cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4521vq2
title: Data from: Wild boar (Sus scrofa) increases species diversity of semi-dry grassland: field experiment with simulated soil disturbances

description: Background Foraging activities of wild boar (Sus scrofa) create
 small-scale soil disturbances in many different vegetation types. Rooting
 alters species composition by opening niches for less-competitive plants
 and as a recurrent factor becomes a part of the community disturbance
 regime. Vegetation responses to wild boar disturbance have mostly been
 studied in the boar’s non-native range or in native forest, rather than in
 open habitats in the native range. We investigate the response of open
 European semi-dry grassland vegetation dominated by (Brachypodium
 pinnatum) to native wild boar pressure in an abandoned agricultural
 landscape. Methods To describe the disturbance regime, we repeatedly
 mapped rooted patches during a 5-year period. Additionally, to study the
 vegetation response, we performed an artificial disturbance experiment by
 creating 30 pairs of simulated disturbances and undisturbed plots. The
 vegetation composition of the paired plots was repeatedly sampled five
 times in eight years of the study. Results Based on repeated mapping of
 disturbances, we predict that if the disturbance regime we observed during
 the 5-year period were maintained over the long term, it would yield a
 stable vegetation ratio consisting of 98.7 % of the grassland undisturbed,
 0.4 % with fresh disturbance and 0.9 % in older successional stages.
 Vegetation composition on the artificially disturbed plots was
 continuously converging to that of undisturbed vegetation, but these
 disturbed plots still differed significantly in composition and had higher
 species number, even after eight years of succession. Synthesis Our
 results thus show that wild boar disturbance regime in its native range
 increases heterogeneity and species diversity of semi-dry grassland
 vegetation.
description: Experimental_disturbances_speciesVegetation composition data from permanent experimental plots (artificial disturbances and undisturbed controls). Plot size is 0.5 × 0.5 m. Cover of all vascular plants are on percentage scale.Natural_disturbances_speciesVegetation composition data from natural disturbances caused by wild boar and undisturbed control plots. Cover of all vascular plants on percentage scale. Plot size is 0.5 × 0.5 m. Columns: Date = date of the data collecting; Age = age of disturbance in years; Year_of_origin = when the disturbance was rootedRooted_areaData from repeated field mapping of natural soil disturbances caused by wild boar. Sheet “Rooting_rerooting_history”: Columns: Rooted area (m2) = area of fragment of disturbance with certain history; Enclave = spatial parameter; Rooting history = history of certain disturbance fragment given by rooting and re-rootings. Sheet “Size (m2)”: Areas (in m2) of all disturbances mapped in certain years.
DOI: 10.5061/dryad.23j8p68
title: Data from: Ionosporus: a new genus for Boletus longipes (Boletaceae), with a new species, I. australis, from Australia

description: Boletus longipes was described in 1909 by George Massee from a specimen
 collected in Singapore. The species was not mentioned again until E.J.H.
 Corner’s book in 1972 on Malaysian boletes. Corner had collected it many
 times during his tenure in Singapore, and he synonymized Boletus tristis
 with B. longipes described nine years after B. longipes by Patouillard and
 Baker from the same site. Among the distinguishing characters of B.
 longipes were deep vinous red spore deposit, red oxidation reaction of the
 hymenophore when bruised, and spores that displayed a strong violet color
 reaction in contact with KOH. C.B. Wolfe ultimately moved both species to
 a new genus Austroboletus. During recent efforts to circumscribe
 Austroboletus in Australasia using morphological and molecular
 phylogenetic inferences, it became clear that B. longipes was neither in
 harmony with Boletus, Porphyrellus, nor Austroboletus. Rather, it is a new
 genus, which we describe here as Ionosporus, allied to Borofutus,
 Spongiforma, and Rhodactina of subfamily Leccinoideae. In addition, recent
 collections from Queensland and New South Wales, Australia, that are
 morphologically similar to I. longipes, are inferred to be a separate new
 species, I. australis.
description: Ionosporus rpb2 fasta
 alignmentA FASTA file of 35
 exemplars with aligned rpb2 sequences. 7 of those exemplars were newly
 seqeunced.Ionosporus rpb2
 alignment.fasta
DOI: 10.5061/dryad.d4s8357
title: Data from: Fluctuating selection strength and intense male competition underlie variation and exaggeration of a water strider’s male weapon

description: Sexually selected traits can reach high degrees of expression and
 variation under directional selection. A growing number of studies suggest
 that such selection can vary in space, time and form within and between
 populations. However, the impact of these fluctuations on sexual trait
 expression is poorly understood. The water strider Microvelia longipes
 displays a striking case of exaggeration and phenotypic variation where
 males display extreme differences in the size of their rear legs. To study
 the origin and maintenance of this exaggerated trait, we conducted
 comparative behavioral and morphometric experiments in a sample of
 Microvelia species. We uncovered differences both in the mating behavior
 and the degree of sexual dimorphism across these species. Interestingly,
 M. longipes evolved a specific mating behavior where males compete for
 egg-laying sites, consisting of small floating objects, to intercept and
 copulate with gravid females. Through male-male competition assays, we
 demonstrated that male rear legs are used as weapons to dominate
 egg-laying sites and that intense competition is associated with the
 evolution of rear leg length exaggeration. Field observations revealed
 rapid fluctuation in M. longipes habitat stability and the abundance of
 egg-laying sites. Paternity tests using genetic markers demonstrated that
 small males could only fertilize about 5% of the eggs when egg-laying
 sites are limiting, whereas this proportion increased to about 20% when
 egg-laying sites become abundant. Furthermore, diet manipulation and
 artificial selection experiments also showed that the exaggerated leg
 length in M. longipes males is influenced by both genetic and nutritional
 factors. Collectively, our results highlight how fluctuation in the
 strength of directional sexual selection, through changes in the intensity
 of male competition, can drive the exaggeration and phenotypic variation
 in this weapon trait.
description: Bayesian tree
 concatenated alignments (6 species) - Posterior
 output.newickConcatenated alignments
 (6 species)ML tree of Concatenated
 alignments (6 species).newickAllometry_all microvelia
 speciesCondition-dependence&selection_experimentsScript allometry Microvelia Speciesscript_condition dependence&selectionscript_male fightingscript_paternity test_FV
DOI: 10.5061/dryad.fq5p33c
title: Data from: Dung beetle activity affects rainforest seed bank dynamics and seedling establishment

description: Dung beetles relocate vertebrate feces under the soil surface, and this
 behavior has many ecological consequences. In tropical forests, for
 example, seeds defecated by mammals that are subsequently buried by dung
 beetles are less likely to suffer predation. While the effects of dung
 beetles on the fate of defecated seeds have been relatively well studied,
 their effect on seeds already buried in the soil has not. To contribute to
 fill this gap we designed a study with three objectives: (1) Describe the
 vertical re-distribution of soil seeds that occurs due to dung beetle
 activity; (2) Determine if beetle activity favors establishment of
 seedlings from the soil seed bank; and (3) Determine if the effect of dung
 beetles is stronger in sites of recurrent mammal defecation. We carried
 out three complementary field experiments, one with artificial seeds
 (plastic beads) of three sizes buried at known depths, one with two
 species of seeds buried at those same depths, and one with the natural
 soil seed bank in sites of single vs. recurrent defecation. Buried beads
 were moved by dung beetles along the vertical axis, both upwards (9.5%)
 and downwards (11.5%); smaller beads were more frequently moved downwards
 while the contrary occurred for larger beads. Dung beetle activity caused
 an increase in seedling establishment, both from experimentally buried
 seeds and from the natural seed bank. Defecation recurrence had no effect
 on seedling establishment. We conclude that dung beetle activity affects
 seed bank dynamics with important consequences for seedling establishment
 in tropical forests.
description: Expe1Experiment 1. Data on
 vertical re-distribution of artificial seeds buried in the soil at three
 depths.Expe2Experiment 2. Data on
 seedlings established from natural seeds buried at three depths and three
 treatment levels of feces and beetle manipulation.Expe3AbundanceExperiment 3-Abundance. Data on cumulative number of seedlings established over time from the natural seed bank in sites of single vs. recurrent defecation.Expe3RichnessExperiment 3-Richness. Data on cumulative number of species established over time from the natural seed bank in sites of single vs. recurrent defecation.ReadmeFile where there is information about the methods used for each experiment and the column names of each data set.
DOI: 10.5061/dryad.rg5s170
title: Data from: Meiotic drive shapes rates of karyotype evolution in mammals

description: Chromosome number is perhaps the most basic characteristic of a genome,
 yet generalizations that can explain the evolution of this trait across
 large clades have remained elusive. Using karyotype data from over 1,000
 mammals, we developed and applied a phylogenetic model of chromosome
 evolution that links chromosome number changes with karyotype morphology.
 Using our model, we infer that rates of chromosome number evolution are
 significantly lower in species with karyotypes that consist of either all
 bibrachial or all monobrachial chromosomes than in species with a mix of
 both types of morphologies. We suggest that species with homogeneous
 karyotypes may represent cases where meiotic drive acts to stabilize the
 karyotype, favoring the chromosome morphologies already present in the
 genome. In contrast, rapid bouts of chromosome number evolution in taxa
 with mixed karyotypes may indicate that a switch in the polarity of female
 meiotic drive favors changes in chromosome number. We do not find any
 evidence that karyotype morphology affects rates of speciation or
 extinction. Furthermore, we document that switches in meiotic drive
 polarity are likely common and have occurred in most major clades of
 mammals, and that rapid remodeling of karyotypes may be more common than
 once thought.
description: supplemental
 filesThis compressed file
 contains all trees and data used in the manuscript. It includes scripts
 used to perform all primary analyses. It includes a readme.txt file that
 provides a short description of all files included.
DOI: 10.5061/dryad.77m6100
title: Data from: Connectivity with primary forest determines the value of secondary tropical forests for bird conservation

description: Predicted species extinctions caused by the destruction and degradation of
 tropical primary forest may be at least partially mitigated by the
 expansion of regenerating secondary forest. However, the conservation
 value of secondary forest remains controversial, and potentially
 underestimated, since most previous studies have focused on young,
 single-aged, or isolated stands. Here we use point count surveys to
 compare tropical forest bird communities in 20–120-yr-old secondary forest
 and primary forest stands in central Panama, with varying connectivity
 between secondary forest sites and extensive primary forest. We found that
 species richness and other metrics of ecological diversity, as well as the
 combined population density of all birds, reached a peak in younger
 (20-yr-old) secondary forests, and appeared to decline in older secondary
 forest stands. This counter-intuitive result can be explained by the
 greater connectivity between younger secondary forests and extensive
 primary forests at our study site, compared with older secondary forests
 that are either (1) more isolated, or (2) connected to primary forests
 that are themselves small and isolated. Our results suggest that
 connectivity with extensive primary forest is a more important determinant
 of avian species richness and community structure than forest age, and
 highlight the vital contribution secondary forests can make in conserving
 tropical bird diversity, so long as extensive primary habitats are
 adjacent and spatially connected.
description: Mayhew et al._Panama
 Bird Data_20190105Panama bird community
 dataset
DOI: 10.5061/dryad.v0861f7
title: Data from: Can we condition native plants to increase drought tolerance and improve restoration success?

description: A common method in ecological restoration is the outplanting of
 nursery-grown seedlings to the field, and with proper resources this
 technique can be highly successful. However, stressors such as drought may
 negatively impact plant performance and restoration success, especially in
 dryland ecosystems. Furthermore, increasing environmental change may
 hamper the ability of practitioners to restore native vegetation. A
 growing body of research suggests that exposing plants to a stressor may
 improve tolerance to subsequent stress events later in life. We sought to
 understand if such a phenomena could be exploited in order to improve
 plant drought-tolerance and aid native plant restoration in southern
 California. In a multi-phase experiment, we first exposed seedlings of
 native perennials to episodic drought, and then later compared the
 response of these plants to a second drought event to that of well-watered
 controls. We also transplanted replicates of both treatments to a
 restoration site in the field to test if exposure to drought as a seedling
 could improve plant performance. Plant species responded to drought
 differently, with species exhibiting the full range of positive, neutral,
 and negative responses to temporal variability in water stress. However,
 some species appeared to benefit from drought preconditioning, exhibiting
 greater growth and increased water-use efficiency compared to well-watered
 plants. This suggests that simple applications of stress treatments could
 improve plant growth and stress tolerance, but the success of this method
 is likely very species-specific. Restoration practitioners should consider
 conducting pilot studies with target plant species to better understand if
 this technique could assist in achieving restoration goals.
description: Can we condition native
 plants to increase drought tolerance and improve restoration
 success?Valliere_etal_EcoApps_Data.xlsx
DOI: 10.5061/dryad.43b7j27
title: Data from: Ectomycorrhizas and tree seedling establishment are strongly influenced by forest edge proximity but not soil inoculum

description: Reforestation is challenging when timber harvested areas have been
 degraded, invaded by non-native species, or are of marginal suitability to
 begin with. Conifers form mutualistic partnerships with ectomycorrhizal
 fungi (EMF) to obtain greater access to soil resources, and these
 partnerships may be especially important in degraded areas. However,
 timber harvest can impact mycorrhizal fungi by removing or compacting
 topsoil, removing host plants, and warming and drying the soil. We used a
 field experiment to evaluate the role of EMF in Douglas-fir reforestation
 in clearcuts invaded by Cytisus scoparius (Scotch broom) where traditional
 reforestation approaches have repeatedly failed. We tested how planting
 distance from intact Douglas-fir forest edges influenced reforestation
 success and whether inoculation with forest soils can be used to restore
 EMF relationships. We used an Illumina DNA sequencing approach to measure
 the abundance, richness and composition of ectomycorrhizal fungi on
 Douglas-fir roots, and assessed differences in Douglas-fir seedling
 survival and growth near to and far from forest edges with and without
 forest soil inoculum. Planting Douglas-fir seedlings near forest edges
 increased seedling survival, growth and EMF root colonization. Edge
 proximity had no effect on EMF richness but did change fungal community
 composition. Inoculations with forest soil did not increase EMF abundance
 or richness or change community composition, nor did it improve seedling
 establishment. With Illumina sequencing we identified two to three times
 greater species richness than described in previous edge effects studies.
 Of the 95 EMF species we identified, 40% of the species occurred on less
 than 5% of the seedlings. The ability to detect fungi at low abundance may
 explain why we did not detect differences in EMF richness with distance to
 hosts as previous studies. Our findings suggest that forest edges are
 suitable for reforestation, even when the interiors of deforested areas
 are not. We advocate for timber harvest designs that maximize edge habitat
 where ectomycorrhizal fungi contribute to tree establishment. However,
 this study does not support the use of inoculation with forest soil as a
 simple method to enhance EMF and seedling survival.
description: Douglas-fir Seedling
 SurvivalSurvival.xlsxDouglas-fir Aboveground BiomassAboveground Biomass.xlsxEctomycorrhizal Fungi AbundanceEMF Abundance.xlsxEctomycorrhizal Fungi CommunityEMF Community.xlsx
DOI: 10.5281/zenodo.18239094
title: TESLA Stock Data_20200823_20250823
DOI: 10.5061/dryad.3k8c480
title: Data from: The role of spore size in the global pattern of co-occurrence among Selaginella species

description: Aim: Separation of regeneration niches may promote coexistence among
 closely related plant species, but there is little evidence that
 regeneration traits affect species ranges at large geographic scales. Here
 we address patterns of co-occurrence within the genus Selaginella, an
 ancient lineage of free-sporing, heterosporous, vascular plants.
 Specifically, we ask whether differences between species in spore size are
 associated with the extent of overlap in their geographic ranges, a
 measure of opportunity for ecological interaction. Taxon: Selaginella
 (Selaginellaceae: Lycopodiales) Methods: We used quantile regression to
 examine the relationship of spore size ratios (pairwise ratios for
 megaspores and microspores of co-occurring species) to the area of range
 overlap and to latitude for a worldwide sample of 112 Selaginella species.
 Phylogenetically informed tests of statistical significance were used for
 each percentile relationship examined in the quantile regressions.
 Results: Large pairwise disparities in megaspore sizes were significantly
 associated with large range overlap. Disparities also tended to be larger
 at low latitudes. Microspore size differences, in contrast, were unrelated
 to shared range area or latitude. Main conclusion: Megaspore size appears
 to affect coexistence at a broad regional scale among Selaginella species,
 in at least some cases. The pattern is consistent with some degree of
 competitive structuring of size-related aspects of dispersal and
 establishment of propagules among some co-occurring species. Habitat
 complexity, such as open microsites within otherwise closed and shaded
 vegetation, seems likely to promote reproductive niche separation and may
 account for the latitudinal structure in Selaginella spore sizes.
description: Margaroni et al. Journal
 of Biogeography Online DataThis single CSV file
 contains the data used in the analysis of S. Margaroni et al., The role of
 spore size in the global pattern of co-occurrence among Selaginella
 species, Journal of Biogeography. Data available for 113 species of
 Selaginella are: species name, average megaspore volume in cubic
 micrometers, average microspore volume in cubic micrometers, area in
 square kilometers of geographic range (estimated as minimum convex polygon
 containing GBIF occurrence points), latitude of centroid of the species
 range polygon in degrees (absolute value, i.e., ignoring N or S latitude),
 and the number of other species ranges that overlap with a given species.
 Data available for 923 instances of pairwise range overlap between species
 are: names of the two species involved, area of overlap between range
 polygons in square kilometers, megaspore volume ratio, and microspore
 volume ratio (ratio of larger spore volume to smaller spore volume of the
 two species in the pair).Margaroni_JBiogeogr_Online_data.csv
DOI: 10.5061/dryad.3tj5c7p
title: Data from: Too much of a good thing? Finding the most informative genetic dataset to answer conservation questions

description: Molecular markers are a useful tool allowing conservation and population
 managers to shed light on genetic processes affecting threatened
 populations. However, as technological advancements in molecular
 techniques continue to evolve, conservationists are frequently faced with
 new genetic markers, each with nuanced variation in their characteristics
 as well as advantages and disadvantages for informing various questions.
 We used a well-studied population of Tasmanian devils from Maria Island to
 illustrate the issues associated with combining multiple genetic datasets
 and to help answer a question posed by many population managers: which
 dataset will provide the most precise and accurate estimates of the
 population processes we are trying to measure? We analysed individual
 heterozygosity (as internal relatedness, IR) of 96 individuals, calculated
 using four genetic marker types (putatively neutral microsatellites,
 MHC-linked microsatellites, reduced representation sequencing, and
 candidate region resequencing). We found no correlation in IR values
 across marker types, suggesting that various genetic markers reflect
 different aspects of genomic diversity. In addition, some marker types
 were more informative than others for conservation decision-making.
 Reduced representation sequencing provided the highest precision (lowest
 error) for estimating population-level genetic diversity, and most closely
 reflected genome-wide heterozygosity both theoretically and empirically.
 Within the conservation context, our results highlight important
 considerations when choosing a molecular technique for wildlife genetics.
description: Data for "Too much
 of a good thing? Finding the most informative genetic dataset to answer
 conservation questions"This data file contains
 the genotypes from 96 devils and four different data types. The
 microsatellite genotypes were generated using the software GeneMarker V
 1.75, the RRS dataset was provided as a proprietary pipline from Diversity
 Array Technologies, and the functional candidate region dataset was
 generated from a previous study (see current paper for details), the raw
 IR values used in the study, and the observed heterozygosities of all loci
 in the study. Detailed descriptions are provided in a "readme"
 tab at the beginning of the file.genotypes_alldatatypes.xlsx