cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d4t7rc3
title: Data from: Contrasting patterns of population history and seed-mediated gene flow in two endemic Costa Rican oak species

description: Lower Central America is an important area to study recent population
 history and diversification of Neotropical species due to its complex and
 dynamic geology and climate. Phylogeographic studies in this region are
 few in comparison with other regions and even less for tree species. The
 aim of the present study was to characterize the phylogeographic structure
 in two partially co-distributed endemic oak species (Quercus costaricensis
 and Q. bumelioides) of the Costa Rican mountains using chloroplast short
 sequence repeats (cpSSRs), and to test for the effect of geological and
 palaeoclimatic processes on their population history. Genetic diversity
 and structure, haplotype networks, patterns of seed-mediated gene flow and
 historical demography were estimated for both species. Results suggested
 contrasting patterns. Quercus costaricensis exhibited high values of
 genetic diversity, a marked phylogeographic structure, a north-to-south
 genetic diversity gradient and evidence of a demographic expansion during
 the Quaternary. Quercus bumelioides did not show significant genetic
 structure and the haplotype network and historical demography estimates
 suggested a recent population expansion probably during the
 Pleistocene-Holocene transition. Phylogeographic structure of Q.
 costaricensis seems to be related to Pleistocene altitudinal migration due
 to its higher altitudinal distribution. Meanwhile, historical
 seed-mediated gene flow through the lower altitudinal distribution of Q.
 bumelioides may have promoted the homogenization of genetic variation.
 Population expansion and stable availability of suitable climatic areas in
 both species probably indicate that palaeoclimatic changes promoted
 downwards altitudinal migration and formation of continuous forests
 allowing oak species to expand their distribution into the Panamanian
 mountains during glacial stages.
description: HernandoRodriguez-Correa_JournalOfHeredity_DryadCpSSR data for two Neotropical oak species (see manuscript for details)
DOI: 10.5061/dryad.g31g3
title: Data from: Outcome after reconstruction of the proximal tibia – complications and competing risk analysis

description: Background and Objectives: The proximal tibia (pT) is a common site for
 bone tumors. Improvements in imaging, chemotherapy and surgical technique
 made limb salvage surgery the treatment of choice. Yet, reconstructions of
 the pT have been associated with less favorable outcome compared to other
 parts of the extremities. The aim of this study was to evaluate the
 outcome of patients with a modular endoprosthetic reconstruction of the
 pT. Methods: Eighty-one consecutive patients with an average age of 29
 years underwent endoprosthetic reconstruction of the pT. Postoperative
 complications were categorized according to the ISOLS classification, and
 revision-free survival until first complication (any Type 1–5), soft
 tissue failure (Type 1), aseptic loosening (Type 2), structural failure
 (Type 3), infection (Type 4), and local tumor progression (Type 5) was
 estimated by using a Fine-Gray model for competing risk analyses for
 univariate and multivariable regression with Firth’s bias correction.
 Results: A total of 45 patients (56%) had at least one complication.
 Cumulative incidence for complication Types 1 to 5 at 5 years with death
 and amputation as competing events revealed a risk of 41% for the first
 complication, 14% for Type 1, 16% for Type 2, 11% for Type 3, 17% for Type
 4, and 1% for Type 5. Conclusion: Despite inclusion of amputation and
 death as strong competing events, pT replacements are still associated
 with a high risk of postoperative failures. The results suggest that
 infection and soft tissue failures (Type 1 and 5) seem to depend from each
 other. Sufficient soft tissue reconstruction and closure allow better
 function and reduce the risk of infection as the most prominent
 complication. The use of a rotating hinge design has significantly reduced
 structural failures over time.
description: Data
DOI: 10.5061/dryad.4gf03
title: Data from: Bayesian species delimitation combining multiple genes and traits in a unified framework

description: Delimitation of species based exclusively on genetic data has been
 advocated despite a critical knowledge gap: how might such approaches fail
 because they rely on genetic data alone, and would their accuracy be
 improved by using multiple data-types. We provide here the requisite
 framework for addressing these key questions. Because both phenotypic and
 molecular data can be analyzed in a common Bayesian framework with our
 program iBPP, we can compare the accuracy of delimited taxa based on
 genetic data alone versus when integrated with phenotypic data. We can
 also evaluate how the integration of phenotypic data might improve species
 delimitation when divergence occurs with gene flow and/or is selectively
 driven. These two realities of the speciation process are ignored by
 currently available genetic approaches. Our model accommodates phenotypic
 characters that exhibit different degrees of divergence, allowing for both
 neutral traits and traits under selection. We found a greater accuracy of
 estimated species boundaries with the integration of phenotypic and
 genetic data, with a strong beneficial influence of phenotypic data from
 traits under selection when the speciation process involves gene flow. Our
 results highlight the benefits of multiple data-types, but also draws into
 question the rationale of species delimitation based exclusively on
 genetic data.
description: perl script to simulate
 data and analyze with iBPPThis perl script can be
 used to reproduce all simulations in the article "Bayesian species
 delimitation combining multiple genes and traits in a unified
 framework".doSimulations_migration.pliBPP v2.1.2iBPP implements a Bayesian method to delimit species, integrating genetic data and trait data. It builds on BPP (Yang and Rannala, 2010). This is a link to version 2.1.2 in Zenodo, doi:10.5281/zenodo.12927iBPPiBPP implements a Bayesian method to delimit species, integrating genetic data and trait data. It builds on BPP (Yang and Rannala, 2010).
DOI: 10.15468/dl.92vju4
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Kalmiopsis leachiana",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 59 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001319-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.50r4t2p
title: Data from: Collective aggressiveness of an ecosystem engineer is associated with coral recovery

description: The ecological impacts of animal groups may be different and predictable
 depending on their collective behavior. Farmerfish (Stegastes nigricans)
 live in social groups and collectively defend gardens of palatable algae.
 These gardens also serve as settlement and nursery habitats for corals
 because farmerfish mob corallivores that attempt to forage on corals
 within their gardens. We detected large among-colony differences in
 farmerfish collective aggression towards intruder fish that persist across
 years. We further found that the territories of aggressive groups and
 territories containing larger farmerfish provided greater protection to
 corals than non-aggressive groups: territories of aggressive groups
 naturally harbored more branching corals than non-aggressive groups, and
 experimentally outplanted branching corals experienced 80% less skeletal
 loss and grew larger over 25 weeks in aggressive territories and in
 territories guarded by larger fish. These findings hint that factors that
 increase farmerfish group aggressiveness (e.g., higher temperatures) could
 enhance the protective value of their territories for the replenishment of
 coral populations.
description: Stegastes behavior and
 coral performanceJMP_Pink Roof bommies for
 Stegastes behavior.xlsx
DOI: 10.5061/dryad.222h3
title: Data from: The evolution of foraging rate across local and geographic gradients in predation risk and competition

description: Multiple theories predict the evolution of foraging rates in response to
 environmental variation in predation risk, intraspecific competition, time
 constraints, and temperature. We tested six hypotheses for the evolution
 of foraging rate in 24 spotted salamander (Ambystoma maculatum)
 populations from three latitudinally divergent sites using structural
 equation models derived from theory and applied to our system. We raised
 salamander larvae in a common-garden experiment and then assayed foraging
 rate under controlled conditions. Gape-limited predation risk from marbled
 salamanders solely explained foraging rate variation among populations at
 the southern site, which was dominated by this form of selection. However,
 at the middle and northern sites, populations evolved different foraging
 rates depending on their unique responses to local intraspecific density.
 The coupling of gape-limited predation risk from marbled salamanders and
 high intraspecific density at the middle site jointly contributed to
 selection for rapid foraging rate. At the northernmost site, intraspecific
 density alone explained 97% of the interpopulation variation in foraging
 rate. These results suggest that foraging rate has evolved multiple times
 in response to varying contributions from predation risk and intraspecific
 competition. Predation risk often varies along environmental gradients,
 and, thus, organisms might often shift evolutionary responses from
 minimizing predation risk to maximizing intraspecific competitive
 performance.
description: Population and
 Environmental CharacteristicsThe file contains two
 spreadsheets. The first provides the full dataset of environmental
 characteristics for all study ponds. The second spreadsheet provides the
 same data but for the subset of populations included in the common garden
 experiment. This file also includes the foraging rate of spotted
 salamanders in the common garden experiment as biomass of zooplankton
 eaten per day.
DOI: 10.5061/dryad.2ck58
title: Data from: Indirect effects of invasive Burmese pythons on ecosystems in southern Florida

description: Invasive predators can dramatically alter ecosystems through both direct
 predation and indirect effects such as tropic cascades. However, most
 examples of top-down effects of invasive predators in terrestrial systems
 stem from islands or similar low-diversity ecosystems. Snakes are an
 emerging guild of damaging invasive predators, but demonstration of
 ecosystem-level impacts of invasive snakes are limited to the single case
 of the brown treesnake on Guam. Invasive Burmese pythons are firmly
 established in southern Florida and have been linked to severe (80–100%)
 declines of several previously common mammal species (e.g. raccoons,
 opossums and rabbits). Specifically, spatiotemporal patterns of mammal
 declines in the Everglades mirror the spread of pythons and experimental
 reintroductions of rabbits to areas where they had been extirpated failed
 due to high (77% of mortalities) rates of predation by pythons. I
 evaluated the potential indirect effects of pythons on the nesting success
 of oviparous species by monitoring artificial turtle nests (N = 183) at 13
 sites across the expanding range of the python population. I documented
 few mammals and low rates of nest predation (average score = 1·5 on a 1–5
 scale) in the southern Everglades where pythons have been established the
 longest, intermediate (average score = 2·3) rates of nest predation at
 recently invaded sites, and very high (average score = 4·6) rates of nest
 predation at sites with few or no pythons. These findings represent the
 first documentation of potential indirect effects of pythons on non-prey
 species, and suggest that loss or decline of mammals is resulting in
 trophic cascades that threaten the Everglades ecosystem. Synthesis and
 applications. My results suggest that an introduction of non-native apex
 predators can result in trophic cascades that alter even complex,
 continental ecosystems. The Burmese python invasion of South Florida shows
 remarkable parallels with the catastrophic case of the brown treesnake in
 Guam, but in some ways is even more worrisome. Documentation of both
 strong direct impacts on prey and potential indirect effects on
 Everglades’ ecosystems within 15 years after being recognized as
 established emphasizes the need to integrate python management into
 restoration of the Greater Everglades Ecosystem. More broadly, non-native
 snakes warrant significant attention for their potential to become
 damaging invasive species.
description: Willson - Python
 Indirect Effects DataMS excel file with
 mammal observation (camera trap) and nest predation rate
 data.
DOI: 10.5061/dryad.1648b
title: Data from: Predation cost of a sexual signal in the threespine stickleback

description: Much evidence exists for sexually selected traits reflecting various
 components of mate quality, but the factors that limit signal expression
 and ensure honest signaling are less well known. Predation risk has been
 proposed to be one factor that could constrain the elaboration of visually
 conspicuous signals and ensure honesty, but little evidence exists because
 of limitations of earlier used methods. We investigated using a
 combination of field observations and experimental work if a conspicuous
 sexual signal of the threespine stickleback Gasterosteus aculeatus, the
 red nuptial coloration of the male, increases predation risk. We compared
 the proportion of colorful males in the gut of a predator in the wild, the
 perch Perca fluviatilis, to that in the population, and found
 proportionally more red-colored stickleback in the gut. This indicates
 that the predator selectively preys on colorful males under natural
 conditions. To differentiate between the effects of color and behavior on
 susceptibility to predation, we experimentally investigated the attack
 behavior of the predator towards breeding stickleback males differing in
 coloration. We found the predator to preferentially attack more colorful
 males, independent of their behavior. These results indicate that
 predation risk is a cost of the sexual signal that could limit expression
 and influence the honesty of the signal as an indicator of mate quality.
description: Predation cost
 dataField data and
 experimental data reported in the paperPerchPredation publ
 051016.xlsx
DOI: 10.5061/dryad.57nm9
title: Data from: New crinoids from the Baltic region (Estonia): fossil tip-dating phylogenetics constrains the origin and Ordovician–Silurian diversification of the Flexibilia (Echinodermata)

description: This study documents previously unknown taxonomic and morphological
 diversity among early Palaeozoic crinoids. Based on highly complete, well
 preserved crown material, we describe two new genera from the Ordovician
 and Silurian of the Baltic region (Estonia) that provide insight into two
 major features of the geological history of crinoids: the early evolution
 of the flexible clade during the Great Ordovician Biodiversification Event
 (GOBE), and their diversification history surrounding the end-Ordovician
 mass extinction. The unexpected occurrence of a highly derived
 sagenocrinid, Tintinnabulicrinus estoniensis gen. et. sp. nov., from Upper
 Ordovician (lower Katian) rocks of the Baltic palaeocontinent provides
 high-resolution temporal, taxonomic and palaeobiogeographical constraints
 on the origin and early evolution of the Flexibilia. The Silurian (lower
 Rhuddanian, Llandovery) Paerticrinus arvosus gen. et sp. nov. is the
 oldest known Silurian crinoid from Baltica and thus provides the earliest
 Baltic record of crinoids following the aftermath of the end-Ordovician
 mass extinction. A Bayesian ‘fossil tip-dating’ analysis implementing the
 fossilized birth–death process and a relaxed morphological clock model
 suggests that flexibles evolved c. 3 million years prior to their oldest
 fossil record, potentially involving an ancestor–descendant relationship
 (via ‘budding’ cladogenesis or anagenesis) with the paraphyletic cladid
 Cupulocrinus. The sagenocrinid subclade rapidly diverged from ‘taxocrinid’
 grade crinoids during the final stages of the GOBE, culminating in maximal
 diversity among Ordovician crinoid faunas on a global scale. Remarkably,
 diversification patterns indicate little taxonomic turnover among
 flexibles across the Late Ordovician mass extinction. However, the
 elimination of closely related clades may have helped pave the way for
 their subsequent Silurian diversification and increased ecological role in
 post-Ordovician Palaeozoic marine communities. This study highlights the
 significance of studies reporting faunas from undersampled
 palaeogeographical regions for clade-based phylogenetic studies and
 improving estimates of global biodiversity through geological time.
description: Master data and command
 fileThis .nex file contains
 all data, PAUP* and MrBayes commands, and R code related to analyses
 described in the text.Wright_and_Toom.nexClade membershipA .csv file needed to run R code from Wright and Toom.MonoPhy.csv
DOI: 10.5061/dryad.6g735
title: Data from: Koalas (Phascolarctos cinereus) from Queensland are genetically distinct from 2 populations in Victoria

description: The koala (Phascolarctos cinereus) suffered population declines and local
 extirpation due to hunting in the early 20th century, especially in
 southern Australia. Koalas were subsequently reintroduced to the Brisbane
 Ranges (BR) and Stony Rises (SR) by translocating individuals from a
 population on French Island descended from a small number of founders. To
 examine genetic diversity and north–south differentiation, we genotyped 13
 microsatellite markers in 46 wild koalas from the BR and SR, and 27
 Queensland koalas kept at the US zoos. The Queensland koalas displayed
 much higher heterozygosity (H O = 0.73) than the 2 southern Australian
 koala populations examined: H O = 0.49 in the BR, whereas H O = 0.41 in
 the SR. This is consistent with the historical accounts of bottlenecks and
 founder events affecting the southern populations and contrasts with
 reports of high genetic diversity in some southern populations. The 2
 southern Australian koala populations were genetically similar (F ST =
 0.018, P = 0.052). By contrast, northern and southern Australian koalas
 were highly differentiated (F ST = 0.27, P &lt; 0.001), thereby
 suggesting that geographic structuring should be considered in the
 conservation management of koalas. Sequencing of 648bp of the mtDNA
 control region in Queensland koalas found 8 distinct haplotypes, one of
 which had not been previously detected among koalas. Queensland koalas
 displayed high mitochondrial haplotype diversity (H = 0.753) and
 nucleotide diversity (π = 0.0072), indicating along with the
 microsatellite data that North American zoos have maintained high levels
 of genetic diversity among their Queensland koalas.
description: koala microsatellite
 genotypesGenomic sequences from
 one Queensland koala were obtained from 454 GS-FLX technology. Using the
 fragments reads from the 454 data, microsatellites repeats were identified
 using MSATCOMMANDER 1.0.8. Alleles were visualized and scored using
 GeneMapper 3.7. The number zero indicates missing genotype
 data.koala_microsatellite_genotypes.xlsx
DOI: 10.5061/dryad.57vh3
title: Data from: Butterfly community ecology: the influences of habitat type, weather patterns, and dominant species in a temperate ecosystem

description: We compared variation in butterfly communities across 3 years at six
 different habitats in a temperate ecosystem near Boulder, Colorado, USA.
 These habitats were classified by the local Open Space consortium as:
 Grasslands, Tallgrass, Foothills Grasslands, Foothills Riparian, Plains
 Riparian, and Montane Woodland. Rainfall and temperature varied
 considerably during these years. We surveyed butterflies using the
 Pollard-Yates method of invertebrate sampling, and compared abundance,
 species richness, and diversity across habitats and years. Communities
 were most influenced by habitat, with all three quantitative measures
 varying significantly across habitats but only two measures showing
 variation across years. Among habitats, butterfly abundance was higher in
 Plains Riparian sites than in Montane Woodland or Grassland sites, though
 diversity was lowest in Plains Riparian areas. Butterfly species richness
 was higher in Foothills Riparian sites than it was in all but one other
 habitat (Tallgrass). Among years, butterfly abundance and species richness
 were lower during the year of least rainfall and highest temperatures,
 suggesting a substantial impact of the hot, dry conditions. Across
 habitats and years, butterfly abundance was consistently high at Plains
 Riparian and Foothills Riparian sites, and richness and diversity were
 consistently high in Foothills Riparian areas These two habitats may be
 highly suitable for butterflies in this ecosystem, regardless of weather
 conditions. Generally low abundance and species richness in Montane
 Woodlands sites, particularly in 2002, suggested low suitability of the
 habitat to butterflies in this ecosystem, and this may be especially
 important during drought-like conditions. Finally, to examine the effect
 that the presence of the very abundant non-native species Pieris rapae L.
 (Lepidoptera: Pieridae) has on these communities, we re-analysed the data
 in the absence of this species. Excluding P. rapae dramatically reduced
 variation of both butterfly abundance and diversity across habitats,
 highlighting the importance of considering community membership in
 analyses like ours.
description: RobinsonEtAl2012_ButterfliesRobinsonEtAl2012_TransectLocations
DOI: 10.5061/dryad.sh45f
title: Data from: The ‘Last Hurrah of the Reigning Darwinulocopines’? Ostracoda (Arthropoda, Crustacea) from the Lower Jurassic Moenave Formation, Arizona and Utah, USA

description: An ostracod fauna is described from lacustrine sediments of the
 Hettangian, Lower Jurassic Whitmore Point Member of the Moenave Formation.
 The Moenave is well known for its rich, Late Triassic?–Early Jurassic
 fossil record, which includes fossil fishes, stromatolites, ostracods,
 spinicaudatans and a diverse ichnofauna of invertebrates and vertebrates.
 Four ostracod species, all belonging to the suborder Darwinulocopina, were
 recovered from these sediments: Suchonellina globosa, Suchonellina
 stricta, Whipplella? sp. 1 and Whipplella? sp. 2. The diversity and
 composition of the Whitmore Point Member ostracod fauna agree with
 previous interpretations about Lake Dixie and nearby paleoenvironments as
 shallow lakes, where darwinulocopine species which survived the effects of
 the Central Atlantic Magmatic Province and the subsequent End-Triassic
 extinction quickly recolonized these areas thanks to asexual reproduction
 by parthenogenesis. The Lake Dixie region, in its geographical isolation,
 may represent the last episode of darwinulocopine dominance in non-marine
 environments before the Late Jurassic diversification of the
 cypridocopine/cytherocopine modern ostracods.
description: Supplemental Data
 11-09-2017Lithology of the Olsen
 Canyon Section (37°01’02” N, 113°23’22” W) near the City of St. George,
 Washington County, Utah State