cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hk400
title: Data from: Controlled comparison of species- and community-level models across novel climates and communities

description: Species distribution models (SDMs) assume species exist in isolation and
 do not influence one another's distributions, thus potentially
 limiting their ability to predict biodiversity patterns. Community-level
 models (CLMs) capitalize on species co-occurrences to fit shared
 environmental responses of species and communities, and therefore may
 result in more robust and transferable models. Here, we conduct a
 controlled comparison of five paired SDMs and CLMs across changing
 climates, using palaeoclimatic simulations and fossil-pollen records of
 eastern North America for the past 21 000 years. Both SDMs and CLMs
 performed poorly when projected to time periods that are temporally
 distant and climatically dissimilar from those in which they were fit;
 however, CLMs generally outperformed SDMs in these instances, especially
 when models were fit with sparse calibration datasets. Additionally, CLMs
 did not over-fit training data, unlike SDMs. The expected emergence of
 novel climates presents a major forecasting challenge for all models, but
 CLMs may better rise to this challenge by borrowing information from
 co-occurring taxa.
description: Pollen
 SitesList of pollen sites
 included in the analysis with their latitude and
 longitude.FinalSiteList_AppendixI_withoutage.pdfPresence/Absence Pollen DataEach .csv file has a presence/absence matrix for the 19 taxa of interest at all sites for every 500 years from 21000BP to 0BP.PollenPA.zip
DOI: 10.5061/dryad.b0q2g
title: Data from: Speciation with gene flow in North American Myotis bats

description: Growing evidence supports the idea that species can diverge in the
 presence of gene flow. However, most methods of phylogeny estimation do
 not consider this process, despite the fact that ignoring gene flow is
 known to bias phylogenetic inference. Furthermore, studies that do
 consider divergence-with-gene-flow typically do so by estimating rates of
 gene flow using a isolation-with-migration model (IM), rather than
 evaluating scenarios of gene flow (such as divergence-with-gene flow or
 secondary contact) that represent very different types of diversification.
 In this investigation, we aim to infer the recent phylogenetic history of
 a clade of western long-eared bats while evaluating a number of different
 models that parameterize gene flow in a variety of ways. We utilize
 PHRAPL, a new tool for phylogeographic model selection, to compare the fit
 of a broad set of demographic models that include divergence, migration,
 or both among Myotis evotis, $M$. thysanodes and M. keenii. A genomic data
 set consisting of 808 loci of ultraconserved elements was used to explore
 such models in three steps using an incremental design where each
 successive set was informed by, and thus more focused than, the previous
 set of models. Specifically, the three steps were to (i) assess whether
 gene flow should be modeled and identify the best topologies, (ii) infer
 directionality of migration using the best topologies, and (iii) estimate
 the timing of gene flow. The best model (AIC model weight ${\sim}0.98$)
 included two divergence events (($M$. evotis, $M$. thysanodes), M. keenii)
 accompanied by gene flow at the initial stages of divergence. These
 results provide a striking example of speciation-with-gene-flow in an
 evolutionary lineage.
description: Morales.etal.Supp_files_dryadData and scripts.SuppMaterial
DOI: 10.5061/dryad.3t6sc
title: Data from: Overview of phase IV clinical trials for postmarket drug safety surveillance: a status report from the ClinicalTrials.gov registry

description: Objective: Phase IV trials are often used to investigate drug safety after
 approval. However, little is known about the characteristics of
 contemporary phase IV clinical trials and whether these studies are of
 sufficient quality to advance medical knowledge in pharmacovigilance. We
 aimed to determine the fundamental characteristics of phase IV clinical
 trials that evaluated drug safety using the ClinicalTrials.gov registry
 data. Methods: A data set of 19 359 phase IV clinical studies registered
 in ClinicalTrials.gov was downloaded. The characteristics of the phase IV
 trials focusing on safety only were compared with those evaluating both
 safety and efficacy. We also compared the characteristics of the phase IV
 trials in three major therapeutic areas (cardiovascular diseases, mental
 health and oncology). Multivariable logistic regression was used to
 evaluate factors associated with the use of blinding and randomisation.
 Results: A total of 4772 phase IV trials were identified, including 330
 focusing on drug safety alone and 4392 evaluating both safety and
 efficacy. Most of the phase IV trials evaluating drug safety (75.9%) had
 enrolment &lt;300 with 96.5% &lt;3000. Among these trials, 8.2%
 were terminated or withdrawn. Factors associated with the use of blinding
 and randomisation included the intervention model, clinical specialty and
 lead sponsor. Conclusions: Phase IV trials evaluating drug safety in the
 ClinicalTrials.gov registry were dominated by small trials that might not
 have sufficient power to detect less common adverse events. An adequate
 sample size should be emphasised for phase IV trials with safety
 surveillance as main task.
description: phase IV clinical
 studies received by ClinicalTrials.gov between 2004-2014This dataset was
 downloaded from the Internet at March 18, 2015study_fields.xlsx
DOI: 10.5061/dryad.p064v
title: Data from: Fitness costs of worker specialisation for ant societies

description: Division of labour is of fundamental importance for the success of
 societies, yet little is known about how individual specialization affects
 the fitness of the group as a whole. While specialized workers may be more
 efficient in the tasks they perform than generalists, they may also lack
 the flexibility to respond to rapid shifts in task needs. Such rigidity
 could impose fitness costs when societies face dynamic and unpredictable
 events, such as an attack by socially parasitic slavemakers. Here, we
 experimentally assess the colony-level fitness consequences of behavioural
 specialization in Temnothorax longispinosus ants that are attacked by the
 slavemaker ant T. americanus. We manipulated the social organization of
 102 T. longispinosus colonies, based on the behavioural responses of all
 3842 workers. We find that strict specialization is disadvantageous for a
 colony's annual reproduction and growth during slave raids. These
 fitness costs may favour generalist strategies in dynamic environments, as
 we also demonstrate that societies exposed to slavemakers in the field
 show a lower degree of specialization than those originating from
 slavemaker-free populations. Our findings provide an explanation for the
 ubiquity of generalists and highlight their importance for the flexibility
 and functional robustness of entire societies.
description: Jongepier_Foitzik_2015_DATA_ProcRSocBConsists of a meta data table with variable descriptions and 5 data tables; Jongepier_data_var, Jongepier_data_pop, Jongepier_data_setup, Jongepier_data_raid and Jongepier_data_scan.Jongepier_Foitzik_2015_SCRIPT_ProcRSocBR script
DOI: 10.5061/dryad.jq933
title: Data from: Temporal and phylogenetic evolution of the sauropod dinosaur body plan

description: The colossal size and body plan of sauropod dinosaurs are unparalleled in
 terrestrial vertebrates. However, to date, there have been only limited
 attempts to examine temporal and phylogenetic patterns in the sauropod
 bauplan. Here, we combine three-dimensional computational models with
 phylogenetic reconstructions to quantify the evolution of whole-body shape
 and body segment properties across the sauropod radiation. Limitations
 associated with the absence of soft tissue preservation in fossils result
 in large error bars about mean absolute body shape predictions. However,
 applying any consistent skeleton : body volume ratio to all taxa does
 yield changes in body shape that appear concurrent with major
 macroevolutionary events in sauropod history. A caudad shift in
 centre-of-mass (CoM) in Middle Triassic Saurischia, associated with the
 evolution of bipedalism in various dinosaur lineages, was reversed in Late
 Triassic sauropodomorphs. A craniad CoM shift coincided with the evolution
 of quadrupedalism in the Late Triassic, followed by a more striking
 craniad shift in Late Jurassic–Cretaceous titanosauriforms, which included
 the largest sauropods. These craniad CoM shifts are strongly correlated
 with neck enlargement, a key innovation in sauropod evolution and pivotal
 to their gigantism. By creating a much larger feeding envelope, neck
 elongation is thought to have increased feeding efficiency and opened up
 trophic niches that were inaccessible to other herbivores. However, we
 find that relative neck size and CoM position are not strongly correlated
 with inferred feeding habits. Instead the craniad CoM positions of
 titanosauriforms appear closely linked with locomotion and environmental
 distributions, potentially contributing to the continued success of this
 group until the end-Cretaceous, with all other sauropods having gone
 extinct by the early Late Cretaceous.
description: ConvexHullsData S1.zipAll_ACE_Results
DOI: 10.5061/dryad.6rv61
title: Data from: Patterns of vertebrate diversity and protection in Brazil

description: Most conservation decisions take place at national or finer spatial
 scales. Providing useful information at such decision-making scales is
 essential for guiding the practice of conservation. Brazil is one of the
 world’s megadiverse countries, and consequently decisions about
 conservation in the country have a disproportionate impact on the survival
 of global biodiversity. For three groups of terrestrial vertebrates
 (birds, mammals, and amphibians), we examined geographic patterns of
 diversity and protection in Brazil, including that of endemic,
 small-ranged, and threatened species. To understand potential limitations
 of the data, we also explored how spatial bias in collection localities
 may influence the perceived patterns of diversity. The highest overall
 species richness is in the Amazon and Atlantic Forests, while the Atlantic
 Forest dominates in terms of country endemics and small-ranged species.
 Globally threatened species do not present a consistent pattern. Patterns
 for birds were similar to overall species richness, with higher
 concentrations of threatened species in the Atlantic Forest, while mammals
 show a more generalized pattern across the country and a high
 concentration in the Amazon. Few amphibians are listed as threatened,
 mostly in the Atlantic Forest. Data deficient mammals occur across the
 country, concentrating in the Amazon and southeast Atlantic Forest, and
 there are no data deficient birds in Brazil. In contrast, nearly a third
 of amphibians are data deficient, widespread across the country, but with
 a high concentration in the far southeast. Spatial biases in species
 locality data, however, possibly influence the perceived patterns of
 biodiversity. Regions with low sampling density need more biological
 studies, as do the many data deficient species. All biomes except the
 Amazon have less than 3% of their area under full protection. Reassuringly
 though, rates of protection do correlate with higher biodiversity,
 including higher levels of threatened and small-ranged species. Our
 results indicate a need for expanded formal protection in Brazil,
 especially in the Atlantic forest, and with an emphasis on fully protected
 areas.
description: GIS
 resultsContains a mix of
 shapefiles and georeferenced TIFF files of the results shown in the
 paper's figures.Jenkins_et_al_2015_GIS_results.zip
DOI: 10.5061/dryad.1p7sf
title: Data from: Genome-wide association reveals the locus responsible for four-horned ruminant

description: Phenotypic variability in horn characteristics, such as their size, number
 and shape, offers the opportunity to elucidate the molecular basis of horn
 development. The objective of this study was to map the genetic
 determinant controlling the production of four horns in two breeds, Jacob
 sheep and Navajo-Churro, and examine whether an eyelid abnormality
 occurring in the same populations is related. Genome-wide association
 mapping was performed using 125 animals from the two breeds that contain
 two- and four-horned individuals. A case–control design analysis of 570
 712 SNPs genotyped with the ovine HD SNP Beadchip revealed a strong
 association signal on sheep chromosome 2. The 10 most strongly associated
 SNPs were all located in a region spanning Mb positions 131.9–132.6,
 indicating the genetic architecture underpinning the production of four
 horns is likely to involve a single gene. The closest genes to the most
 strongly associated marker (OAR2_132568092) were MTX2 and the HOXD
 cluster, located approximately 93 Kb and 251 Kb upstream respectively. The
 occurrence of an eyelid malformation across both breeds was restricted to
 polled animals and those carrying more than two horns. This suggests the
 eyelid abnormality may be associated with departures from the normal
 developmental production of two-horned animals and that the two conditions
 are developmentally linked. This study demonstrated the presence of
 separate loci responsible for the polled and four-horned phenotypes in
 sheep and advanced our understanding of the complexity that underpins horn
 morphology in ruminants.
description: GWAS_SNP_GenotypesSNP genotypes formatted as ped and map files for analysis using PLINK v1.7 or later.Dryad_Submission.7z
DOI: 10.5061/dryad.1041
title: Data from: Epidermal growth factor receptor and transforming growth factor-ß signaling contributes to variation for wing shape in Drosophila melanogaster

description: Wing development in Drosophila is a common model system for the dissection
 of genetic networks and their roles during development. In particular, the
 RTK and TGF-ß regulatory networks appear to be involved with numerous
 aspects of wing development, including patterning, cell determination,
 growth, proliferation, and survival in the developing imaginal wing disc.
 However, little is known as to how subtle changes in the function of these
 genes may contribute to quantitative variation for wing shape, per se. In
 this study 50 insertional mutations, representing 43 loci in the RTK,
 Hedgehog, TGF-ß pathways, and their genetically interacting factors were
 used to study the role of these networks on wing shape. To concurrently
 examine how genetic background modulates the effects of the mutation, each
 insertion was introgressed into two wild-type genetic backgrounds. Using
 geometric morphometric methods, it is shown that the majority of these
 mutations have profound effects on shape but not size of the wing when
 measured as heterozygotes. To examine the relationships between how each
 mutation affects wing shape hierarchical clustering was used. Unlike
 previous observations of environmental canalization, these mutations did
 not generally increase within-line variation relative to their wild-type
 counterparts. These results provide an entry point into the genetics of
 wing shape and are discussed within the framework of the dissection of
 complex phenotypes.
description: Supplementary
 DataSupplInfo14.pdf
DOI: 10.5061/dryad.310nt
title: Data from: Flexibility and control of thorax deformation during hawkmoth flight

description: The interaction between neuromuscular systems and body mechanics plays an
 important role in the production of coordinated movements in animals.
 Lepidopteran insects move their wings by distortion of the thorax
 structure via the indirect flight muscles (IFMs), which are activated by
 neural signals at every stroke. However, how the action of these muscles
 affects thorax deformation and wing kinematics is poorly understood. We
 measured the deformation of the dorsal thorax (mesonotum) of tethered
 flying hawkmoths, Agrius convolvuli, using a high-speed laser profilometer
 combined with simultaneous recordings of electromyograms and wing
 kinematics. We observed that locally amplified mesonotum deformation near
 the wing hinges ensures sufficient wing movement. Furthermore, phase
 asymmetry in IFM activity leads to phase asymmetry in mesonotum
 oscillations and wingbeats. Our results revealed the flexibility and
 controllability of the single structure of the mesonotum by neurogenic
 action of the IFMs.
description: DatasetsThe datasets include text files (z-position of thorax morphology), an R script file for visualization and sample reconstructed images (bmp, avi and webGL).datasets.zip
DOI: 10.5061/dryad.cp4mb
title: Data from: Comparative analysis of Begonia plastid genomes and their utility for species-level phylogenetics

description: Recent, rapid radiations make species-level phylogenetics difficult to
 resolve. We used a multiplexed, high-throughput sequencing approach to
 identify informative genomic regions to resolve phylogenetic relationships
 at low taxonomic levels in Begonia from a survey of sixteen species. A
 long-range PCR method was used to generate draft plastid genomes to
 provide a strong phylogenetic backbone, identify fast evolving regions and
 provide informative molecular markers for species-level phylogenetic
 studies in Begonia.
description: Region21_Mulitiple_alignment(ndhI-ndhG) Plastid sequences containing high sequence divergence that could be suitable for phylogenetic analyses at the species level in Begonia. Short (804 bp), Sanger-sequence-able region with average pairwise identity of 86.7%. Bayesian inference phylogenetic reconstruction analysed under a GTR+I+G model performed in MrBayes, with 13 taxa rooted on B.varipeltata.Region24_multiple_alignment(rpoB–psbD) Plastid sequences containing high sequence divergence that could be suitable for phylogenetic analyses at the species level in Begonia. Medium length (1360 bp), with average pairwise identity of 93.9%. Bayesian inference phylogenetic reconstruction analysed under a GTR+I+G model performed in MrBayes, with 16 taxa rooted on B.bogneri.Whole_plastid_alignmentThe draft sequence generated for B. peltata was used as a reference to map each set of assembled contigs for all sixteen Begonia species (including B. peltata). Plastid genome contigs were aligned to B. peltata using MAFFT v6.717 (Multiple Alignment using Fast Fourier Transform) (30) applying the iterative refinement method (FFT-NS-i) and using default parameter settings (gap opening penality: 1.53, offset-value: 0.0) and then visually inspected and manually adjusted in the software program Geneious Pro 5.6.3 (http://www.geneious.com/).
DOI: 10.5285/6ecfd160-4740-491e-a8b3-8cbb3a4c8701
title: Functional traits of the tallest tropical tree species in Borneo, 2022

description: This dataset comprises 25 traits related to plant hydraulic function and wood anatomy for 38 individual trees of five dipterocarp species from a site in Borneo. Traits were measured at multiple positions along each tree: at the bottom and the top of the trunk, then at 3 positions along a lower, a middle, and an upper branch in the crown of the tree - so 12 measurement points per tree for the traits. The trees that were measured ranged in height from 7.7 to 71 m in height. These data were all collected following standardised methodologies for each trait sampled and they were all collected during one very large field campaign which took place during 2022. Following this anatomy samples and data were processed. The aim of this data set was to test whether tree height alters the water transport system of trees to make them more vulnerable to the impacts of drought.
description: Samples were collected from 38 individual trees of five Dipterocarp species throughout May-July 2022. To measure trait values 1-2m length branches were extracted from each sample location in the tree crowns (upper crown, and when crown depth allowed, also mid-crown and lower-crown). Vertical height and horizontal distance from the main stem were recorded for each excised branch to enable hydraulic path length to be calculated. In addition, wood cores were extracted with increment borers at breast height (1.3m, or just above any buttresses). Immediately after sampling material was sealed in moist bags and transported to laboratories at the Sabah Forest Research Centre (10-30 minutes' walk), where functional traits were measured. The traits measured included leaf and wood structural traits, leaf and wood hydraulic traits and wood anatomy traits. The full list of traits measures and procedures used to measure the traits are laid out in the supporting information. All data were entered into a excel spreadsheet and saved as a .csv file.
DOI: 10.5061/dryad.ch4nr
title: Data from: Effects of chronic consumption of sugar-enriched diets on brain metabolism and insulin sensitivity in adult Yucatan Minipigs

description: Excessive sugar intake might increase the risk to develop eating disorders
 via an altered reward circuitry, but it remains unknown whether different
 sugar sources induce different neural effects and whether these effects
 are dependent from body weight. Therefore, we compared the effects of
 three high-fat and isocaloric diets varying only in their carbohydrate
 sources on brain activity of reward-related regions, and assessed whether
 brain activity is dependent on insulin sensitivity. Twenty-four minipigs
 underwent 18FDG PET brain imaging following 7-month intake of high-fat
 diets of which 20% in dry matter weight (36.3% of metabolisable energy)
 was provided by starch, glucose or fructose (n = 8 per diet). Animals were
 then subjected to a euglycemic hyperinsulinemic clamp to determine
 peripheral insulin sensitivity. After a 7-month diet treatment, all groups
 had substantial increases in body weight (from 36.02±0.85 to 63.33±0.81
 kg; P&lt;0.0001), regardless of the diet. All groups presented similar
 insulin sensitivity index (ISI = 1.39±0.10 mL·min-1·μUI·kg). Compared to
 starch, chronic exposure to fructose and glucose induced bilateral brain
 activations, i.e. increased basal cerebral glucose metabolism, in several
 reward-related brain regions including the anterior and dorsolateral
 prefrontal cortex, the orbitofrontal cortex, the anterior cingulate
 cortex, the caudate and putamen. The lack of differences in insulin
 sensitivity index and body weight suggests that the observed differences
 in basal brain glucose metabolism are not related to differences in
 peripheral insulin sensitivity and weight gain. The differences in basal
 brain metabolism in reward-related brain areas suggest the onset of
 cerebral functional alterations induced by chronic consumption of dietary
 sugars. Further studies should explore the underlying mechanisms, such as
 the availability of intestinal and brain sugar transporter, or the
 appearance of addictive-like behavioral correlates of these brain
 functional characteristics.
description: PET raw
 dataRaw FDG PET images in
 nifty format. Images were obtained 45 minutes after FDG injection. See
 additional file for animals groups.Images.zipClamp Data & animals groups assignmentExcel file with all data required to calculate M value from Defronzo formula plus animal assignment to three different groups defined by their dietClamp Data.xlsx