cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9tb73
title: Data from: Angiosperm fleshy fruits and seed dispersers: a comparative analysis of adaptation and constraints in plant-animal interactions

description: Variation in phenotypic traits of angiosperm fleshy fruits has been
 explained as the result of adaptations to their mutualistic seed
 dispersers. By analyzing the information available on fleshy fruit
 characteristics of 910 angiosperm species, I assess the hypothesis of
 evolutionary association between fruit phenotypic traits and type of seed
 disperser (birds, mammals, and mixed dispersers) and address explicitly
 and quantitatively alternative null hypotheses about phylogenetic effects.
 Phylogenetic affinity among plant taxa is accounted for by comparative
 methods including nested ANOVA, phylogenetic autocorrelation, and
 independent contrasts. Averaging over the 16 fruit traits examined,
 phylogenetic effects down to genus level explain 61% of total variance.
 Phylogenetic autocorrelations are strong among close relatives, reaching
 significance for 11 of the 16 fruit traits examined. When assessed by
 independent contrast methods, correlated evolution between type of
 disperser and fruit traits is confined to fruit diameter. Differences
 among dispersal syndromes in other traits vanish after accounting for
 phylogenetic effects. These analyses reveal that seed dispersal syndromes
 are not entirely interpretable as current adaptations to seed dispersers.
 Their status as exaptations can be assessed by combining experimental
 studies of natural selection on fruit size and rigorous comparative and
 cladistic tests of adaptational hypotheses.
description: FRUBASE
 datasetThe FRUBASE database, a
 huge dataset of fleshy fruit traits compiled from bibliographic references
 and my own work. Data are provided for more than 1000 plant species from
 all around the world. The FRUBASE package accompanies: Jordano, P. 1995.
 Angiosperm fleshy fruits and seed dispersers: a comparative analysis of
 adaptation and constraints in plant-animal interactions. American
 Naturalist 145: 163-191. It contains a copy of the main data file used for
 this paper, as well as other accompanying files (see below). Nomenclature
 and taxonomic arrangement follows Stevens, P. F. (2001 onwards).
 Angiosperm Phylogeny Website. Version 8, June 2007.
 http://www.mobot.org/MOBOT/research/APweb/. This scheme follows: A.P.G. [=
 Angiosperm Phylogeny Group] II. 2003. An update of the Angiosperm
 Phylogeny Group classification for the orders and families of flowering
 plants: APG II. Bot. J. Linnean Soc. 141: 399-436. Also see
 https://github.com/pedroj/FRUBASE.FRUBASE_2008.xls
DOI: 10.5061/dryad.3vb73
title: Data from: Contemporary ecological interactions improve models of past trait evolution

description: Despite the fact that natural selection underlies both traits and
 interactions, evolutionary models often neglect that ecological
 interactions may, and in many cases do, influence the evolution of traits.
 Here, we explore the interdependence of ecological interactions and
 functional traits in the pollination associations of hawkmoths and
 flowering plants. Specifically, we develop an adaptation of the
 Ornstein-Uhlenbeck model of trait evolution that allows us to study the
 influence of plant corolla depth and observed hawkmoth-plant interactions
 on the evolution of hawkmoth proboscis length. Across diverse modelling
 scenarios, we find that the inclusion of contemporary interactions can
 provide a better description of trait evolution than the null expectation.
 Moreover, we show that the pollination interactions provide more-likely
 models of hawkmoth trait evolution when interactions are considered at
 increasingly fine-scale groups of hawkmoths. Finally, we demonstrate how
 the results of best-fit modelling approaches can implicitly support the
 association between interactions and trait evolution that our method
 explicitly examines. In showing that contemporary interactions can provide
 insight into the historical evolution of hawkmoth proboscis length, we
 demonstrate the clear utility of incorporating additional ecological
 information to models designed to study past trait evolution.
description: Hawkmoth proboscis
 length optimaThe optima calculated
 based on selective regimes, pollination interactions, and plant corolla
 lengths. Original trait and interaction data can be found at:
 http://dx.doi.org/10.5061/dryad.qn83roptimas.RDataHawkmoth phylogenyThe dated phylogeny used for this study. Tree was compiled from the species presence data of: http://dx.doi.org/10.5061/dryad.qn83r. Nodes were dated with the phylogeny of: http://dx.doi.org/10.5061/dryad.3450rhawkmoth.nexSupplementary MaterialAdditional analyses including model-fits where EIT is not weighted by interaction frequency, output of SURFACE, and comparisons to the SLOUCH model.supporting_information.pdfProboscis lengths for hawkmoth speciesA two-column data frame containing species names and the proboscis length corresponding to each species. These data are drawn from https://doi.org/10.5061/dryad.qn83r and the original publication should be cited when referring to this data. In cases where a species occurred in more than one network in the aforementioned paper, the mean proboscis length is given in this file.hm_traits.csvModel implementation exampleTwo R scripts. One containing the functions that implement the model and one containing a short script to run the model.model_code.tar.gz
DOI: 10.5061/dryad.mb64cr8
title: Data from: Venom of prey-specialised spiders is more toxic to their preferred prey: a result of prey-specific toxins

description: 1. In specialised predators a variety of adaptations have evolved to such
 a level of specificity that they allow very effective exploitation of
 focal prey. Venom is an essential adaptive trait of predatory venomous
 species, such as spiders, yet our knowledge of spider venom is incomplete.
 2. In agreement with the prey preference hypothesis, we expected that the
 venom of spider specialists should be more toxic to focal than to
 alternative prey, because it is composed of prey-specific toxins. 3. Here
 we used spiders with three types of trophic specialisations: specialists
 that were ant-eating, termite-eating, and spider-eating. We compared the
 efficacy of prey capture of preferred and alternative prey (measured as
 paralysis latency) with that of related generalists and profiled the venom
 of the studied species using proteomic methods. We used 22 spider species:
 six myrmecophagous, two termitophagous, three araneophagous, and 11
 euryphagous generalist species belonging to different families. 4. We
 found that ten of the eleven specialist species induced significantly
 shorter paralysis latency in preferred prey than in alternative prey.
 Generalists exhibited either similar efficiency on both prey types or
 slightly higher efficiency on preferred prey. 5. Multivariate analysis of
 proteomic profiles (peptides and proteins) revealed significant
 differences between trophic specialisations, particularly in peptides.
 Specialists appear to have venom composed of unique specific compounds as
 revealed by the multivariate ordination and indicator analysis. These
 components are likely prey-specific toxins.
description: venomMALDI-TOF MS and
 SDS-PAGE data of venom of sampled species
DOI: 10.5061/dryad.1307
title: Data from: Complete mitochondrial DNA replacement in a Lake Tanganyika cichlid fish

description: We used nuclear and mitochondrial DNA sequences from specimens collected
 throughout Lake Tanganyika to clarify the evolutionary relationship
 between Lamprologus callipterus and Neolamprologus fasciatus. The nuclear
 data supports the reciprocal monophyly of these two shell breeding
 lamprologine cichlids. However, mitochondrial DNA (mtDNA) sequences show
 that 1) L. callipterus includes two divergent and geographically disjunct
 (North-South) mtDNA lineages; and that 2) N. fasciatus individuals cluster
 in a lineage sister group to the northern lineage of L. callipterus. The
 two mtDNA lineages of L. callipterus diverged c. 684 Kya to 1.2 Mya,
 coinciding with a major water level low stand in Lake Tanganyika, which
 divided the lake into isolated sub-lakes. This suggests that the two mtDNA
 lineages originated as the result of the separation of L. callipterus
 populations in different sub-basins. The incongruent phylogenetic position
 of N. fasciatus can best be explained by an ancient unidirectional
 introgression from L. callipterus into N. fasciatus. Remarkably, our data
 indicate that this event resulted in the complete mtDNA replacement in N.
 fasciatus. Our data suggest that hybridization occurred soon after the
 divergence of the two L. callipterus mtDNA lineages, probably still during
 the water level low stand, and that subsequently the invading mtDNA
 lineage spread throughout the lake.
description: Dataset used for nuclear
 reconstruction of nuclear phylogenyFile used for inference
 of nuclearDNA relationships of focal species (L. callipterus and N.
 fasciatus) within Lamprologini. Specimens names correspond to isolate
 names in SOM file 1 of the paper. For commands given to MrBayes when
 reading this file see ReadMe below.ITS_LSU_RAG1.nxsDataset used for reconstruction of mtDNA phylogenyATPCYTBDLOOP.nxsData used in phylogeographic analysisDloop.fas
DOI: 10.5061/dryad.85569
title: Data from: Multi-locus phylogeny of the Afrotropical freshwater crab fauna reveals historical drainage connectivity and transoceanic dispersal since the Eocene

description: Phylogenetic reconstruction, divergence time estimations and ancestral
 range estimation were undertaken for 66% of the Afrotropical freshwater
 crab fauna (Potamonautidae) based on four partial DNA loci (12S rRNA, 16S
 rRNA, cytochrome oxidase one [COI], and histone 3). The present study
 represents the most comprehensive taxonomic sampling of any freshwater
 crab family globally, and explores the impact of paleodrainage
 interconnectivity on cladogenesis among freshwater crabs. Phylogenetic
 analyses of the total evidence data using maximum-likelihood (ML), maximum
 parsimony (MP), and Bayesian inference (BI) produced a robust
 statistically well-supported tree topology that reaffirmed the monophyly
 of the Afrotropical freshwater crab fauna. The estimated divergence times
 suggest that the Afrotropical Potamonautidae diverged during the Eocene.
 Cladogenesis within and among several genera occurred predominantly during
 the Miocene, which was associated with major tectonic and climatic
 ameliorations throughout the region. Paleodrainage connectivity was
 observed with specimens from the Nilo-Sudan and East African coast proving
 to be sister to specimens from the Upper Guinea Forests in West Africa. In
 addition, we observed strong sister taxon affinity between specimens from
 East Africa and the Congo basin, including specimens from Lake Tanganyika,
 while the southern African fauna was retrieved as sister to the Angolan
 taxa. Within the East African clade we observed two independent
 transoceanic dispersal events, one to the Seychelles Archipelago and a
 second to Madagascar, while we observe a single transoceanic dispersal
 event from West Africa to São Tomé. The ancestral area estimation
 suggested a West African/East African ancestral range for the family with
 multiple dispersal events between southern Africa and East Africa, and
 between East Africa and Central Africa The taxonomic implications of our
 results are discussed in light of the widespread paraphyly evident among a
 number of genera.
description: long_realignThe DNA data file of the four partial loci sequenced during the present studyFIGURE S1Comparison of selected node ages based on different calibration schemes.Supplementary materialDNA substitution models for each of the four lociTable S1Testing between different models for the divergence time estimation using external rates and one fossil point.Table S2Testing of different biogeographic scenarios using BioGeoBears.Table S3Results of the test correlating the biogeographic areas.
DOI: 10.5061/dryad.5gs1v
title: Data from: Latitude drives diversification in Madagascar’s endemic dry forest rodent, Eliurus myoxinus (sub-family Nesomyinae)

description: Numerous hypotheses have been proposed for the historical processes
 governing the rich endemism of Madagascar's biodiversity. The
 ‘watershed model’ suggests that drier climates in the recent geological
 past have resulted in the contraction of forests around major watersheds,
 thereby defining areas of endemism. We test whether this hypothesis
 explains phylogeographical patterns in a dry forest-dependent rodent,
 Eliurus myoxinus, an endemic species widely distributed through western
 Madagascar. We sequenced the mitochondrial cytochrome b locus and nuclear
 introns of the β-fibrinogen and the growth hormone receptor genes for E.
 myoxinus. Using a parametric bootstrapping approach, we tested whether the
 mitochondrial gene tree data fit expectations of local differentiation
 given the watershed model. We additionally estimated population
 differentiation and historical demographic parameters, and reconstructed
 the spatial history of E. myoxinus to highlight spatial and temporal
 patterns of differentiation. The data do not support the watershed model
 as a clear explanation for the genetic patterns of diversity within extant
 E. myoxinus populations. We find striking patterns of latitudinal genetic
 structure within western Madagascar, and indicate possible roles for
 environmental and ecological gradients along this axis in generating
 phylogeographical diversity.
description: Cytochrome-b
 alignmentCytochrome-b DNA
 sequence alignment for all individuals included.cytb_eliurus.nexBeta-fibrinogen alignmentBeta-fibrinogen DNA sequence alignment for all individuals included. Includes two alleles per individual determined either by TA cloning, or computationally in PHASE.bfib_eliurus.nexGHR alignmentGHR DNA sequence alignment for all individuals included. Includes two alleles per individual determined either by TA cloning, or computationally in PHASE.ghr_eliurus.nexSpecimen numbersField collection numbers and associated museum collection specimen numbers for a subset of individuals that are referred to by both numbers.specimen_numbers.txtBEAST infile for continuous diffusion model analysisInfile generated by BEAUTi 1.7.5 for analysis in BEAST 1.7.5 of Eliurus myoxinus data of under a continuous diffusion model. Cytochrome-b sequences and locality data for each individual are included in this XML.eliurus_cdm_C01.xml
DOI: 10.25919/69jy-nn19
title: Parkes observations for project PX137 semester 2025OCTS_11

description: Pulsar data from Parkes (Murriyang) Target of Opportunity (ToO) observations
DOI: 10.5061/dryad.646
title: Data from: Generalized Frequency Coding: A Method of Preparing Polymorphic Multistate Characters for Phylogenetic Analysis

description: A new method of coding polymorphic multistate characters for phylogenetic
 analysis is presented. By dividing such characters into subcharacters,
 their frequency distributions can be represented with discrete states.
 Differential weighting is employed to counter the effect of using multiple
 characters to represent one character. The new method, termed generalized
 frequency coding (GFC), is potentially superior to previously used methods
 in that it incorporates more information and can be applied to both
 qualitative and quantitative characters. The method was applied to a
 previously published data set that includes both types of polymorphic
 multistate characters, and performed well according to congruence with
 other studies and the g1 and nonparametric bootstrap statistics. The data
 set was also used to compare GFC to both gap-weighting and Manhattan
 distance step matrix coding. On these grounds and for philosophical
 reasons, GFC was found to be a better estimator of phylogeny.
description: Smith and Gutberlet
 computer program "CodeThis"50ways.exe"CodeThis" Excel fileCodeThis.xls
DOI: 10.5061/dryad.45j84
title: Data from: Sex-chromosome differentiation parallels post-glacial range expansion in European tree frogs (Hyla arborea).

description: Occasional XY recombination is a proposed explanation for the
 sex-chromosome homomorphy in European tree frogs. Numerous laboratory
 crosses, however, failed to detect any event of male recombination, and a
 detailed survey of NW-European Hyla arborea populations identified
 male-specific alleles at sex-linked loci, pointing to the absence of XY
 recombination in their recent history. Here we address this paradox in a
 phylogeographic framework, by genotyping sex-linked microsatellite markers
 in populations and sibships from the entire species range. Contrasting
 with postglacial populations of NW Europe, which display complete absence
 of XY recombination and strong sex-chromosome differentiation, refugial
 populations of the southern Balkans and Adriatic coast show limited XY
 recombination and large overlaps in allele frequencies. Geographically and
 historically intermediate populations of the Pannonian Basin show
 intermediate patterns of XY differentiation. Even in populations where X
 and Y occasionally recombine, the genetic diversity of Y haplotypes is
 reduced below the levels expected from the four-fold drop in copy numbers.
 This study is the first in which X and Y haplotypes could be phased over
 the distribution range in a species with homomorphic sex chromosomes; it
 shows that XY-recombination patterns may differ strikingly between
 conspecific populations, and that recombination arrest may evolve rapidly
 (&lt; 5000 generations).
description: Sex-linked
 microsatellite genotypes of Hyla arborea adultsIndividual genotypes of
 14 sex-linked microsattelites in Hyla arborea populations. In males,
 colors show inferred Y haplotypes, when identifiable (colors are
 independent between populations). Individuals highlighted in bold were
 involved in crossings. 0: null alleles, NA: missing
 data.AdultData.xlsxSex-linked microsatellite genotypes of Hyla arborea familiesGenotypes of 14 sex-linked microsatellites in families from different populations. Each family consist of a mother (first row), a father (second row) and the offspring. Blue colors show male alleles at heterozygous loci. 0: null alleles, NA: missing data.FamilyData.xlsxSex-linked microsatellite genotypes of phenotypically sexed offspringSex-linked microsatellite genotypes and phenotypic sex in a family from loc. 1 (Greece, Crete). Blue colors show male alleles at heterozygous loci. 0: null allelesSexedOffspring_loc.1.xlsx
DOI: 10.25934/pr00010120
title: A Bayesian borrowing-by-parts method integrated with propensity score stratification for borrowing adult data for pediatric patients

description: In medical research, it's essential to find the most effective treatments for every patient group, including children. However, because children are less often included in clinical trials, it can be challenging to gather enough data to determine the best treatments for them. This project aims to address this challenge by using advanced statistical methods to better estimate how well treatments work for children by leveraging adult studies' data.

To explain our approach, let's break down some key terms and concepts: Bayesian methods are like making an educated guess that you continually improve as you gather more information. Bayesian borrowing is when we use information from one group (adults) to help make better guesses for another group (children). Propensity score stratification helps us make fair comparisons by ensuring that the groups we're comparing are similar in important ways. By combining these methods, we can make the most of the available data to estimate treatment effects more accurately for pediatric patients.

This research is crucial because it can lead to better-informed medical decisions and improve care for children, who often have fewer treatment options supported by strong evidence. The Belimumab treatment being studied, which is a drug that is used to treat certain autoimmune diseases, such as lupus, could impact thousands of children suffering from Systemic lupus erythematosus (SLE) disease, a chronic autoimmune disease where the immune system attacks the body's own tissues (causing inflammation and damage to various organs). By using data from adult studies to enhance our understanding of how these treatments work in children, we can improve healthcare outcomes for a large and vulnerable segment of the population. This research has the potential to directly benefit millions of children by providing them with more effective and safer treatment options.
DOI: 10.25934/00000458
title: A Phase 3, Multi-Center, Randomized, Double-Blind, Placebo-Controlled, 52-Wk Study to Evaluate the Efficacy and Safety of Belimumab (HGS1006, LymphoStat-B™), a Fully Human Monoclonal Anti-BLyS Antibody, in Subjects With Systemic Lupus Erythematosus (SLE)

description: The purpose of this study is to evaluate the efficacy, safety, tolerability, and impact on quality of life of two different doses of belimumab administered in addition to standard therapy in subjects with active, autoantibody-positive systemic lupus erythematosus (SLE) disease.
DOI: 10.25934/00006096
title: A Multi-center, Randomized, Placebo-Controlled Trial to Evaluate the Safety, Efficacy, and Pharmacokinetics of Belimumab, a Human Monoclonal Anti-BLyS Antibody, Plus Standard Therapy in Pediatric Patients With Systemic Lupus Erythematosus

description: This is a multi-center study to evaluate the safety, pharmacokinetics, and efficacy of belimumab intravenous (IV) in pediatric patients 5 to 17 years of age with active systemic lupus erythematosus
DOI: 10.25934/00000447
title: A Phase 3, Multi-Center, Randomized, Double-Blind, Placebo-Controlled, 76-Week Study to Evaluate the Efficacy and Safety of Belimumab (HGS1006, LymphoStat-B™), a Fully Human Monoclonal Anti-BLyS Antibody, in Subjects With Systemic Lupus Erythematosus (SLE)

description: The purpose of this study is to evaluate the efficacy, safety, tolerability, and impact on quality of life of two different doses of belimumab administered in addition to standard therapy in subjects with active, autoantibody-positive systemic lupus erythematosus (SLE) disease.