cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h77tb
title: Data from: An invasive non-native mammal population conserves genetic diversity lost from its native range

description: Invasive, non-native species are one of the major causes of global
 biodiversity loss. Although they are, by definition, successful in their
 non-native range, their populations generally show major reductions in
 their genetic diversity during the demographic bottleneck they experience
 during colonization. By investigating the mitochondrial genetic diversity
 of an invasive non-native species, the stoat Mustela erminea, in New
 Zealand and comparing it to diversity in the species’ native range in
 Great Britain, we reveal the opposite effect. We demonstrate that the New
 Zealand stoat population contains four mitochondrial haplotypes that have
 not been found in the native range. Stoats in Britain rely heavily on
 introduced rabbits Oryctolagus cuniculus as their primary prey and were
 introduced to New Zealand in a misguided attempt at biological control of
 rabbits, which had also been introduced there. While invasive stoats have
 since decimated the New Zealand avifauna, native stoat populations were
 themselves decimated by the introduction to Britain of Myxoma virus as a
 control measure for rabbits. We highlight the irony that while introduced
 species (rabbits) and subsequent biocontrol (myxomatosis) have caused
 population crashes of native stoats, invasive stoats in New Zealand, which
 were also introduced for biological control, now contain more genetic
 haplotypes than their most likely native source.
description: British Stoat Simulation
 R codeThis file contains the
 annotated R code for the mitochondrial genetic drift simulation for stoats
 in Britain since 1883.British_Stoat_Simulation.RNZ Stoat Simulation R codeThis file contains the annotated R code for the mitochondrial genetic drift simulation for the New Zealand stoat population since 1883 - showing the consequences of the founding bottleneck size.NZ_Stoat_Simulation.RStoat d-loop alignmentFASTA file containing the alignment of stoat (Mustela erminea) d-loop sequences from Europe and the haplotypes found in New Zealand (with genbank accession numbers).Stoat_dloop_Alignment.fastaSampling location map and coordinatesThis file contains a map showing the sampling locations and a table providing the coordinates for each location.Sampling location map & coordinates.pdf
DOI: 10.5061/dryad.52qk8
title: Data from: Impact of helminth infections and nutritional constraints on the small intestine microbiota

description: Helminth infections and nutrition can independently alter the composition
 and abundance of the gastrointestinal microbiota, however, their combined
 effect is poorly understood. Here, we used the T. retortaeformis-rabbit
 system to examine how the helminth infection and host restriction from
 coprophagy/ready-to-absorb nutrients affected the duodenal microbiota, and
 how these changes related to the acquired immune response at the site of
 infection. A factorial experiment was performed where the bacterial
 community, its functionality and the immune response were examined in four
 treatments (Infect, Infect+Collar, Control+Collar and Control). Helminths
 reduced the diversity and abundance of the microbiota while the
 combination of parasites and coprophagic restriction led to a more
 diversified and abundant microbiota than infected cases, without
 significantly affecting the intensity of infection. Animals restricted
 from coprophagy and free from parasites exhibited the richest and most
 abundant bacterial community. By forcing the individuals to absorb
 nutrients from less digested food, the coprophagic restriction appears to
 have facilitated the diversity and proliferation of bacteria in the
 duodenum. Changes in the microbiota were more clearly associated with
 changes in the immune response for the infected than the nutrient
 restricted animals. The functional and metabolic characteristics of the
 duodenal microbiota were not significantly different between treatments.
 Overall, infection and diet affect the gut microbiota but their
 interactions and outcome can be complex. These findings can have important
 implications for the development of control measures to helminth
 infections where poor nutrition/malnutrition can also be a concern.
description: Cattadori et al.
 parasites and nutrition on gut microbiota raw filesThis zip folder has all
 the original microbiome, immunity and parasite data used in this study. A
 readMe file is also included that explain each file. Please, contact
 Isabella Cattadori if additional details are needed.Cattadori et al. parasites and
 nutrition on gut microbiota.zip
DOI: 10.5061/dryad.661jb
title: Data from: High levels of genetic structure and striking phenotypic variability in a sexually dimorphic suckermouth catfish from the African Highveld

description: Uncovering biological diversity to more accurately understand diversity
 patterns, and ultimately the processes driving diversification, is
 important not only from an evolutionary perspective but also a
 conservation perspective. This is particularly pertinent in Africa's
 rivers in which overall diversity, as well as how it arose, is poorly
 understood in comparison with lacustrine environments. Here we investigate
 population divergence in the sexually dimorphic suckermouth catfish
 species Chiloglanis anoterus (Crass, 1960) from the African Highveld, in
 which we observe striking variability in exaggerated male caudal fins
 across its range. As this trait is likely to be indirect evidence for
 sexual selection by female choice, a mechanism that has been shown to
 increase species diversity in different taxa, we used an integrated
 approach to test if current diversity in this species is underestimated.
 Results based on phylogenetic inference, population genetics and geometric
 morphometrics indicate that the recognized species C. anoterus represents
 five distinct lineages that may be considered confirmed candidate species.
 We suggest that diversification in these highland catfish has been
 facilitated through geographical isolation in upper river catchments, and
 that sexual selection through female choice has probably driven variation
 in male caudal fin morphology. In contrast to the relatively large range
 size of the currently recognized species (C. anoterus), our findings
 highlight highly restricted ranges of the lineages identified here,
 indicating that these highland habitats may harbour higher levels of
 endemic diversity than previously thought.
description: mtDNA matrix Chiloglanis
 anoterusControl region and CO1
 sequence datamtDNA_Canoterus.nexAFLP matrix Chiloglanis anoterusconfigured for structure inputAFLP-structure-ordered_run4_input_28Aug14.txt
DOI: 10.5061/dryad.274b1
title: Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates

description: We propose a two-step procedure for estimating multiple migration rates in
 an approximate Bayesian computation (ABC) framework, accounting for global
 nuisance parameters. The approach is not limited to migration, but
 generally of interest for inference problems with multiple parameters and
 a modular structure (e.g. independent sets of demes or loci). We condition
 on a known, but complex demographic model of a spatially subdivided
 population, motivated by the reintroduction of Alpine ibex (Capra ibex)
 into Switzerland. In the first step, the global parameters ancestral
 mutation rate and male mating skew have been estimated for the whole
 population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second
 step, we estimate in this study the migration rates independently for
 clusters of demes putatively connected by migration. For large clusters
 (many migration rates), ABC faces the problem of too many summary
 statistics. We therefore assess by simulation if estimation per pair of
 demes is a valid alternative. We find that the trade-off between reduced
 dimensionality for the pairwise estimation on the one hand and lower
 accuracy due to the assumption of pairwise independence on the other
 depends on the number of migration rates to be inferred: the accuracy of
 the pairwise approach increases with the number of parameters, relative to
 the joint estimation approach. To distinguish between low and zero
 migration, we perform ABC-type model comparison between a model with
 migration and one without. Applying the approach to microsatellite data
 from Alpine ibex, we find no evidence for substantial gene flow via
 migration, except for one pair of demes in one direction.
description: Microsatellite genotypes
 of Alpine ibex demes in the Swiss AlpsThis file contains raw
 data (genotypes of 37 microsatellites) of 954 individuals sampled in 31
 Alpine ibex demes in the Swiss Alps. These data were collected and
 processed between 2005 and 2008 by Iris Biebach (iris.biebach@ieu.uzh.ch)
 and collaborators in the lab of Lukas Keller (lukas.keller@ieu.uzh.ch) at
 the University of Zurich, Switzerland. The content of this file has the
 following format: First line: number of loci (37). Lines 2 to n-1 (one
 line per individual): deme_id allele1_of_locus1; allele2_of_locus1;
 allele1_of_locus2; allele2_of_locus2. Names of demes (deme_id; first
 column in lines 2 to n-1) correspond to those given in Table S1 in the
 Supporting Information.genotypes_neutral_Aug10_geneflow_all_casus_37loci.txtCensus sizes of Alpine ibex demes in the Swiss AlpsThis file contains census population sizes of Alpine ibex in the Swiss Alps from 1906 to 2007.census_sizes.csvTransfer by humans of Alpine ibexThis file contains numbers of male and female Alpine ibex transferred by humans between demes during the process of reintroduction into the Swiss Alps. The entries cover the time between 1906 and 1993.transfers.csv
DOI: 10.5061/dryad.63m03
title: Data from: Genes and group membership predict gidgee skink (Egernia stokesii) reproductive pairs

description: Due to their role in mate choice, disease resistance and kin recognition,
 genes of the major histocompatibility complex (MHC) are good candidates
 for investigating genetic-based mate choice. MHC based mate choice is
 context dependent and influenced by many factors including social
 structure. Social structure diversity makes the Egernia group of lizards
 suitable for comparative studies of MHC based mate choice. We investigated
 mate choice in the gidgee skink (Egernia stokesii), a lizard that exhibits
 high levels of social group and spatial stability. Group membership was
 incorporated into tests of the good genes as heterozygosity and compatible
 genes hypotheses for adaptive (MHC) and neutral (microsatellite) genetic
 diversity (n = 47 individuals genotyped). Females were more likely to pair
 with a male with higher MHC diversity and with whom they had a lower
 degree of microsatellite relatedness. Males were more likely to pair with
 a female with higher microsatellite heterozygosity and with whom they
 shared a lower proportion of MHC alleles. Lizards were more likely to mate
 with an individual from within, rather than outside, their social group,
 which confirmed earlier findings for this species and indicated mate
 choice had already largely occurred prior to either social group formation
 or acceptance of an individual into an existing group. Thus, a combination
 of genes and group membership, rather than group membership alone,
 predicted mate choice in this species. This work will contribute to an
 enhanced understanding of squamate group formation and a deeper
 understanding of the evolution of sociality within all vertebrates.
description: MHCgenotypesContains MHC I genotypes for 47 adult E. stokesii and MHC II genotypes for 46 adult E. stokesii, utilised in mate choice tests.MICSATgenotypesMicrosatellite genotype data (six loci) for adult E. stokesii, utilised in mate choice tests.MHCsequencesNucleotide sequences pertaining to 31 MHC I alleles and 5 MHC II alleles used to derive measures in E. stokesii mate choice tests.PairDataData used in GLMM analyses for E. stokesii mate choice tests.
DOI: 10.5281/zenodo.18382020
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Henry Wormsbacher, http://www.wikidata.org/entity/Q137883435. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q137883435
DOI: 10.5061/dryad.fm23dq6
title: Data from: Herbarium specimens reveal increasing herbivory over the past century

description: Predicting how ecological interactions will respond to global change is a
 major challenge. Plants and their associated insect herbivores compose
 much of macroscopic diversity, yet how their interactions have been
 altered by recent environmental change remains underexplored. To address
 this gap, we quantified herbivory on herbarium specimens of four plant
 species with records extending back 112 years. Our study focused on the
 northeastern US, where temperatures have increased rapidly over the last
 few decades. This region also represents a range of urban development, a
 form of global change that has shown variable effects on herbivores in the
 past studies. Herbarium specimens collected in the early 2000s were 23%
 more likely to be damaged by herbivores than those collected in the early
 1900s. Herbivory was greater following warmer winters and at low
 latitudes, suggesting that climate warming may drive increasing insect
 damage over time. In contrast, human population densities were negatively
 associated with herbivore damage. To explore whether changes in insect
 occurrence or abundance might explain shifts in herbivory, we used insect
 observational records to build climate occupancy models for lepidopteran
 herbivores (butterflies and moths) of our focal plant species. These
 models show that higher winter temperatures were associated with higher
 probability of insect herbivore presence, while urbanization was
 associated with reduced probability of herbivore presence, supporting a
 link between insect herbivore occurrence and herbivory mediated through
 environment. Synthesis. Using a temporal record of plant herbivory that
 spans over a century, we show that both temperature and urbanization
 influence insect damage to plants, but in very different ways. Our results
 indicate that damage to plants by insect herbivores will likely continue
 to increase through time in the northeastern US as global temperatures
 rise, but that urbanization may disrupt local effects of winter warming on
 herbivory by excluding certain herbivores. These changes may scale to
 shape ecosystem processes that are driven by herbivory, including plant
 productivity.
description: Meinekeetal_2018_JOE_DryadsubmissionEach row in this file represents an herbarium specimen. For each specimen, associated herbivory data and climatic metadata are included.Meinekeetal._DRYAD_JOE_2018.xlsx
DOI: 10.5061/dryad.vt84k
title: Data from: Direct and indirect impacts of climate change on microbial and biocrust communities alter the resistance of the N cycle in a semiarid grassland

description: 1. Climate change will raise temperatures and modify precipitation
 patterns in drylands worldwide, affecting their structure and functioning.
 Despite the recognized importance of soil communities dominated by mosses,
 lichens and cyanobacteria (biocrusts) as a driver of nutrient cycling in
 drylands, little is known on how biocrusts will modulate the resistance
 (i.e., the amount of change caused by a disturbance) of the N cycle in
 response to climate change. 2. Here, we evaluate how warming (ambient vs.
 ~2.5ºC increase), rainfall exclusion (ambient vs. ~30% reduction of total
 annual rainfall) and biocrust cover (incipient vs. well-developed
 biocrusts) affect multiple variables linked to soil N availability
 (inorganic and organic N and potential net N mineralization rate) and its
 resistance to climate change during four years in a field experiment. We
 also evaluate how climate change-induced modifications in biocrust and
 microbial communities indirectly affect such resistance. 3. Biocrusts
 promoted the resistance of soil N availability regardless of the climatic
 conditions considered. However, the dynamics of N availability diverged
 progressively from their original conditions with warming and/or rainfall
 exclusion, as both treatments enhanced N availability and promoted the
 dominance of inorganic over organic N. In addition, the increase of
 fungal: bacterial ratio and the decrease of biocrust cover observed under
 warming had a negative indirect effect on the resistance of N cycle
 variables. 4. Synthesis. Our results indicate that climate change will
 have negative direct and indirect (i.e. through changes in biocrust and
 microbial communities) impacts on the resistance of the N cycle in dryland
 soils. While biocrusts can play an important role slowing down the impacts
 of climate change on the N cycle due to their positive and continued
 effects on the resistance of multiple variables from the N cycle, such
 change will progressively alter N cycling in biocrust-dominated
 ecosystems, enhancing both N availability and inorganic N dominance.
description: DatasetThere are three spreadsheets with data. The spreadsheet "Soil_dataset" contains the raw soil data, as well as the values of the RS index derived from them. The spreadsheet "IEMs_dataset" contains the raw amonium and nitrate values obtained from ion-exchange membranes, as well as the values of the RS index derived from them. The spreadsheet "SEM_dataset" contains the data used in the SEM models. After each data spreadsheet there is a spreadshet with the associated metadata, where a description of all the variables and units can be found.
DOI: 10.5281/zenodo.18371163
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Henry Wormsbacher, http://www.wikidata.org/entity/Q137883435. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q137883435
DOI: 10.5061/dryad.b73c68f
title: Data from: Trajectories of motor abnormalities in milder phenotypes of ataxia telangiectasia

description: Objective: To describe and classify the neurological trajectories in
 patients with mild neurological forms of ataxia telangiectasia (A-T) from
 the Dutch A-T cohort, combined with patients reported in the literature.
 Methods: Clinical, genetic and laboratory data of 14 A-T patients with
 mild neurological phenotypes from the Dutch cohort were analyzed and
 combined with corresponding data from the literature. A mild neurological
 phenotype was defined by a later onset, non-ataxia presenting or dominant
 feature, or slower progression compared to the classical A-T phenotype.
 Neurological trajectories were classified based on age of onset,
 presenting feature and follow-up data. Results: 105 patients were included
 in the study. Neurological trajectories were categorized into six groups:
 patients with childhood-onset extrapyramidal features with cerebellar
 symptoms developing later (group 1; 18 patients), childhood-onset
 cerebellar symptoms, with extrapyramidal features developing later (group
 2; 35 patients), childhood to adolescence-onset dystonia, without
 cerebellar symptoms (group 3; 23 patients), childhood to adolescence-onset
 isolated cerebellar symptoms (group 4; 22 patients), childhood to
 adult-onset prominent muscle weakness (group 5; 2 patients), and patients
 with adult-onset extrapyramidal features, with anterior horn cell disease
 arising subsequently (group 6; 5 patients). Conclusions: This systematic
 study of the different motor abnormalities and their course over time in
 A-T patients with mild phenotypes, enabled us to recognize six essentially
 different phenotypic patterns. Awareness of these different trajectories
 of motor abnormalities in milder forms of A-T will contribute to a
 reduction of diagnostic delay in this severe multisystem disorder.
description: Table e-1: Clinical and
 laboratory data of 105 A-T patients with mild phenotypes from the Dutch
 cohort and literature.Table
 e-1_revision.docxTable e-2: Serum
 alpha-fetoprotein levels of patients with mild A-T.Table
 e-2_revision.docxTable e-3: Genetic data
 of A-T patients with mild phenotypes from the Dutch cohort and
 literature.Table
 e-3_revision.docxTable e-4: First
 diagnoses of patients with mild forms of A-T.Table e-4_revision__no
 changes.docx
DOI: 10.5061/dryad.86f1m6g
title: Data from: Refining eligibility criteria for amyotrophic lateral sclerosis clinical trials

description: Objective: To assess the effect of eligibility criteria on exclusion
 rates, generalizability and outcome heterogeneity in ALS clinical trials,
 and to assess the value of a risk-based inclusion criterion. Methods: A
 literature search was performed to summarize eligibility criteria of
 clinical trials. The extracted criteria were applied to an incidence
 cohort of 2,904 consecutive ALS patients to quantify their effects on
 generalizability and outcome heterogeneity. We evaluated the effect of a
 risk-based selection approach on trial design using a personalized
 survival prediction model. Results: We identified 38 trials: enrolled
 patients reveal a large variability between trials of all patient
 characteristics (p &lt; 0.001), except for the proportion of males (p
 = 0.21). Exclusion rates varied widely (from 14% to 95%; mean 59.8% (95%
 CI 52.6-66.7)). Stratification of the eligible populations into prognostic
 subgroups showed that eligibility criteria lead to exclusion of patients
 in all prognostic groups. Eligibility criteria neither reduce
 heterogeneity in survival time (from 22.0 to 20.5 months, p = 0.09) nor
 affect between-patient variability in functional decline (from 0.62 to
 0.65, p = 0.25). In none of the 38 trials were the eligibility criteria
 found to be more efficient than the prediction model in optimizing sample
 size and eligibility rate. Conclusions: The majority of ALS patients are
 excluded from trial participation, which questions the generalizability of
 trial results. Importantly, eligibility criteria only minimally improve
 homogeneity in trial endpoints. An individualized risk-based criterion
 could be used to balance the gains in trial design and loss in
 generalizability.
description: Supplemental
 dataData
 supplementSupplement_v20.docx