cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zw3r2287v
title: Data from: Global change on the Roof of the World: vulnerability of Himalayan otter species to land-use and climate alterations

description: Climate Change Vulnerability Assessment (CCVA) prescribes the
 quantification of species vulnerability based on three components:
 sensitivity, adaptive capacity and exposure. Such assessments should be
 performed through combined approaches that integrate trait-based elements
 (e.g., measures of species sensitivity such as niche width) with
 correlative tools quantifying exposure (magnitude of changes in climate
 within species habitat). Furthermore, as land-use alterations may increase
 climate impacts on biodiversity, CCVAs should focus on both climate and
 land-use change effects. Unfortunately, most of such assessments have so
 far focused exclusively on exposure to climate change.  We
 evaluated the vulnerability of three otter species occurring in the
 Himalayan region, i.e. Aonyx cinereus, Lutra lutra and Lutrogale
 perspicillata, to 2050 climate and land-use through the recently-proposed
 Climate Niche Factor Analysis (CNFA) framework combined with Species
 Distribution Models. Future climate and land-use change will reduce (6 –
 15%) and shift (10 – 18%) the geographic range of the three species in the
 Himalaya, with land-use alterations exerting far more severe effects than
 climate change. Among vulnerability components, sensitivity played a
 greater role than exposure in determining the vulnerability of the otters.
 Specifically, the most specialist species, L. perspicillata showed the
 highest vulnerability in comparison with the most generalist, L. lutra.
 Our results underline how coupling climate and land-use change components
 in CCVAs can generate diverging predictions of species vulnerability
 compared to approaches relying on climate change only. Moreover, intrinsic
 components, such as species sensitivity, proved significantly more
 important in determining vulnerability than extrinsic metrics such as
 habitat exposure. The dataset contains XY coordinates of Himalayan otter
 species used in the study. Since Himalayan otters are listed as
 threatened or vulnerable in several of the regions covered by the
 study, original coordinates were rounded to 1 degree. Specific data
 sources are provided in the coupled table.
DOI: 10.5061/dryad.8kprr4xnt
title: Association of neighborhood-level material deprivation with healthcare costs and outcome after stroke

description: The objective was to determine the association between material
 deprivation and direct healthcare costs and clinical outcomes following
 stroke in the context of a publicly funded universal healthcare system. In
 this population-based cohort study of patients with ischemic and
 hemorrhagic stroke admitted to hospital between 2008 and 2017 in Ontario,
 Canada, we used linked administrative data to identify the cohort,
 predictor variables, and outcomes. The exposure was a five-level
 neighborhood material deprivation index. The primary outcome was direct
 healthcare costs incurred by the public payer in the first year. Secondary
 outcomes were death and admission to long-term care. Among 90,289 patients
 with stroke, the mean (standard deviation) per-person costs increased with
 increasing material deprivation, from $50,602 ($55,582) in the least
 deprived quintile to $56,292 ($59,721) in the most deprived quintile
 (unadjusted relative cost ratio and 95% confidence intervals 1.11
 [1.08,1.13] and adjusted relative cost ratio 1.07 [1.05,1.10] for least
 compared to most deprived quintile). People in the most deprived quintile
 had higher mortality within one year compared to the least deprived
 quintile (adjusted hazard ratio (HR) 1.07 [1.03,1.12]) as well as within
 three years (adjusted HR 1.09 [1.05,1.13]). Admission to long-term care
 increased incrementally with material deprivation and those in the most
 deprived quintile had an adjusted HR of 1.33 [1.24,1.43]) compared to
 those in the least deprived quintile. Material deprivation is a risk
 factor for increased costs and poor outcomes after stroke. Interventions
 targeting health inequities due to social determinants of health are
 needed.
DOI: 10.5061/dryad.3ffbg79hx
title: Ecological causes of fluctuating natural selection on habitat choice in an amphibian

description: We estimated natural selection targeting three traits related to habitat
 choice in a frog (Pseudacris maculata) breeding in pools on the rocky
 shores of Isle Royale, Michigan, over 16 years. Our aim was to identify
 the form and ecological causes of annual variation in directional and
 correlational selection as expressed in the survival and growth of
 tadpoles. We found directional selection favoring early breeding, but pool
 choice was under weak stabilizing selection. However, the form of
 stabilizing selection and the position of the optimum trait value shifted
 among years with the severity of disturbance and the intensity of biotic
 interactions. In years when wave wash and pool desiccation were severe,
 selection shifted to favor tadpoles in habitats where these risks were
 less pronounced. If predatory dragonfly larvae were abundant, selection
 favored tadpoles in small pools where dragonflies did not occur. When
 intraspecific competition was strong, selection favored early broods
 within a broader range of pool types. The agents of selection in this
 study – biotic interactions and disturbance – are common to many
 ecological systems and frequently exhibit temporal variation; this
 suggests that fluctuating selection may be widespread in natural
 populations.
description: Detailed description in the published paper.
description: For details about the data sets, read the file called
 README.txt
DOI: 10.5061/dryad.63xsj3v29
title: Genome and transcriptome assemblies of TIL11

description: Here, we employed single-molecule long-read sequencing of cDNA libraries
 from five tissues of the teosinte inbred line TIL11 and identified 70,044
 non-redundant transcript isoforms. 23,527 predicted genes were identified
 using our state-of-the-art, machine learning-based bioinformatics
 pipeline DenovoAS_Finder without a complete reference genome.
 Additionally, we constructed a draft TIL11 genome based on a Nanopore
 sequencing dataset with 16,633 high-quality contigs and a N50 of 112 kb.
DOI: 10.5061/dryad.31zcrjdkj
title: Black Scoter habitat use along the southeastern coast of the United States

description: While the Atlantic Coast of the United States and Canada is a major
 wintering area for sea ducks, knowledge about their wintering habitat use
 is relatively limited. Black Scoters have a broad wintering distribution
 and are the only open water species of sea duck that is abundant along the
 southeastern coast of the United States. Our study identified variables
 that affected Black Scoter (Melanitta americana) distribution and
 abundance in the Atlantic Ocean along the southeastern coast of the United
 States. We used aerial survey data from 2009 to 2012 provided by the
 United States Fish and Wildlife Service to identify variables that
 influenced Black Scoter distribution. We used indicator variable selection
 to evaluate relationships between Black Scoter habitat use and a variety
 of broad- and fine-scale oceanographic and weather variables. Average time
 between waves, ocean floor slope, and the interaction of bathymetry and
 distance to shore had the strongest association with southeastern Black
 Scoter distribution.
description: Count data were collected from aerial surveys. Further
 information is available in associatead manuscript.
DOI: 10.5061/dryad.6djh9w11h
title: Ants of the State of Pará, Brazil: a historical and comprehensive dataset of a key biodiversity hotspot in the Amazon Basin

description: The state of Pará in northern Brazil is located entirely within the Amazon
 Basin and harbors a great diversity of landscape and vegetation types that
 support high levels of biodiversity. Here, we provide a comprehensive
 inventory of ant species and their distribution in Pará. This regional
 list is based on an extensive review of species records from published and
 unpublished sources covering a period of 134 years (1886–2020) and
 includes the five most representative ant collections in Brazil. In total,
 we documented 12 subfamilies, 90 genera and 753 ant species, including 97
 species recorded for the first time in Pará and 12 species newly reported
 in Brazil. Sampling effort across the state is highly uneven, and most
 records may be associated with research areas near the state capital,
 mining areas, hydroelectric dams, and research field stations run by the
 state or universities. In addition, our results suggest a strong bias in
 ant collection in Pará in terms of proximity of sampled sites to access
 routes, such as roads and rivers. We also found that species records were
 highly unevenly distributed based on areas of endemism within the Amazon,
 vegetation type, and protected areas within the state. Ant surveys are
 still lacking from most protected areas of Pará, and further sampling is
 urgently needed in view of the current trend of expansion of major
 infrastructure projects and natural resource harvesting within protected
 areas of Pará. Our database represents an extremely valuable and rich
 source of information for further studies on ant biodiversity and
 conservation in the Amazon Basin.
description: We compiled a dataset of ant species from Pará recorded in the
 literature from 1886 (the first record in the literature of ants collected
 in Pará) to 2020. Most published data records were provided by the Global
 Ant Biodiversity (GABI) project (Guénard et al. 2017), including data
 extracted from AntWeb (AntWeb 2020). Next, we extracted geographical
 information from labels of specimens collected in Pará and deposited in
 one of the five main Brazilian entomological collections, namely Museu
 Paraense Emílio Goeldi (MPEG); Coleção Entomológica Padre Jesus Santiago
 Moure at Universidade Federal do Paraná (DZUP); Centro de Pesquisas do
 Cacau at Comissão Executiva do Plano de Lavoura Cacaueira (CPDC); Museu de
 Zoologia da Universidade de São Paulo (MZSP); and Instituto Nacional de
 Pesquisas da Amazônia (INPA). Thirdly, for the MPEG dataset, we retrieved
 records from the Brazilian Biodiversity Information System (SiBBr), a
 national online biodiversity database (https://www.sibbr.gov.br/). The
 SiBBr repository hosts and mirrors the information available from GBIF
 (Global Biodiversity Information Facility; https://www.gbif.org). Lastly,
 material from recent surveys conducted by the authors in the state of Pará
 were also used to update the database.
DOI: 10.5061/dryad.t4b8gtj24
title: Global impact of lightning-produced oxidants

description: Lightning plays a major role in tropospheric oxidation, and its role on
 modulating tropospheric chemistry was thought to be emissions of nitrogen
 oxides (NOx). Recent field and laboratory measurements demonstrate that
 lightning generates extremely large amounts of oxidants, including
 hydrogen oxides (HOx) and O3. We here implement the lightning-produced
 oxidants in a global chemical transport model to examine its global impact
 on tropospheric composition. We find that lightning-produced oxidants can
 increase global mass weighted OH by 0.3-10%, and affect CO, O3, and
 reactive nitrogen substantially, depending on the emission strength of
 oxidants from lightning. Our work highlights the importance and
 uncertainties of lightning-produced oxidants, as well as the need for
 rethinking the role of lightning in tropospheric oxidation chemistry.
description: Please refer to Table 1 in the paper for the names of each model
 run.
DOI: 10.5061/dryad.nvx0k6dsm
title: COVID-19 PHAC Agent-Based Model for age-stratified intervention and herd immunity study

description: The PHAC agent-based model was used to explore the progression of
 the COVID-19 epidemic under three intervention scenarios
 (infection-preventing vaccination, illness-preventing vaccination and
 shielding) in individuals above three age thresholds (≥45, ≥55 and ≥65
 years) while lifting shutdowns and physical distancing in the community.
 This data repository contains the PHAC
 modelling code in Anylogic used for this study. 
description: The following link contains instructions for using the COVID-19
 PHAC Agent-Based Model, as well as information on where to get a free
 version of AnyLogic and how to use an older version of the PHAC
 Agent-based model that was accepted for a previous manuscript:<br>
 https://nccid.ca/phac-agent-based-model-on-covid-19/
DOI: 10.5061/dryad.mkkwh710k
title: Adaptation without specialization early in a host shift: fecundity data

description: Students of speciation debate the role of performance trade-offs across
 different environments early in speciation. We tested for early
 performance trade-offs with a host shift experiment using a member of
 the Enchenopa binotata species complex of treehoppers
 (Hemiptera: Membracidae). In this clade of plant-feeding insects,
 different species live on different host plants and exhibit strong
 behavioral and physiological host specialization. After five generations,
 the experimental host shifts resulted either in no adaptation or in
 adaptation without specialization. The latter result was more likely in
 sympatry; in allopatry, populations on novel host plants were more likely
 to go extinct. We conclude that in the early stages of speciation,
 adaptation to novel host plants does not necessarily bring about
 performance trade-offs on ancestral environments. Adaptation may be
 facilitated rather than hindered by gene flow, which prevents extinction.
 Additional causes of specialization and assortative mating may be required
 if colonization of novel environments is to result in speciation.
description: "Quasinatural" selection experiment followed by
 reciprocal transplant rearing experiment; fecundity measured as # nymphs
 eclosing from eggs
DOI: 10.5061/dryad.f4qrfj6w2
title: Data from: First evidence of deviation from Mendelian proportions in a conservation program

description: Classic Mendelian inheritance is the bedrock of population genetics and
 underpins pedigree-based management of animal populations. However,
 assumptions of Mendelian inheritance might not be upheld in conservation
 breeding programs if early viability selection occurs, even when efforts
 are made to equalise genetic contributions of breeders. To test this
 possibility, we investigated deviations from Mendelian proportions in a
 captive meta-population of the endangered Tasmanian devil. This marsupial
 population is ideal for addressing evolutionary questions in conservation
 due to its large size, range of enclosure types (varying in environmental
 conditions), good genomic resources (which aid interpretation), and the
 species’ biology. Devil mothers give birth to more offspring than they can
 nurse in the pouch, providing the potential for intense viability
 selection amongst embryos. We used data from 140 known sire-dam-offspring
 triads to isolate within-family selection from population-level mechanisms
 (such as mate choice or inbreeding), and compared observed offspring
 genotypes at 123 targeted SNPs to neutral (i.e. Mendelian) expectations.
 We found lower offspring heterozygosity than expected, and subtle patterns
 of differential effects across a gradient of management intensity from
 zoo-like enclosures to semi-wild environments for some loci. Meiotic drive
 or maternal-foetal incompatibilities are consistent with our results,
 although we cannot statistically confirm these mechanisms. We found some
 evidence that maternal genotype affects annual litter size, suggesting
 that family-level effects are driven by differential offspring mortality
 before birth or during early development. Our results show that deviations
 from Mendelian inheritance can occur in conservation programs, despite
 best-practice management to prevent selection.
DOI: 10.5061/dryad.pk0p2ngnr
title: Environmental gradients predict the ratio of environmentally acquired carotenoids to self-synthesised pteridine pigments

description: Carotenoids are important pigments producing integument coloration;
 however, their dietary availability may be limited in some environments.
 Many species produce red to yellow hues using a combination of carotenoids
 and self-synthesised pteridine pigments. A compelling but untested
 hypothesis is that pteridines replace carotenoids in environments where
 carotenoid availability is limited. Based on a phylogenetic comparative
 analysis of pigment concentrations in agamid lizards, we show that
 environmental gradients predict the ratio of carotenoids to pteridines;
 carotenoid concentrations are lower and pteridine concentrations higher in
 arid environments with low vegetation productivity. Both carotenoid and
 pteridine pigments were present in all species, but only pteridine
 concentrations explained colour variation among species and there were no
 correlations between carotenoid and pteridine pigments with similar hue.
 These results suggest that pteridine pigments replace carotenoids in
 carotenoid-limited environments, irrespective of skin hue, presumably
 because it is metabolically cheaper to synthesise pteridines than to
 acquire and sequester carotenoids when carotenoids are rare.
description: Dataset with pigment information in lizards, from liquid
 chromatography-mass spectrometry. Multiple species distributed in
 Australia, pigments extracted for multiple species and multiple
 individuals per species and multiple tissues per individual. Dataset
 contains final concentrations for 11 pigments (carotenoids and
 pteridines) after taking into account blanks and tissue weight.
description: There are no missing values for pigment information, but some
 missing values for sexual selection indices which were not available in
 the literature. Information on each column in the dataset is provided in a
 Metadata tab. Code to reproduce all analyses and graphs is also
 attached.
DOI: 10.5061/dryad.95x69p8kp
title: Geographical and ecological variables of Pseudotaxus chienii populations

description: Pseudotaxus chienii, belonging to the monotypic
 genus Pseudotaxus (Taxaceae), is a relict conifer endemic to China. Its populations are usually small and patchily distributed, having a low capacity of natural regeneration. To gain a clearer understanding of how landscape variables affect the local adaptation of P. chienii, we applied EST-SSR markers in conjunction with landscape genetics methods: (1) to examine the population genetic pattern and spatial genetic structure; (2) to perform genome scan and selection scan to identify outlier loci and the associated landscape variables; and (3) to model the ecological niche under climate change. As a result, P. chienii was found to have a moderate level of genetic variation and a high level of genetic differentiation. Its populations displayed a significant positive relationship between the genetic and geographical distance (i.e., “isolation by distance” pattern) and a strong fine scale spatial genetic structure within 2 km. A putatively adaptive locus EMS6 (functionally annotated to cellulose synthase A catalytic subunit 7) was identified, which was found significantly associated with soil Cu, K, and Pb content and the combined effects of temperature and precipitation. Moreover, P. chienii was predicted to experience significant range contractions in future climate change scenarios. Our results highlight the potential of specific soil metal content and climate variables as the driving force of adaptive genetic differentiation in P. chienii. The data would also be useful to develop a conservation action plan for P. chienii.
DOI: 10.5061/dryad.xsj3tx9ff
title: Bird pollination syndrome is the plant’s adaptation to ornithophily, but nectarivorous birds are not so selective

description: Many tropical plants are pollinated by birds and several bird
 phylogenetical lineages have specialised to a nectar diet. The
 long-assumed, intimate ecological and evolutionary relationship between
 ornithophilous plants and phenotypically specialised nectarivorous birds
 has nevertheless been questioned in recent decades, where such
 plant-pollinator interactions have been shown to be highly
 generalised.    In our study, we analysed two
 extensive interaction datasets: bird-flower and insect-flower
 interactions, both collected on Mt. Cameroon, West-Central Africa. We
 tested if 1) insects and birds interact with distinct groups of plants; 2)
 plants with a typical set of ornithophilous floral traits (i.e. bird
 pollination syndrome) interact mainly with birds; 3) birds favour plants
 with bird pollination syndrome; and 4) if and how the individual floral
 traits and plant level nectar production predict bird
 visitation.      Bird-visited
 plants were typically also visited by insects, while approximately half of
 the plants were visited by insects only. We confirmed the validity of the
 bird pollination syndrome hypothesis, as plants with bird-pollination
 syndrome traits were visited by birds at a higher rate and mostly hosted a
 lower frequency of visiting insects. However, these ornithophilous plants
 were not more attractive than the other plants for nectar-feeding birds.
 Nectar production per plant individual was a better predictor of bird
 visitation than any other floral trait traditionally related to the bird
 pollination syndrome. Our study thus demonstrated the highly asymmetrical
 relationship between ornithophilous plants and nectarivorous
 birds.
DOI: 10.5061/dryad.3r2280gg5
title: Data from: Wolbachia and host intrinsic reproductive barriers contribute additively to post-mating isolation in spider mites

description: Wolbachia are maternally-inherited bacteria that induce cytoplasmic
 incompatibility in many arthropod species. However, the ubiquity of this
 isolation mechanism for host speciation processes remains elusive, as only
 few studies have examined Wolbachia-induced incompatibilities when host
 populations are not genetically compatible. Here, we used three
 populations of two genetically differentiated colour forms of the
 haplodiploid spider mite Tetranychus urticae to dissect the interaction
 between Wolbachia-induced and host-associated incompatibilities, and their
 relative contribution to post-mating isolation. We found that these two
 sources of incompatibility act through different mechanisms in an additive
 fashion. Host-associated incompatibility contributes 1.5 times more than
 Wolbachia-induced incompatibility in reducing hybrid production, the
 former through an overproduction of haploid sons at the expense of diploid
 daugters (ca. 75% decrease) and the latter by increasing the embryonic
 mortality of daughters (by ca. 49%). Furthermore, regardless of cross
 direction, we observed near-complete F1 hybrid sterility and complete F2
 hybrid breakdown between populations of the two forms, but Wolbachia did
 not contribute to this outcome. We thus show mechanistic independence and
 an additive nature of host-intrinsic and Wolbachia-induced sources of
 isolation. Wolbachia may contribute to reproductive isolation in this
 system, thereby potentially affecting host differentiation and
 distribution in the field.