cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fj7cc64
title: Data from: A new actinopterygian from the Late Devonian Gogo Formation, Western Australia

description: The study of early actinopterygians (ray-finned fishes) from the Devonian
 has been hampered by imperfect preservation in the majority of taxa. The
 Late Devonian (early Frasnian) Gogo Formation of north-western Western
 Australia is notable in producing complete fossil actinopterygians with
 exceptional three-dimensional preservation of both the dermal and
 endoskeletal anatomy. Four taxa have been described and have proved
 invaluable in understanding the anatomy of early representatives of this
 clade. Here, we present a fifth Gogo taxon, based on a single
 exceptionally preserved specimen and representing a new genus and species
 of early ray-finned fish. The neurocranium was CT scanned, permitting a
 detailed examination of the endocast. The new taxon possesses unusual
 features including a greatly enlarged spiracular opening and extensive
 spinose ornamentation on the dermal skull bones, median ridge scutes and
 lepidotrichia. The endocast displays a mosaic of characters, some of which
 are similar to Mimipiscis and non-actinopterygian outgroups, while other
 features are more akin to Raynerius from the Late Devonian of France as
 well as several stratigraphically younger taxa. A phylogenetic analysis
 resolves the new form as sister taxon to fishes from the Late Devonian of
 the Northern Hemisphere and all post-Devonian actinopterygians, confirming
 that the assemblage of fossil ray fins from the Gogo Formation is part of
 the wider Devonian actinopterygian radiation.
description: Supplemental file 1 =
 Expanded cladogramPhylogenetic placement
 of Pickeringius acanthophorus n. gen. et sp. Expanded version of the tree
 presented in Figure 14, detailing unambiguous character changes. Optimised
 in MacClade 4.08.Supplement_1.pdfSupplemental file 2 = Apomorphy listDetailed apomorphy list of the phylogenetic analysis presented in Figure 14 and Supplemental .Supplement_2.docxSupplemental File 3 = Character matrixNexus file of the character matrix used in the phylogenetic analysis.Supplement_3.nex
DOI: 10.5281/zenodo.17967553
title: How does habitat use influence PFAS contamination in wildlife? Combining stable isotopes and GPS tracking in three gull species

description: Raw data and scripts of the analyses of the article " How does habitat use influence PFAS contamination in wildlife? Combining stable isotopes and GPS tracking in three gull species" by Rozen-Rechels D., Lemesle P. (co-first authors) et al., published in Environmental Pollution (https://doi.org/10.1016/j.envpol.2025.127556). These data are freely available in csv format. Tracking data are available on Movebank under the project LARUS SP Ile de Ré [ID PROG_533] (https://www.movebank.org/cms/webapp?gwt_fragment=page%3Dstudies%2Cpath%3Dstudy603876591) on reasonable request to the Ligue pour la Protection des Oiseaux (project manager Pamela Lagrange) and authors; the csv dataset used in the study is also available on reasonable request to the Ligue pour la Protection des Oiseaux (project manager Pamela Lagrange) and authors. See the readme file for metadata explanation.

Data and scripts were formatted by the first authors David Rozen-Rechels and Prescillia Lemesle and data curators Manrico Sebastiano and William Jouanneau (physiological data) and LPO data curators for tracking data : Frédéric Robin (curator at the time of study) and Pamela Lagrange (actual curator) and collected according to standards and procedures described in the companion journal article.

CORINE Land Cover data used are part of the CORINE Land Cover - France Métropolitaine - 2012 data, published in 2015 for regions Aquitaine-Limousin-Poitou-Charentes and Pays de la Loire. See for example: https://www.data.gouv.fr/datasets/corine-land-cover-occupation-des-sols-en-france
DOI: 10.5061/dryad.0b3k209
title: Data from: Group and kin recognition via olfactory cues in chimpanzees (Pan troglodytes)

description: Primates were traditionally thought to have a reduced sense of smell.
 Although there is now evidence that olfaction plays a greater role in
 primate social life than previously assumed, research on the sense of
 smell in non-human apes is scarce. Chimpanzees sniff the ground and
 vegetation on boundary patrols, but the function of this behaviour is
 unclear. Since chimpanzees are highly territorial and can kill individuals
 that do not belong to their own community, sniffing might function to
 gather information about conspecifics, particularly concerning group
 membership and kinship. To investigate whether chimpanzees recognize group
 members and kin via olfactory cues, we conducted behavioural bioassays on
 two groups of chimpanzees at Leipzig Zoo. In a pilot study, we found that
 chimpanzees responded more strongly to urine than to faeces or body odour.
 We then presented urine from group members, outgroup individuals and an
 unscented control in aerated boxes using a simultaneous discrimination
 task. The first behaviour after a chimpanzee first approached a box was
 related to olfaction (sniffing, nose within 20 cm, licking) in 83% of
 cases, highlighting the importance of olfaction as a general investigation
 mechanism in this species. Chimpanzees sniffed significantly longer at
 urine stimuli than the control and significantly longer at odours from
 outgroup individuals than those from group members. Furthermore, the
 duration of sniffing was positively correlated with relatedness. Our
 results suggest that chimpanzees use olfactory cues to obtain information
 about social relationships and fill a gap in our understanding of primate
 chemical communication.
description: Data_Ingroup-Outgroup_BioassayData and R-script used for analysis of the ingroup-outgroup bioassayData_Odour_Source_Preference_Pilot_StudyData and R-script used for analysis of the odour source preference pilot studyData_Intensity_ScoresData and R-script used for analysis of the influence of odour intensity
DOI: 10.5281/zenodo.17967552
title: How does habitat use influence PFAS contamination in wildlife? Combining stable isotopes and GPS tracking in three gull species

description: Raw data and scripts of the analyses of the article " How does habitat use influence PFAS contamination in wildlife? Combining stable isotopes and GPS tracking in three gull species" by Rozen-Rechels D., Lemesle P. (co-first authors) et al., published in Environmental Pollution (https://doi.org/10.1016/j.envpol.2025.127556). These data are freely available in csv format. Tracking data are available on Movebank under the project LARUS SP Ile de Ré [ID PROG_533] (https://www.movebank.org/cms/webapp?gwt_fragment=page%3Dstudies%2Cpath%3Dstudy603876591) on reasonable request to the Ligue pour la Protection des Oiseaux (project manager Pamela Lagrange) and authors; the csv dataset used in the study is also available on reasonable request to the Ligue pour la Protection des Oiseaux (project manager Pamela Lagrange) and authors. See the readme file for metadata explanation.

Data and scripts were formatted by the first authors David Rozen-Rechels and Prescillia Lemesle and data curators Manrico Sebastiano and William Jouanneau (physiological data) and LPO data curators for tracking data : Frédéric Robin (curator at the time of study) and Pamela Lagrange (actual curator) and collected according to standards and procedures described in the companion journal article.

CORINE Land Cover data used are part of the CORINE Land Cover - France Métropolitaine - 2012 data, published in 2015 for regions Aquitaine-Limousin-Poitou-Charentes and Pays de la Loire. See for example: https://www.data.gouv.fr/datasets/corine-land-cover-occupation-des-sols-en-france
DOI: 10.5061/dryad.n8h5147
title: Data from: New locus reveals the genetic architecture of sex reversal in the Chinese tongue sole (Cynoglossus semilaevis)

description: Sex reversal in insects, amphibians, reptiles, and fishes is a complicated
 and interesting biological phenomenon. Sex reversal changes the sex ratio
 of populations and may complicate breeding schemes. In the Chinese tongue
 sole (Cynoglossus semilaevis), genetic females may change into
 pseudomales, thereby increasing aquaculture costs because of the lower
 growth rate of the males than that of the females. Here, we identify a new
 locus associated with sex reversal; this single nucleotide polymorphism
 (SNP) is located in the third intron of the doublesex and mab-3 related
 transcription factor 1 (Dmrt1) gene on the Z chromosome (named
 Cyn_Z_8564889) and has two alleles, A and G. Cyn_Z_8564889 regulates sex
 reversal interactively with our previously detected SNP (Cyn_Z_6676874),
 with the genetic females simultaneously carrying the T allele of
 Cyn_Z_6676874 and the A allele of Cyn_Z_8564889 changing into pseudomales.
 Other Dmrt1 polymorphisms were detected, which formed two haplotypes. Two
 SNPs in the second exon of Dmrt1 result in amino acid changes, suggesting
 that Dmrt1 is essential in sex reversal. We also verified that pseudomales
 produce no or little W sperm. The interaction and linkage between
 Cyn_Z_6676874 and Cyn_Z_8564889 and the absence of W sperm from
 pseudomales unravel the genetic architecture of sex reversal in C.
 semilaevis.
description: sex reversal of tongue
 solesupplementary data
 description File_S1_phenotypes.txt contains fish ID, genotypic sex,
 phenotypic sex, allele at SNP Cyn_Z_6676874, incidence of sex reversal.
 File_S2_genotypes.txt contains ID and genotypes of 33410 markers, which
 are expressed as 012, 0 and 2 stand for homozygotes of each alleles, and 1
 for heterozygote. File_S3_SNP_info.txt contains three columns, they are
 marker name, chromosome, and position in order.supplementary
 file.rar
DOI: 10.5061/dryad.1858
title: Data from: Multielement stoichiometry in aquatic invertebrates: when growth dilution matters

description: Element concentrations in organisms can be variable, often causing
 deviations from otherwise consistent, taxon-specific multielement
 stoichiometries. Such variation can have considerable ecological
 consequences, yet physiological mechanisms remain unclear. We tested the
 influence of somatic growth dilution (SGD) on multiple element
 concentrations under different bioenergetic conditions. SGD occurs when
 rapid individual growth causes a disproportional gain in biomass relative
 to gain of a specific element. SGD can strongly affect elements in various
 organisms, but we lack a general framework to unify results across studies
 and assess its overall importance. We derived the general conditions that
 trigger SGD from an element accumulation model. We parameterized the model
 with bioenergetic and element-specific rates summarized from the
 literature to compare SGD effects on 15 elements (nonessential metals,
 essential trace elements, macronutrients) in three aquatic invertebrate
 taxa. For all taxa, we found that SGD: (1) occurs to some degree for all
 15 elements over realistic ranges of growth and ingestion rates, and (2)
 has the greatest effect on elements with low efflux (excretion) rates,
 including certain nonessential metals (e.g., MeHg, Po), essential trace
 elements and macronutrients (e.g., N, Fe). Thus, SGD can strongly affect
 concentrations of a spectrum of elements under natural conditions. These
 results provide a framework for predicting variation in elemental
 composition of animals.
description: DryadDataKarimietal2010.docNOTE: THIS FILE CONTAINS ERRORS. Please use the updated version of the file, found at http://dx.doi.org/10.5061/dryad.1858/2DryadDataKarimietal2010 correctedTables summarizing bioenergetic rates and element kinetics reported in published studies for select aquatic invertebrate taxa: Daphnia, marine copepods and mytilid mussels. Values include growth rates, ingestion rates, element assimilation efficiencies and element efflux rates.
DOI: 10.5061/dryad.4006fm8
title: Data from: Correlates of rate heterogeneity in avian ecomorphological traits

description: Heterogeneity in rates of trait evolution is widespread, but it remains
 unclear which processes drive fast and slow character divergence across
 global radiations. Here, we test multiple hypotheses for explaining rate
 variation in an ecomorphological trait (beak shape) across a globally
 distributed group (birds). We find low support that variation in
 evolutionary rates of species is correlated with life history,
 environmental mutagenic factors, range size, number of competitors, or
 living on islands. Indeed, after controlling for the negative effect of
 species' age, 80% of variation in species‐specific evolutionary rates
 remains unexplained. At the clade level, high evolutionary rates are
 associated with unusual phenotypes or high species richness. Taken
 together, these results imply that macroevolutionary rates of
 ecomorphological traits are governed by both ecological opportunity in
 distinct adaptive zones and niche differentiation among closely related
 species.
description: Landmark
 configurationsUser-averaged landmark
 configurations for 3D scans of bird beaks. The two lists cover species for
 which genetic data is available (Gsubset) and also the full list of
 species (full_subset).landmark_configurations.rarTable1 and table 2Tree and trait data files used to calculate species-specific and clade rates of evolution, as well as data for candidate predictor variables (data used to obtain the results in tables 1 and 2).table1_2.rarTable S3Trees and trait data files used to calculate species-specific rates of evolution (data used to obtain the results in table S3).tableS3.rarTable S5Trees and trait data files used to calculate species-specific rates of evolution, as well as data for candidate predictor variables (data used to obtain the results in Table S5).tableS5.rarTable S6Trees and trait data files used to calculate clade rates of evolution, as well as data for candidate predictor variables (data used to obtain the results in table S6).tableS6.rarTable S7Tree and trait data file used to calculate clade rates of evolution, as well as data for candidate predictor variables (data used to obtain the results in table S7).tableS7.rar
DOI: 10.5061/dryad.cr6dm10
title: Data from: Low-smoke chulha in Indian slums: study protocol for a randomised controlled trial

description: Background: Biomass fuel is used as a primary cooking source by more than
 half of the world’s population, contributing to a high burden of disease.
 Although cleaner fuels are available, some households continue using solid
 fuels because of financial constraints and absence of infrastructure,
 especially in non-notified slums. The present study documents a randomised
 controlled study investigating the efficacy of improved cookstove on the
 personal exposure to air pollution and the respiratory health of women and
 children in an Indian slum. The improved cookstove was based on
 co-creation of a low-smoke chulha with local communities in order to
 support adaption and sustained uptake. Methods: The study will be
 conducted in a non-notified slum called Ashrayanagar in Bangalore, India.
 The study design will be a 1:1 randomised controlled intervention trial,
 including 250 households. The intervention group will receive an improved
 cookstove (low-smoke chulha) and the control group will continue using
 either the traditional cookstove (chulha) or a combination of the
 traditional stove and the kerosene/diesel stove. Follow-up time is 1 year.
 Outcomes include change in lung function (FEV1/FVC), incidence of
 pneumonia, change in personal PM2.5 and CO exposure, incidence of
 respiratory symptoms (cough, phlegm, wheeze and shortness of breath),
 prevalence of other related symptoms (headache and burning eyes), change
 in behaviour and adoption of the stove. Ethical clearance was obtained
 from the Institutional Ethics Committee of the Indian Institute of Public
 Health HyderabadBengaluru Campus. Discussion: The findings from this study
 aim to provide insight into the effects of improved cookstoves in urban
 slums. Results can give evidence for the decrease of indoor air pollution
 and the improvement of respiratory health for children and women.
description: Report from improved
 cook stove tests in Bangalore slumsCONCLUSION
 REPORT.pdf
DOI: 10.5061/dryad.h55p1q5
title: Data from: Dogs accompanied humans during the Neolithic expansion into Europe

description: Near Eastern Neolithic farmers introduced several species of domestic
 plants and animals as they dispersed into Europe. Dogs were the only
 domestic species present in both Europe and the Near East prior to the
 Neolithic. Here, we assessed whether early Near Eastern dogs possessed a
 unique mitochondrial lineage that differentiated them from Mesolithic
 European populations. We then analysed mitochondrial DNA sequences from 99
 ancient European and Near-Eastern dogs spanning the Upper Palaeolithic to
 the Bronze Age to assess if incoming farmers brought Near Eastern dogs
 with them, or instead primarily adopted indigenous European dogs after
 they arrived. Our results show that European pre-Neolithic dogs all
 possessed the mitochondrial haplogroup C, and that the Neolithic and
 Post-Neolithic dogs associated with farmers from Southeastern Europe
 mainly possessed haplogroup D. Thus, the appearance of haplogroup D most
 likely resulted from the dissemination of dogs from the Near East into
 Europe. In Western and Northern Europe, the turnover is incomplete and C
 haplogroup persists well into the Chalcolithic at least. These results
 suggest that dogs were an integral component of the Neolithic farming
 package and a mitochondrial lineage associated with the Near East was
 introduced into Europe alongside pigs, cows, sheep, and goats. It got
 diluted into the native dog population when reaching the Western and
 Northern margins of Europe.
description: modern and ancient dog
 mt sequence (HVR1)all-sequence
 file.fst
DOI: 10.5061/dryad.3v9v238
title: Data from: A dedicated target capture approach reveals variable genetic markers across micro- and macro-evolutionary time scales in palms

description: Understanding the genetics of biological diversification across micro- and
 macro-evolutionary time scales is a vibrant field of research for
 molecular ecologists as rapid advances in sequencing technologies promise
 to overcome former limitations. In palms, an emblematic, economically and
 ecologically important plant family with high diversity in the tropics,
 studies of diversification at the population and species levels are still
 hampered by a lack of genomic markers suitable for the genotyping of large
 numbers of recently diverged taxa. To fill this gap, we used a whole
 genome sequencing approach to develop target sequencing for molecular
 markers in 4,184 genome regions, including 4,051 genes and 133 non-genic
 putatively neutral regions. These markers were chosen to cover a wide
 range of evolutionary rates allowing future studies at the family, genus,
 species and population levels. Special emphasis was given to the avoidance
 of copy number variation during marker selection. In addition, a set of
 149 well-known sequence regions previously used as phylogenetic markers by
 the palm biological research community were included in the target
 regions, to open the possibility to combine and jointly analyse already
 available data sets with genomic data to be produced with this new
 toolkit. The bait set was effective for species belonging to all three
 palm subfamilies tested (Arecoideae, Ceroxyloideae and Coryphoideae), with
 high mapping rates, specificity and efficiency. The number of high quality
 Single Nucleotide Polymorphisms (SNPs) detected at both the subfamily and
 population levels facilitates efficient analyses of genomic diversity
 across micro- and macro-evolutionary time scales.
description: PopcornPalm_AllBaitListList of the baits, in fasta format, of the PopcornPalm target capture kit including all 59,264 baits of 120bp.PopcornPalm57K_baitListList of the baits, in fasta format, of the PopcornPalm57K target capture kit including 57,061 baits of 120bp.PopcornPalm54K_baitListList of the baits, in fasta format, of the PopcornPalm54K target capture kit including 54,090 baits of 120bp.
DOI: 10.5061/dryad.n2r370n
title: Data from: Accounting for uncertainty in the evolutionary timescale of green plants through clock-partitioning and fossil calibration strategies

description: Establishing an accurate evolutionary timescale for green plants
 (Viridiplantae) is essential to understanding their interaction and
 coevolution with the Earth’s climate and the many organisms that rely on
 green plants. Despite being the focus of numerous studies, the timing of
 the origin of green plants and the divergence of major clades within this
 group remain highly controversial. Here, we infer the evolutionary
 timescale of green plants by analysing 81 protein-coding genes from 99
 chloroplast genomes, using a core set of 21 fossil calibrations. We test
 the sensitivity of our divergence-time estimates to various components of
 Bayesian molecular dating, including the tree topology, clock models,
 clock-partitioning schemes, rate priors, and fossil calibrations. We find
 that the choice of clock model affects date estimation and that the
 independent-rates model provides a better fit to the data than the
 autocorrelated-rates model. Varying the rate prior and tree topology had
 little impact on age estimates, with far greater differences observed
 among calibration choices and clock-partitioning schemes. Our analyses
 yield date estimates ranging from the Paleoproterozoic to Mesoproterozoic
 for crown-group green plants, and from the Ediacaran to Middle Ordovician
 for crown-group land plants. We present divergence-time estimates of the
 major groups of green plants that take into account various sources of
 uncertainty. Our proposed timeline lays the foundation for further
 investigations into how green plants shaped the global climate and
 ecosystems, and how embryophytes became dominant in terrestrial
 environments.
description: SI_alignment_99_taxa_cp12Alignment (in nexus format) of 1st and 2nd codon positions of 81 protein-coding chloroplast genes from 97 green plants and two red algae outgroup taxa.SI_alignment_99_taxa_cp3Alignment (in nexus format) of 3rd codon positions of 81 protein-coding chloroplast genes from 97 green plants and two red algae outgroup taxa.Supplementary_InformationThis file contains all of the supplementary information from the study "Accounting for uncertainty in the evolutionary timescale of green plants through clock-partitioning and fossil calibration strategies". In total, there are 7 supplementary tables and 11 supplementary figures within.