cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wstqjq2rp
title: Armed to the teeth: Supplementary material, R code, Rdata, mesh, landmarks

description: The structure, composition, and shape of teeth have been related to
 dietary specialization in many vertebrate species, but comparative studies
 on snakes’ teeth are lacking. Yet, snakes have diverse dietary habits that
 may impact the shape of their teeth. We hypothesize that prey properties,
 such as hardness and shape, as well as feeding behavior, such as aquatic
 or arboreal predation, or holding vigorous prey, impose constraints on the
 evolution of tooth shape in snakes. We compared the morphology of the
 dentary teeth of 63 species that cover the phylogenetic and dietary
 diversity of snakes, using 3D geometric morphometrics and linear
 measurements. Our results show that prey hardness, foraging substrate, and
 the main foraging mechanical challenge are important drivers of tooth
 shape, size, and curvature. Overall, long, slender, curved teeth with a
 thin layer of hard tissue are observed in species that need to maintain a
 grip on their prey.  Short, stout, less curved teeth are
 associated with species that undergo high or repeated loads. Our study
 demonstrates the diversity of tooth morphology in snakes and the need to
 investigate its underlying functional implications to better understand
 the evolution of teeth in vertebrates.
description: We microCT scanned the dentary teeth of 63 species of snakes
 using a Phoenix Nanotom S μCT‐scanner (General Electric, Fairfield, CT,
 USA). The 3D reconstruction was done using Phoenix datos|x2 (v2.3.0,
 General Electric, Fairfield, CT, USA) and the subsequent segmentation was
 performed using VGStudioMax (v1.0, Volume Graphics GmbH, Heidelberg,
 Germany). We then compare the shape of these teeth using 3D geometric
 morphometrics. We used phylogenetic comparative analysis to investigate
 the relationship between shape and diet. We provide the R code, Rdata, and
 all necessary files to reproduce our results. We also
 added the supplementary material related to our publication.
description: R, Meshlab, MorphoDig
DOI: 10.5061/dryad.b8gtht7hj
title: Data for: Genetic control of grain amino acid composition in a UK soft wheat mapping population

description: Wheat is a major source of nutrients for populations across the globe, but
 the amino acid composition of wheat grain does not provide optimal
 nutrition. The nutritional value of wheat grain is limited by low
 concentrations of lysine (the most limiting essential amino acid) and high
 concentrations of free asparagine (precursor to the processing contaminant
 acrylamide). There are currently few available solutions for asparagine
 reduction and lysine biofortification through breeding. In this study, we
 investigated the genetic architecture controlling grain-free amino acid
 composition and its relationship to other traits in a Robigus × Claire
 doubled haploid population. Multivariate analysis of amino acids and other
 traits showed that the two groups are largely independent of one another,
 with the largest effect on amino acids being from the environment. Linkage
 analysis of the population allowed the identification of QTL controlling
 free amino acids and other traits, and this was compared against genomic
 prediction methods. Following the identification of a QTL controlling free
 lysine content, wheat pangenome resources facilitated analysis of
 candidate genes in this region of the genome. These findings can be used
 to select appropriate strategies for lysine biofortification and free
 asparagine reduction in wheat breeding programmes.
DOI: 10.5061/dryad.3j9kd51pk
title: Data from: Sulfur isotopic discrimination factors differ among avian tissues and diets: Insights from a case study in Gentoo Penguins (Pygoscelis papua)

description: The use of stable isotopes of sulfur (δ34S) to infer avian diets, foraging
 habitats, and movements is relatively uncommon, resulting in a lack of
 information on patterns of δ34S incorporation in avian tissue. In a
 controlled study of Gentoo Penguins (Pygoscelis papua), we found that
 diet-tissue isotopic discrimination factors (Δ34Sdiet-tissue) differed
 among egg components and feathers synthesized from a common diet, ranging
 from -0.4 to -1.7 ‰. We also found that methodical choices such as lipid
 extraction and prey tissue selection influenced calculated Δ34Sdiet-tissue
 values. Specifically, Δ34Sdiet-tissue values were lower (i.e., more
 negative) when calculated using whole fish relative to fish muscle and
 lipid-extraction biased egg yolk, but not fish tissue, δ34S values.
 Δ34Sdiet-tissue values obtained for Gentoo Penguins fed a marine fish diet
 were generally lower than those reported for freshwater-fish-consuming
 Double-crested Cormorants (Phalacrocorax auritus), the only other bird
 species in which Δ34Sdiet-tissue has been quantified. We found support for
 the hypothesis that tissue Δ34Sdiet-tissue values are inversely related to
 dietary δ34S values in birds, similar to what has been observed in
 mammals. Given this relationship, the discrimination factors reported here
 for Gentoo Penguins may be broadly applicable to other avian species with
 a similar marine diet. Finally, we provide recommendations for future
 studies seeking to quantify Δ34Sdiet-tissue in avian tissues and guidance
 to allow for greater application of sulfur stable isotope analysis in
 ornithological research.
description: Data was collected from a captive breeding population of Gentoo
 Penguins (<em>Pygoscelis</em> <em>papua</em>) at
 the Henry Doorly Zoo in Omaha, Nebraska, USA. Penguins were hand-fed ad libitum a consistent diet
 of Atlantic Herring (<em>Clupea harengus</em>) for eight and
 ten months prior to the start of egg tissue collection and feather molt,
 respectively.  Samples of herring (whole fish and muscle tissue), body
 feathers, eggshell membrane, albumen and yolk were analyzed for sulfur (S)
 elemental concentration (%S) and stable isotope values
 (δ<sup>34</sup>S) using an elemental analyzer system coupled
 to a continuous-flow stable isotope ratio mass spectrometer. A sub-sample
 of whole fish, fish muscle, and yolk samples were lipid extracted using a
 Soxhlet apparatus with a 1:1 Petroleum–Ether: Ethyl–Ether prior to
 analyses. We calculated
 Δ<sup>34</sup>S<sub>diet-tissue</sub> by
 subtracting the δ<sup>34</sup>S values of each individual egg
 tissue and feather sample from the mean isotopic values of the diets
 (whole herring and herring muscle) consumed prior to tissue
 synthesis.
DOI: 10.5061/dryad.m37pvmd6p
title: Results of linear ocean model experiment for: Dual wave energy sources for the Atlantic Niño events identified by wave energy flux in case studies

description: These are sensitivity experiments designed by manipulating the wind
 forcing that drives the linear ocean model to investigate the difference
 in equatorial waves in 1999, 2019, and 2021. 
description: Three forcing regions are marked as R1 (the western equatorial
 Atlantic region), R2 (the whole equatorial Atlantic region), and R3 (the
 off-equatorial region).  Selecting one region where the zonal forcing is
 applied and elsewhere it is eliminated to initiate the event in the three
 selected years respectively. Thus one group of the experiments for a
 certain selected year includes five scenarios marked from T0 to T4, where
 T0 is the reference run, T4 is the scenario excluding the zonal forcing in
 the whole selected forcing domain and other numbers indicate the selected
 region where the zonal forcing is still applied. In each scenario, we
 integrated the LOM for two years from the initial condition by the
 reference run (T0) at the beginning of the selected year to excite the
 1st-4th BCMs independently.
DOI: 10.5061/dryad.z34tmpgk1
title: Dataframes for: Postpartum cessation of urban space use by a female baboon living at the edge of the City of Cape Town

description: Species with slow life history strategies that invest in few offspring
 with extended parental care need to adapt their behaviour to cope with
 anthropogenic changes that occur within their lifetime. Here we show that
 a female chacma baboon (Papio ursinus) who commonly ranges within urban
 space in the City of Cape Town, South Africa, stops using urban space
 after giving birth. This change of space use occurs without any
 significant change in daily distance travelled or social interactions that
 would be expected with general risk-sensitive behaviour after birth.
 Instead, we suggest this change occurs because of the specific and greater
 risks the baboons experience within the urban space compared to natural
 space, and because leaving the troop (to enter urban space) may increase
 infanticide risk. This case study can inform methods used to manage the
 baboon’s urban space use in Cape Town and provides insight into how life
 history events alter individuals’ use of anthropogenic environments.
description: This dataset was calculated from high-resolution GPS data,
 recording at 1Hz from individual tracking collars deployed on n = 16 adult
 baboons. GPS data was cleaned as processed as per procedures outlined in
 the manuscript.
description: Dataframes are supplied in csv format.
DOI: 10.25338/b8qm06
title: Partial NADH dehydrogenase subunit 2 (ND2) gene sequences for Trochilidae hummingbirds

description: Anthropogenic changes have altered the historical distributions of many
 North American taxa.  As environments shift, ecological and
 evolutionary processes can combine in complex ways to either stimulate or
 inhibit range expansion. Here we examine the role of evolution in a rapid
 range expansion whose ecological context has been well-documented, Anna’s
 Hummingbird (Calypte anna). Previous work suggests that the C. anna range
 expansion is the result of an ecological release facilitated by
 human-mediated environmental changes, where access to new food sources has
 allowed further filling of the abiotic niche. We examine the role of gene
 flow and adaptation during range expansion from their native California
 breeding range, north into Canada and east into New Mexico and Texas, USA.
 Using low-coverage whole genome sequencing, we found high genetic
 diversity, low divergence, and little evidence of selection on the
 northern and eastern expansion fronts. Additionally, there are no clear
 barriers to gene flow across the native and expanded range. The lack of
 selective signals between core and expanded ranges could reflect i) an
 absence of novel selection pressure in the expanded range (supporting the
 ecological release hypothesis), ii) swamping of adaptive variation due to
 high gene flow, or iii) limitations of genome scans for detecting small
 shifts in allele frequencies across many loci. Nevertheless, our results
 provide an example where strong selection is not apparent during a rapid,
 contemporary range shift.
description: To identify potential Anna’s Hummingbird <em>(Calypte
 anna)</em> samples, we sequenced nestlings and fledglings of unknown
 hummingbird species and samples that had been identified as Anna’s
 Hummingbird (<em>C. anna</em>) and other hummingbird species
 likely to be collected in the region: Costa’s (<em>C.
 costae</em>), Allen’s (<em>Selasphorus sasin</em>),
 Calliope (<em>S. calliope</em>), and Rufous (<em>S.
 rufus</em>) Hummingbirds. Tissue samples were provided by Dr. Lisa
 Tell at UC Davis and we extracted genomic DNA using DNeasy Blood &
 Tissue Kit (Qiagen). We amplified part of the NADH dehydrogenase subunit 2
 (ND2) gene using H6313, H6316, and L5219 primers (Sorenson et al., 1999),
 cleaned the products using an ExoSAP protocol, then sequenced them at
 UCDNA Sequencing Facility at the University of California,
 Davis. For more information, see Adams et al. 2023.
 Widespread gene flow following range expansion in Anna's Hummingbird.
 Molecular Ecology. Accepted. DOI:10.1111/mec.16928.
description: Any program that can read .ab1 files. Popular software includes
 FinchTV, Sequence Scanner, and 4Peaks, among others.
DOI: 10.5061/dryad.vdncjsz06
title: The role of abiotic and biotic factors in the unequal body shape diversification of a Gondwanan fish radiation (Otophysi:Characiformes)

description: Understanding why some clades diversify greatly, while others do not, is a
 major goal of evolutionary biology. Both abiotic and biotic factors are
 important in driving unequal morphological diversity across the tree of
 life. However, few studies have quantified how differences in abiotic
 habitat and community composition influence unequal morphological
 diversification in spatiotemporally diffuse radiations. Here we use
 geometric morphometrics, abiotic habitat data generated by Geographic
 Information Systems (GIS) analyses, evolutionary simulations, and
 phylogenetic comparative methods to determine whether random evolution,
 habitat variation, competition for niches or a combination of factors
 influenced the unequal body shape diversity of a Gondwanan freshwater fish
 radiation. We find that neotropical characiform lineages, which exhibit
 substantially more body shape diversity than their African counterparts,
 occupy significantly more slope and elevation habitats than African
 lineages. Differences in habitat occupation between the continental
 radiations occur by a combination of competition with cypriniform fishes
 in Africa restricting access to higher slope and elevation habitats and
 significantly more low elevation and slope habitat available in the
 neotropics. Our findings suggest that spatiotemporally widespread
 radiations, like the Characiformes, do not diversify across homogenized
 habitats and biotic assemblages, with differences in community structure
 and physical habitat important in driving unequal morphological
 diversification.
DOI: 10.6084/m9.figshare.31169518.v1
title: Raw data of selective chiral multistate switching via the dynamic interplay of diabolic and exceptional points

description: All raw data supporting the selective chiral multistate switching.
DOI: 10.5061/dryad.p2ngf1vvx
title: The role of irradiance in controlling coralline algal calcification

description: Coralline algae are an essential element of benthic ecosystems throughout
 the ocean’s photic zone. Yet, the role of light in shaping the physiology
 of coralline algae from cold-water, low-light habitats is poorly
 understood. Here, we assess the calcification physiology of five
 cool-temperate coralline algae in response to different irradiances over
 three months. We show that in contrast to current models focused on warmer
 water species, previously observed enhancement of calcification rates by
 photosynthesis is largely limited to lower irradiances, and that the
 removal of CO2 from the calcifying fluid is not the underlying mechanism
 of this enhancement. Instead, this likely occurs via two processes: 1)
 increased ion pumping rates to elevate the calcium carbonate saturation
 state in the calcifying fluid; and 2) a higher daytime pH in the diffusion
 boundary layer that raises calcifying fluid pH. However, as irradiance
 increases, ion pumping becomes increasingly saturated limiting further
 enhancements. Our results also suggest the existence of two calcification
 strategies in coralline algae and indicate that magnesium incorporation is
 determined by the magnesium-to-calcium ratio in the calcifying fluid
 ([Mg]CF/[Ca]CF). This study adds to our mechanistic understanding of
 calcification in coralline algae and fills in much-needed knowledge about
 the role of light in controlling their physiology.
description: Chlorophyll flourometry was used to obtain Fv/Fm
 (variable fluorescence [Fv] normalised to maximal fluorescence [Fm]),
 rETRmax (maximum relative elctron transport rate), Ek (minimum saturation
 intensity) and alpha (light use efficiency). Skeletal
 magnesium content in mol% and Full-Width-Half-Maximum were measured using
 confocal Raman spectroscopy. Chlorophyll a,
 phycoerything and phycocyanin content was calculated from absorbance
 readings (UV-vis spectrophotometer). Calcification
 rates were calculated from changes in weight (buoyant weight) which were
 normalised for surface area (cm<sup>-2</sup>) and time
 (d<sup>-1</sup>). Short-term
 calcification rates in the dark and the light were calculated from changes
 in total alkalinity which were normalised for surface area (cm-2) and time
 (h-1). Photosynthetic rates (gross) were calculated
 from changes in oxygen (O<sub>2</sub>) during the day (net
 photosynthesis) and the night (dark respiration) which were normalised for
 surface area (cm<sup>-2</sup>) and time
 (h<sup>-1</sup>). Organic tissue carbon
 isotope values were calculated from the ratio between
 <sup>13</sup>C and <sup>12</sup>C
DOI: 10.5061/dryad.p5hqbzktd
title: Intensified livestock farming increases antibiotic resistance genotypes and phenotypes in animal feces

description: Animal feces from livestock farming can be a major source of antibiotic
 resistance to the environment, but a clear gap exists on how the
 resistance reservoir in feces alters as farming activities intensify.
 Here, we sampled feces from eight Chinese farms, where yak, sheep, pig,
 and horse were reared under free-range to intensive conditions, and
 determined fecal resistance using both genotype and phenotype approaches.
 Animals reared intensively exhibited increased
 diversity of antibiotic resistance genes (ARGs) and greater
 resistance phenotypes in feces, which were cross-correlated. Furthermore,
 at the metagenome contig level, ARGs were
 co-located with mobile genetic elements at a higher frequency
 (27.38%) as farming intensified, with associated resistance
 phenotypes being less coupled with bacterial phylogeny. Intensified
 farming also expanded the multidrug resistance preferentially carried on
 pathogens in fecal microbiomes. Overall, farming intensification
 can increase antibiotic resistance genotypes and phenotypes in
 domestic animal feces, with implications for environmental health.
  
description: We sampled feces from eight Chinese farms, where animals (yak, sheep, pig, and horse) were reared under free range to more intensive conditions, to determine the extent to which intensified farming expands antibiotic resistance in fecal matter, using both genotype and phenotype approaches.The datasets of Ct values from high-throughput qPCR analyses are shown in supplementary Data 1 (*.xlsx). The datasets of TPM values from metagenomic sequencing analyses are shown in Supplementary Data 2 (*.xlsx). All isolated and then identified strains with their sequenced reads are listed in Supplementary Data 3 (*.xlsx). Supplementary Data 4 (*.xlsx) contains all recorded diameters of the inhibition zone (IZD) for these strains tested using the standard disc diffusion assay. Please see the README document for detailed information. 
description: We sampled feces from eight Chinese farms, where animals (yak, sheep, pig, and horse) were reared under free range to more intensive conditions, to determine the extent to which intensified farming expands antibiotic resistance in fecal matter, using both genotype and phenotype approaches.The datasets of Ct values from high-throughput qPCR analyses are shown in supplementary Data 1 (*.xlsx). The datasets of TPM values from metagenomic sequencing analyses are shown in Supplementary Data 2 (*.xlsx). All isolated and then identified strains with their sequenced reads are listed in Supplementary Data 3 (*.xlsx). Supplementary Data 4 (*.xlsx) contains all recorded diameters of the inhibition zone (IZD) for these strains tested using the standard disc diffusion assay. Please see the README document for detailed information.
DOI: 10.5061/dryad.qnk98sfmr
title: Species diagnosis tables for: Crinoids from the Wooster Shale Member of the Cuyahoga Formation, Carboniferous (Mississippian, Tournaisian) of Northeastern Ohio

description: Nine crinoids are described from the Wooster Shale Member of the Cuyahoga
 Formation from Wayne and Ashland counties, Ohio, USA. Identifiable
 elements of the fauna include five camerate crinoids, one flexible
 crinoid, and three other eucladid crinoids. Five new species are
 described, including Cactocrinus woosterensis n. sp., Cusacrinus brushi n.
 sp., Agaricocrinus murphyi n. sp., Decadocrinus laevis n. sp., and
 Decadocrinus inordinatus n. sp. Overall, the distribution of crinoid
 clades in the Wooster Shale is similar to that of the stratigraphically
 lower Meadville Shale Member of the Cuyahoga Formation, although less
 diverse and with only one species (Cyathocrinites simplex) in common. Many
 of the Wooster Shale crinoids are completely or partially preserved with
 siderite in either nodules or within siderite beds. These crinoids are
 commonly preserved in trauma postures, which is characteristic of burial
 in episodic high turbulence events. The paleoenvironments and taxa of the
 two Cuyahoga Formation crinoid faunas more closely resemble Viséan faunas
 in siliciclastic settings than typical carbonate faunas of the
 Tournaisian. Supplemental tables included here are species diagnostic
 tables listing characters for differentiating species in the following
 Mississippian crinoid (Phylum Echinodermata) genera: Agaricocrinus,
 Cactocrinus, Cusacrinus, and Decadocrinus. 
description: These data were compiled from the 19th, 20th, and 21st century
 literature on fossil crinoids.
DOI: 10.24378/exe.31161238
title: Anonymised qualitative interview excerpts underpinning Phase 2 of the RecoverED programme theory development process

description: This dataset is associated with the publication <i>Developing a programme theory of a complex, home-based rehabilitation intervention for recovery after an episode of delirium</i> (PLOS ONE, accepted).The publication reports the process of developing and refining a programme theory underpinning RecoverED, a novel, home-based, multicomponent rehabilitation intervention designed to support recovery following an episode of delirium in older adults. The paper focuses on the methodological process and synthesis of evidence and does not report primary qualitative findings in detail.The dataset shared here comprises anonymised qualitative interview excerpts from Phase 2 of the programme theory development process. Phase 2 involved semi-structured qualitative interviews with key stakeholders, including older adults with lived experience of delirium, family carers, and healthcare professionals. These interviews were conducted to explore experiences of delirium and recovery, perceived support needs, and views on intervention components, mechanisms, and delivery.The interview data were used to inform, refine, and substantiate the developing programme theory, contributing to the identification of key intervention components, hypothesised mechanisms of action, and contextual factors. The excerpts provided represent the minimal qualitative dataset underpinning the analytic interpretations presented in the paper and are shared to support transparency, reproducibility, and reuse.All data have been fully anonymised in accordance with ethical approvals and participant consent. The dataset contains coded interview excerpts linked to analytic themes and does not include full interview transcripts.