cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4s6m3
title: Data from: Woody climbers show greater population genetic differentiation than trees: insights into the link between ecological traits and diversification

description: The climbing habit is a key innovation in plants: climbing taxa have
 higher species richness than non-climbing sister groups. We evaluated the
 hypothesis that climbing plant species show greater among-population
 genetic differentiation than non-climber species. We compared the
 among-population genetic distance in woody climbers (8 species, 30
 populations) and trees (7 species, 29 populations) coexisting in 9
 communities in a temperate rainforest. We also compared within-population
 genetic diversity in co-occurring woody climbers and trees in two
 communities. Mean genetic distance between populations of climbers was
 twice that of trees. Isolation by distance (increase in genetic distance
 with geographic distance) was greater for climbers. Climbers and trees
 showed similar within-population genetic diversity. Our longevity estimate
 suggested that climbers had shorter generation times, while other
 biological features often associated with diversification (dispersal and
 pollination syndromes, mating system, size and metabolic rate) did not
 show significant differences between groups. We hypothesize that the
 greater population differentiation in climbers could result from greater
 evolutionary responses to local selection acting on initially higher
 within-population genetic diversity, which could be driven by neutral
 processes associated with shorter generation times. Increased population
 genetic differentiation could be incorporated as another line of evidence
 when testing for key innovations.
description: Genetic and geographic
 distancesPairwise genetic (after
 AFLP markers) and geographic distances between populations of trees and
 woody climbersData Evolution
 16-0307.xlsx
DOI: 10.5061/dryad.k6916
title: Data from: Differential predation drives the geographical divergence in multiple traits in aposematic frogs

description: Prey have evolved a range of traits to enhance their survival against
 predators. These traits often show geographical variation due to the
 differences in local predation pressure. To date, there exists ample
 evidence of the geographical variation in single anti-predator traits such
 as coloration induced by differential predation. However, predation
 pressure often induces the shift in a suite of (correlated) prey traits,
 such as coloration and behavior, rather than a single trait in nature. In
 this study, we investigated the nature and extent of geographical
 variation in both color and behavioral traits in the oriental fire-bellied
 toad, Bombina orientalis, testing whether the frogs experience different
 predation pressure in different sites and evaluating how this might affect
 a range of traits associated with predator avoidance. Specifically, we
 quantified dorsal/ventral coloration, daytime resting place (i.e. the
 place where each frog was first spotted), and activity levels of natural
 populations of the frogs in 9 geographically distinct sites distributed
 across South Korea. We found the clearest differences in these traits
 between mainland and Jeju Island populations, with Jeju Island frogs
 exhibiting 1) less bright and less chromatic aposematic ventral coloration
 than mainland frogs, 2) lower activity during both day and night, and 3) a
 tendency to rest underwater. Follow-up predation experiments using clay
 frog models found that frogs in Jeju Island suffer higher predation
 pressure than mainland frogs, which readily explains the divergence in
 behavioral and morphological traits among populations.
description: Colour and behavioural
 data, Activity level survey data, and predation experiments data
 fileKang et
 al_2017_BehavioralEcology_Data.xlsx
DOI: 10.5061/dryad.pq1js52
title: Data from: Wild and laboratory exposure to cues of predation risk increases relative brain mass in male guppies

description: There is considerable diversity in brain size within and among species,
 and substantial dispute over the causes, consequences and importance of
 this variation. Comparative and developmental studies are essential in
 addressing this controversy. Predation pressure has been proposed as a
 major force shaping brain, behaviour and life history. The Trinidadian
 guppy, Poecilia reticulata, shows dramatic variation in predation pressure
 across populations. We compared the brain mass of guppies from high and
 low predation populations collected in the wild. Male but not female
 guppies exposed to high predation possessed heavier brains for their body
 size compared to fish from low predation populations. The brain is a
 plastic organ, so it is possible that the population differences we
 observed were partly due to developmental responses rather than evolved
 differences. In a follow‐up study, we raised guppies under cues of
 predation risk or in a control condition. Male guppies exposed to predator
 cues early in life had heavier brains relative to their body size than
 control males, while females showed no significant effect of treatment.
 Collectively our results suggest that male guppies exposed to predation
 invest more in neural tissue, and that these differences are at least
 partly driven by plastic responses.
description: Brain mass and body size
 dataBrain mass and body size
 data from field collections of guppies from high and low predation
 populations (sheet 1) and from guppies exposed to cues of predation or
 control cues in the laboratory (sheet 2).data.xlsx
DOI: 10.5061/dryad.f57k3
title: Data from: Glucocorticoid metabolism in the in ovo environment modulates exposure to maternal corticosterone in Japanese quail embryos (Coturnix japonica)

description: Maternal effects have gained attention as a method by which mothers may
 alter the physiological condition and phenotype of their offspring based
 upon current environmental conditions. The physiological and phenotypic
 outcomes of glucocorticoid-mediated maternal effects have been extensively
 studied in a variety of vertebrates; however, the underlying mechanism is
 currently unclear. Here, we injected tritiated corticosterone into the
 yolks of freshly laid Japanese quail eggs (Coturnix japonica) and traced
 its movement and metabolism through the in ovo development period. We
 found that corticosterone was extensively conjugated throughout the egg by
 the end of development, and while minimal corticosterone was detected
 within the embryo during development, accumulation of a conjugated
 metabolite in the embryo started to occur on day 6 of development. Because
 no movement and metabolism of corticosterone occurred in infertile eggs,
 our findings suggest that embryos are not passive recipients of maternal
 steroids, but instead appear to possess extensive metabolic capabilities,
 which may modulate their exposure to maternal steroids.
description: Yolk corticosterone
 dataIncludes data on
 tritiated steroids found in the three egg components over the course of
 egg development as well as TLC data in two different solvent
 systems.RSBL-2014-0502
 data.xlsx
DOI: 10.5061/dryad.3r041
title: Data from: Trade-offs and tritrophic consequences of host shifts in specialized root herbivores

description: Trade-offs in an herbivore's ability to feed, avoid predation and
 succeed on alternative hosts are thought to be major driving factors in
 host specialization. In this study, we compared how two closely related
 milkweed beetles (Tetraopes spp.) that have specialized on separate
 Asclepias species respond to host switching to alternative milkweed
 plants. By additionally examining effects on the beetles’ entomopathogenic
 natural enemies, we test whether host plant specialization is driven by
 plant–herbivore interactions alone or whether there is a role for the
 tritrophic interactions. Tetraopes beetles feed on milkweed roots as
 larvae and on milkweed shoots as adults, and they sequester toxic
 cardenolides from their host plants. We predicted that growth and
 sequestration would be compromised on alternative hosts as a consequence
 of specialization. Larvae of each Tetraopes species were reared on their
 native host plant, the host plant of the other species and two closely
 related Asclepias species that do not typically host Tetraopes. Regardless
 of beetle specialization, survival of both beetles was highest on A.
 syriaca, which has the second-to-lowest levels of root cardenolides and is
 the native host for T. tetraophthalmus. Larval growth was not affected by
 host plant for T. texanus, but T. tetraophthalmus grew best on A.
 exaltata, a close relative of A. syriaca that does not typically
 experience beetle feeding. We found that larval sequestration of
 cardenolides largely mirrored host plant values in the roots, with the
 exception of T. texanus on A. asperula, which sequestered a low proportion
 of the cardenolides from this host. Although all larvae were susceptible
 to entomopathogenic nematodes (EPNs), the number of EPNs emerging from
 cadavers depended on the beetle–plant combination, with more EPNs produced
 when beetles were feeding on native compared to non-native hosts. The
 observed consequences for tritrophic interactions did not fit expectations
 for specialized herbivores (i.e. EPN predation was highest when beetles
 were on their native hosts), suggesting that specialization may be driven
 primarily by a plant–herbivore interaction in this system, not by a
 tritrophic effect.
description: ALI_ AGRAWAL
 2016_DATALarval weight data,
 Larval survival data, HPLC cardenolide determinations from plant and
 larval tissue, Entomopathogenic nematode performance data. The excel file
 contains two sheets listing experimental data and a short descriptions of
 abbreviations where necessary.
DOI: 10.5061/dryad.sn42f
title: Data from: Colour misbinding during motion rivalry

description: When two dissimilar colours are displayed to the two eyes at overlapping
 retinal locations, binocular rivalry typically results: a fluctuating
 struggle for perceptual dominance of each eye’s stimulus. We found instead
 that isoluminant counter-rotating patterns consisting of coloured and
 achromatic portions can promote an illusory colour “misbinding”, where the
 colours from both eyes were perceived within a single rotating pattern.
 The achromatic portion of one rotating pattern thus appeared to take on
 the colour of the other, oppositely-rotating pattern. The results suggest
 that the neural mechanisms of colour binding can operate even while
 representations of the same patterns’ motions are undergoing rivalry, and
 support the idea that rivalry can occur in isolation within the motion
 system.
description: MaloneyLamClifford_dataHuman behavioural data as presented in main experiment of the article.MaloneyLamClifford_ESM_dataPilot data presented in the electronic supplementary material of the paper.
DOI: 10.5061/dryad.2dc34
title: Data from: Sublethal streptomycin concentrations and lytic bacteriophage together promote resistance evolution

description: Sub-minimum inhibiting concentrations (sub-MICs) of antibiotics frequently
 occur in natural environments owing to wide-spread antibiotic leakage by
 human action. Even though the concentrations are very low, these sub-MICs
 have recently been shown to alter bacterial populations by selecting for
 antibiotic resistance and increasing the rate of adaptive evolution.
 However, studies are lacking on how these effects reverberate into key
 ecological interactions, such as bacteria–phage interactions. Previously,
 co-selection of bacteria by phages and antibiotic concentrations exceeding
 MICs has been hypothesized to decrease the rate of resistance evolution
 because of fitness costs associated with resistance mutations. By
 contrast, here we show that sub-MICs of the antibiotic streptomycin (Sm)
 increased the rate of phage resistance evolution, as well as causing
 extinction of the phage. Notably, Sm and the phage in combination also
 enhanced the evolution of Sm resistance compared with Sm alone. These
 observations demonstrate the potential of sub-MICs of antibiotics to
 impact key ecological interactions in microbial communities with
 evolutionary outcomes that can radically differ from those associated with
 high concentrations. Our findings also contribute to the understanding of
 ecological and evolutionary factors essential for the management of the
 antibiotic resistance problem.
description: Bacterial
 densitiesDensities of bacteria
 during 66-day experimentBacterial_densities.xlsxPhage densitiesPhage densities during 66-day experimentPhage_densities.xlsxPhage resistancePhage resistance data for 66-day experimentPhageres.csv12-day experimentData from 12-day experiment12daydata.xlsx
DOI: 10.5061/dryad.3sm6t
title: Data from: A new basal chaeomysticete (Mammalia: Cetacea) from the late Oligocene Pysht Formation of Washington, USA

description: Modern baleen-bearing mysticetes are descendant from archaic, toothed
 mysticetes known from the Late Eocene and Oligocene of the Pacific Ocean.
 These toothed mysticetes, such as aetiocetids and mammalodontids, dominate
 the Oligocene fossil record. However, larger bodied eomysticetids have
 recently been described from the Oligocene of the Pacific and western
 Atlantic. These eomysticetids lack functional teeth as adults and are thus
 considered to be the earliest members of Chaeomysticeti. A new fossil from
 the Olympic Peninsula, Washington State, including a partial skull,
 tympanic bullae, mandibles and postcrania, is here described as Sitsqwayk
 cornishorum gen. et sp. nov. S. cornishorum is a Late Oligocene mysticete
 lacking functional teeth and is the most phylogenetically basal
 chaeomysticete. Accordingly, S. cornishorum exhibits a mosaic of
 aetiocetid and eomysticetid characteristics. The presence of S.
 cornishorum in the North Pacific, and its phylogenetic position relative
 to the eomysticetids from the Southern Ocean, suggests a possible a North
 Pacific point of origin for Chaeomysticeti.
description: Peredo and Uhen
 MatrixA nexus file containing
 the matrix used for the phylogenetic analysisPeredo and Uhen
 Mesquite.nex
DOI: 10.5061/dryad.q9d6s
title: Data from: Genetic differentiation of eastern wolves in Algonquin Park despite bridging gene flow between coyotes and grey wolves

description: Distinguishing genetically differentiated populations within hybrid zones
 and determining the mechanisms by which introgression occurs are crucial
 for setting effective conservation policy. Extensive hybridization among
 grey wolves (Canis lupus), eastern wolves (C. lycaon) and coyotes (C.
 latrans) in eastern North America has blurred species distinctions,
 creating a Canis hybrid swarm. Using complementary genetic markers, we
 tested the hypotheses that eastern wolves have acted as a conduit of
 sex-biased gene flow between grey wolves and coyotes, and that eastern
 wolves in Algonquin Provincial Park (APP) have differentiated following a
 history of introgression. Mitochondrial, Y chromosome and autosomal
 microsatellite genetic data provided genotypes for 217 canids from three
 geographic regions in Ontario, Canada: northeastern Ontario, APP and
 southern Ontario. Coyote mitochondrial DNA (mtDNA) haplotypes were common
 across regions but coyote-specific Y chromosome haplotypes were absent;
 grey wolf mtDNA was absent from southern regions, whereas grey wolf Y
 chromosome haplotypes were present in all three regions. Genetic
 structuring analyses revealed three distinct clusters within a genetic
 cline, suggesting some gene flow among species. In APP, however, 78.4% of
 all breeders and 11 of 15 known breeding pairs had assignment probability
 of Qgreater than or equal to0.8 to the Algonquin cluster, and the
 proportion of eastern wolf Y chromosome haplotypes in APP breeding males
 was higher than expected from random mating within the park
 (P&lt;0.02). The data indicate that Algonquin wolves remain
 genetically distinct despite providing a sex-biased genetic bridge between
 coyotes and grey wolves. We speculate that ongoing hybridization within
 the park is limited by pre-mating reproductive barriers.
description: Structure Assignment and
 Microsatellite ScoresThis file contains raw
 micro satellite scores and the Q value probability of assignment (mean of
 10 runs in Structure) to each of the three identified clusters as
 described in the manuscript.Rutledge et al. 2010 Heredity
 K
DOI: 10.5061/dryad.qf414sb
title: Data from: Ants on Clerodendrum infortunatum: disentangling effects of larceny and herbivory

description: Nectar larcenists extract nectar from flowers without pollinating them. A
 reasonable expectation is that any form of nectar larceny should have a
 detrimental effect on the plant’s reproductive success. However, studies
 reveal an entire range of effects, from highly negative to highly
 positive. This variation in effect may be partly explained by additional,
 unmeasured, effects of nectar larcenists on plants. In a study system
 where two ant species Tapinoma melanocephalum (Fabr.) and Trichomyrmex
 destructor (Jerd.) act as nectar larcenists, we examined the effect of
 larceny on the female reproductive success of Clerodendrum infortunatum
 Gaertn. in rain forest fragments of the Western Ghats, India. This was
 done through a combination of field observations and a series of field
 experiments looking at the effects of excluding ants from inflorescences.
 We found that T. destructor reduces fruit set considerably. Rather than
 this being a consequence of nectar larceny, however, our experiments show
 that the negative effect arises instead from the herbivorous behaviour of
 the ant. At a population level, both ant species prefer edges over
 interiors of forest patches, spatially concentrating the interaction zone
 to forest edges. Simultaneously considering multiple ecological
 interactions and disentangling their relative contributions might explain
 the large variation across species in the observed effect of larceny. The
 overall population effect of nectar larceny and herbivory is likely to
 depend on the spatial structuring of plants and ants.
description: Mukhopadhyay2018NectarLarcenyIt is a zip file which contains all the data files, codes and the README file.Mukhopadhyay2018.zip
DOI: 10.5061/dryad.7s3b8
title: Data from: Experimental sexual selection and sex comb evolution in Drosophila

description: Sexual selection can drive rapid evolutionary change in reproductive
 behaviour, morphology and physiology. This often leads to the evolution of
 sexual dimorphism, and continued exaggerated expression of dimorphic
 sexual characteristics, although a variety of other alternative selection
 scenarios exist. Here, we examined the evolutionary significance of a
 rapidly evolving, sexually dimorphic trait, sex comb tooth number, in two
 Drosophila species. The presence of the sex comb in both D. melanogaster
 and D. pseudoobscura is known to be positively related to mating success,
 although little is yet known about the sexually selected benefits of sex
 comb structure. In this study, we used experimental evolution to test the
 idea that enhancing or eliminating sexual selection would lead to
 variation in sex comb tooth number. However, the results showed no effect
 of either enforced monogamy or elevated promiscuity on this trait. We
 discuss several hypotheses to explain the lack of divergence, focussing on
 sexually antagonistic coevolution, stabilizing selection via species
 recognition and nonlinear selection. We discuss how these are important,
 but relatively ignored, alternatives in understanding the evolution of
 rapidly evolving sexually dimorphic traits.
description: Snook et al data
 Dryad
DOI: 10.5281/zenodo.17864120
title: Acute oral toxicity (LD50) of PFAS in mice rats datastes (ChemPharos datasets)

description: ChemPharos dataset description

·        Mouse dataset

A curated and enriched dataset for PFAS acute oral toxicity in mice (NEMESIS project) . The dataset was compiled from two previous studies by Chen et al. (2024) (https://doi.org/10.1016/j.jhazmat.2024.136071) and da Silva and de Melo (2024) (https://doi.org/10.1080/1062936X.2024.2417250). The curated oral toxicity dataset comprises 133 PFAS molecules and 777 molecular descriptors extracted from their 2D structure using the EnalosMold2 KNIME node. Useful metadata include CAS Numbers, SMILES representations, IUPAC names, MW values etc. Modelling subset information is additionally provided to support model reproducibility and transparency. Compounds are classified as “High” or “Low” toxicity based on their LD50 (mg/kg) values and the toxicity category thresholds proposed by US EPA. chemPharos link: https://db.chempharos.eu/datasets/Datasets.zul?datasetID=ds16 

·        Rat dataset

A curated and enriched dataset for PFAS acute oral toxicity in mice (INSIGHT project) . The dataset was compiled from three previous studies by Chen et al. (2024) (https://doi.org/10.1016/j.jhazmat.2024.136071), da Silva and de Melo (2024) (https://doi.org/10.1080/1062936X.2024.2417250), and Lu et al. (2024) (https://doi.org/10.1007/s00204-024-03739-w). The curated oral toxicity dataset comprises 307 PFAS molecules and 777 molecular descriptors extracted from their 2D structure using the EnalosMold2 KNIME node. Useful metadata include CAS Numbers, SMILES representations, IUPAC names, MW values etc. Modelling subset information is additionally provided to support model reproducibility and transparency. Compounds are classified as “High” or “Low” toxicity based on their LD50 (mg/kg) values and the toxicity category thresholds proposed by US EPA. chemPharos link: https://db.chempharos.eu/datasets/Datasets.zul?datasetID=ds17
DOI: 10.5281/zenodo.17864121
title: Acute oral toxicity (LD50) of PFAS in mice rats datastes (ChemPharos datasets)

description: ChemPharos dataset description

·        Mouse dataset

A curated and enriched dataset for PFAS acute oral toxicity in mice (NEMESIS project) . The dataset was compiled from two previous studies by Chen et al. (2024) (https://doi.org/10.1016/j.jhazmat.2024.136071) and da Silva and de Melo (2024) (https://doi.org/10.1080/1062936X.2024.2417250). The curated oral toxicity dataset comprises 133 PFAS molecules and 777 molecular descriptors extracted from their 2D structure using the EnalosMold2 KNIME node. Useful metadata include CAS Numbers, SMILES representations, IUPAC names, MW values etc. Modelling subset information is additionally provided to support model reproducibility and transparency. Compounds are classified as “High” or “Low” toxicity based on their LD50 (mg/kg) values and the toxicity category thresholds proposed by US EPA. chemPharos link: https://db.chempharos.eu/datasets/Datasets.zul?datasetID=ds16 

·        Rat dataset

A curated and enriched dataset for PFAS acute oral toxicity in mice (INSIGHT project) . The dataset was compiled from three previous studies by Chen et al. (2024) (https://doi.org/10.1016/j.jhazmat.2024.136071), da Silva and de Melo (2024) (https://doi.org/10.1080/1062936X.2024.2417250), and Lu et al. (2024) (https://doi.org/10.1007/s00204-024-03739-w). The curated oral toxicity dataset comprises 307 PFAS molecules and 777 molecular descriptors extracted from their 2D structure using the EnalosMold2 KNIME node. Useful metadata include CAS Numbers, SMILES representations, IUPAC names, MW values etc. Modelling subset information is additionally provided to support model reproducibility and transparency. Compounds are classified as “High” or “Low” toxicity based on their LD50 (mg/kg) values and the toxicity category thresholds proposed by US EPA. chemPharos link: https://db.chempharos.eu/datasets/Datasets.zul?datasetID=ds17