cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6bs40
title: Data from: Nest signature changes throughout colony cycle and after social parasite invasion in social wasps

description: Social insects recognize their nestmates by means of a cuticular
 hydrocarbon signature shared by colony members, but how nest signature
 changes across time has been rarely tested in longitudinal studies and in
 the field. In social wasps, the chemical signature is also deposited on
 the nest surface, where it is used by newly emerged wasps as a reference
 to learn their colony odor. Here, we investigate the temporal variations
 of the chemical signature that wasps have deposited on their nests. We
 followed the fate of the colonies of the social paper wasp Polistes
 biglumis in their natural environment from colony foundation to decline.
 Because some colonies were invaded by the social parasite Polistes
 atrimandibularis, we also tested the effects of social parasites on the
 nest signature. We observed that, as the season progresses, the nest
 signature changed; the overall abundance of hydrocarbons as well as the
 proportion of longer-chain and branched hydrocarbons increased. Where
 present, social parasites altered the host-nest signature qualitatively
 (adding parasite-specific alkenes) and quantitatively (by interfering with
 the increase in overall hydrocarbon abundance). Our results show that 1)
 colony odor is highly dynamic both in colonies controlled by legitimate
 foundresses and in those controlled by social parasites; 2) emerged
 offspring contribute little to colony signature, if at all, in comparison
 to foundresses; and 3) social parasites, that later mimic host signature,
 initially mark host nests with species-specific hydrocarbons. This study
 implies that important updating of the neural template used in nestmate
 recognition should occur in social insects.
description: Nest odor changes
 connected with season and parasite presence in P. biglumis
 nestsData collected in the
 field, analyzed with SPSS statistic. Px = Peak number x; FACx = Principal
 Component x; Perc x = Percentage of the peak x; QTot = Total concentration
 of hydrocarbons; IdNest = Sample ID; dx = right side; sx = left side; mtg
 = Montgenèvre, fer = Ferrere;Nest season_in
 uso.xlsx
DOI: 10.5061/dryad.156j4
title: Data from: A phylogeny of the genus Amaranthus (Amaranthaceae), based on several low-copy nuclear loci and chloroplast regions

description: The genus Amaranthus (pigweeds) is a group of ∼74 monoecious or dioecious
 annual species native to every continent but Antarctica, frequently
 associated with natural and human disturbance, with several economically
 important domesticated and weedy species. We set out to reconstruct the
 phylogeny of Amaranthus, with broad geographic sampling, in order to
 answer questions about biogeographic relationships in the genus and the
 monophyly of the subgenera. Fifty-eight species were included inmaximum
 parsimony and Bayesian phylogenetic analyses based on ITS and three
 low-copy nuclear genes (A36, G3PDH, and Waxy), as well as two chloroplast
 regions (trnL5′-trnL3′ and matK/trnK). Topology tests were also employed
 to test taxonomic hypotheses about incongruence between trees and the
 monophyly of clades containing Galápagos species. Our analyses support the
 origin of the genus in the Americas, with a single long-distance dispersal
 event to the Old World, and both nuclear and chloroplast trees recover
 three to fourmajor clades, roughly corresponding to three subgenera
 recognized based on morphology. However, there are species in all of these
 clades that were not predicted based on morphology, and we discover
 previously unsuspected relationships between Galápagos species and species
 from the North American Southwest, which comprise small monophyletic
 groups outside of the three recognized subgenera. Additionally, an
 important herbicide resistant weed species (A. palmeri) and its sister
 species are placed into different large clades based on nuclear or
 chloroplast data, suggesting a chloroplast capture event. These results
 will provide a basis for further exploration of the evolution of weedy
 ecological strategies in the group.
description: Waselkov Data SysBot
 2018Data (sequence
 alignments, tree files, and supplementary information) associated with
 Waselkov et al. 2018, Systematic Botany.
DOI: 10.5061/dryad.20g1d
title: Data from: Robustness of the approximate likelihood of the protracted speciation model

description: The protracted speciation model presents a realistic and parsimonious
 explanation for the observed slowdown in lineage accumulation through
 time, by accounting for the fact that speciation takes time. A method to
 compute the likelihood for this model given a phylogeny is available and
 allows estimation of its parameters (rate of initiation of speciation,
 rate of completion of speciation, and extinction rate) and statistical
 comparison of this model to other proposed models of diversification.
 However this likelihood computation method makes an approximation of the
 protracted speciation model to be mathematically tractable: it sometimes
 counts fewer species than one would do from a biological perspective. This
 approximation may have large consequences for likelihood-based inferences:
 it may render any conclusions based on this method completely irrelevant.
 Here we study to what extent this approximation affects parameter
 estimations. We simulated phylogenies from which we reconstructed the tree
 of extant species according to the original, biologically meaningful
 protracted speciation model and according to the approximation. We then
 compared the resulting parameter estimates. We found that the differences
 were larger for high values of extinction rates and small values of
 speciation-completion rates. Indeed, a long speciation-completion time and
 a high extinction rate promote the appearance of cases to which the
 approximation applies. However, surprisingly, the deviation introduced is
 largely negligible over the parameter space explored, suggesting that this
 approximate likelihood can be applied reliably in practice to estimate
 biologically relevant parameters under the original protracted speciation
 model.
description: R scripts and
 resultsThe zip-file contains R
 scripts used to simulate and estimate parameters. See the readme.txt file
 for more info.Simonet et al - data
 archive.zip
DOI: 10.5061/dryad.d08g0
title: Data from: Behavioral tactic predicts preoptic-hypothalamic gene expression more strongly than developmental morph in fish with alternative reproductive tactics

description: Reproductive success relies on the coordination of social behaviors, such
 as territory defense, courtship, and mating. Species with extreme
 variation in reproductive tactics are useful models for identifying the
 neural mechanisms underlying social behavior plasticity. The plainfin
 midshipman (Porichthys notatus) is a teleost fish with two male
 reproductive morphs that follow widely divergent developmental
 trajectories and display alternative reproductive tactics (ARTs). Type I
 males defend territories, court females, and provide paternal care, but
 will resort to cuckoldry if they cannot maintain a territory. Type II
 males reproduce only through cuckoldry. We sought to disentangle gene
 expression patterns underlying behavioral tactic, in this case ARTs, from
 those solely reflective of developmental morph. Using RNA-sequencing, we
 investigated differential transcript expression in the preoptic
 area-anterior hypothalamus (POA-AH) of courting type I males, cuckolding
 type I males, and cuckolding type II males. Unexpectedly, POA-AH
 differential expression was more strongly coupled to behavioral tactic
 than morph. This included a suite of transcripts implicated in hormonal
 regulation of vertebrate social behavior. Our results reveal that
 divergent expression patterns in a conserved neuroendocrine center known
 to regulate social-reproductive behaviors across vertebrate lineages may
 be uncoupled from developmental history to enable plasticity in the
 performance of reproductive tactics.
description: b2g_PN_ref_transcriptome_annotationBlast2Go annotation of spawning male plainfin midshipman (Porichthys notatus) preoptic area-anterior hypothalamus
DOI: 10.5061/dryad.9b3r0
title: Data from: Dominance and the initiation of group feeding events: the modifying effect of sociality

description: Individuals can differ in how much they benefit from being in a group
 depending on characteristics such as their dominance rank or their
 behaviour. Understanding which categories of individuals influence the
 decisions of a group could help understand which individuals are
 benefiting the most. We examine these ideas in wild flocks of black-capped
 chickadees (Poecile atricapillus), which feature stable group membership
 and linear dominance hierarchies. We attempt to infer which individuals
 are influencing group movement by examining how individuals initiate and
 join foraging events in relation to their dominance rank, exploratory
 personality type and position within a social network. We find that the
 influence of dominance on these behaviours heavily depends on the social
 connections an individual has, and that the effect of exploratory
 personality was small. Dominant individuals with a high eigenvector
 centrality were more likely to initiate a foraging event, while among
 individuals with a low eigenvector centrality this relationship was
 reversed, with subordinates being slightly more likely to initiate a
 foraging event. Analysis also suggested that individuals with a large
 number of strong social connections would be less affected by dominance
 than less social individuals. This suggests a system where individuals
 might adopt different foraging strategies depending on their position
 within a social network, and highlights the importance of individuals’
 social phenotype when studying group decision making.
description: Static RFID
 dataVisits to static RFID
 feeders used to generate social networksstaticdata.csvGBI dataGroup by individual matrices for each siteGBIdata.zipIndividual measuresIndividual measures of dominance and latency to exploreinddata.csvArrival dataArrival of individuals to forage while feeder was in novel environment - restricted to each individual's first arrival only.arrivaldata.csv
DOI: 10.5061/dryad.68pc2
title: Data from: Macroalgal-bacterial interactions: role of dimethylsulfoniopropionate in microbial gardening by Ulva (Chlorophyta)

description: The marine macroalga Ulva mutabilis (Chlorophyta) develops into
 callus-like colonies consisting of undifferentiated cells and abnormal
 cell walls under axenic conditions. U. mutabilis is routinely cultured
 with two bacteria, the Roseovarius sp. MS2 strain and the Maribacter sp.
 MS6 strain, which release morphogenetic compounds and ensure proper algal
 morphogenesis. Using this tripartite community as an emerging model
 system, we tested the hypothesis that the bacterial-algal interactions
 evolved as a result of mutually taking advantage of signals in the
 environment. Our study aimed to determine whether cross-kingdom cross-talk
 is mediated by the attraction of bacteria through algal chemotactic
 signals. Roseovarius sp. MS2 senses the known osmolyte
 dimethylsulfoniopropionate (DMSP) released by Ulva into the growth medium.
 Roseovarius sp. is attracted by DMSP and takes it up rapidly. Therefore,
 the compound can only be determined in axenic growth media. As DMSP did
 not promote bacterial growth under the tested conditions, Roseovarius
 benefited solely from glycerol as the carbon source provided by Ulva.
 Roseovarius quickly catabolized DMSP into methanethiol (MeSH) and
 dimethylsulfide (DMS). We conclude that many bacteria can use DMSP as a
 reliable signal indicating a food source and promote the subsequent
 development and morphogenesis in Ulva.
description: Determination of
 dimethylsulfoniopropionate (DMSP) in Ulva(1) Raw file: DMSP can
 be directly quantified in Ulva mutabilis using liquid chromatography
 coupled to mass spectrometry (HILIC-ESI-Q-ToF-MS). A representative raw
 data file (MassLynx V4.1) was uploaded. DMSP (M+H = m/z 135) was produced
 by blade cells of the Ulva thallus. [2H6]-DMSP (M+H = m/z 141) was added
 as an internal standard for reference and quantification. (2) Excel file:
 Values of the DMSP quantification and the uptake
 experiment.Data_DMSP_ Kessler et
 al.zip
DOI: 10.15468/dl.m24bac
title: Occurrence Download

description: A dataset containing 2490 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseudacris ornata (Holbrook, 1836)"
 ]
}

 The dataset includes 2490 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075968-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2d27a2
title: Occurrence Download

description: A dataset containing 59329 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseudacris crucifer (Wied-Neuwied, 1838)"
 ]
}

 The dataset includes 59329 records from 111 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0076210-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xdbu54
title: Occurrence Download

description: A dataset containing 3808 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseudacris nigrita (LeConte, 1825)"
 ]
}

 The dataset includes 3808 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0076200-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ucfd5c
title: Occurrence Download

description: A dataset containing 36069 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lithobates sphenocephalus (Cope, 1886)"
 ]
}

 The dataset includes 36069 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0077413-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.c8b66
title: Data from: The reluctant visitor: an alkaloid in toxic nectar can reduce olfactory learning and memory in Asian honey bees

description: The nectar of the thunder god vine, Tripterygium hypoglaucum, contains a
 terpenoid, triptolide (TRP), that is toxic to the sympatric Asian honey
 bee, Apis cerana. However, these bees will forage on, recruit for, and
 pollinate this plant during a seasonal dearth of preferred food sources.
 Olfactory learning plays a key role in forager constancy and pollination,
 and we therefore tested the effects of acute and chronic TRP feeding on
 forager olfactory learning, using proboscis extension reflex conditioning.
 At a concentration of 0.5ug TRP/ml, within the natural range, there were
 no learning effects. However, memory retention (1 h after the last
 learning trial) significantly decreased by 56% following acute consumption
 of 0.5 ug TRP/ml. Chronic exposure did not alter learning or memory,
 except at high concentrations (5 and 10 ug TRP/ml) that are likely not
 biologically relevant. Natural TRP concentrations in nectar should
 therefore not significantly harm plant pollination. Long term exposure to
 TRP could have colony effects, but these may be ameliorated by the bees
 aversion to T. hypoglaucum nectar when other food sources are available
 and, perhaps, by detoxification mechanisms. The co-evolution of this plant
 and its reluctant mutualist may therefore illustrate a classic compromise
 between the interests of both actors.
description: Toxic nectar
 r1Toxic
 nectar
DOI: 10.15468/dl.etgek2
title: Occurrence Download

description: A dataset containing 780 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseudacris brimleyi Brandt & Walker, 1933"
 ]
}

 The dataset includes 780 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0076221-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z6ur9y
title: Occurrence Download

description: A dataset containing 2923 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseudacris ocularis (Holbrook, 1838)"
 ]
}

 The dataset includes 2923 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0076218-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.94z5v2
title: Occurrence Download

description: A dataset containing 107260 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lithobates clamitans (Latreille, 1801)"
 ]
}

 The dataset includes 107260 records from 124 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0076223-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9kbh4s
title: Occurrence Download

description: A dataset containing 6279 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseudacris feriarum (Baird, 1854)"
 ]
}

 The dataset includes 6279 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0076225-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.edskxn
title: Occurrence Download

description: A dataset containing 17881 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hyla chrysoscelis Cope, 1880"
 ]
}

 The dataset includes 17881 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0076230-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hr744
title: Data from: Oxidation of linoleic and palmitic acid in pre-hibernating and hibernating common noctule bats revealed by 13C breath testing

description: Mammals fuel hibernation by oxidizing saturated and unsaturated fatty
 acids from triacylglycerols in adipocytes, yet the relative importance of
 these two categories as an oxidative fuel may change during hibernation.
 We studied the selective use of fatty acids as an oxidative fuel in
 noctule bats (Nyctalus noctula). Pre-hibernating noctule bats that were
 fed 13C-enriched linoleic acid (LA) showed 12 times higher tracer
 oxidation rates compared to conspecifics fed 13C-enriched palmitic acid
 (PA). After this experiment, we supplemented the diet of bats with the
 same fatty acids on 5 subsequent days to enrich their fat depots with the
 respective tracer. We then compared the excess 13C enrichment (APE) in
 breath of bats for torpor and arousal events during early and late
 hibernation. We observed higher APE values in breath of bats fed
 13C-enriched LA than in bats fed 13C-enriched PA for both states, torpor
 and arousal, and also for both periods. Thus, hibernating bats oxidized
 selectively endogenous LA instead of PA, most likely because of faster
 transportation rates of PUFA compared with SFA. We did not observe changes
 in APE values in the breath of torpid animals between early and late
 hibernation. Skin temperature of torpid animals increased by 0.7oC between
 early and late hibernation in bats fed PA, whereas it decreased by -0.8oC
 in bats fed LA, highlighting that endogenous LA may fulfil two functions
 when available in excess: serving as an oxidative fuel and supporting cell
 membrane functionality.
description: Data_RosnerVoigtMetabolic rate, APE values and TOR for pre-hibernating common noctule bats (Fig. 1), body temperature, metabolci rate and APE values for hibernating noctule bats (early Fig. 2, late Fig. 3)
DOI: 10.17632/6nt9t4bmyp.1
title: Proteolytic Enzymes in Dentin Erosion: Roles of Matrix Metalloproteinases and Cathepsins and the Effectiveness of Synthetic and Natural Inhibitors—A Systematic Review

description: This systematic review synthesizes and critically appraises the current evidence on the role of proteolytic enzymes in dentin erosion, with a specific focus on matrix metalloproteinases (MMPs) and cathepsins, and evaluates the effectiveness of synthetic and natural inhibitors in modulating their activity. Dentin erosion is a multifactorial process in which acid-mediated demineralization is exacerbated by endogenous enzymatic degradation of the exposed organic matrix, compromising structural integrity and accelerating tissue loss. Evidence indicates that MMPs and cysteine cathepsins act synergistically under erosive conditions, amplifying collagen breakdown and hindering remineralization.

Following PRISMA guidelines, electronic searches were conducted across major databases to identify in vitro, ex vivo, and clinical studies assessing proteolytic activity in eroded dentin and the impact of inhibitory strategies. The review summarizes the mechanisms of enzyme activation, spatial distribution, and interaction, and compares the efficacy of commonly investigated inhibitors, including chlorhexidine, metal ions, polyphenols, and other naturally derived compounds.

Overall, the findings highlight that targeted inhibition of proteolytic enzymes—particularly combined or dual-inhibition approaches—represents a promising adjunctive strategy for controlling dentin erosion. The review also identifies methodological limitations and research gaps, providing directions for future translational and clinical studies.
DOI: 10.5061/dryad.fg189
title: Data from: No evidence of inbreeding depression in sperm performance traits in wild song sparrows

description: Inbreeding is widely hypothesized to shape mating systems and population
 persistence, but such effects will depend on which traits show inbreeding
 depression. Population and evolutionary consequences could be substantial
 if inbreeding decreases sperm performance and hence decreases male
 fertilisation success and female fertility. However, the magnitude of
 inbreeding depression in sperm performance traits has rarely been
 estimated in wild populations experiencing natural variation in
 inbreeding. Further, the hypothesis that inbreeding could increase
 within-ejaculate variation in sperm traits, and thereby further affect
 male fertilisation success has not been explicitly tested. We used a wild
 pedigreed song sparrow (Melospiza melodia) population, where frequent
 extra-pair copulations likely create strong post-copulatory competition
 for fertilisation success, to quantify effects of male coefficient of
 inbreeding (f) on key sperm performance traits. We found no evidence of
 inbreeding depression in sperm motility, longevity or velocity, and the
 within-ejaculate variance in sperm velocity did not increase with male f.
 Contrary to inferences from highly inbred captive and experimental
 populations, our results imply that moderate inbreeding will not
 necessarily constrain sperm performance in wild populations. Consequently,
 the widely observed individual-level and population-level inbreeding
 depression in male and female fitness may not stem from reduced sperm
 performance in inbred males.
description: Data for inbreeding
 depression in sperm performance (Losdat et al. 2017)Losdat et al_ ID in sperm song
 sparrows.txt
DOI: 10.17632/hh9wr3ydd7.1
title: Code: Towards Operational Tree-Level Timber Quality and Volume Estimation Using UAV Multi-Sensor Remote Sensing

description: LiDAR-related code for the estimation of stem straightness. Additionally, code for the segmenteation and stem diameter estimation based on previous work added.