cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q90fm
title: Data from: Sex-specific and individual preferences for hunting strategies in white sharks

description: Fine-scale predator movements may be driven by many factors including sex,
 habitat, and distribution of resources. There may also be individual
 preferences for certain movement strategies within a population which can
 be hard to quantify. Within top predators, movements are also going to be
 directly related to the mode of hunting; for example sit-and-wait or
 actively searching for prey. Although there is mounting evidence that
 different hunting modes can cause opposing trophic cascades, there has
 been little focus on the modes used by top predators, especially those in
 the marine environment. Adult white sharks (Carcharhodon carcharias) are
 well known to forage on marine mammal prey, particularly pinnipeds. Sharks
 primarily ambush pinnipeds on the surface but there has been less focus on
 the strategies they use to encounter prey. We applied mixed hidden Markov
 models to acoustic tracking data of white sharks in a coastal aggregation
 area in order to quantify changing movement states (Area Restricted
 Searching (ARS) vs. patrolling) and the factors that influenced them.
 Individuals were re-tracked over multiple days throughout a month to see
 if state-switching dynamics varied or if individuals preferred certain
 movement strategies. Sharks were more likely to use ARS movements in the
 morning and during periods of chumming by ecotourism operators.
 Furthermore, the proportion of time individuals spent in the two different
 states and the state-switching frequency, differed between the sexes and
 between individuals. Predation attempts/success on pinnipeds were observed
 for sharks in both ARS and patrolling movement states and within all
 random effects groupings. Therefore white sharks can use both a
 ‘sit-and-wait’ (ARS) and ‘active searching’ (patrolling) movements to
 ambush pinniped prey on the surface. White sharks demonstrate individual
 preferences for fine scale movement patterns which may be related to their
 use of different hunting modes. Marine top predators are generally assumed
 to use only one type of hunting mode, but we show that there is likely a
 mix within populations. As such, individual variability should be
 considered when modelling behavioural effects of predators on prey
 species.
description: GWS TRACKING DATA GB_
 2010-2014_ATAcoustic tracking data
 of Carcharodon carcharias in Gansbaai South Africa.
DOI: 10.5061/dryad.mq61g
title: Data from: Binary-state speciation and extinction method is conditionally robust to realistic violations of its assumptions

description: Background: Phylogenetic comparative methods allow us to test evolutionary
 hypotheses without the benefit of an extensive fossil record. These
 methods, however, make simplifying assumptions, among them that clades are
 always increasing or stable in diversity, an assumption we know to be
 false. This study simulates hypothetical clades to test whether the Binary
 State Speciation and Extinction (BiSSE) method can be used to correctly
 detect relative differences in diversification rate between ancestral and
 derived character states even as net diversification rates are declining
 overall. We simulate clades with declining but positive diversification
 rates, as well those in which speciation rates decline below extinction
 rates so that they are losing richness for part of their history. We run
 these analyses both with simulated symmetric and asymmetric speciation
 rates to test whether BiSSE can be used to detect them correctly. Results:
 For simulations with a neutral character, the fit for a BiSSE model with a
 neutral character is better than alternative models so long as net
 diversification rates remain positive. Once net diversification rates
 become negative, the BiSSE model with the greatest likelihood often has a
 non-neutral character, even though there is no such character in the
 simulation. BiSSE's usefulness in detecting real asymmetry in
 speciation rates improves with clade age, even well after net
 diversification rates have become negative. Conclusions: BiSSE is most
 useful in analyzing clades of intermediate age, before they have reached
 peak diversity and gone into decline. After this point, users of BiSSE
 risk incorrectly inferring differential evolutionary rates when none
 exist. Fortunately, most studies using BiSSE and similar models focus on
 rapid, recent diversifications, and are less likely to encounter the
 biases BiSSE models are subject to for older clades. For extant groups
 that were once more diverse than now, however, caution should be taken in
 inferring past diversification patterns without fossil data.
description: BiSSE sim
 dataAll of the data that we
 used to conduct our titular study. Data are sorted based on models,
 etc.R script
 runR
 script used to automate the simulation model and then analyze the
 simulation model outputBiSSE
 Sim.RSpeciationExtinctionModel.cSource code for the simulation we used to create taxa (requires a c compiler)Biota.txtSample biota input file for the simulation (failure to use such a file will cause the simulation to crash and output a sample file such as this one)Model.txtSample model input file for the simulation (failure to use such a file will cause the simulation to crash and output a sample file such as this one)
DOI: 10.6075/j0hd7vvf
title: BindingDB: Measured Binding Data for Protein-Ligand and Other Molecular Systems

description: This collection contains the data in BindingDB, a large database launched in 2000 that supports research, education and practice in drug discovery, pharmacology, computer-aided drug design, machine-learning and artificial intelligence, and related fields by collecting experimentally measured protein-small molecule binding data, as well as selected collections of other types of binding data, such as host-guest and protein-protein, chiefly from scientific articles and patents.
DOI: 10.5061/dryad.bh8n5j8
title: Data from: Stochastic and deterministic effects on interactions between canopy and recruiting species in forest communities

description: 1. Interactions between established (canopy) and recruiting individuals
 (recruits) are pervasive in plant communities. Studies on recruitment in
 forests have mainly focused on negative density-dependent conspecific
 interactions, while the outcomes of heterospecific canopy-recruit
 interactions have received much less attention and are generally assumed
 to be driven by stochastic processes. 2. Herein, we explore the relative
 influence of stochastic (abundance) and deterministic (species identity
 and phylogenetic distance) effects on the frequency of canopy-recruit
 interactions, and characterise the interactions in terms of their spatial
 consistency and effect on recruitment (depressing, neutral or enhancing).
 3. In 12 plots (50  50 m) of mixed pine-oak forests in Southern Spain we
 identified all saplings recruiting beneath 56 shrub and tree species, and
 in open areas not covered by woody plants. We used generalised linear
 mixed models to investigate the influence of stochastic and deterministic
 processes on the frequency of canopy-recruit interactions, on their
 spatial consistency and their effects on recruitment, and applied neutral
 null models to evaluate the spatial consistency in the occurrence of
 interactions across plots. 4. Deterministic and stochastic interactions
 were equally common emphasizing the prevalence of non-neutral effects.
 Among the realized interactions, 36.8% enhanced recruitment, 49.05% were
 neutral, and 14.1% depressed recruitment. Many potential interactions
 (42.08%) were not observed in any study sites, presumably due to the
 scarcity of the interacting species. Moreover, the probability that two
 species formed a canopy-recruit interaction, the frequency of their
 interaction, and the probability that the interaction had an enhancing
 effect on recruitment, all increased with the phylogenetic distance
 between the interacting species. However, the prevalence of these effects
 depended on the recruitment environment (heterospecific, conspecific or
 open). Recruitment-enhancing interactions between heterospecifics were
 more consistently realized in different sites than neutral or depressing
 interactions. 5. The establishment of canopy-recruit interactions (which
 species recruits beneath which others, and how often) is not simply
 determined by stochastic events. Indeed, due to their prevalence we argue
 that deterministic canopy-recruit interactions are important drivers of
 plant community dynamics.
description: field.dataStudy species and locations (Table 1-2); interactions frequency by site (Table 3); interactions tested for their effect on recruitment (Table 4); and interaction consistency across plots (Table 5).phylo.dataPhylip file with the sequences used to construct the phylogeny in Appendix S1.
DOI: 10.5061/dryad.r95c6
title: Data from: Local adaptation with high gene flow: temperature parameters drive adaptation to altitude in the common frog (Rana temporaria)

description: Both environmental- and genetic-influences can result in phenotypic
 variation. Quantifying the relative contributions of local adaptation and
 phenotypic plasticity to phenotypes is key to understanding the effect of
 environmental variation on populations. Identifying the selective
 pressures that drive divergence is an important, but often lacking, next
 step. High gene flow between high- and low-altitude common frog (Rana
 temporaria) breeding sites has previously been demonstrated in Scotland.
 The aim of this study was to assess whether local adaptation occurs in the
 face of high gene flow and to identify potential environmental selection
 pressures that drive adaptation. Phenotypic variation in larval traits was
 quantified in R. temporaria from paired high- and low-altitude sites using
 three common temperature treatments. Local adaptation was assessed using
 QST-FST analyses, and quantitative phenotypic divergence was related to
 environmental parameters using Mantel tests. Although evidence of local
 adaptation was found for all traits measured, only variation in larval
 period and growth rate was consistent with adaptation to altitude.
 Moreover, this was only evident in the three mountains with the highest
 high-altitude sites. This variation was correlated with mean summer and
 winter temperatures, suggesting temperature parameters are potentially
 strong selective pressures maintaining local adaptation, despite high gene
 flow.
description: Study
 sitesSite name
 (abbreviation), location (latitude and longitude) and altitude (metres
 above sea level).Temperature data
 fileAir temperature data
 collected every two hours, by site. Date, Time: when air temperature was
 recorded. Temperature in degrees centigrade by site.Environmental
 parameterspH, conductivity (μS),
 total dissolved solids (ppm) and dissolved oxygen content (mg/l)
 measurements by site.Phenotypic trait
 dataFor each individual:
 Mountain of origin (Mountain), Site abbreviation (Population), Altitude
 (low or high), Egg mass of origin (Family), Treatment (temperature; oC),
 Basket (within Treatment), Weight at metamorphosis (Weight; g), Snout-vent
 length change from start to end of experiment (SVL; mm), Larval Period
 (days), Growth rate (Rate; g/day), Egg diameter (Egg, mm),
 SurvivalR-script for QST
 modelFor QST model using lme4
 packageReadMeReadMe file for all
 data
DOI: 10.15468/dl.kr49um
title: Occurrence Download

description: A dataset containing 150 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erythranthe marmorata"
 ]
}

 The dataset includes 150 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000597-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j04q7vzg
title: BindingDB Dataset, October 1, 2025. In BindingDB: Measured Binding Data for Protein-Ligand and Other Molecular Systems

description: Data curated by BindingDB were collected from articles and patents using a semi-automated procedure. We first work from the source document to automatically preload a representation of the data into a web-based curation interface. Human curators then examine the preloaded data, compare it with the source document, and make corrections as needed. The corrected curation is then inspected by a second curator and any proposed corrections are discussed and made if needed. Occasionally, a user will contact BindingDB with a proposed correction. Each such proposal is reviewed individually and made if warranted.
description: This object is the BindingDB dataset as of October 1, 2025. 

The core data for a given binding measurement comprises the identity of the two molecules involved, usually a protein and a small organic molecule; a measured indicator of their affinity, such as a dissociation constant or IC50; and the identity of the document from which the measurement was curated. Proteins are identified primarily by UniProt ID and small organic molecules by SMILES strings. 

This BindingDB release contains about 3.08 million experimental binding data.
description: The Oracle data dump was exported from Oracle 12c Enterprise Edition release 12.2.0.1.0- 64-bit production. The MySQL dump was exported from MySQL version 8.0.26.
DOI: 10.5061/dryad.mb2gb
title: Data from: Inbreeding depression does not increase after exposure to a stressful environment: a test using compensatory growth

description: Background: Inbreeding is often associated with a decrease in offspring
 fitness (‘inbreeding depression’). Moreover, it is generally assumed that
 the negative effects of inbreeding are exacerbated in stressful
 environments. This G × E interaction has been explored in many taxa under
 different environmental conditions. These studies usually manipulate
 environmental conditions either in adulthood or throughout an individual’s
 entire life. Far fewer studies have tested how stressful environments only
 experienced during development subsequently influence the effects of
 inbreeding on adult traits. Results: We experimentally manipulated the
 diet (control versus low food) of inbred and outbred juvenile Eastern
 mosquitofish (Gambusia holbrooki) for three weeks (days 7-28) to test
 whether experiencing a presumably stressful environment early in life
 influences their subsequent growth and adult phenotypes. The control diet
 was a standard laboratory food regime, while fish on the low food diet
 received less than 25 % of this amount of food. Unexpectedly, despite a
 large sample size (237 families, 908 offspring) and a quantified 23 %
 reduction in genome-wide heterozygosity in inbred offspring from matings
 between full-siblings (f = 0.25), neither inbreeding nor its interaction
 with early diet affected growth trajectories, juvenile survival or adult
 size. Individuals did not mitigate a poor start in life by showing
 ‘compensatory growth’ (i.e. faster growth once the low food treatment
 ended), but they showed ‘catch-up growth’ by delaying maturation. There
 was, however, no effect of inbreeding on the extent of catch-up growth.
 Conclusions: There were no detectable effects of inbreeding on growth or
 adult size, even on a low food diet that should elevate inbreeding
 depression. Thus, the long-term costs of inbreeding due to lower male
 reproductive success we have shown in another study appear to be unrelated
 to inbreeding depression for adult male size or the growth rates that are
 reported in the current study.
description: Vega-Trejo et.al.
 2016.BMC Evol Biol.Data
DOI: 10.6075/j0v40w61
title: BindingDB Dataset, January 1, 2026. In BindingDB: Measured Binding Data for Protein-Ligand and Other Molecular Systems

description: This object is the BindingDB dataset as of January 1, 2026. 

The core data for a given binding measurement comprises the identity of the two molecules involved, usually a protein and a small organic molecule; a measured indicator of their affinity, such as a dissociation constant or IC50; and the identity of the document from which the measurement was curated. Proteins are identified primarily by UniProt ID and small organic molecules by SMILES strings. 

This BindingDB release contains about 3.18 million experimental binding data.
description: Data curated by BindingDB were collected from articles and patents using a semi-automated procedure. We first work from the source document to automatically preload a representation of the data into a web-based curation interface. Human curators then examine the preloaded data, compare it with the source document, and make corrections as needed. The corrected curation is then inspected by a second curator and any proposed corrections are discussed and made if needed. Occasionally, a user will contact BindingDB with a proposed correction. Each such proposal is reviewed individually and made if warranted.
description: The Oracle data dump was exported from Oracle 12c Enterprise Edition release 12.2.0.1.0- 64-bit production. The MySQL dump was exported from MySQL version 8.0.26.
DOI: 10.5061/dryad.57vf3fr
title: Data from: Sulettaria: a new ginger genus disjunct from Elettaria cardamomum

description: In 1950, Holttum placed species from Malaysia in the cardamom genus,
 Elettaria, while noting that they may, in fact, belong elsewhere in the
 tribe Alpinieae. We tested this hypothesis applying phylogenetic methods
 using nuclear ITS and At103, and plastid matK, ndhF and trnL-F sequences
 from several samples of the genus. In the resulting molecular phylogeny,
 these samples appeared in three separate places of the Alpinieae.
 Elettaria s. str. is endemic in India and Sri Lanka while all species from
 Peninsular Malaysia, Sumatra and Borneo are placed in a new genus,
 Sulettaria which, furthermore, includes six species with basionyms in
 Amomum, A. kandariense from Sulawesi and the other five from Borneo.
 Fifteen new combinations are made, an identification key provided and
 lectotypes designated for three species. Plants labelled as cardamom and
 exhibited in some botanic gardens have been misidentified and represent a
 species in the Alpinia zerumbet clade.
description: Concatenated
 DataThis data is a
 concatenated sequences of ITS, matK, ndhF, trnL-F and
 At103konkatenert7.fasConcatenated Data of Nuclear DNA SequencesConcatenated data of ITS (base 1-674) and at103 (base 675-1210)konkatenert_nuclear_fas.fasConcatenated Data of Chloroplast DNA SequencesConcatenated data of matK (base 1-1042), trnLcd (base 1043-1679), trnLef (base 1680-2047) and ndhF (2048-2748)konkatenert_chloroplast_fas.fas
DOI: 10.6075/j0wq040d
title: BindingDB Dataset, October 1, 2023. In BindingDB: Measured Binding Data for Protein-Ligand and Other Molecular Systems

description: This object is the BindingDB dataset as of October 1, 2023. 

The core data for a given binding measurement comprises the identity of the two molecules involved, usually a protein and a small organic molecule; a measured indicator of their affinity, such as a dissociation constant or IC50; and the identity of the document from which the measurement was curated. Proteins are identified primarily by UniProt ID and small organic molecules by SMILES strings. 

This BindingDB release contains about 2.6 million experimental binding data.
description: Data curated by BindingDB were collected from articles and patents using a semi-automated procedure. We first work from the source document to automatically preload a representation of the data into a web-based curation interface. Human curators then examine the preloaded data, compare it with the source document, and make corrections as needed. The corrected curation is then inspected by a second curator and any proposed corrections are discussed and made if needed. Occasionally, a user will contact BindingDB with a proposed correction. Each such proposal is reviewed individually and made if warranted.
description: The Oracle data dump was exported from Oracle 12c Enterprise Edition release 12.2.0.1.0- 64-bit production. The MySQL dump was exported from MySQL version 8.0.26.
DOI: 10.5061/dryad.8987
title: Data from: Is sexual selection driving diversification of the bioluminescent ponyfishes (Teleostei: Leiognathidae)?

description: Sexual selection is a mechanism of speciation that theoretically could
 provide genetic isolation among populations and lead to an increase in
 diversification rates. In this study, we investigate the impact of
 potential sexual selection on the tempo and mode of ponyfish evolution.
 Ponyfishes (Leiognathidae) are bioluminescent marine fishes that exhibit
 sexually-dimorphic features of their unique light-organ system (LOS).
 Given that some leiognathid species have a sexually dimorphic LOS, whereas
 others do not, this family provides an excellent system within which to
 study the potential role of sexual selection in diversification and
 morphological differentiation. We estimate the phylogenetic relationships
 and divergence times of Leiognathidae, investigate the tempo and mode of
 ponyfish diversification, and explore morphological shape disparity among
 clades. We recover strong support for a monophyletic Leiognathidae, and
 estimate that all major ponyfish lineages initially evolved during the
 Paleogene. We conclude that if sexual selection is occurring in ponyfish
 evolution, it is likely only as a genetic isolating mechanism that has
 allowed ponyfishes to continuously diversify over time, with no overall
 impact on increases in diversification rate or morphological disparity.
description: TotalPonyfishMolEcol65_SimpleNexus file of genetic data
DOI: 10.6075/j0ks6rrw
title: BindingDB Dataset, April 1, 2024. In BindingDB: Measured Binding Data for Protein-Ligand and Other Molecular Systems

description: The Oracle data dump was exported from Oracle 12c Enterprise Edition release 12.2.0.1.0- 64-bit production. The MySQL dump was exported from MySQL version 8.0.26.
description: This object is the BindingDB dataset as of April 1, 2024. 

The core data for a given binding measurement comprises the identity of the two molecules involved, usually a protein and a small organic molecule; a measured indicator of their affinity, such as a dissociation constant or IC50; and the identity of the document from which the measurement was curated. Proteins are identified primarily by UniProt ID and small organic molecules by SMILES strings. 

This BindingDB release contains about 2.6 million experimental binding data.
description: Data curated by BindingDB were collected from articles and patents using a semi-automated procedure. We first work from the source document to automatically preload a representation of the data into a web-based curation interface. Human curators then examine the preloaded data, compare it with the source document, and make corrections as needed. The corrected curation is then inspected by a second curator and any proposed corrections are discussed and made if needed. Occasionally, a user will contact BindingDB with a proposed correction. Each such proposal is reviewed individually and made if warranted.