{"conditionsOfAccess":"Data is accessible online and may be reused in accordance with licence conditions","copyrightNotice":"All Rights (including copyright) CSIRO, University of Adelaide, University of Western Sydney, Royal Botanic Gardens and Domain Trust, Taronga Conservation Society, University of Sydney, University of Queensland, Parks Australia 2023.","creditText":"The full credit for the data generation of many direct and indirect individuals. Credit to Kyle N. Armstrong from Environment Institute, University of Adelaide; Christopher M. Todd, Annabel Dorrestein, Justin A. Welbergen and John M. Martin from The Hawkesbury Institute for the Environment, Western Sydney University; Karrie Rose, and Jane Hall at Australian Registry of Wildlife Health, Taronga Conservation Society Australia; David N. Phalen from Sydney School of Veterinary Science, University of Sydney; Nicholas A. Macgregor from Parks Australia, Canberra and Luke R. Lloyd-Jones, Pierre Feutry and David A. Westcott from CSIRO.\n\nWe gratefully acknowledge the Christmas Island National Park staff who supported this work directly and indirectly, particularly Samantha Flakus, Brendan Tiernan and Kerrie Bennison. We are thankful for the support provided for field data collection and genetic data generation by the Director of National Parks, Western Sydney University, Taronga Conservation Society, and CSIRO Land and Water. We are grateful for the help of Libby Timmiss, Richard Askew, Zoia Wowk, Georgie Custance, Varsha Raj, Bryony Hitchcock, Hannah Carson, Laura Pulscher, Ariana Ananda, Sophie Hall, Ari Drummond and Lauren Bassett, who assisted with capture and tissue collection. ","datePublished":"2023-06-26","description":"The data and files in these directories underpin the extension and application\nof close-kin mark-recapture (CKMR) to the critically endangered Christmas Island \nflying-fox. The data were generated over a set of collaborative projects between \nthe Commonwealth Scientific and Industrial Research Organisation and the CIFF \nEcology Team, which included members from West. Syd University, Taronga Zoo, \nUni SA, and Parks Australia. \n\nThe data were generated across two rounds of data generation and \nreporting, where round 1 was, in a sense, a pilot CKMR study that set the \nfoundation for the generation of more genetic data in round 2. \n\nThe primary data are SNP genotype data generated using the DArTSeq technology, \nmtDNA sequences in Fasta format, and the important covariate data gathered through\nfield studies on CIFF.\n\nThe data further accompany the manuscript \"Lloyd-Jones, L et al.\nClose-kin mark-recapture informs critically endangered terrestrial mammal \nstatus\", 2022\". The results summarised in that manuscript appear in their\nraw form in this directory along with the scripts used to generate them.\n\n\n\nLineage: Christmas Island is a territory of Australia located 1,500 km west of the Australian mainland. Samples and measurements from individual CIFF were collected across the island during multiple sampling exercises for several different studies (19,24,39,40).\n\nSamples\n------------\n      Those studies detail the capture, morphological measurements, and tissue sampling procedure of the samples included in this analysis. Briefly, CIFFs were caught using nets at both foraging and roost sites between August 2015 and February 2019. Capture locations were distributed across the island and the net location within each roost site was randomly selected. Foraging sites were chosen using night driving surveys from random starting locations and fruiting trees selected as a capture site were random on any given night 40.\n      Captured animals were processed at the capture site where they were anaesthetised and sex and age determined, and morphological measurements recorded; one of the capture sites was a field laboratory (The ?Pink House? building in Christmas Island National Park). Age class was determined using morphologic measurements and secondary sex characteristics, including tooth staining and wear and in females, teat elongation. For each individual, wing-membrane biopsies were taken and stored in ethanol for genetic analyses. \nApproval for animal experiments - The research protocols used across the fieldwork adhered to the guidelines of the American Society of Mammalogists for research on live mammals 54 with approval from the Animal Care and Ethics Committee of Western Sydney University (Project Protocol No. A11140). Permits to capture, handle, band and measure bats were issued by the Christmas Island National Park (Permit No. CINP-2015-6-1).\n\nGenetic data\n------------------\n\nGenetic single nucleotide polymorphism data were generated by Diversity Arrays Pty. Ltd. (Canberra, Australia) for each available CIFF tissue sample using the DArTseq technology. The DNA sample preparation and arrangement were performed through a multi-stage collaborative effort between\nWestern Sydney University, Taronga Conservation Society at University of Sydney, University of Adelaide and CSIRO. \n\nMitochondrial DNA data were generated by amplicon sequencing in both directions using the PCR primers by AGRF Ltd, Adelaide, South Australia. See associated manuscript for more information.\n\n19.\tPulscher, L. A. et al. Evidence of chronic cadmium exposure identified in the critically endangered Christmas Island flying-fox (Pteropus natalis). Science of The Total Environment 766, 144374 (2021).\n24.\tTodd, C. M. et al. Body-size dependent foraging strategies in the Christmas Island flying-fox: implications for seed and pollen dispersal within a threatened island ecosystem. Movement Ecology 10, 1?15 (2022).\n39.\tPhalen, D. N. et al. Genetic diversity and phylogeny of the Christmas Island flying fox (Pteropus melanotus natalis). Journal of Mammalogy 98, 428?437 (2017).\n40.\tTodd, C. M., Westcott, D. A., Rose, K., Martin, J. M. & Welbergen, J. A. Slow growth and delayed maturation in a Critically Endangered insular flying fox (Pteropus natalis). Journal of Mammalogy 99, 1510?1521 (2018).","keywords":["abundance estimation","bats","flying fox","genetic mark-recapture","kinship","threatened species",{"name":"Genetics not elsewhere classified","termCode":"310599","url":"https://linked.data.gov.au/def/anzsrc-for/2020/310599","inDefinedTermSet":"https://linked.data.gov.au/def/anzsrc-for/2020/","@type":"DefinedTerm"},{"name":"Ecological applications not elsewhere classified","termCode":"410299","url":"https://linked.data.gov.au/def/anzsrc-for/2020/410299","inDefinedTermSet":"https://linked.data.gov.au/def/anzsrc-for/2020/","@type":"DefinedTerm"},{"name":"Applied statistics","termCode":"490501","url":"https://linked.data.gov.au/def/anzsrc-for/2020/490501","inDefinedTermSet":"https://linked.data.gov.au/def/anzsrc-for/2020/","@type":"DefinedTerm"}],"name":"Data and code associated with manuscript \"Close-kin mark-recapture informs critically endangered terrestrial mammal status\".","producer":{"description":"Conduct CKMR population estimation based on existing CIFF genomic data","identifier":"csiro:R-13612","name":"CLSD CIFF CKMR","parentOrganization":{"name":"Commonwealth Scientific and Industrial Research Organisation","url":"https://www.csiro.au","@type":"Organization"},"@type":"ResearchProject"},"publisher":{"name":"Commonwealth Scientific and Industrial Research Organisation","@id":"https://www.csiro.au","@type":"Organization"},"spatialCoverage":{"geo":{"box":"105.5049 -10.6084 105.7496 -10.3898","@type":"GeoShape"},"@type":"Place"},"temporalCoverage":"2015-08-01/2019-02-28","url":"https://data.csiro.au/collection/csiro:58766","version":"v1","citation":[],"funder":[{"name":"CSIRO","contactPoint":[{"areaServed":"AU","telephone":"1300 363 400","type":"ContactPoint"},{"areaServed":"Worldwide","telephone":"+61 3 9545 2176","type":"ContactPoint"},{"contactType":"CSIRO Enquiries","type":"ContactPoint","url":"https://www.csiro.au/en/Contact"}],"@type":"Organization"},{"name":"University of Adelaide","@type":"Organization"},{"name":"University of Western Sydney","@type":"Organization"},{"name":"Royal Botanic Gardens and Domain Trust","@type":"Organization"},{"name":"Taronga Conservation Society","@type":"Organization"},{"name":"University of Sydney","@type":"Organization"},{"name":"University of Queensland","@type":"Organization"},{"name":"Parks Australia","@type":"Organization"}],"creator":[{"familyName":"Lloyd-Jones","givenName":"Luke","name":"Luke Lloyd-Jones","@type":"Person"},{"familyName":"Bravington","givenName":"Mark V.","name":"Mark V. Bravington","@type":"Person"},{"familyName":"Armstrong","givenName":"Kyle","name":"Kyle Armstrong","@type":"Person"},{"familyName":"Lawrence","givenName":"Emma","name":"Emma Lawrence","@type":"Person"},{"familyName":"Feutry","givenName":"Pierre","name":"Pierre Feutry","@type":"Person"},{"familyName":"Todd","givenName":"Christopher","name":"Christopher Todd","@type":"Person"},{"familyName":"Dorrestein","givenName":"Annabel","name":"Annabel Dorrestein","@type":"Person"},{"familyName":"Welbergen","givenName":"Justin A.","name":"Justin A. Welbergen","@type":"Person"},{"familyName":"Martin","givenName":"John M.","name":"John M. Martin","@type":"Person"},{"familyName":"Rose","givenName":"Karrie","name":"Karrie Rose","@type":"Person"},{"familyName":"Hall","givenName":"Jane","name":"Jane Hall","@type":"Person"},{"familyName":"Phalen","givenName":"David","name":"David Phalen","@type":"Person"},{"familyName":"Peters","givenName":"Isabel","name":"Isabel Peters","@type":"Person"},{"familyName":"Baylis","givenName":"Shane","name":"Shane Baylis","sameAs":"https://orcid.org/0000-0002-2373-1311","@type":"Person"},{"familyName":"Macgregor","givenName":"Nicholas A.","name":"Nicholas A. Macgregor","@type":"Person"},{"familyName":"Westcott","givenName":"David A.","name":"David A. Westcott","@type":"Person"}],"includedInDataCatalog":{"id":"https://www.re3data.org/repository/r3d100010734","name":"CSIRO Data Access Portal","url":"https://data.csiro.au","@type":"DataCatalog"},"funding":[],"identifier":[{"url":"https://doi.org/10.25919/2k26-t773","value":"doi:10.25919/2k26-t773","@id":"https://doi.org/10.25919/2k26-t773","propertyID":"https://registry.identifiers.org/registry/doi","@type":"PropertyValue"},"http://hdl.handle.net/102.100.100/487002?index=1"],"isAccessibleForFree":true,"license":{"name":"Creative Commons Attribution-Noncommercial 4.0 Licence","url":"https://creativecommons.org/licenses/by-nc/4.0/","@type":"CreativeWork","additionalType":"http://purl.org/au-research/vocabulary/RIFCS/RIFCSLicenceType/CC-BY-NC"},"@type":"Dataset","distribution":{"url":"https://data.csiro.au/collection/csiro:58766?tab=data","@type":"DataDownload"},"@context":"https://schema.org"}