian model of indel rate variation for phylogenetic tree inference

description: While indel rate variation has been observed and analyzed in detail, it is
 not taken into account by current indel-aware phylogenetic reconstruction
 methods. In this work, we introduce a continuous time stochastic process,
 the geometric Poisson indel process, that generalizes the Poisson indel
 process by allowing insertion and deletion rates to vary across sites. We
 design an efficient algorithm for computing the probability of a given
 multiple sequence alignment based on our new indel model. We describe a
 method to construct phylogeny estimates from a fixed alignment using
 neighbor joining. Using simulation studies, we show that ignoring indel
 rate variation may have a detrimental effect on the accuracy of the
 inferred phylogenies, and that our proposed method can sidestep this issue
 by inferring latent indel rate categories. We also show that our
 phylogenetic inference method may be more stable to taxa subsampling than
 methods that either ignore indels or indel rate variation.
description: Molluscan RNA
 dataThis dataset is obtained
 from http://www.rna.icmb.utexas.edu/SIM/4D/Mollusk/alignment.gb. This
 dataset in nexus format is converted from the original dataset in GenBank
 format using EMBOSS. The dataset in fasta format used in the data analysis
 section of the paper can be obtained directly from
 https://github.com/yzhai220/geopip together with the source
 code.molluscan.nexus.txt
DOI: 10.5061/dryad.pn795
title: Data from: Assessing cumulative impacts of forest development on the distribution of furbearers using expert-based habitat modeling

description: Cumulative impacts of anthropogenic landscape change must be considered
 when managing and conserving wildlife habitat. Across the central-interior
 of British Columbia, Canada, industrial activities are altering the
 habitat of furbearer species. This region has witnessed unprecedented
 levels of anthropogenic landscape change following rapid development in a
 number of resource sectors, particularly forestry. Our objective was to
 create expert-based habitat models for three furbearer species: fisher
 (Pekania pennanti), Canada lynx (Lynx canadensis), and American marten
 (Martes americana) and quantify habitat change for those species. We
 recruited 10 biologist and 10 trapper experts and then used the analytical
 hierarchy process to elicit expert knowledge of habitat variables
 important to each species. We applied the models to reference landscapes
 (i.e., registered traplines) in two distinct study areas and then
 quantified the change in habitat availability from 1990 to 2013. There was
 strong agreement between expert groups in the choice of habitat variables
 and associated scores. Where anthropogenic impacts had increased
 considerably over the study period, the habitat models showed substantial
 declines in habitat availability for each focal species (78% decline in
 optimal fisher habitat, 83% decline in optimal lynx habitat, and 79%
 decline in optimal marten habitat). For those traplines with relatively
 little forest harvesting, the habitat models showed no substantial change
 in the availability of habitat over time. The results suggest that habitat
 for these three furbearer species declined significantly as a result of
 the cumulative impacts of forest harvesting. Results of this study
 illustrate the utility of expert knowledge for understanding large-scale
 patterns of habitat change over long time periods.
description: Habitat variable voting
 & AHP evaluation of variables by expertsThis Excel file contains
 four worksheets. The first worksheet contains the results of the voting
 for the inclusion of habitat variables into the habitat models for fisher,
 lynx, and marten, as voted by the biologist and trapper experts. The next
 three worksheets contain the eigenvector scores resulting from the AHP
 elicitation, where the biologists and trappers evaluated the importance of
 each habitat variable for fisher, lynx, and marten.DATA_ESA_SUBMISSION.xlsx
DOI: 10.5061/dryad.20d67
title: Data from: Consequences of symbiont co-infections for insect host phenotypes

description: 1. Most animals host communities of symbiotic bacteria. In insects, these
 symbionts may have particularly intimate interactions with their hosts:
 many are intracellular and can play important roles in host ecology and
 evolution, including protection against natural enemies. 2. We
 investigated how interactions between different species or strains of
 endosymbiotic bacteria within an aphid host influence the outcome of
 symbiosis for both symbiont and host. 3. We first asked whether different
 combinations of facultative symbiont species or strains can exist in
 stable co-infections. We then investigated whether the benefits that
 facultative bacteria confer on their hosts (protection against natural
 enemies) are enhanced, reduced or unaltered by the presence of a
 co-infecting symbiont. We asked this both for co-infecting symbionts that
 confer different phenotypes on their hosts (protection against fungal
 pathogens vs. parasitoid wasps) and symbionts with overlapping functions.
 Finally, we investigated the additional survival costs to aphids of
 carrying multiple infections of symbiont species or strains, and compared
 symbiont titres in double and single infections. 4. We found that stable
 co-infections were possible between all of the combinations of facultative
 symbiont species (Regiella insecticola + Hamiltonella defensa, Regiella +
 Rickettsiella sp., Regiella + Spiroplasma sp.) and strains (Hamiltonella)
 that we studied. Where symbionts provided protection against different
 natural enemies, no alteration in protection was observed in the presence
 of co-infections. Where symbionts provided protection against the same
 natural enemy, the level of protection corresponded to the higher of the
 two symbionts present. In some instances, aphid hosts suffered additional
 survival costs when hosting double infections. In the case of
 Hamiltonella, however, infection with multiple strains of the same
 symbiont led to lower symbiont titres than single infections, and actually
 improved aphid survival. 5. We conclude that the long-term maintenance of
 symbiont co-infections in aphids is likely to be determined primarily by
 costs of co-infections and in some instances by redundancy of symbiont
 benefits.
description: Complete_data_fileDryad.xlsx
DOI: 10.5061/dryad.5g7nq49
title: Data from: Multiple mating is linked to social setting, and benefits the males in a communally rearing mammal

description: Individuals in social species may mate with multiple opposite sex
 individuals, including members of the same or different social groups.
 This variation may be linked to genetic benefits, where multiple mating
 decreases risk of inbreeding. Multiple mating also may be constrained by
 the socio-spatial setting through its effect on availability of mates.
 Since multiple mating with individuals from same or different groups may
 determine sex-specific fitness effects, we also examined how multiple
 mating modulates social benefits of females and males. We used 7 years of
 data on demography, social organization, and genetics of a natural
 population of the group-living and colonial rodent, Octodon degus, to
 determine how kin and sex composition within social groups, and spatial
 relations between these groups (i.e., colonial habits) influence multiple
 mating and its fitness consequences. 81.3% of males and 64.9% of females
 produced offspring with multiple opposite sex individuals within groups
 and with individuals of neighboring groups. Thus, polygynandry was the
 dominant mating system in the degu population examined. Multiple mating in
 degus was high when compared with estimates reported in other social
 mammals. Variation in female and male multiple mating was better explained
 by social setting through its effect on availability of potential mates
 rather than by benefits derived from decreasing risk of inbreeding.
 Finally, our study revealed how multiple mating enhances male, but not
 female reproductive success.
description: Data file
 1Sheet 1: Data on
 individual subjects (sex, social group ID), social organization (group
 size, male-to-female ratio), distance to mates, genetic relatedeness.
 Sheet 2: data on individual offspring survivalMaster Data File Ebensperger et
 al.xlsx
DOI: 10.5061/dryad.s42n1
title: Data from: Role of sex and migration in adaptation to sink environments

description: Understanding the effects of sex and migration on adaptation to novel
 environments remains a key problem in evolutionary biology. Using a
 single-cell alga Chlamydomonas reinhardtii, we investigated how sex and
 migration affected rates of evolutionary rescue in a sink environment, and
 subsequent changes in fitness following evolutionary rescue. We show that
 sex and migration affect both the rate of evolutionary rescue and
 subsequent adaptation. However, their combined effects change as the
 populations adapt to a sink habitat. Both sex and migration independently
 increased rates of evolutionary rescue, but the effect of sex on
 subsequent fitness improvements, following initial rescue, changed with
 migration, as sex was beneficial in the absence of migration but
 constraining adaptation when combined with migration. These results
 suggest that sex and migration are beneficial during the initial stages of
 adaptation, but can become detrimental as the population adapts to its
 environment.
description: Lagator et al. Effects
 of sex and migration in adaptation to sink environments
 datasetExperimental data:
 Optical density measurements of growth of experimentally selected
 populations of Chlamydomonas reinhardtiiLagator et al. Effects of Sex
 and Migration in Adaptation to Sink Environments
 dataset.xlsx
DOI: 10.5061/dryad.r620r
title: Data from: Perceptual impairment in face identification with poor sleep

description: Previous studies have shown impaired memory for faces following restricted
 sleep. However, it is not known whether lack of sleep impairs performance
 on face identification tasks that do not rely on recognition memory,
 despite these tasks being more prevalent in security and forensic
 professions—for example, in photo-ID checks at national borders. Here we
 tested whether poor sleep affects accuracy on a standard test of
 face-matching ability that does not place demands on memory: the Glasgow
 Face-Matching Task (GFMT). In Experiment 1, participants who reported
 sleep disturbance consistent with insomnia disorder show impaired accuracy
 on the GFMT when compared with participants reporting normal sleep
 behaviour. In Experiment 2, we then used a sleep diary method to compare
 GFMT accuracy in a control group to participants reporting poor sleep on
 three consecutive nights—and again found lower accuracy scores in the
 short sleep group. In both experiments, reduced face-matching accuracy in
 those with poorer sleep was not associated with lower confidence in their
 decisions, carrying implications for occupational settings where
 identification errors made with high confidence can have serious outcomes.
 These results suggest that sleep-related impairments in face memory
 reflect difficulties in perceptual encoding of identity, and point towards
 metacognitive impairment in face matching following poor sleep.
description: Experiment 1
 dataS1: GFMT performance and
 sleep measure data from Experiment 1.S1_exp1data.xlsxExperiment 2 dataS2: GFMT performance and sleep measure data for Experiment 2S2_exp2data.xlsx
DOI: 10.15468/dl.w2x49y
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-219.46867 37.98657,-218.77284 37.98657,-218.77284 38.44769,-219.46867 38.44769,-219.46867 37.98657))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Acrocephalus orientalis",
 "Year 2020-2026"
 ]
}

 The dataset includes 96 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000977-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mv32t
title: Data from: Biodiversity dynamics and environmental occupancy of fossil azooxanthellate and zooxanthellate scleractinian corals

description: Scleractinian corals have two fundamentally different life strategies,
 which can be inferred from morphological criteria in fossil material. In
 the non-photosymbiotic group nutrition comes exclusively from
 heterotrophic feeding, whereas the photosymbiotic group achieves a good
 part of its nutrition from algae hosted in the coral’s tissue. These
 ecologic differences arose early in the evolutionary history of corals but
 with repeated evolutionary losses and presumably also gains of symbiosis
 since then. We assessed the biodiversity dynamics and environmental
 occupancy of both ecologic groups to identify times when the evolutionary
 losses of symbiosis as inferred from molecular analyses might have
 occurred and if these can be linked to environmental change. Two episodes
 are likely: The first was in the mid-Cretaceous when non-symbiotic corals
 experienced an origination pulse and started to become more common in
 deeper, non-reef habitats and on siliciclastic substrates initiating a
 long-term offshore trend in occupancy. The second was around the
 Cretaceous/Paleogene boundary with another origination pulse and increased
 occupancy of deep-water settings in the non-symbiotic group. Environmental
 factors such as rapid global warming associated with mid-Cretaceous anoxic
 events and increased nutrient concentrations in Late Cretaceous–Cenozoic
 deeper waters are plausible mechanisms for the shift. Turnover rates and
 durations are not significantly different between the two ecologic groups
 when compared over the entire history of scleractinians. However, the
 deep-water shift of non-symbiotic corals was accompanied by reduced
 extinction rates, supporting the view that environmental occupancy is a
 prominent driver of evolutionary rates.
description: Table
 S1List of valid
 scleractinian genera in the Paleobiology Database and their inferred
 symbiotic mode.TableS1.xlsx
DOI: 10.15468/dl.953qvb
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plowmania nyctaginoides",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 74 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000978-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.85qd6
title: Data from: The impact of Wolbachia, male age and mating history on cytoplasmic incompatibility and sperm transfer in Drosophila simulans

description: Most insects harbour a variety of maternally inherited endosymbionts, the
 most widespread being Wolbachia pipientis that commonly induce cytoplasmic
 incompatibility (CI) and reduced hatching success in crosses between
 infected males and uninfected females. High temperature and increasing
 male age are known to reduce the level of CI in a variety of insects. In
 Drosophila simulans, infected males have been shown to mate at a higher
 rate than uninfected males. By examining the impact of mating rate
 independent of age, this study investigates whether a high mating rate
 confers an advantage to infected males through restoring their
 compatibility with uninfected females over and above the effect of age.
 The impact of Wolbachia infection, male mating rate and age on the number
 of sperm transferred to females during copulation and how it relates to CI
 expression was also assessed. As predicted, we found that reproductive
 compatibility was restored faster in males that mate at higher rate than
 that of low mating and virgin males, and that the effect of mating history
 was over and above the effect of male age. Nonvirgin infected males
 transferred fewer sperm than uninfected males during copulation, and
 mating at a high rate resulted in the transfer of fewer sperm per mating
 irrespective of infection status. These results indicate that the
 advantage to infected males of mating at a high rate is through
 restoration of reproductive compatibility with uninfected females, whereas
 uninfected males appear to trade off the number of sperm transferred per
 mating with female encounter rate and success in sperm competition. This
 study highlights the importance Wolbachia may play in sexual selection by
 affecting male reproductive strategies.
description: Figure 1
 dataCytoplasmic
 incompatibility induction experiment data. This data has been used to
 produce figure 1.Sperm transfer
 experimentThis data has been used
 for sperm transfer experiment and production of figure
 2.Sperm_experiment_data.xlsxFigure 3 data% hatching success per sperm has been calculated and figure 3 has been produced.
DOI: 10.5061/dryad.1999
title: Data from: Landscape effects on extremely fragmented populations of a rare solitary bee, Colletes floralis

description: Globally there is concern over the decline of bees, an ecologically
 important group of pollinating insects. Genetic studies provide insights
 into population structure that are crucial for conservation management but
 that would be impossible to obtain by conventional ecological methods. Yet
 conservation genetic studies of bees have primarily focussed on social
 species rather than the more species-rich solitary bees. Here we
 investigate the population structure of Colletes floralis, a rare and
 threatened solitary mining bee, in Ireland and Scotland using nine
 microsatellite loci. Genetic diversity was surprisingly as high in
 Scottish (Hebridean island) populations at the extreme northwestern edge
 of the species range as in mainland Irish populations further south.
 Extremely high genetic differentiation among populations was detected;
 multilocus FST was up to 0.53, and G'ST and Dest were even higher
 (maximum: 0.85 and 1.00 respectively). A pattern of isolation by distance
 was evident for sites separated by land. Water appears to act as a
 substantial barrier to gene flow yet sites separated by sea did not
 exhibit isolation by distance. Colletes floralis populations are extremely
 isolated and probably not in regional migration-drift equilibrium.
 GIS-based landscape genetic analysis reveals urban areas as a potential
 and substantial barrier to gene flow. Our results highlight the need for
 urgent site-specific management action to halt the decline of this and
 potentially other rare solitary bees.
description: Genepop file of 12
 populationsGenepop file of 12
 populations used for genetic analysis. Individuals were collected in the
 field. DNA was extracted and analysed by authors (ED &
 TM).All 12
 pops.txt
DOI: 10.5061/dryad.m6f93
title: Data from: Inbreeding ratio and genetic relationships among strains of the Western clawed frog, Xenopus tropicalis

description: The Western clawed frog, Xenopus tropicalis, is a highly promising model
 amphibian, especially in developmental and physiological research, and as
 a tool for understanding disease. It was originally found in the West
 African rainforest belt, and was introduced to the research community in
 the 1990s. The major strains thus far known include the Nigerian and Ivory
 Coast strains. However, due to its short history as an experimental
 animal, the genetic relationship among the various strains has not yet
 been clarified, and establishment of inbred strains has not yet been
 achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima
 University has maintained stocks of multiple X. tropicalis strains and
 conducted consecutive breeding as part of the National BioResource
 Project. In the present study we investigated the inbreeding ratio and
 genetic relationship of four inbred strains at IAB, as well as stocks from
 other institutions, using highly polymorphic microsatellite markers and
 mitochondrial haplotypes. Our results show successive reduction of
 heterozygosity in the genome of the IAB inbred strains. The Ivory Coast
 strains clearly differed from the Nigerian strains genetically, and three
 subgroups were identified within both the Nigerian and Ivory Coast
 strains. It is noteworthy that the Ivory Coast strains have an
 evolutionary divergent genetic background. Our results serve as a guide
 for the most effective use of X. tropicalis strains, and the long-term
 maintenance of multiple strains will contribute to further research
 efforts.
description: genotypic data of seven
 strains of Xenopus tropicalisdata in genepop
 format.genotypicdata_genepop.txtGenotypicdata of eleven strains for sixty SSLP markersGenepop formatgenotypicdata_new_genepop_for_dryad.txt