cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k5786
title: Data from: The population biology of fungal invasions

description: Fungal invasions are increasingly recognized as a significant component of
 global changes, threatening ecosystem health and damaging food production.
 Invasive fungi also provide excellent models to evaluate the generality of
 results based on other eukaryotes. We first consider here the reasons why
 fungal invasions have long been overlooked: they tend to be inconspicuous,
 and inappropriate methods have been used for species recognition. We then
 review the information available on the patterns and mechanisms of fungal
 invasions. We examine the biological features underlying invasion success
 of certain fungal species. We review population structure analyses,
 revealing native source populations and strengths of bottlenecks. We
 highlight the documented ecological and evolutionary changes in invaded
 regions, including adaptation to temperature, increased virulence,
 hybridization, shifts to clonality and association with novel hosts. We
 discuss how the huge census size of most fungi allows adaptation even in
 bottlenecked, clonal invaders. We also present new analyses of the
 invasion of the anther-smut pathogen on white campion in North America, as
 a case study illustrating how an accurate knowledge of species limits and
 phylogeography of fungal populations can be used to decipher the origin of
 invasions. This case study shows that successful invasions can occur even
 when life history traits are particularly unfavourable to long-distance
 dispersal and even with a strong bottleneck. We conclude that fungal
 invasions are valuable models to contribute to our view of biological
 invasions, in particular by providing insights into the traits as well as
 ecological and evolutionary processes allowing successful introductions.
description: dataset_gladieux_et_al_population_biology_fungal_invasionsMultilocus microsatellite genotypes with GPS data, for all Microbotryum lychnidis-dioicae samples
DOI: 10.5061/dryad.kb175
title: Data from: Dispersal constraints for the conservation of the grassland herb Thymus pulegioides L. in a highly fragmented agricultural landscape

description: Species-rich grassland communities are one of the most important habitats
 for biodiversity and of high conservation priority in Europe. Restoration
 actions are mainly focused on the improvement of abiotic conditions, such
 as nutrient depletion techniques, and are generally based on the
 assumption that the target community will re-establish at the restored
 site when the target species exist in the neighborhood. Information on the
 contemporary seed-dispersal range is therefore crucial to develop
 effective conservation measures. Here, we investigated the contemporary
 long-distance seed dispersal and genetic structure of the grassland herb
 Thymus pulegioides in an intensively managed agricultural landscape in
 Flanders (Northern Belgium). Assignment tests based on amplified fragment
 length polymorphisms revealed very low levels of effective seed dispersal
 between populations although seed availability and seed viability was not
 a limiting factor. The process of fragmentation has resulted in a high
 population differentiation and without further incoming gene flow the
 remnant populations are prone to further genetic erosion and perhaps
 extinction. Our findings illustrate that restoring suitable abiotic
 habitat conditions in the neighborhood of existing populations does likely
 not guarantee colonization for this grassland specialist. For the survival
 of the species, existing populations should be functionally connected and
 seed addition may be necessary for successful conservation to overcome
 dispersal-limitation.
description: Thymus pulegioides AFLP
 dataThe file Thymus
 pulegioides AFLP data.csv includes the binary matrix of AFLP band presence
 (1) – absence (0) for 155 AFLP-markers and 287 individuals of Thymus
 pulegioides sampled in 19 populations in central-east Flanders (Northern
 Belgium). The matrix also include the spatial coordinates of each sampled
 population, given in the two last columns. The markers are numbered M1 to
 M155.
DOI: 10.5061/dryad.r6ng71d4
title: Data from: Peptidomics-based phylogeny and biogeography of Mantophasmatodea (Hexapoda)

description: The insect order Mantophasmatodea was described in 2002. Prior to that
 time, several generations of entomologists had assumed that all major
 insect taxa were known; thus, its description was a sensation for
 zoologists. Since then, a surprising abundance and species diversity of
 this taxon have been found, particularly in the winter rainfall region of
 South Africa. To learn more about the evolutionary lineages, speciation,
 and biogeography of Mantophasmatodea, we applied an unusual peptidomics
 approach. We collected specimens of almost all known and novel taxa of
 these insects, developed methods for immediate sample preparation in the
 field, introduced peptide mass fingerprints for the unambiguous
 identification of taxa, and subsequently analyzed the most extensive
 dataset on peptide hormones ever compiled for insect taxa. To account for
 intraspecific variation, we analyzed several individuals per putative
 species. Increased taxon sampling was preferred over a further increase in
 the number of characters to optimize the accuracy of phylogenetic
 analyses. The large dataset made it possible to test the validity of using
 neuropeptide sequences, which co-evolve with their respective receptors,
 to analyze phylogenetic relationships among closely related taxa.
 Altogether, the data from 71 populations of Mantophasmatodea were
 sufficient to clearly separate the major clades of Mantophasmatodea,
 including previously undescribed taxa such as Pachyphasma, Striatophasma,
 and Austrophasmatidae gen. et sp. nov. ‘RV’. The data confirm the
 monophyly of Austrophasmatidae and show a relatively recent and extensive
 radiation in the winter rainfall region of South Africa but also suggest
 that the species-level diversification of Namibian Mantophasma is less
 marked than previously thought. We discuss the biogeographical and
 ecological factors that may have resulted in different regional patterns
 of endemism and species diversity in Mantophasmatodea. The unique
 development of the neuroendocrine capa-neurons in the ventral nervous
 system is described as synapomorphy of Mantophasmatodea + Grylloblattodea
 and is a further argument for a close relationship between these insect
 taxa.
description: Predel_SystBiol_supplMat1Predel_SystBiol_supplMat2
DOI: 10.5061/dryad.sr2hd7md
title: Data from: Species and phylogenetic nomenclature

description: The motivation for the development of phylogenetic nomenclature
 (originally called “phylogenetic taxonomy”) was to allow biological
 classification (or “systematization”) to represent phylogenetic
 relationships, and to embody important principles such as “the
 untenability of paraphyletic groups” (de Queiroz and Gauthier 1990). From
 this starting point de Queiroz and Gauthier developed a creative new basis
 for systematization in which the entities are not ranked taxa but clades
 (de Queiroz and Gauthier 1990, 1992, 1994; de Queiroz 1992, 1994). Instead
 of attaching names to taxa by reference to a type and a rank, as in
 traditional biological nomenclature, phylogenetic nomenclature labels taxa
 by the use of multiple “specifiers” – specimens or apomorphic traits that
 unambiguously refer to a particular monophyletic taxon. The subsequent
 development of phylogenetic nomenclature included formation of a scholarly
 society, the International Society for Phylogenetic Nomenclature, and
 development of a formal Code, the PhyloCode (http://www.phylocode.org),
 that is now in final preparation for publication at University of
 California Press. The hope for many phylogenetic systematists was for a
 new system of nomenclature that would firmly connect taxonomy to phylogeny
 and would allow for more stable ways to name the many significant clades
 that make up the Tree of Life. However, a major challenge for the
 development of the PhyloCode has been the treatment of species. We argue
 in this paper that the approach taken to species in the PhyloCode is at
 odds with the motivations that drove many to support phylogenetic
 nomenclature and that these problems should be fixed before the PhyloCode
 is published and officially implemented.
description: Cellinese_Appendix1This document represents the proposal for changes to the PhyloCode, with respect to species. It was submitted on October 5, 2011 to the Committee of Phylogenetic Nomenclature, International Society for Phylogenetic Nomenclature.
DOI: 10.5061/dryad.118ph65
title: Data from: Understanding co-occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM)

description: A primary goal of ecology is to understand the fundamental processes
 underlying the geographic distributions of species. Two major strands of
 ecology – habitat modelling and community ecology – approach this problem
 differently. Habitat modellers often use species distribution models
 (SDMs) to quantify the relationship between species’ and their
 environments without considering potential biotic interactions. Community
 ecologists, on the other hand, tend to focus on biotic interactions and,
 in observational studies, use co‐occurrence patterns to identify
 ecological processes. Here, we describe a joint species distribution model
 (JSDM) that integrates these distinct observational approaches by
 incorporating species co‐occurrence data into a SDM. JSDMs estimate
 distributions of multiple species simultaneously and allow decomposition
 of species co‐occurrence patterns into components describing shared
 environmental responses and residual patterns of co‐occurrence. We provide
 a general description of the model, a tutorial and code for fitting the
 model in R. We demonstrate this modelling approach using two case studies:
 frogs and eucalypt trees in Victoria, Australia. Overall, shared
 environmental correlations were stronger than residual correlations for
 both frogs and eucalypts, but there were cases of strong residual
 correlation. Frog species generally had positive residual correlations,
 possibly due to the fact these species occurred in similar habitats that
 were not fully described by the environmental variables included in the
 JSDM. Eucalypt species that interbreed had similar environmental responses
 but had negative residual co‐occurrence. One explanation is that
 interbreeding species may not form stable assemblages despite having
 similar environmental affinities. Environmental and residual correlations
 estimated from JSDMs can help indicate whether co‐occurrence is driven by
 shared environmental responses or other ecological or evolutionary process
 (e.g. biotic interactions), or if important predictor variables are
 missing. JSDMs take into account the fact that distributions of species
 might be related to each other and thus overcome a major limitation of
 modelling species distributions independently.
description: Eucalypt Grampians Site
 by Environment OccurrenceThis file contains site
 data with environmental variables and occurrence of each eucalypt species.
 This is the original species set, of which some species were aggregated
 for the analyses in Pollock et al. 2014 (see methods).SiteEnviroOccurData.csvEucalypt species traits GrampiansThis file contains species-level traitsEucSpeciesTraits.csv
DOI: 10.5061/dryad.m574rq8
title: Data from: Good parenting may not increase reproductive success under environmental extremes

description: For species exhibiting parental care, the way in which parents adjust care
 behaviour to compensate for environmental change potentially influences
 offspring survival and, ultimately, population viability. Using the
 three-spined stickleback (Gasterosteus aculeatus) – a species in which
 males provide parental care by building and tending a nest and fanning the
 eggs – we examined how low dissolved oxygen (DO) levels affect paternal
 care, embryo development and survival. While levels of nest tending were
 unaffected by DO level, we found that larger males fanned their embryos
 more under low oxygen conditions. This resulted in faster rates of embryo
 development within the clutches of these larger males, but reduced embryo
 survival at 7d post-fertilisation compared to clutches of smaller males.
 Our results suggest that although parents may attempt to compensate for
 environmental change via alterations to care behaviour, their ability to
 do so can be dependent on parental phenotype. This sets up the potential
 for oxygen levels to act on the strength and direction of selection within
 populations. We discuss possible explanations for the surprising result
 that supposedly adaptive changes in care behaviour by large males (i.e.
 increased fanning) led to reduced embryo survival at 7d
 post-fertilisation, and whether, as a consequence, acute environmental
 conditions may have the potential to overwhelm selection on sexual traits.
description: DATA from Fox et al
 (2018) Good parenting may not increase reproductive success under
 environmental extremesExcel file containing
 raw data underlying the analyses conducted in Fox et al (2018) Good
 parenting may not increase reproductive success under environmental
 extremesDATA_Fox et
 al_Environmentally-dependent parental
 care.xlsx
DOI: 10.5061/dryad.255qd
title: Data from: Female polyandry and size-assortative mating in isolated local populations of the Japanese common toad Bufo japonicus

description: In anurans, female polyandry under male harassment is distributed across
 taxa because of external aquatic fertilisation. According to the sexual
 selection theory, male–male competition for access to females is affected
 by the operational sex ratio (OSR) and population density. The Japanese
 common toad, Bufo japonicus, is widespread in mainland Japan, and like the
 European common toad, B. bufo, it engages in explosive breeding. We
 observed the breeding behaviour of B. japonicus in isolated local
 populations for three years in two breeding ponds with different
 population sizes and densities: large-low (L-pond) and small-high
 (S-pond). We analysed the relative polyandry ratio in egg clutches laid by
 females and estimated the size-assortative mating pattern to be an
 indicator of male–male competition in the two ponds. Both ponds tended to
 exhibit a size-assortative mating pattern; however, the frequency of
 polyandry was different in the two ponds (L-pond = 20% and S-pond = 90%).
 We also found that polyandry could occur without multiple amplexus with a
 high population density, i.e. eggs were often fertilised by free-swimming
 sperm in the small shallow pond. We propose that high female polyandry
 ratios without continuous male harassment are generated because of a
 male-biased OSR and a high population density in the small pond.
description: Genotype and body size
 dataGenotyping data for
 paternity analysis: genotype of seven microsatellite loci for adults and
 offspring from two ponds. And body size data of adult toads: snout-to-vent
 length (SVL) of amplectant pairs and non-amplectant males in the two ponds
 for three years.genotype and body size
 data.xlsx
DOI: 10.5061/dryad.18p73
title: Data from: The behavioral trade-off between thermoregulation and foraging in a heat-sensitive species

description: The range-shifts of many species are lagging behind climate change,
 meaning that those species are likely to experience increases in average
 ambient temperature. Heat-sensitive species may experience increasingly
 precarious trade-offs between investment in thermoregulation versus other
 key processes as the climate warms. We investigated the potential for
 trade-offs to exist between behavioral thermoregulation and foraging,
 studying a typical heat-sensitive endotherm: the Alpine ibex (Capra ibex).
 Ibex use higher altitudes when it is hotter, which could restrict them
 from more profitable foraging areas at lower altitudes. We investigated
 this potential trade-off using data on the altitude-use and activity
 budgets of 43 marked males collected during the vegetation growing season
 in Gran Paradiso National Park, Italy. We used structural equation
 modeling to assess the support for models linking ambient temperature,
 altitude-use, vegetation productivity, and foraging time. Ibex migrated to
 higher altitudes during spring and summer, maintaining their ambient
 temperature within a very narrow band. Consequently, when it was warmer
 ibex utilized areas that were less productive, as indicated by lower
 normalized difference vegetation indices, and consumed lower quality
 forage, as indicated by lower levels of fecal crude protein. Ibex did not
 compensate behaviorally for reduced forage productivity by adjusting their
 foraging effort. We identify a trade-off between thermoregulation and
 foraging in ibex, which could affect this species negatively in the
 future. Such trade-offs could be a general phenomenon for heat-sensitive
 species. Our study reveals that behavioral thermoregulation can exert a
 strong influence on animal distributions, even overriding resource
 productivity in importance.
description: Alpine ibex behavioral
 and environmental data used in structural equation
 modelsData collected on male
 Alpine ibex behavior and environmental conditions in Gran Paradiso
 National Park, Italy, between May and October 2011.Ibex SEM data for
 Dryad.csvAlpine ibex fecal crude
 protein and environmental dataData collected on male
 Alpine ibex fecal crude protein content and environmental conditions in
 Gran Paradiso National Park, Italy, between May and October
 2011.Ibex
 FCP data for Dryad.csv
DOI: 10.5061/dryad.586b5
title: Data from: Restriction to large-scale gene flow versus regional panmixia among cold seep Escarpia spp. (Polychaeta, Siboglinidae)

description: The history of colonization and dispersal in fauna distributed among
 deep-sea chemosynthetic ecosystems remains enigmatic and poorly understood
 because of an inability to mark and track individuals. A combination of
 molecular, morphological and environmental data improves understanding of
 spatial and temporal scales at which panmixia, disruption of gene flow or
 even speciation may occur. Vestimentiferan tubeworms of the genus Escarpia
 are important components of deep -sea cold seep ecosystems, as they
 provide long-term habitat for many other taxa. Three species of Escarpia,
 Escarpia spicata [Gulf of California (GoC)], Escarpia laminata [Gulf of
 Mexico (GoM)] and Escarpia southwardae (West African Cold Seeps), have
 been described based on morphology, but are not discriminated through the
 use of mitochondrial markers (cytochrome oxidase subunit 1; large
 ribosomal subunit rDNA, 16S; cytochrome b). Here, we also sequenced the
 exon-primed intron-crossing Haemoglobin subunit B2 intron and genotyped 28
 microsatellites to (i) determine the level of genetic differentiation, if
 any, among the three geographically separated entities and (ii) identify
 possible population structure at the regional scale within the GoM and
 West Africa. Results at the global scale support the occurrence of three
 genetically distinct groups. At the regional scale among eight sampling
 sites of E. laminata (n = 129) and among three sampling sites of E.
 southwardae (n = 80), no population structure was detected. These findings
 suggest that despite the patchiness and isolation of seep habitats,
 connectivity is high on regional scales.
description: Escarpia_spicata_MetadataMetadata for Escarpia spicata individuals in this studyEscarpia_southwardae_MetadataMetadata for Escarpia southwardae individuals in this studyEscarpia_laminata_MetadataMetadata for Escarpia laminata individuals in this studyAdditional_Escarpia_MetadataAdditional samples added to study, requested by reviewersEscarpia Raw Allele CallsRaw allele calls for all three Escarpia groups. Loci name in row, individual name in columnEscarpia laminata raw allele callsE. laminata raw allele calls. Loci name in row; individual name in column.Escarpia_southwardae raw allele callsE. southwardae raw allele calls. Loci name in row; individual name in column.
DOI: 10.5061/dryad.ps736
title: Data from: Genetic restoration in the eastern collared lizard under prescribed woodland burning

description: Eastern collared lizards of the Ozarks live in glades—open, rocky habitats
 embedded in a woodland matrix. Past fire suppression had made the
 woodlands a barrier to dispersal, leading to habitat destruction,
 fragmentation and local extinction. Reintroduced populations of lizards
 were subjected to 10 years of habitat fragmentation under continued fire
 suppression followed by twelve years of landscape restoration with
 prescribed burns. Prior to prescribed burning, genetic diversity decreased
 within glades and differentiation increased among glades. With woodland
 burning, genetic diversity within glades first decreased during an
 expanding colonization phase, but then increased as a dynamically stable
 metapopulation was established. Population differentiation among glades
 also stabilized in the metapopulation under weak isolation-by-distance.
 This study is one of the first to examine the genetic changes in a species
 of conservation concern throughout all the stages of decline and recovery
 and shows the importance of landscape-level restoration for maintaining
 the genetic integrity of populations. This study also demonstrates how
 mark–recapture and genetic data together can yield detailed insight into
 metapopulation dynamics that would be impossible from just one type of
 data alone.
description: Stegall All glades All
 yearsMicrosatellite two-digit
 data in Genepop format from all samples collected between 1984 and 2006.
 Missing values are represented by zero. Data is partitioned such that each
 year represents a Genepop "population = 'Pop'". Each
 sample ID includes the year collected, the glade, and the unique ID (e.g.
 "1984-SM7-S030" is sample ID S030 collected on glade SM7 in
 1984).Stegall Mtn All glades all
 years.txt
DOI: 10.15468/dl.e6tzvt
title: Occurrence Download

description: A dataset containing 702 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Indotyphlops braminus",
 "Year 1960-2026"
 ]
}

 The dataset includes 702 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000884-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8376
title: Data from: Evidence for canalization of Distal-less function in the leg of Drosophila melanogaster

description: A considerable body of theory pertaining to the evolution of canalization
 has emerged recently, yet there have been few empirical investigations of
 their predictions. To address this, patterns of canalization and trait
 correlation were investigated under the individual and joint effects of
 the introgression of a loss-of-function allele of the Distal-less gene and
 high-temperature stress on a panel of iso-female lines. Variation was
 examined for number of sex comb teeth and the length of the basi-tarsus on
 the pro-thoracic leg of male Drosophila melanogaster. I demonstrate that
 whereas there is evidence for trait canalization, there is no evidence to
 support the hypothesis of the evolution of genetic canalization as a
 response to microenvironmental canalization. Furthermore, I demonstrate
 that although there are genetic correlations between these traits, there
 is no association between their measures of canalization. I discuss the
 prospects of the evolutionary lability of the Distal-less gene within the
 context of changes in genetic variation and covariation.
description: dll