cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dd30d
title: Data from: Herbivores safeguard plant diversity by reducing variability in dominance

description: 1. Reductions in community evenness can lead to local extinctions as
 dominant species exclude subordinate species; however, herbivores can
 prevent competitive exclusion by consuming otherwise dominant plant
 species, thus increasing evenness. While these predictions logically
 result from chronic, gradual reductions in evenness, rapid, temporary
 pulses of dominance may also reduce species richness. Short pulses of
 dominance can occur as biotic or abiotic conditions temporarily favor one
 or a few species, manifested as increased temporal variability (the
 inverse of temporal stability) in community evenness. Here, we tested
 whether consumers help maintain plant diversity by reducing the temporal
 variability in community evenness. 2. We tested our hypothesis by reducing
 herbivore abundance in a detailed study of a developing, tallgrass prairie
 restoration. To assess the broader implications of the importance of
 herbivory on community evenness as well as potential mechanisms, we paired
 this study with a global herbivore-reduction experiment. 3. We found that
 herbivores maintained plant richness in a tallgrass prairie restoration by
 limiting temporary pulses in dominance by a single species. Dominance by
 an annual species in a single year was negatively associated with species
 richness, suggesting that short pulses of dominance may be sufficient to
 exclude subordinate species. 4. The generality of this site-level
 relationship was supported by the global experiment in which inter-annual
 variability in evenness declined in the presence of vertebrate herbivores
 over timeframes ranging in length from 2-5 years, preventing declines in
 species richness. Furthermore, inter-annual variability of community
 evenness was also negatively associated with pre-treatment species
 richness. 5. Synthesis: A loss or reduction of herbivores can destabilize
 plant communities by allowing brief periods of dominance by one or a few
 species, potentially triggering a feedback cycle of dominance and
 extinction. Such cycles may not occur immediately following the loss of
 herbivores, being delayed until conditions allow temporary periods of
 dominance by a subset of plant species.
description: Nutrient Network
 dataPlant cover data
 collected from the Nutrient Network and submitted prior to April 19, 2016.
 Data are limited to plots without nutrient additions at sites with at
 least two years of herbivore reduction data.NutNet
 data.csvRestoration
 dataPlant cover data
 collected from the Oakridge Research and Education Prairie in Ames, IA,
 USA from 2012-2015. Cover values represent percent aerial cover for each
 species following a modified Daubenmire method.
DOI: 10.5061/dryad.54722
title: Data from: Genetic architecture of sexual dimorphism in a subdioecious plant with a proto-sex chromosome

description: The rise of sexual dimorphism is thought to coincide with the evolution of
 sex chromosomes. Yet because sex chromosomes in many species are ancient,
 we lack empirical evidence of the earliest stages of this transition. We
 use QTL analysis to examine the genetic architecture of sexual dimorphism
 in subdioecious octoploid Fragaria virginiana. We demonstrate that the
 region housing the male-function locus controls the majority of
 quantitative variation in proportion fruit set, confirming the existence
 of a proto-sex chromosome, and houses major QTL for eight additional
 sexually dimorphic traits, consistent with theory and data from animals
 and plants with more advanced sex chromosomes. We also detected autosomal
 QTL, demonstrating contributions to phenotypic variation in sexually
 dimorphic traits outside the sex-determining region. Moreover, for
 proportion seed set we found significant epistatic interactions between
 autosomal QTL and the male-function locus, indicating sex-limited QTL. We
 identified linked QTL reflecting trade-offs between male and female traits
 expected from theory and positive integration of male traits. These
 findings indicate the potential for the evolution of greater sexual
 dimorphism. Involvement of linkage groups homeologous to the proto-sex
 chromosome in these correlations reflects the polyploid origin of F.
 virginiana and raises the possibility that chromosomes in this homeologous
 group were predisposed to become the sex chromosome.
description: Spigler_etalEVOL_DRYAD_traitdataQuantitative trait data for Fragaria mapping populationSpigler_etalEVOL_DRYAD_HermGenotypesGenotypic data for male fertile individuals (males and hermaphrodites)Spigler_etalEVOL_DRYAD_FemaleGenotypesGenotypic data for male sterile individuals (female and neuter individuals)Spigler_etalEVOL_DRYAD_FemandHerm_MAPFILEMaternal ("female") and paternal ("hermaphrodite") map files
DOI: 10.5061/dryad.rq163
title: Data from: Genetic variation for mitochondrial function in the New Zealand freshwater snail Potamopyrgus antipodarum

description: The proteins responsible for mitochondrial function are encoded by two
 different genomes with distinct inheritance regimes, rendering rigorous
 inference of genotype–phenotype connections intractable for all but a few
 model systems. Asexual organisms provide a powerful means to address these
 challenges because offspring produced without recombination inherit both
 nuclear and mitochondrial genomes from a single parent. As such, these
 offspring inherit mitonuclear genotypes that are identical to the
 mitonuclear genotypes of their parents and siblings and different from
 those of other asexual lineages. Here, we compared mitochondrial function
 across distinct asexual lineages of Potamopyrgus antipodarum, a New
 Zealand freshwater snail model for understanding the evolutionary
 consequences of asexuality. Our analyses revealed substantial phenotypic
 variation across asexual lineages at three levels of biological
 organization: mitogenomic, organellar, and organismal. These data
 demonstrate that different asexual lineages have different mitochondrial
 function phenotypes, likely reflecting heritable variation (that is, the
 raw material for evolution) for mitochondrial function in P. antipodarum.
 The discovery of this variation combined with the methods developed here
 sets the stage to use P. antipodarum to study central evolutionary
 questions involving mitochondrial function, including whether
 mitochondrial mutation accumulation influences the maintenance of sexual
 reproduction in natural populations.
description: mtDNA_copy_numberContains mtDNA and nuclear gene rad51 qPCR results.copy_number.xlsxrespirometryContains all raw oxygen consumption data.MTTContains all MTT assay (electron flux) dataHeat_stressContains all raw heat stress dataJC1Contains all JC-1 assay (mitochondrial membrane potential) dataAll JC1MTTLactate work for lineages as of 4.2013.xlsx
DOI: 10.5061/dryad.v550k
title: Data from: Experimental test of plant defense evolution in four species using long-term rabbit exclosures

description: Plant defense traits have evolved over macro- and microevolutionary
 timescales in response to herbivores. Although a number of studies have
 investigated the evolutionary impacts of herbivores over short timescales,
 few studies have experimentally examined what defense traits most commonly
 evolve and whether multiple coexisting species exhibit similar
 evolutionary responses to herbivores. We addressed these questions using a
 long-term experiment at Silwood Park, England, United Kingdom, where we
 excluded rabbits from 38 grassland plots for &lt;1 to 34 years. To
 assess the evolutionary impacts of rabbits on plant defense traits, we
 collected seeds from plots containing the following perennial species:
 Anthoxanthum odoratum L. (Poaceae), Festuca rubra L. spp. rubra (Poaceae),
 Holcus lanatus L. (Poaceae), and Stellaria graminea L. (Caryophyllaceae).
 We then grew these plants in a common garden, and measured defensive and
 morphological traits. We found some evidence for evolutionary change of
 defense traits in three of the four species following the exclusion of
 rabbits. We observed the clearest changes in F. rubra, which showed a 9%
 decline in tolerance to herbivory and a 26% decline in leaf number. We
 also observed weak evidence for a change in all grass species towards a
 more erect growth form suggesting that grazing selects for plants that
 grow close to the ground. Although our results are most consistent with
 evolution due to changes in the frequency of alleles and genotypes, we
 cannot rule out that epigenetic changes (e.g., methylation) or maternal
 environmental effects also contributed to or caused the observed long-term
 phenotypic responses. Synthesis: Our study provides an experimental test
 of the evolutionary effects of an ecologically important herbivore. We
 found evidence for plant defense evolution following &gt;20 years of
 rabbit exclusion, however the evidence was only strong in 1 species for
 multiple traits, weak in all 3 grass species for avoidance, and absent in
 an herb species. This suggests that the evolutionary effects of an
 ecologically important herbivore on plants will be variable and difficult
 to predict in nature.
description: Data for Didiano et al
 2014 Journal of EcologyData on plant traits
 looking at evolution of plants following the experimental exclusion of
 rabbits. Traits measured on plants grown in a common garden experiment at
 University of Toronto. Seeds from rabbit exclosures at Silwood Park,
 England.20140208_Didionao_JEcol_Data_Final.xlsx
DOI: 10.5061/dryad.38gr5821
title: Data from: Testing and quantifying phylogenetic signals and homoplasy in morphometric data

description: The relationship between morphometrics and phylogenetic analysis has long
 been controversial. Here we propose an approach that is based on mapping
 morphometric traits onto phylogenies derived from other data and thus
 avoids the pitfalls encountered by previous studies. This method treats
 shape as a single, multidimensional character. We propose a test for the
 presence of a phylogenetic signal in morphometric data, which simulates
 the null hypothesis of the complete absence of phylogenetic structure by
 permutation of the shape data among the terminal taxa. We also propose 2
 measures of the fit of morphometric data to the phylogeny that are direct
 extensions of the consistency index and retention index used in
 traditional cladistics. We apply these methods to a small study of the
 evolution of wing shape in the Drosophila melanogaster subgroup, for which
 a very strongly supported phylogeny is available. This case study reveals
 a significant phylogenetic signal and a relatively low degree of
 homoplasy. Despite the low homoplasy, the shortest tree computed from
 landmark data on wing shape is inconsistent with the well-supported
 phylogenetic tree from molecular data, underscoring that morphometric data
 may not provide reliable information for inferring phylogeny.
description: Landmark coordinates of
 fly wingsThe file contains the x
 and y coordinates of 15 landmarks for all nine species of the Drosophila
 melanogaster subgroup. The file is a tab-delimited text file, and the data
 for each fly wing are on one line.DrosoRaw9species.txtPhylogeny of Drosophila melanogaster subgroupThe phylogeny of the 9 species in the study, as a Nexus fileDroso_phylo.nex
DOI: 10.5061/dryad.6ch89
title: Data from: The nervous system does not compensate for an acute change in the balance of passive force between synergist muscles

description: It is unclear how muscle activation strategies adapt to differential acute
 changes in the biomechanical characteristics between synergist muscles.
 This issue is fundamental to understanding the control of almost every
 joint in the body. The aim of this human experiment was to determine
 whether the relative activation of the heads of the triceps surae
 (Gastrocnemius medialis [GM], Gastrocnemius lateralis [GL] and Soleus
 [SOL]) compensates for differential changes in passive force between these
 muscles. Twenty-four participants performed isometric ankle plantarflexion
 at 20N.m and 20% of the active torque measured during a maximal
 contraction, at three ankle angles (30&[deg] of plantarflexion,
 0&[deg] and 25&[deg] of dorsiflexion; knee fully
 extended). Myoelectric activity (electromyography) provided an index of
 neural drive. Muscle shear modulus (elastography) provided an index of
 muscle force. Passive dorsiflexion induced a much larger increase in
 passive shear modulus for GM (+657.6&[plusmn]257.7%) than GL
 (+488.7&[plusmn]257.9%) and SOL (+106.6&[plusmn]93.0%).
 However, the neural drive during submaximal tasks did not compensate for
 this change in the balance of the passive force. Instead, when considering
 the contraction at 20% MVC, GL RMS EMG was reduced at both 0&[deg]
 (-39.4&[plusmn]34.5%) and DF 25&[deg]
 (-20.6&[plusmn]58.6%) compared to PF 30&[deg], while GM
 and SOL RMS EMG did not change. As a result, the GM/GL ratio of shear
 modulus was higher at 0&[deg] and DF 25&[deg] than PF
 30&[deg], indicating that the greater the dorsiflexion angle, the
 stronger the bias of force to GM compared to GL. The magnitude of this
 change in force balance varied greatly between participants.
description: Dryad_DemographicsThis file contains participant characteristics and demographics (24 human participants)Dryad_TorqueThis file contains data measured during the maximal voluntary isometric plantarflexions.Dryad_Passive_shear_modulusThis file contains passive shear modulus values measured at 30°, 0° and -25° of plantarflexion.Dryad_NeuralDriveThis file contains data of EMG RMS values for the trial 1 and trial 2 measured during the isometric plantarflexion tasks performed at 20% of MVC and 20 N.m and normalized to that measured during maximal isometric for plantarflexion. Note that data for trial 1 and 2 are averaged within the manuscript.Dryad_Shear_modulus_Submaximal_tasksThis file contains the shear modulus values measured during the isometric plantarflexion tasks performed at 20% of MVC and 20 N.m.
DOI: 10.6084/m9.figshare.31151968
title: Entrepreneurial Ecosystem Indicators for Small and Medium-sized Cities in South Korea (2012–2023)

description: This dataset provides a balanced panel of 151 South Korean municipalities from 2012 to 2023, integrating demographic, economic, fiscal, and entrepreneurship-related indicators at the municipal level. It is intended for research on entrepreneurial ecosystems, regional inequality, and urban sustainability in non-metropolitan contexts.
DOI: 10.6084/m9.figshare.31151968.v1
title: Entrepreneurial Ecosystem Indicators for Small and Medium-sized Cities in South Korea (2012–2023)

description: This dataset provides a balanced panel of 151 South Korean municipalities from 2012 to 2023, integrating demographic, economic, fiscal, and entrepreneurship-related indicators at the municipal level. It is intended for research on entrepreneurial ecosystems, regional inequality, and urban sustainability in non-metropolitan contexts.
DOI: 10.5061/dryad.15500
title: Data from: Exosomes in mammals with greater habitat variability contain more proteins and RNAs

description: Factors determining habitat variability are poorly understood despite
 possible explanations based on genome and physiology. This is because
 previous studies only focused on primary measures such as genome size and
 body size. In this study, we hypothesize that specific gene functions
 determine habitat variability in order to explore new factors beyond
 primary measures. We comprehensively evaluate the relationship between
 gene functions and the climate envelope while statistically controlling
 for potentially confounding effects by using data on the habitat range,
 genome, body size and metabolism of various mammals. Our analyses show
 that the number of proteins and RNAs contained in exosomes is
 predominantly associated with the climate envelope. This finding indicates
 the importance of exosomes to habitat range expansion of mammals and
 provides a new hypothesis for the relationship between the genome and
 habitat variability.
description: RSOS-170162_R1_data
DOI: 10.5061/dryad.0nh60
title: Data from: Repeated and predictable patterns of ecotypic differentiation during a biological invasion: lake-stream divergence in parapatric Swiss stickleback

description: The relative importance of ecological selection and geographical isolation
 in promoting and constraining genetic and phenotypic differentiation among
 populations is not always obvious. Interacting with divergent selection,
 restricted opportunity for gene flow may in some cases be as much a cause
 as a consequence of adaptation, with the latter being a hallmark of
 ecological speciation. Ecological speciation is well studied in parts of
 the native range of the three-spined stickleback. Here, we study this
 process in a recently invaded part of its range. Switzerland was colonized
 within the past 140 years from at least three different colonization
 events involving different stickleback lineages. They now occupy diverse
 habitats, ranging from small streams to the pelagic zone of large lakes.
 We use replicated systems of parapatric lake and stream populations, some
 of which trace their origins to different invasive lineages, to ask (i)
 whether phenotypic divergence occurred among populations inhabiting
 distinct habitats, (ii) whether trajectories of phenotypic divergence
 follow predictable parallel patterns and (iii) whether gene flow
 constrains divergent adaptation or vice versa. We find consistent
 phenotypic divergence between populations occupying distinct habitats.
 This involves parallel evolution in several traits with known ecological
 relevance in independent evolutionary lineages. Adaptive divergence
 supersedes homogenizing gene flow even at a small spatial scale. We find
 evidence that adaptive phenotypic divergence places constraints on gene
 flow over and above that imposed by geographical distance, signalling the
 early onset of ecological speciation.
description: Genetic, stable isotope
 & phenotypic data for Swiss sticklebacksThis file contains the
 combined data set collected on sticklebacks (Gasterosteus aculeatus) from
 5 different lake systems in Switzerland. Provided are individual data for
 microsatellites, stable isotopes and linear as well as geometric
 morphometric phenotypes.Lucek et al
 JEB.xlsx
DOI: 10.5061/dryad.m61t20h4
title: Data from: Social organisation and genetic structure: insights from co-distributed bat populations

description: The impact of ecology and social organisation on genetic structure at
 landscape spatial scales, where gene dynamics shape evolution as well as
 determine susceptibility to habitat fragmentation, is poorly understood.
 Attempts to assess these effects must take into account the potentially
 confounding effects of history. We used microsatellites to compare genetic
 structure in seven bat species with contrasting patterns of roosting
 ecology and social organisation, all of which are co-distributed in an
 ancient forest habitat that has been exceptionally buffered from radical
 habitat shifts. Over one thousand individuals were captured at foraging
 sites and genotyped at polymorphic microsatellite loci. Analyses of
 spatially explicit genotype data revealed inter-species differences in the
 extent of movement and gene flow and genetic structure across continuous
 intact forest. Highest positive genetic structure was observed in
 tree-roosting taxa that roost either alone or in small groups. By
 comparison, a complete absence of genetic autocorrelation was noted in the
 cave-roosting colonial species across the study area. Our results thus
 reveal measurable inter-species differences in the natural limits of gene
 flow in an unmodified habitat, which we attribute to contrasting roosting
 ecology and social organisation. The consequences of ecology and behaviour
 for gene flow have important implications for conservation. In particular,
 tree-roosting species characterised by lower vagility and thus gene flow
 will be disproportionally impacted by landscape-scale forest clearance and
 habitat fragmentation, which are prevalent in the study region. Our method
 also highlights the usefulness of rapid sampling of foraging bats for
 assaying genetic structure, particularly where roosting sites are not
 always known.
description: Rossiter et al DRYAD
 uploadMicrosatellite data with
 coordinates
DOI: 10.5061/dryad.9r0n681
title: Data from: Characteristics determining host suitability for a generalist parasite

description: Host quality is critical for parasites. The common cuckoo Cuculus canorus
 is a generalist avian brood parasite, but individual females show strong
 preference for a specific host species. Here, we use three extensive
 datasets to investigate different host characteristics determining cuckoo
 host selection at the species level: (i) 1871 population-specific
 parasitism rates collected across Europe; (ii) 14 K cases of parasitism in
 the United Kingdom; and (iii) 16 K cases of parasitism in Germany, with
 data collected during the period 1735–2013. We find highly consistent
 effects of the different host species traits across our three datasets:
 the cuckoo prefers passerine host species of intermediate size that breed
 in grass- or shrubland and that feed their nestlings with insects, and
 avoids species that nest in cavities. Based on these results, we construct
 a novel host suitability index for all passerine species breeding in
 Europe, and show that host species known to have a corresponding cuckoo
 host race (gens) rank among the most suitable hosts in Europe. The
 distribution of our suitability index shows that host species cannot be
 classified as suitable or not but rather range within a continuum of
 suitability.
description: Stokke_data_parasitism_rates_Dryad_ESM1Parasitism ratesStokke_data_passerines_Dryad_ESM2Species traitsStokke_data_parasitism_UK_Dryad_ESM3Parasitism rates UKStokke_data_parasitism_Germany_Dryad_ESM4Parasitism rates GermanyStokke_data_sources_Dryad_ESM5Data sources
DOI: 10.5061/dryad.52mp1
title: Data from: Divergence-with-gene-flow within the recent chipmunk radiation (Tamias)

description: Increasing data have supported the importance of divergence with gene flow
 (DGF) in the generation of biological diversity. In such cases, lineage
 divergence occurs on a shorter timescale than does the completion of
 reproductive isolation. Although it is critical to explore the mechanisms
 driving divergence and preventing homogenization by hybridization, it is
 equally important to document cases of DGF in nature. Here we synthesize
 data that have accumulated over the last dozen or so years on DGF in the
 chipmunk (Tamias) radiation with new data that quantify very high rates of
 mitochondrial DNA (mtDNA) introgression among para- and sympatric species
 in the T. quadrivittatus group in the central and southern Rocky
 Mountains. These new data (188 cytochrome b sequences) bring the total
 number of sequences up to 1871; roughly 16% (298) of the chipmunks we have
 sequenced exhibit introgressed mtDNA. This includes ongoing introgression
 between subspecies and between both closely related and distantly related
 taxa. In addition, we have identified several taxa that are apparently
 fixed for ancient introgressions and in which there is no evidence of
 ongoing introgression. A recurrent observation is that these
 introgressions occur between ecologically and morphologically diverged,
 sometimes non-sister taxa that engage in well-documented niche
 partitioning. Thus, the chipmunk radiation in western North America
 represents an excellent mammalian example of speciation in the face of
 recurrent gene flow among lineages and where biogeography, habitat
 differentiation and mating systems suggest important roles for both
 ecological and sexual selection.
description: Nexus
 Filequadgroup.nex