cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8k821ds
title: Data from: Evaluating statistical multiple sequence alignment in comparison to other alignment methods on protein data sets

description: The estimation of multiple sequence alignments of protein sequences is a
 basic step in many bioinformatics pipelines, including protein structure
 prediction, protein family identification, and phylogeny estimation.
 Statistical co-estimation of alignments and trees under stochastic models
 of sequence evolution has long been considered the most rigorous technique
 for estimating alignments and trees, but little is known about the
 accuracy of such methods on biological benchmarks. We report the results
 of an extensive study evaluating the most popular protein alignment
 methods as well as the statistical co-estimation method BAli-Phy on 1192
 protein data sets from established benchmarks as well as on 120 simulated
 data sets. Our study (which used more than 230 CPU years for the BAli-Phy
 analyses alone) shows that BAli-Phy has better precision and recall (with
 respect to the true alignments) than the other alignment methods on the
 simulated data sets, but has consistently lower recall on the biological
 benchmarks (with respect to the reference alignments) than many of the
 other methods. In other words, we find that BAli-Phy systematically
 under-aligns when operating on biological sequence data, but shows no sign
 of this on simulated data. There are several potential causes for this
 change in performance, including model misspecification, errors in the
 reference alignments, and conflicts between structural alignment and
 evolutionary alignments, and future research is needed to determine the
 most likely explanation. We conclude with a discussion of the potential
 ramifications for each of these possibilities.
description: Alignment
 DataContains reference
 alignments and BAli-Phy Posterior Decoding alignments for all data
 referred to in the manuscript.data_for_dryad.zipS2-supplementary_information_spreadsheet_v5_resubmissionAn excel spreadsheet with all of the detailed results of the study described in the paper.S1 - SupplementContains supplementary tables and exhibits referred to in the manuscript.revision-systematic-biology-supplement.pdf
DOI: 10.5061/dryad.6t5m946
title: Data from: Increases in sampling support the southern Gondwanan hypothesis for the origin of dinosaurs

description: Dinosaurs were ubiquitous in terrestrial ecosystems through most of the
 Mesozoic and are still diversely represented in the modern fauna in the
 form of birds. Recent efforts to better understand the origins of the
 group have resulted in the discovery of many new species of early
 dinosaurs and their closest relatives (dinosauromorphs). In addition,
 recent re-examinations of early dinosaur phylogeny have highlighted
 uncertainties regarding the interrelationships of the main dinosaur
 lineages (Sauropodomorpha, Theropoda and Ornithischia), and questioned the
 traditional hypothesis that the group originated in South Gondwana and
 gradually dispersed over Pangaea. Here, we use a historical approach to
 examine the impact of new fossil discoveries and changing phylogenetic
 hypotheses on biogeographic scenarios for dinosaur origins over 20 years
 of research time, and analyse the results in the light of different fossil
 record sampling regimes. Our results consistently optimize South Gondwana
 as the ancestral area for Dinosauria, as well as for more inclusive clades
 including Dinosauromorpha, and show that this hypothesis is robust to
 increased taxonomic and geographic sampling and divergent phylogenetic
 results. Our results do not find any support for the recently proposed
 Laurasian origin of dinosaurs and suggest that a southern Gondwanan origin
 is by far the most plausible given our current knowledge of the diversity
 of early dinosaurs and non-dinosaurian dinosauromorphs.
description: R
 packagesR packages to run the
 biogeographical analyses.Supplementary
 filesThis folder includes all
 data required to run the biogeographic analyses (Ages, Areas, Distance
 multipliers, Time periods and Newick trees) and the resulting Tests tables
 (LRT and AICc) of our analyses.Appendix
 S1This file includes all
 results of the analysis, including the exploratory analysis which consider
 the ichnological record of possible dinosauromorphs in the Early-Middle
 Triassic of Europe.
DOI: 10.5061/dryad.s22s280
title: Data from: Why less complexity produces better forecasts: an independent data evaluation of kelp habitat models

description: Understanding how species are distributed in the environment is
 increasingly important for natural resource management, particularly for
 keystone and habitat forming species, and those of conservation concern.
 Habitat suitability models are fundamental to developing this
 understanding; however their use in management continues to be limited due
 to often-vague model objectives and inadequate evaluation methods. Along
 the Northeast Pacific coast, canopy kelps (Macrocystis pyrifera and
 Nereocystis luetkeana) provide biogenic habitat and considerable primary
 production to nearshore ecosystems. We investigated the distribution of
 these species by examining a series of increasingly complex habitat
 suitability models ranging from process-based models based on
 species' ecology to complex Generalised Additive Models applied to
 purpose-collected survey data. Seeking limits on model complexity, we
 explored the relationship between model complexity and forecast skill,
 measured using both cross-validation and independent data evaluation. Our
 analysis confirmed the importance of predictors used in models of coastal
 kelp distributions developed elsewhere (i.e., depth, bottom type, bottom
 slope, and exposure); it also identified additional important factors
 including salinity, and interactions between exposure and salinity, and
 slope and tidal energy. Comparative results showed that cross-validation
 can lead to over-fitting, while independent data evaluation clearly
 identified the appropriate model complexity for generating habitat
 forecasts. Our results also illustrate that, depending on the evaluation
 data, predictions from simpler models can out-perform those from more
 complex models. Collectively, the insights from evaluating multiple models
 with multiple data sets contribute to the holistic assessment of model
 forecast skill. The continued development of methods and metrics for
 evaluating model forecasts with independent data, and the explicit
 consideration of model objectives and assumptions, promise to increase the
 utility of model forecasts to decision makers.
description: dataGregrEcography_2018Includes: 1) Kelp survey and remote sensing data as csv files; 2) various processed results in RData format.scriptsGregrEcography_2018R scripts for processing and analysing the data.
DOI: 10.5061/dryad.sh4m4s6
title: Data from: Ant colonies maintain social homeostasis in the face of decreased density

description: Interactions lie at the heart of social organization, particularly in ant
 societies. Interaction rates are presumed to increase with density, but
 there is little empirical evidence for this. We manipulated density within
 carpenter ant colonies of the species Camponotus pennsylvanicus by
 quadrupling nest space and by manually tracking 6.9 million ant locations
 and over 3200 interactions to study the relationship between density,
 spatial organization and interaction rates. Colonies divided into distinct
 spatial regions on the basis of their underlying spatial organization and
 changed their movement patterns accordingly. Despite a reduction in both
 overall and local density, we did not find the expected concomitant
 reduction in interaction rates across all colonies. Instead, we found
 divergent effects across colonies. Our results highlight the remarkable
 organizational resilience of ant colonies to changes in density, which
 allows them to sustain two key basic colony life functions, that is food
 and information exchange, during environmental change.
description: Modlmeier et al data
 set
DOI: 10.5061/dryad.6jk8h77
title: Data from: Lake regionalization and diatom metacommunity structuring in tropical South America

description: Lakes and their topological distribution across Earth’s surface impose
 ecological and evolutionary constraints on aquatic metacommunities. In
 this study, we group similar lake ecosystems as metacommunity units
 influencing diatom community structure. We assembled a database of 195
 lakes from the tropical Andes and adjacent lowlands (8ºN–30ºS and 58–79ºW)
 with associated environmental predictors to examine diatom metacommunity
 patterns at two different levels: taxon and functional (deconstructed
 species matrix by ecological guilds). We also derived spatial variables
 that inherently assessed the relative role of dispersal. Using
 complementary multivariate statistical techniques (Principal Component
 Analysis, cluster analysis, non-metric multidimensional scaling,
 Procrustes, variance partitioning), we examined diatom-environment
 relationships among different lake habitats (sediment surface, periphyton
 and plankton) and partitioned community variation to evaluate the
 influence of niche- and dispersal-based assembly processes in diatom
 metacommunity structure across lake clusters. The results showed a
 significant association between geographic clusters of lakes based on
 gradients of climate and landscape configuration and diatom assemblages.
 Six lake clusters distributed along a latitudinal gradient were identified
 as functional metacommunity units for diatom communities. Variance
 partitioning revealed that dispersal mechanisms were a major contributor
 to diatom metacommunity structure, but in a highly context-dependent
 fashion across lake clusters. In the Andean Altiplano and adjacent
 lowlands of Bolivia, diatom metacommunities are niche assembled but
 constrained by either dispersal limitation or mass effects, resulting from
 area, environmental heterogeneity, and ecological guild relationships.
 Topographic heterogeneity played an important role in structuring planktic
 diatom metacommunities. We emphasize the value of a guild-based
 metacommunity model linked to dispersal for elucidating mechanisms
 underlying latitudinal gradients in distribution. Our findings reveal the
 importance of shifts in ecological drivers across climatic and
 physiographically distinct lake clusters, providing a basis for comparison
 of broad-scale community gradients in lake-rich regions elsewhere. This
 may help guide future research to explore evolutionary constraints on the
 rich Neotropical benthic diatom species pool.
description: Tropical South America
 Diatom DatabaseThis database consists
 in two different datasets: 1) Diatom dataset: include the individual
 diatom datasets (presence/absence data) of the study regions 2)
 Environment dataset: include limnological and geo-climatic variables of
 the study lakesTropicalSA-DiatomDB.xlsx
DOI: 10.5061/dryad.9pr1476
title: Data from: The importance of core habitat for a threatened species in changing landscapes

description: 1. Habitat loss, fragmentation and alteration of the landscape matrix are
 interdependent processes, collectively responsible for most recent species
 extinctions. Thus, determining the extent to which these landscape
 processes affect animals is critical for conservation. However,
 researchers have often assumed that interdependent effects are
 independently related to animals’ responses, underestimating the
 importance of one or several landscape processes in driving species
 declines. 2. We demonstrate how to disentangle the interdependent effects
 of habitat area, fragmentation, and edge context on population size by
 assessing abundance of a rapidly-declining grassland songbird species
 (Grasshopper Sparrow, Ammodramus savannarum) in eastern Kansas (USA). We
 conducted &gt; 7,000 point-count bird surveys at &gt; 2,000 sites
 over two breeding seasons, then modelled the direct, interactive, and
 indirect effects of landscape factors on abundance within spatial scales
 (200-, 400-, 800-, 1600-m radii) relevant to our focal species’ dispersal
 behavior. 3. Sparrow abundance correlated most strongly with landscape
 structure within 400-m radii, increasing non-linearly with grassland area
 and decreasing with the proportion of grassland near cropland or woody
 edges. Sparrows’ negative response to cropland edges was mostly an added,
 indirect consequence of reduced grassland area, whereas sparrows’ stronger
 negative response to woody edges was not attributable to variation in
 grassland area. Fragmentation and edge context mattered most in landscapes
 comprising ~ 50–80% grassland. 4. Synthesis and applications. Abundance of
 a threatened grassland songbird was influenced more by core grassland area
 (a function of total grassland area, fragmentation, and edge context) than
 total grassland area per se. Moreover, a local extinction threshold of ~
 50% grassland indicated that small amounts of habitat were unsuitable for
 our focal species regardless of habitat configuration or matrix type.
 Local extinction thresholds in response to habitat area provide clear
 baseline targets for land managers; above those thresholds, configuration
 and the matrix can be modified to increase abundance of edge-sensitive
 animals. Conflicting evidence in the literature regarding the importance
 of fragmentation and matrix features could be partially explained by
 species-level traits, or methodological issues such as defining landscapes
 at ecologically-arbitrary spatial scales, assessing landscape quality
 using species richness, and ignoring interactive and indirect effects.
description: Input
 dataThis file contains all
 of the data used for conducting analyses and plotting results for this
 study.grsp_glmm_input_data.csvR codeThis file contains the R script used for conducting all analyses and plotting results for this study.grsp_glmm_code.r
DOI: 10.5061/dryad.v7k54df
title: Data from: Crop-to-wild hybridization in cherries – empirical evidence from Prunus fruticosa

description: Crop cultivation can lead to genetic swamping of indigenous species and
 thus pose a serious threat for biodiversity. The rare Eurasian tetraploid
 shrub Prunus fruticosa (ground cherry) is suspected of hybridizing with
 cultivated allochthonous tetraploid P. cerasus and autochthonous diploid
 P. avium. Three Prunus taxa (447 individuals of P. fruticosa, 43 of P.
 cerasus and 73 of P. avium) and their hybrids (198 individuals) were
 evaluated using analysis of absolute genome size/ploidy level and
 multivariate morphometrics. Flow cytometry revealed considerable
 differentiation in absolute genome size at the tetraploid level (average
 2C of P. fruticosa = 1.30 pg, average 2C of P. cerasus = 1.42 pg, i.e. a
 9.2% difference). The combination of methods used allowed us to ascertain
 the frequency of hybrids occurring under natural conditions in Central
 Europe. The morphological evaluation of leaves was based upon
 distance-based morphometrics supplemented by elliptic Fourier analysis.
 The results provided substantial evidence for ongoing hybridization
 (hybrids occurred in 39.5% of P. fruticosa populations). We detected
 homoploid introgressive hybridization with alien P. cerasus at the
 tetraploid level. We also found previously overlooked but frequent
 triploid hybrids resulting from heteroploid hybridization with indigenous
 P. avium, which, however, probably represent only the F1 generation.
 Although both hybrids differ in ploidy, they cannot be distinguished using
 morphometrics. Hybrids are frequent and may endanger wild populations of
 genuine P. fruticosa via direct niche competition or, alternatively or in
 addition, via introgression at the homoploid level (i.e. genetic
 swamping). The cultivation of cherries thus substantially threatens the
 existence of genuine P. fruticosa.
description: raw data: FCM, distance
 based and elliptic Fourier morphometricsraw
 dataraw
 data_FCM+morphometrics.xlsx
DOI: 10.5061/dryad.467hp97
title: Data from: In situ reference datasets from the TropiSAR and AfriSAR campaigns in support of upcoming spaceborne biomass missions

description: Tropical forests are a key component of the global carbon cycle. Yet,
 there are still high uncertainties in forest carbon stock and flux
 estimates, notably because of their spatial and temporal variability
 across the tropics. Several upcoming spaceborne missions have been
 designed to address this gap. High-quality ground data are essential for
 accurate calibration/validation so that spaceborne biomass missions can
 reach their full potential in reducing uncertainties regarding forest
 carbon stocks and fluxes. The BIOMASS mission, a P-band SAR satellite from
 the European Space Agency (ESA), aims at improving carbon stock mapping
 and reducing uncertainty in the carbon fluxes from deforestation, forest
 degradation, and regrowth. In situ activities in support of the BIOMASS
 mission were carried out in French Guiana and Gabon during the TropiSAR
 and AfriSAR campaigns. During these campaigns, airborne P-band SAR, forest
 inventory, and lidar data were collected over six study sites. This paper
 describes the methods used for forest inventory and lidar data collection
 and analysis, and presents resulting plot estimates and aboveground
 biomass maps. These reference datasets along with intermediate products
 (e.g., canopy height models) can be accessed through ESA's Forest
 Observation System and the Dryad data repository and will be useful for
 BIOMASS but also to other spaceborne biomass missions such as GEDI, NISAR,
 and Tandem-L for calibration/validation purposes. During data quality
 control and analysis, prospects for reducing uncertainties have been
 identified, and this paper finishes with a series of recommendations for
 future tropical forest field campaigns to better serve the remote sensing
 community.
description: In situ datasets from
 the TropiSAR and AfriSAR campaignsThree types of data are
 provided in the different folders: (1) Tabular data files (.csv)
 containing plot-based estimates of aboveground biomass and lidar-derived
 metrics for calibration points of 1ha or 0.25ha (0.16ha in case relative
 tree coordinates were missing); (2) Raster files (.tif) corresponding to
 maps of predicted aboveground biomass (at 50-m, 100-m and 200-m
 resolution). Digital terrain models (DTM) and canopy height models (CHM)
 at 1-m resolution are available upon request to the study site PIs
 (contact details provided in the README file); (3) Vector files (.shp)
 containing polygons corresponding to the location of calibration points of
 1ha or 0.25ha (0.16ha in case relative tree coordinates were missing).
 PLEASE SEE README FILE FOR MORE INFORMATIONIN_SITU_DATA_TropiSAR_AfriSAR.zip
DOI: 10.15468/dl.bkw8zw
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Corydalis yanhusuo",
 "Year 1975-2026"
 ]
}

 The dataset includes 46 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001546-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18376054
title: DZD Core Data Set - Metadata and SOP

description: DZD Core Data Set - Metadata and SOPs contains documentation for the DZD Core Data Set. The German Center for Diabetes Research (DZD) conducts large clinical multicenter studies in the field of diabetes and metabolic research. The DZD has established the DZD Core Data Set which contains a list of clinical parameters relevant for diabetes research in related clinical studies. The Core Data Set itself is published at MDM Portal.
description: Metadata and SOPs are a supplement for the DZD Core Data Set. The DZD Core Data Set is published at MDM Portal.
DOI: 10.5281/zenodo.7360000
title: DZD Core Data Set - Metadata and SOP

description: DZD Core Data Set - Metadata and SOPs contains documentation for the DZD Core Data Set. The German Center for Diabetes Research (DZD) conducts large clinical multicenter studies in the field of diabetes and metabolic research. The DZD has established the DZD Core Data Set which contains a list of clinical parameters relevant for diabetes research in related clinical studies. The Core Data Set itself is published at MDM Portal.
description: Metadata and SOPs are a supplement for the DZD Core Data Set. The DZD Core Data Set is published at MDM Portal.
DOI: 10.15468/dl.2ezngf
title: Occurrence Download

description: A dataset containing 2326 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Philippines",
 "Geometry POLYGON((120.21671 19.7098,122.73204 19.7098,122.73204 22.04766,120.21671 22.04766,120.21671 19.7098))",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 2326 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001544-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kj8kp94
title: Data from: Rapid evolution and the genomic consequences of selection against interspecific mating

description: While few species introduced into a new environment become invasive, those
 that do provide critical information on ecological mechanisms that
 determine invasions success and the evolutionary responses that follow
 invasion. Aedes albopictus (the Asian tiger mosquito) was introduced into
 the naturalized range of Aedes aegypti (the yellow fever mosquito) in the
 USA in the mid-1980s, resulting in the displacement of A. aegypti in much
 of the southeastern USA. The rapid displacement was likely due to the
 superior competitive ability of A. albopictus as larvae and asymmetric
 mating interference competition, in which male A. albopictus mate with and
 sterilize A. aegypti females, a process called “satyrization”. The goal of
 this study was to examine the genomic responses of a resident species to
 an invasive species in which the mechanism of character displacement is
 understood. We used double-digest restriction enzyme DNA sequencing
 (ddRADseq) to analyze outlier loci between selected and control lines of
 laboratory-reared A. aegypti females from two populations (Tucson, AZ and
 Key West, Florida, USA), and individual females classified as either
 “resisted” or “mated with” A. albopictus males via mating trials of
 wild-derived females from four populations in Florida. We found
 significant outlier loci in comparing selected and control lines and
 between mated and non-mated A. aegypti females in the laboratory and
 wild-derived populations, respectively. We found overlap in specific
 outlier loci between different source populations that support consistent
 genomic signatures of selection within A. aegypti. Our results point to
 regions of the A. aegypti genome and potential candidate genes that may be
 involved in mating behavior, and specifically in avoiding interspecific
 mating choices.
description: 31OutlierSequencesBED file for genomic placement of mapped reads from selection experiment42seqsOf49SNPs_ForMappingToGenomeShared outlier sequences from selected lines.FloridaPopMap of Florida Populations "Wild Derived"FloridaPopFlorida population genetics file (.ped)P-val-for -LD_49LociRevisedRevisedP-values for pairwise exact tests.SelectedvsWild-expermt.map file for population genomic comparisons of the wild derived mosquitoes.SelectedvsWild-expermt.ped file for comparisons of population genomics for field populations from FloridaYvsNOutlierLoci.bed file for the outlier loci comparing "yes" and "no" phenotypes from wild-derived populations in Florida.