{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T11:55:01Z","timestamp":1791287701881,"version":"4.1.0"},"reference-count":0,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T00:00:00Z","timestamp":1791244800000},"content-version":"am","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Genomic tools are increasingly important for conservation and wildlife health surveillance, yet their use is often constrained by limited resources, sample quality, and the need for minimally invasive approaches. Here we show that untargeted low-coverage sequencing applied to scale-clip DNA can jointly address population structure, genotype\u2013phenotype associations, and pathogen surveillance in timber rattlesnakes (Crotalus horridus), a species threatened by habitat fragmentation, human encroachment, and the emerging fungal pathogen Ophidiomyces ophidiicola. We sequenced 107 snakes sampled from eight populations in the Appalachian Mountains of the northeastern United States to a mean depth of 0.94x per individual. Population differentiation is pronounced and only weakly correlated with geographic distance, and inbreeding coefficients in some populations are high enough to suggest fitness consequences. Genome-wide association analysis identifies a locus for black-to-yellow color morph containing ALDH4A1, a member of a gene family implicated in vertebrate pigmentation but distinct from melanin pathway pigmentation genes. Our untargeted sequencing method also captures host-associated microbes: O. ophidiicola loads are higher in snakes with clinical signs of snake fungal disease, though some asymptomatic individuals carry substantial loads, and skin-associated microbial communities are disrupted in snakes with higher fungal burdens. That all of these inferences derive from the same minimally invasive sampling and sequencing workflow highlights the scalability of this approach for biodiversity conservation.<\/jats:p>","DOI":"10.1093\/jhered\/esag080","type":"journal-article","created":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T11:38:58Z","timestamp":1791027538000},"source":"Crossref","is-referenced-by-count":0,"title":["Population genetics, trait mapping and fungal pathogen surveillance using untargeted sequencing in timber rattlesnakes (\n                    <i>Crotalus horridus)<\/i>"],"prefix":"10.1093","author":[{"given":"Christopher","family":"Husted","sequence":"first","affiliation":[{"name":"Genomics and Computational Biology, UMass Chan Medical School , Worcester, MA ,","place":["United States"]},{"name":"Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School , Worcester, MA \u00a0","place":["United States"]},{"name":"Broad Institute of MIT & Harvard , Cambridge, MA \u00a0","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob","family":"Alonso","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT & Harvard , Cambridge, MA \u00a0","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ross","family":"Swofford","sequence":"additional","affiliation":[{"name":"Genomics and Computational Biology, UMass Chan Medical School , Worcester, MA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne G","family":"Stengle","sequence":"additional","affiliation":[{"name":"Division of Science, Engineering, and Mathematics, Holyoke Community College , Holyoke, MA \u00a0","place":["United States"]},{"name":"Department of Chemistry, Smith College , Northampton, MA \u00a0","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucas R","family":"Moreira","sequence":"additional","affiliation":[{"name":"Genomics and Computational Biology, UMass Chan Medical School , Worcester, MA ,","place":["United States"]},{"name":"Broad Institute of MIT & Harvard , Cambridge, MA \u00a0","place":["United States"]},{"name":"Colossal Biosciences , Dallas, TX ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel E","family":"Neafsey","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT & Harvard , Cambridge, MA \u00a0","place":["United States"]},{"name":"Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health , Boston, MA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel A","family":"Johnston","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT & Harvard , Cambridge, MA \u00a0","place":["United States"]},{"name":"Zoo New England , Boston, MA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Baitchman","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT & Harvard , Cambridge, MA \u00a0","place":["United States"]},{"name":"Zoo New England , Boston, MA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diane P","family":"Genereux","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT & Harvard , Cambridge, MA \u00a0","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Daniels","sequence":"additional","affiliation":[{"name":"Genomics and Computational Biology, UMass Chan Medical School , Worcester, MA ,","place":["United States"]},{"name":"Broad Institute of MIT & Harvard , Cambridge, MA \u00a0","place":["United States"]},{"name":"RNA Therapeutics Institute, UMass Chan Medical School , Worcester, MA \u00a0","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4343-3776","authenticated-orcid":false,"given":"Elinor K","family":"Karlsson","sequence":"additional","affiliation":[{"name":"Genomics and Computational Biology, UMass Chan Medical School , Worcester, MA ,","place":["United States"]},{"name":"Broad Institute of MIT & Harvard , Cambridge, MA \u00a0","place":["United States"]},{"name":"Program in Molecular Medicine, UMass Chan Medical School , Worcester, MA \u00a0","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,6]]},"container-title":["Journal of Heredity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jhered\/advance-article-pdf\/doi\/10.1093\/jhered\/esag080\/71626267\/esag080.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jhered\/advance-article-pdf\/doi\/10.1093\/jhered\/esag080\/71626267\/esag080.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T11:30:27Z","timestamp":1791286227000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jhered\/advance-article\/doi\/10.1093\/jhered\/esag080\/8868895"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,6]]},"references-count":0,"URL":"https:\/\/doi.org\/10.1093\/jhered\/esag080","relation":{},"ISSN":["0022-1503","1465-7333"],"issn-type":[{"value":"0022-1503","type":"print"},{"value":"1465-7333","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,6]]},"article-number":"esag080"}}