cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5th45
title: Data from: Size structuring and allometric scaling relationships in coral reef fishes

description: Temperate marine fish communities are often size structured, with
 predators consuming increasingly larger prey and feeding at higher trophic
 levels as they grow. Gape limitation and ontogenetic diet shifts are key
 mechanisms by which size structuring arises in these communities. Little
 is known, however, about size structuring in coral reef fishes. Here, we
 aimed to advance understanding of size structuring in coral reef food webs
 by examining the evidence for these mechanisms in two groups of reef
 predators. Given the diversity of feeding modes amongst coral reef fishes,
 we also compared gape size—body size allometric relationships across
 functional groups to determine if they are reliable indicators of size
 structuring. We used gut content analysis and quantile regressions of
 predator size—prey size relationships to test for evidence of gape
 limitation and ontogenetic niche shifts in reef piscivores (n=13 species)
 and benthic invertivores (n=3 species). We then estimated gape size—body
 size allometric scaling coefficients for 21 different species from four
 functional groups, including herbivores/detritivores, which are not
 expected to be gape-limited. We found evidence of both mechanisms for size
 structuring in coral reef piscivores, with maximum prey size scaling
 positively with predator body size, and ontogenetic diet shifts including
 prey type and expansion of prey size. There was, however, little evidence
 of size structuring in benthic invertivores. Across species and functional
 groups, absolute and relative gape sizes were largest in piscivores as
 expected, but gape size—body size scaling relationships were not
 indicative of size structuring. Instead, relative gape sizes and mouth
 morphologies may be better indicators. Our results provide evidence that
 coral reef piscivores are size-structured, and that gape limitation and
 ontogenetic niche shifts are the mechanisms from which this structure
 arises. Although gape allometry was not indicative of size structuring, it
 may have implications for ecosystem function: positively allometric gape
 size—body size scaling relationships in herbivores/detritivores suggests
 that loss of large-bodied individuals of these species will have a
 disproportionately negative impact on reef grazing pressure.
description: predator-size-prey-size-dataThis csv contains the data used for the predator size - prey size analysis.predator-size-prey-size-metadataThis csv contains the column names and descriptions for gape-size-body-size-dataThis csv contains the data for the gape size - body size analysis.gape-size-body-size-column-metadataThis csv contains the column descriptions for the gape size-body size data.
DOI: 10.5281/zenodo.18373889
title: Sparse tensor dataset

description: This archive contains sparse tensor data for Hubbard-2D models and nwchem models.
DOI: 10.5281/zenodo.18373890
title: Sparse tensor dataset

description: This archive contains sparse tensor data for Hubbard-2D models and nwchem models.
DOI: 10.5061/dryad.7898
title: Data from: Can clone size serve as a proxy for clone age? An exploration using microsatellite divergence in Populus tremuloides

description: In long-lived clonal plant species, the overall size of a clone has
 previously been used to estimate clone age. The size of a clone, however,
 might be largely determined by physical or biotic interactions, obscuring
 the relationship between clone size and age. Here, we use the accumulation
 of mutations at 14 microsatellite loci to estimate clone age in trembling
 aspen, Populus tremuloides, from southwestern Canada. We show that the
 observed patterns of genetic divergence are consistent with a model of
 clonal growth, allowing us to use pairwise genetic divergence as an
 estimator of clone age. In the populations studied, clone size did not
 exhibit a significant relationship with microsatellite divergence,
 indicating that clone size is not a good proxy for clone age.
description: SSR_Data_11905036MEC-08-0315.R1This data was collected in two geographical locations: Riske Creek, British Columbia and Waterton Lakes National Park, Alberta. The data represent 14 microsatellite loci. See Ally et al. 2008 for a description of the SSRs. Any loci that did not amplify are indicated with an question mark.Riske_Creek_sizedataSee the README_SIZEDATA fileRR_SizeDataSee README_SIZEDATA File
DOI: 10.15468/dl.cy3twh
title: Occurrence Download

description: A dataset containing 232053 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Canis lupus"
 ]
}

 The dataset includes 232053 records from 810 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000708-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.57t4q
title: Data from: Morphology and genetics reveal an intriguing pattern of differentiation at a very small geographic scale in a bird species, the forest thrush Turdus lherminieri

description: Mobile organisms are expected to show population differentiation only over
 fairly large geographical distances. However, there is growing evidence of
 discrepancy between dispersal potential and realized gene flow. Here we
 report an intriguing pattern of differentiation at a very small spatial
 scale in the forest thrush (Turdus lherminieri), a bird species endemic to
 the Lesser Antilles. Analysis of 331 individuals from 17 sampling sites
 distributed over three islands revealed a clear morphological and genetic
 differentiation between these islands isolated by 40–50 km. More
 surprisingly, we found that the phenotypic divergence between the two
 geographic zones of the island of Guadeloupe was associated with a very
 strong genetic differentiation (Fst from 0.073–0.153), making this pattern
 a remarkable case in birds given the very small spatial scale considered.
 Molecular data (mitochondrial control region sequences and microsatellite
 genotypes) suggest that this strong differentiation could have occurred in
 situ, although alternative hypotheses cannot be fully discarded. This
 study suggests that the ongoing habitat fragmentation, especially in
 tropical forests, may have a deeper impact than previously thought on
 avian populations.
description: Genetic and
 Morphological data from Arnoux etal Heredity 2014Genetic (10
 microsatellite loci) and morphological data (5 variables) collected in the
 field from 327 forest thrush individuals (3 islands, 17
 populations).Genetic and morphological data
 from Arnoux etal Heredity 2014.xls
DOI: 10.5061/dryad.8pv40
title: Data from: Solidago altissima differs with respect to ploidy frequency and clinal variation across the prairie-forest biome border in Minnesota

description: PREMISE OF THE STUDY: Although our awareness of ploidy diversity has
 expanded with the application of flow cytometry, we still know little
 about the extent to which cytotypes within mixed-ploidy populations are
 genetically differentiated across environmental gradients. METHODS: To
 address this issue, we reared 14 populations of Solidago altissima
 spanning the prairie–forest ecotone in Minnesota in a common garden with a
 watering treatment. We assessed ploidy frequencies and measured survival,
 flowering phenology, and plant architectural traits for 4 years. KEY
 RESULTS: All populations harbored multiple cytotypes; prairie populations
 were dominated by tetraploids, forest populations by hexaploids. Diploids
 and polyploids differed significantly for 84% of the traits. Beyond
 average differences, the slope of trait values covaried with latitude and
 longitude, but this relationship was stronger for diploids than the other
 two polyploid cytotypes as indicated by numerous ploidy × latitude and
 ploidy × longitude interactions. For example, the timing of flowering of
 the cytotypes overlapped in populations sampled from the northeastern
 hemiboreal forest but differed significantly between cytotypes sampled
 from populations in the southwestern prairie. The watering treatments had
 weak effects, and there were no ploidy differences for phenotypic
 plasticity. CONCLUSIONS: Our data show that diploids have diverged
 genetically to a greater extent than polyploids along the environmental
 clines sampled in this study. Moreover, different environments favor
 phenotypic convergence over divergence among cytotypes for some traits.
 Differences in ploidy frequency and phenotypic divergence among cytotypes
 across gradients of temperature and precipitation are important
 considerations for restoration in an age of climate change.
description: Prairie_Forest_Precip_Gradient_DRYADThis file includes all original data related to the analysis published by the American Journal of Botany including: 1) The original radomized block design, 2) the rearranged split-plot block design, 3) the population code as it appears in the manuscript, 4) a genotype number, 5) the watering treatment (D=dry; W = wet), 6) Biome (P=prairie, F=forest), 7) latitude and longitude of wild population, 8) flow cytometry peaks and pg DNA calculation, 9) original rhizome weight at planting, and for each year 2007-2010 when measured, 10) date of first flower, 11) leaf number, 12) height, 13) basal stem diameter, 14) abaxial and adaxial stomatal counts and their ratio, 15) clone number, 16) branch number 17) dried biomass. Herbivory (yes/no) for 2008 is also included.
DOI: 10.5061/dryad.j0p62
title: Data from: Biogeography and host-related factors trumps parasite life-history: limited congruence among the genetic structures of specific ectoparasitic lice and their rodent hosts

description: Parasites and hosts interact across both micro- and macroevolutionary
 scales where congruence among their phylogeographic and phylogenetic
 structures may be observed. Within southern Africa, the four-striped mouse
 genus, Rhabdomys, is parasitized by the ectoparasitic sucking louse,
 Polyplax arvicanthis. Molecular data recently suggested the presence of
 two cryptic species within P. arvicanthis that are sympatrically
 distributed across the distributions of four putative Rhabdomys species.
 We tested the hypotheses of phylogeographic congruence and cophylogeny
 among the two parasite lineages and the four host taxa, utilizing
 mitochondrial and nuclear sequence data. Despite the documented
 host-specificity of P. arvicanthis, limited phylogeographic correspondence
 and nonsignificant cophylogeny was observed. Instead, the parasite–host
 evolutionary history is characterized by limited codivergence and several
 duplication, sorting and host-switching events. Despite the elevated
 mutational rates found for P. arvicanthis, the spatial genetic structure
 was not more pronounced in the parasite lineages compared with the hosts.
 These findings may be partly attributed to larger effective population
 sizes of the parasite lineages, the vagility and social behaviour of
 Rhabdomys, and the lack of host-specificity observed in areas of host
 sympatry. Further, the patterns of genetic divergence within parasite and
 host lineages may also be largely attributed to historical biogeographic
 changes (expansion-contraction cycles). It is thus evident that the
 association between P. arvicanthis and Rhabdomys has been shaped by the
 synergistic effects of parasite traits, host-related factors and
 biogeography over evolutionary time.
description: Polyplax_COI_DyradMItochondrial Cytochrome Oxidase subunit 1 nexus alignment file for Polyplax arvicanthisRhabdomys_COI_DyradMitochondrial Cytochrome Oxidase subunit 1 nexus alignment file for RhabdomysPolyplax_CAD_DyradNuclear CAD rudimentary gene nexus alignment file for Polyplax arvicanthisRhabdomys_Eef1a1_DyradNuclear Eukaryotic elongation factor 1 alpha 1 nexus alignment file for Rhabdomys
DOI: 10.5061/dryad.p71bv
title: Data from: Changes in biotic and abiotic drivers of seedling species composition during forest recovery following shifting cultivation on Hainan Island, China

description: Seedlings play an important role in the processes of plant community
 succession. We compared seedling (dbh &lt; 1 cm) species composition
 and diversity over a chronosequence (18-, 30-, 60-year-old second growth
 and old growth forest) after shifting cultivation in a tropical lowland
 rain forest area on Hainan Island, China. Seedling diversity reached a
 maximum in the 60-year-old second growth forest, which is consistent with
 the intermediate disturbance hypothesis. With the progression of secondary
 succession, canopy openness (CO), soil organic matter, soil phosphorus
 content, and tree abundance showed a general decreasing trend; soil water
 content and tree basal area showed a general trend of increase, while soil
 pH and other nutrients reached maximum values and tree richness reached a
 minimum value at intermediate stages of succession. Seedling composition
 and diversity were significantly affected by soil water, pH, soil nutrient
 content, and biotic factors in the 18-year-old second growth forests; by
 soil pH, soil nutrient content, and biotic factors in the 30-year-old
 second growth forests; by CO, soil nutrient content and tree abundance in
 the 60-year-old second growth forests; and by CO, soil pH, and soil
 nutrient content in the old growth forests. At earlier stages of
 succession, the effect of the proportion of old growth forest in the
 surrounding landscape on seedling diversity was greater than that of
 land-use history, but the importance of these drivers was reversed at
 later stages of succession.
description: Xinghui Lu et al. 2016.
 Biotropica.Data BaseData description of plot
 species and environment factorsData.xlsx
DOI: 10.5061/dryad.60pq3
title: Data from: Shape up or ship out: migratory behaviour predicts morphology across spatial scale in a freshwater fish

description: 1. Migration is a widespread phenomenon, with powerful ecological and
 evolutionary consequences. Morphological adaptations to reduce the
 energetic costs associated with migratory transport are commonly
 documented for migratory species. However, few studies have investigated
 whether variation in body morphology can be explained by variation in
 migratory strategy within a species. 2. We address this question in roach
 Rutilus rutilus, a partially migratory freshwater fish that migrates from
 lakes into streams during winter. We both compare body shape between
 populations that differ in migratory opportunity (open vs. closed lakes),
 and between individuals from a single population that vary in migratory
 propensity (migrants and residents from a partially migratory population).
 Following hydrodynamic theory, we posit that migrants should have a more
 shallow body depth, to reduce the costs associated with migrating into
 streams with higher flow conditions than the lakes the residents occupy
 all year round. 3. We find evidence both across and within populations to
 support our prediction, with individuals from open lakes and migrants from
 the partially migratory population having a more slender, shallow-bodied
 morphology than fish from closed lakes and all-year residents. 4. Our data
 suggest that a shallow body morphology is beneficial to migratory
 individuals and our study is one of the first to link migratory strategy
 and intraspecific variation in body shape.
description: Data from Chapman et al
 (JAE)All data, raw and
 summarized. All analyses were performed in SPSS (release
 21.0.0.0)Chapman_et_al_2014_JAE.xlsx
DOI: 10.5061/dryad.2ff8mv9
title: Data from: Limited influence of landscape on the genetic structure of three small mammals in a heterogeneous arid environment

description: Aim: The complexity and biologically challenging nature of arid landscapes
 can generate high inter- and intra-species diversity, although these
 biomes remain poorly studied. We investigated whether prominent geomorphic
 features in an Australian arid landscape had similar influences on
 patterns of intra-specific genetic diversity of three small mammals with
 different distribution and life history traits. Specifically, we tested
 (1) whether mountain ranges harbour high diversity and act as refugia, (2)
 the extent to which ephemeral river systems pose barriers to gene flow, or
 (3) whether environmental differences explain genetic structure in these
 species. Location: The topographically complex Pilbara bioregion of the
 Australian arid zone. Taxa: Two native rodents, the Western pebble-mound
 mouse, Pseudomys chapmani, and the Sandy inland mouse, Pseudomys
 hermannsburgensis, and a dasyurid, Ningaui timealeyi. Methods: We used
 maximum parsimony networks of mitochondrial haplotypes and
 spatially-explicit Bayesian clustering analysis of microsatellite
 genotypes to identify historical and contemporary genetic structure in
 each species. Based on measures of individual diversity and genetic
 distance, we distinguished ‘hotspots’ and ‘coldspots’ (greater than 1.5
 standard deviations from the mean) of genetic diversity and genetic
 connectivity and assessed their concordance with landscape features. The
 influence of environmental dissimilarity on observed genetic
 differentiation was evaluated using generalised dissimilarity modelling.
 Results: Patterns of genetic diversity and connectivity were complex, with
 few consistent patterns across species. Both microsatellite and
 mitochondrial diversity were high across species, with limited spatial
 genetic structure. Rivers had the most influence on genetic patterns but
 were not consistently identified as barriers. Environmental dissimilarity
 amongst sampling sites had low explanatory power. Main Conclusions:
 Limited genetic structure in each of the three species suggests that the
 structurally complex Pilbara landscape remains relatively permeable to
 species with high dispersal capacity. Additionally, population responses
 to boom-bust cycles in arid environments are likely to obscure spatial
 genetic patterns.
description: Levy_DataContains microsatellite and mitochondrial haplotype data used to estimate genetic diversity and genetic connectivity of three small mammal species (Ningaui timealeyi, Pseudomys chapmani, Pseudomys hermannsburgensis) in the Pilbara bioregion of Western Australia, Australia.
DOI: 10.5061/dryad.51696
title: Data from: Two-module organization of the mandible in the yellow-necked mouse: a comparison of two different morphometric approaches

description: Mandibles of yellow-necked mouse (Apodemus flavicollis) were used to
 explore modularity. We tested a biological hypothesis that two separate
 modules (alveolar region and ascending ramus) can be recognized within the
 mandible. As a second research goal, we compared two different
 morphometric procedures under the assumption that methodological
 approaches that use either geometric or traditional morphometric
 techniques should give similar results. Besides confirmation of the
 predicted hypothesis of modularity, the application of both approaches
 revealed that: 1) Modularity was somewhat more evident when it was
 analyzed on the asymmetric (fluctuating asymmetry, FA) than on the
 symmetric (individual variation) component of variation; 2) There is
 correspondence in the patterns of individual variation and FA, which
 indicates that integration of mandibular traits among individuals is
 primarily due to direct developmental interactions and 3) Allometry does
 not obscure the hypothesized modularity for individual variation or for
 FA. In addition, traditional morphometric method allowed us to check if
 allometry influenced each module to the same extent, and to conclude that
 the ascending ramus is more heavily influenced by general size than the
 alveolar region. In studies of modularity, differences in methods can lead
 to discrepancies in the results, and therefore some caution is required
 when comparing findings from different investigations. The substantial
 agreement between our results provides evidence that, when considering
 two-module organization of the mouse mandible, direct comparison among
 studies that use the methods applied herein is, in great part, reliable.
description: Raw_coordinatesX and Y coordinates of each landmark
DOI: 10.5061/dryad.j968847
title: Data from: Species pools and differential performance generate variation in leaf nutrients between native and exotic species in succession

description: 1. A central aim of invasion biology has been to identify key functional
 differences between native and exotic species to determine which traits
 may be responsible for invasion success and impacts. There are two primary
 ways that differences may exist between native and exotic species - the
 traits of the local species pools may differ, or the way that the traits
 interact with their environment may differ. 2. We explored leaf nutrient
 concentrations as functional traits that directly link to plant metabolic
 processes by sampling healthy, mature leaves from 119 native and exotic
 taxa across a wide range of successional statuses in New Jersey, USA. Leaf
 nutrient concentration data (carbon, calcium, magnesium, nitrogen,
 potassium) were paired with long-term community dynamics from the
 Buell-Small Succession Study to evaluate abundance-weighted trait values
 over succession for native and exotic species. 3. After accounting for
 differences across growth forms, there were minimal differences in foliar
 nutrients based on plant origin, with only lower leaf carbon and higher
 leaf potassium in exotic species. However, these differences were not
 sufficient to generate overall differences between native and exotic
 species in a multivariate analysis. In contrast, the successional
 trajectories of the abundance-weighted trait values for most leaf
 nutrients differed strongly between native and exotic plants. While this
 pattern may be partially attributable to variation in the species pool for
 carbon and potassium, successional processes generated differential
 sorting, suggesting underlying differences in how the same traits function
 in native and exotic assemblages. 4. Synthesis: These results suggest that
 both variation in the species pool and variation in the successional
 selection of plant traits can generate functional differences between
 native and exotic plants. Assessments of trait differences between native
 and exotic species will require information on traits and plant
 performance to unambiguously link traits to function in dynamic plant
 communities.
description: C3Cover over successional
 timeC4 cover
 dataCover over successional
 timeC4.csvC5Cover over successional timeC6Cover over successional timeC7Cover over successional timeD1Cover over successional timeD2Cover over successional timeD3Cover over successional timeE1cover over successional timeE2Cover over successional timeLeaf_nutrient_and_species_dataLeaf nutrient data