cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sc983fc
title: Data from: Habitat segregation between brown bears and gray wolves in a human-dominated landscape

description: Identifying how sympatric species belonging to the same guild coexist is a
 major question of community ecology and conservation. Habitat segregation
 between two species might help reduce the effects of interspecific
 competition and apex predators are of special interest in this context,
 because their interactions can have consequences for lower trophic levels.
 However, habitat segregation between sympatric large carnivores has seldom
 been studied. Based on monitoring of 53 brown bears (Ursus arctos) and 7
 sympatric adult gray wolves (Canis lupus) equipped with GPS collars in
 Sweden, we analyzed the degree of interspecific segregation in habitat
 selection within their home ranges in both late winter and spring, when
 their diets overlap the most. We used the K-select method, a multivariate
 approach that relies on the concept of ecological niche, and randomization
 methods to quantify habitat segregation between bears and wolves. Habitat
 segregation between bears and wolves was greater than expected by chance.
 Wolves tended to select for moose occurrence, young forests, and rugged
 terrain more than bears, which likely reflects the different requirements
 of an omnivore (bear) and an obligate carnivore (wolf). However, both
 species generally avoided human-related habitats during daytime.
 Disentangling the mechanisms that can drive interspecific interactions at
 different spatial scales is essential for understanding how sympatric
 large carnivores occur and coexist in human-dominated landscapes, and how
 coexistence may affect lower trophic levels. The individual variation in
 habitat selection detected in our study may be a relevant mechanism to
 overcome intraguild competition and facilitate coexistence.
description: dataData from Milleret et
 al. Ecology and Evolution (Habitat segregation between brown bears and
 gray wolves in a human-dominated landscape)
DOI: 10.5061/dryad.j9m4cm6
title: Data from: Highest plasticity of carbon concentrating mechanisms in earliest evolved phytoplankton

description: Phytoplankton photosynthesis strongly relies on the operation of
 carbon‐concentrating mechanisms (CCMs) to accumulate CO2 around their
 carboxylating enzyme ribulose‐1,5‐bisphosphate carboxylase/oxygenase
 (RuBisCO). Earlier evolved phytoplankton groups were shown to exhibit
 higher CCM activities to compensate for their RuBisCO with low CO2
 specificities. Here, we tested whether earlier evolved phytoplankton
 groups also exhibit a higher CCM plasticity. To this end, we collected
 data from literature and applied a Bayesian linear meta‐analytic model.
 Our results show that with elevated pCO2, photosynthetic CO2 affinities
 decreased strongest and most consistent for the earlier evolved groups,
 i.e., cyanobacteria and dinoflagellates, while CO2‐dependent changes in
 affinities for haptophytes and diatoms were smaller and less consistent.
 In addition, responses of maximum photosynthetic rates toward elevated
 pCO2 were generally small and inconsistent across species. Our results
 demonstrate that phytoplankton groups with an earlier origin possess a
 high CCM plasticity, whereas more recently evolved groups do not, which
 likely results from evolved differences in the CO2 specificity of RuBisCO.
description: R script for a Bayesian
 linear meta-analytic modelThis file provides the R
 script used in the publication "Highest plasticity of carbon
 concentrating mechanisms in earliest evolved phytoplankton" by Dedmer
 Van de Waal, Karen Brandenburg, Joost Keuskamp, Scarlett Trimborn,
 Sebastian Rokitta, Sven Kranz, Björn Rost. For details we refer to the
 publication.final5.RData on CCM regulation of marine phytoplankton to elevated pCO2mydata3.csv
DOI: 10.5061/dryad.8570
title: Data from: A phylogeographic, demographic and historical analysis of the short-tailed pit viper (Gloydius brevicaudus): evidence for early divergence and late expansion during the Pleistocene

description: The impact of quaternary glaciation in eastern China on local fanua and
 flora has been a topic of considerable interest. We used mitochondrial DNA
 (mtDNA) sequence data and coalescent simulations to test two general
 biogeographic hypothesis related to the effects of Pleistocene climatic
 fluctuations for a widespread ophidian species (Gloydius brevicaudus) in
 eastern China and Korean Peninsula. The phylogenetic analysis revealed
 three major lineages, the southeast Coastal, Yangtze and North Lineages.
 The latter two are closely related and jointly form a continental lineage.
 Divergence dating and coalescent simulations indicate a Late Pliocene to
 Early Pleistocene divergence between lineages from the southeast coast and
 continental interior, followed by a mid-to-late Pleistocene divergence
 between lineages from the north and the middle–lower Yangtze Valley across
 East China, suggesting that all these lineages predated the last glacial
 maximum. An overlapping range between the two lineages within the
 continental lineage and a secondary contact associated with ecological
 transition zones on the margins of the North China Plain were also
 observed. These results show that vicariance patterns dominated the
 history of G. brevicaudus. Though the climatic events of the Pleistocene
 have had a marked effect on the historical distribution and intra-specific
 divergence of reptiles in China, coalescent and non-coalescent demographic
 analyses indicate that all lineages of G. brevicaudus seem not to have
 been adversely affected by glacial cycles during the Late Pleistocene,
 presumably because of an increase in the amount of climatically mild
 habitat in East Asia due to a decline in elevation and the development of
 monsoons since the Mid-End Pleistocene.
description: sequinThis Zip file includes
 ND4 and cyt-b sequences created using sequin. The text file shows the
 Genbank Nos. of each sequence.
DOI: 10.5061/dryad.f8j0n
title: Data from: Evolution of pre-copulatory and post-copulatory strategies of inbreeding avoidance and associated polyandry

description: Inbreeding depression is widely hypothesised to drive adaptive evolution
 of pre-copulatory and post-copulatory mechanisms of inbreeding avoidance,
 which in turn are hypothesised to affect evolution of polyandry (i.e.,
 female multiple mating). However, surprisingly little theory or modelling
 critically examines selection for pre-copulatory or post-copulatory
 inbreeding avoidance, or both strategies, given evolutionary constraints
 and direct costs, or examines how evolution of inbreeding avoidance
 strategies might feed back to affect evolution of polyandry. Selection for
 post-copulatory inbreeding avoidance, but not for pre-copulatory
 inbreeding avoidance, requires polyandry, while interactions between
 pre-copulatory and post-copulatory inbreeding avoidance might cause
 functional redundancy (i.e., ‘degeneracy’) potentially generating complex
 evolutionary dynamics among inbreeding strategies and polyandry. We used
 individual-based modelling to quantify evolution of interacting
 pre-copulatory and post-copulatory inbreeding avoidance and associated
 polyandry given strong inbreeding depression and different evolutionary
 constraints and direct costs. We found that evolution of post-copulatory
 inbreeding avoidance increased selection for initially rare polyandry, and
 that evolution of a costly inbreeding avoidance strategy became negligible
 over time given a lower cost alternative strategy. Further, fixed
 pre-copulatory inbreeding avoidance often completely precluded evolution
 of polyandry and hence post-copulatory inbreeding avoidance, but fixed
 post-copulatory inbreeding avoidance did not preclude evolution of
 pre-copulatory inbreeding avoidance. Evolution of inbreeding avoidance
 phenotypes and associated polyandry are therefore affected by evolutionary
 feedbacks and degeneracy. All else being equal, evolution of
 pre-copulatory inbreeding avoidance and resulting low polyandry is more
 likely when post-copulatory inbreeding avoidance is precluded or costly,
 and evolution of post-copulatory inbreeding avoidance greatly facilitates
 evolution of costly polyandry.
description: pre_post_cop_code.tarThis compressed directory contains the 45 files needed to compile the code underlying the paper and run all simulations. Parameter values for simulations are set in the PolyIn.c file, which outputs results in three separate TXT files. The output TXT files can be used in the analysis.R file to recreate all analyses and figures from the paper. This code is also publicly available, with additional documentation, on Brad Duthie's GitHub repository: https://github.com/bradduthie/pre_post_cop
DOI: 10.5061/dryad.4kb77
title: Data from: Reverse evolution: selection against costly resistance in disease-free microcosm populations of Paramecium caudatum

description: Evolutionary costs of parasite resistance arise if genes conferring
 resistance reduce fitness in the absence of parasites. Thus,
 parasite-mediated selection may lead to increased resistance and a
 correlated decrease in fitness, whereas relaxed parasite-mediated
 selection may lead to reverse evolution of increased fitness and a
 correlated decrease in resistance. We tested this idea in experimental
 populations of the protozoan Paramecium caudatum and the parasitic
 bacterium Holospora undulata. After 8 years, resistance to infection and
 asexual reproduction were compared among paramecia from (i) infected
 populations, (ii) uninfected naive populations and (iii) previously
 infected, parasite-free (recovered) populations. Paramecia from infected
 populations were more resistant (+12%), but had lower reproduction (-15%)
 than naive paramecia, indicating an evolutionary trade-off between
 resistance and fitness. Recovered populations showed similar reproduction
 to naive populations; however, resistance of recently (&lt;3 years)
 recovered populations was similar to paramecia from infected populations,
 while longer (&gt;3 years) recovered populations were as susceptible
 as naive populations. This suggests a weak, convex trade-off between
 resistance and fitness, allowing recovery of fitness, without complete
 loss of resistance, favouring the maintenance of a generalist strategy of
 intermediate fitness and resistance. Our results indicate that
 (co)evolution with parasites can leave a genetic signature in disease-free
 populations.
description: reproductive_ratedata file for analysis of reproductive rate; text file with column headers; further details see Materials and methods in the paperresistancedata file for analysis of resistance (= proportion infected individuals); text file with column headers; further details see Materials and methods in the papercorrelation_reproduction_resistancedata file for analysis of correlation between resistance and reproductive rate; text file with column headers; further details see Materials and methods in the paper
DOI: 10.5061/dryad.p1s20
title: Data from: Association between inbreeding depression and floral traits in a generalist-pollinated plant

description: Individual variation in the magnitude of inbreeding depression (ID) in
 plants and its association with phenotypic traits may have important
 consequences for mating system evolution. This association has been
 investigated only scarcely, and always considering traits functionally
 related to autogamy. Here, we explore the association between individual
 variation in ID and plant traits associated with pollinator attractiveness
 (related to plant size, corolla size and corolla shape) in two populations
 of Erysimum mediohispanicum (Brassicaceae). ID was calculated along the
 entire life cycle of the plants. In addition, we also explored the
 relationship between phenotypic traits and the individual levels of
 heterozygosity. We found significant associations between ID and corolla
 diameter and stalk height, being taller plants with larger corollas those
 undergoing a lower intensity of ID. Furthermore, we found a negative
 relationship between corolla diameter and heterozygosity, suggesting that
 plants with large flowers have purged their genetic load. Finally, we
 found a significant effect of corolla diameter on the intrapopulation
 genetic structure. All these findings suggest that plants with large
 flowers have secularly suffered frequent inbreeding in the study
 populations. Because corolla diameter is a trait frequently selected by
 pollinators in E. mediohispanicum, we believe that the observed
 relationship between this trait and ID could be mediated by pollinators,
 probably throughout an increasing in biparental inbreeding, geitonogamy or
 autogamy.
description: ID_PhenIndividual inbreeding depression values and their phenotypes associated to each plant.Homozi_EmIndividual homozygous values and their phenotypes associated in E. mediohispanicum
DOI: 10.5061/dryad.vn269
title: Data from: Investigation of the effect of cochlear implant electrode length on speech comprehension in quiet and noise compared with the results with users of electro-acoustic-stimulation, a retrospective analysis

description: Objectives: This investigation evaluated the effect of cochlear implant
 (CI) electrode length on speech comprehension in quiet and noise and
 compare the results with those of EAS users. Methods: 91 adults with some
 degree of residual hearing were implanted with a FLEX20, FLEX24, or FLEX28
 electrode. Some subjects were postoperative electric-acoustic-stimulation
 (EAS) users; the other subjects were in the groups of electric
 stimulation-only (ES-only). Speech perception was tested in quiet and
 noise at 3 and 6 months of ES or EAS use. Speech comprehension results
 were analyzed and correlated to electrode length. Results: While the
 FLEX20 ES and FLEX24 ES groups were still in their learning phase between
 the 3 to 6 months interval, the FLEX28 ES group was already reaching a
 performance plateau at the three months appointment yielding remarkably
 high test scores. EAS subjects using FLEX20 or FLEX24 electrodes outscored
 ES-only subjects with the same short electrodes on all 3 tests at each
 interval, reaching significance with FLEX20 ES and FLEX24 ES subjects on
 all 3 tests at the 3-months interval and on 2 tests at the 6- months
 interval. Amongst ES-only subjects at the 3- months interval, FLEX28 ES
 subjects significantly outscored FLEX20 ES subjects on all 3 tests and the
 FLEX24 ES subjects on 2 tests. At the-6 months interval, FLEX28 ES
 subjects still exceeded the other ES-only subjects although the difference
 did not reach significance. Conclusions: Among ES-only users, the FLEX28
 ES users had the best speech comprehension scores, at the 3- months
 appointment and tendentially at the 6 months appointment. EAS users showed
 significantly better speech comprehension results compared to ES-only
 users with the same short electrodes.
description: FLEX_row_data_anonym_englishEvery patient got an ID number, all dates were reduced to years, ages were aggregated and we removed data which are not necessary for analysis.
DOI: 10.15468/dl.8y8fuv
title: Occurrence Download

description: A dataset containing 2129 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Actinidia chinensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2129 records from 108 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001102-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d3m1j
title: Data from: High adult mortality in disease-challenged frog populations increases vulnerability to drought

description: Pathogen emergence can drive major changes in host population demography,
 with implications for population dynamics and sensitivity to environmental
 fluctuations. The amphibian disease chytridiomycosis, caused by infection
 with the fungal pathogen Batrachochytrium dendrobatidis (Bd), is
 implicated in the severe decline of over 200 amphibian species. In species
 that have declined but not become extinct, Bd persists and can cause
 substantial ongoing mortality. High rates of mortality associated with Bd
 may drive major changes in host demography, but this process is poorly
 understood. Here, we compared population age structure of Bd-infected
 populations, Bd-free populations and museum specimens collected prior to
 Bd emergence for the endangered Australian frog, Litoria verreauxii alpina
 (alpine tree frog). We then used population simulations to investigate how
 pathogen-associated demographic shifts affect the ability of populations
 to persist in stochastic environments. We found that Bd-infected
 populations have a severely truncated age structure associated with very
 high rates of annual adult mortality. Near-complete annual adult turnover
 in Bd-infected populations means that individuals breed once, compared
 with Bd-free populations where adults may breed across multiple years. Our
 simulations showed that truncated age structure erodes the capacity of
 populations to withstand periodic recruitment failure; a common challenge
 for species reproducing in uncertain environments. We document previously
 undescribed demographic shifts associated with a globally emerging
 pathogen and demonstrate how these shifts alter host ecology. Truncation
 of age structure associated with Bd effectively reduces host niche width
 and can help explain the contraction of L. v. alpina to perennial
 waterbodies where the risk of drought-induced recruitment failure is low.
 Reduced capacity to tolerate other sources of mortality may explain
 variation in decline severity among other chytridiomycosis-challenged
 species and highlights the potential to mitigate disease impacts through
 minimizing other sources of mortality.
description: Individual frog
 measurement dataThis file contains
 measurement data for individual frogs, along with information on
 population origin and disease status for populations and individuals.
 Museum registration details refer to specimen I.D. for the Museum
 Victoria, Australia.
DOI: 10.5061/dryad.37ns0
title: Data from: Abiotic environmental variation drives virulence evolution in a fish host-parasite geographic mosaic

description: 1.Parasite virulence varies greatly. Theory predicts that this arises from
 parasites optimising a trade-off between the mortality they inflict on
 current hosts, and their transmission to future hosts. The effect of the
 environment on this coevolution is rarely considered. 2.Geographic mosaics
 are fertile systems for studying coevolution, but again, the diversity of
 outcomes is often assumed to result from co-evolutionary dynamism, rather
 than being moulded by the environment. 3.Here we quantify variation in
 virulence among lakes in a geographic mosaic of coevolution between a
 trematode ectoparasite (Gyrodactylus arcuatus) and its three-spined
 stickleback (Gasterosteus aculeatus) host. 4.Virulence varies greatly in
 this system, and parasites are generally locally adapted to their hosts.
 5.Parasites are also locally adapted to the water in their own lake, and
 virulence is strongly related to lake pH, the dominant axis of abiotic
 environmental variation in this system. 6.These results suggest that the
 evolution of virulence can be substantially affected by the abiotic
 environment, which has important implications for understanding
 coevolution. There are also implications for the evolutionary management
 of disease e.g. ectoparasites in aquaculture, the impacts of which might
 be expected to reduce given ongoing acidification of aquatic ecosystems.
description: Gasterosteus and
 Gyrodactylus: results of artificial infection experiments showing local
 adaptationThe file contains the
 results from five experiments. Experiments 1 to 4 show the outcome of
 artificial infections of stickleback hosts from different populations
 (lakes) with Gyrodactylus parasites from different lakes. Data shown are
 the populations of origin of the host and parasite, the sex, length (mm)
 and family (where applicable) of hosts, and the total number of parasites
 counted on the host over the course of the experiment. Different
 experiments are for different combinations of host and parasite
 populations, and had slightly different experimental conditions (e.g.
 number of parasites used to start an infection, and frequency of counts).
 Experiment 5 shows the results (in hours until death) of an experiment in
 which parasites from different lakes (and detached from hosts), were
 reciprocally exposed to water from the same lakes.Func Ecol DRYAD
 data.xlsx
DOI: 10.5061/dryad.pg034
title: Data from: Small-scale intraspecific patterns of adaptive immunogenetic polymorphisms and neutral variation in Lake Superior lake trout

description: Many fishes express high levels of intraspecific variability, often linked
 to resource partitioning. Several studies show that a species’
 evolutionary trajectory of adaptive divergence can undergo reversals
 caused by changes in its environment. Such a reversal in neutral genetic
 and morphological variation among lake trout Salvelinus namaycush
 ecomorphs appears to be underway in Lake Superior. However, a water depth
 gradient in neutral genetic divergence was found to be associated with
 intraspecific diversity in the lake. To investigate patterns of adaptive
 immunogenetic variation among lake trout ecomorphs, we used Illumina
 high-throughput sequencing. The population’s genetic structure of the
 major histocompatibility complex (MHC Class IIβ exon 2) and 18
 microsatellite loci were compared to disentangle neutral and selective
 processes at a small geographic scale. Both MHC and microsatellite
 variation were partitioned more by water depth stratum than by ecomorph.
 Several metrics showed strong clustering by water depth in MHC alleles,
 but not microsatellites. We report a 75% increase in the number of MHC
 alleles shared between the predominant shallow and deep water ecomorphs
 since a previous lake trout MHC study at the same locale (c. 1990s data).
 This result is consistent with the reverse speciation hypothesis, although
 adaptive MHC polymorphisms persist along an ecological gradient. Finally,
 results suggested that the lake trout have multiple copies of the MHC II
 locus consistent with a historic genomic duplication event. Our findings
 indicated that conservation approaches for this species could focus on
 managing various ecological habitats by depth, in addition to regulating
 the fisheries specific to ecomorphs.
description: Genepop_MHC_DominantBinary_DryadGenepop_Msats_Dryad