{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:52:12Z","timestamp":1753876332505,"version":"3.41.2"},"reference-count":86,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,2,11]],"date-time":"2025-02-11T00:00:00Z","timestamp":1739232000000},"content-version":"vor","delay-in-days":10,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Understanding how organisms adapt to their environments is a central question in evolutionary biology. Limestone langurs are unique among primates, as they are exclusively found in karst limestone habitats and have evolved mechanisms to tolerate high levels of mineral ions, which are typically associated with metal toxicity affecting organs, cells, and genetic material. We generated a high-quality reference genome (Tfra_5.0) for the limestone langur (Trachypithecus francoisi), along with genome resequencing data for 48 langurs representing 15 Trachypithecus species. Genes encoding ion channels (e.g., Na+, K+, and Ca2+) exhibited significantly accelerated evolution in limestone langurs. Limestone langur-specific mutations in Na+ and Ca2+ channels were experimentally confirmed to modify inward ion currents in vitro. Unexpectedly, scans for positive selection also identified genes involved in DNA damage response\/repair pathways, a previously unknown adaptation. This finding highlights an evolutionary adaptation in limestone langurs that mitigates the increased risk of DNA damage posed by elevated metal ion concentrations. Notably, a limestone langur-specific mutation (E94D) of the melanocortin 1 receptor (MC1R) was associated with increased basal cyclic adenosine monophosphate (cAMP) production, contributing to the species\u2019 darker coat color, which likely serves as camouflage on limestone rocks. Our findings reveal novel adaptive evolutionary mechanisms of limestone langurs and offer broader insights into organismal adaptation to extreme environments, with potential implications for understanding human health, biological evolution, and biodiversity conservation.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzaf007","type":"journal-article","created":{"date-parts":[[2025,2,11]],"date-time":"2025-02-11T18:05:12Z","timestamp":1739297112000},"source":"Crossref","is-referenced-by-count":1,"title":["Living on the Rocks: Genomic Analysis of Limestone Langurs Provides Novel Insights into the Adaptive Evolution in Extreme Karst Environments"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-9550-5803","authenticated-orcid":false,"given":"Zhijin","family":"Liu","sequence":"first","affiliation":[{"name":"College of Life Sciences, Capital Normal University , Beijing 100048,","place":["China"]},{"name":"CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-0253-3976","authenticated-orcid":false,"given":"Xiongfei","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Capital Normal University , Beijing 100048,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-2474-4327","authenticated-orcid":false,"given":"Peipei","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Capital Normal University , Beijing 100048,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-5843-9323","authenticated-orcid":false,"given":"Minheng","family":"Hong","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Capital Normal University , Beijing 100048,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-1041-9718","authenticated-orcid":false,"given":"Xiaochan","family":"Yan","sequence":"additional","affiliation":[{"name":"Center for the Evolutionary Origins of Human Behavior, Kyoto University , Inuyama 484-8506,","place":["Japan"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-2130-9844","authenticated-orcid":false,"given":"Xiaoqiu","family":"Qi","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Capital Normal University , Beijing 100048,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-8157-8300","authenticated-orcid":false,"given":"Qian","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Capital Normal University , Beijing 100048,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-0846-4683","authenticated-orcid":false,"given":"Zhenghao","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Capital Normal University , Beijing 100048,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-1935-9685","authenticated-orcid":false,"given":"Huajian","family":"Nie","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Capital Normal University , Beijing 100048,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-5774-5410","authenticated-orcid":false,"given":"Hui","family":"Li","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Capital Normal University , Beijing 100048,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-8556-0949","authenticated-orcid":false,"given":"Ziwen","family":"Li","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Capital Normal University , Beijing 100048,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8829-0588","authenticated-orcid":false,"given":"Liye","family":"Zhang","sequence":"additional","affiliation":[{"name":"Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research , 37077 G\u00f6ttingen,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-2023-091X","authenticated-orcid":false,"given":"Jiwei","family":"Qi","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-1250-9428","authenticated-orcid":false,"given":"Chaolei","family":"He","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Capital Normal University , Beijing 100048,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2004-6658","authenticated-orcid":false,"given":"Nguyen","family":"Van Truong","sequence":"additional","affiliation":[{"name":"Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research , 37077 G\u00f6ttingen,","place":["Germany"]},{"name":"Institute for Biochemistry and Biology, University of Potsdam , 14476 Potsdam,","place":["Germany"]},{"name":"Central Institute for Natural Resources and Environmental Studies, Vietnam National University , Hanoi 110403, Vietnam"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2953-2815","authenticated-orcid":false,"given":"Minh D","family":"Le","sequence":"additional","affiliation":[{"name":"Central Institute for Natural Resources and Environmental Studies, Vietnam National University , Hanoi 110403, Vietnam"},{"name":"Faculty of Environmental Sciences, University of Science, Vietnam National University , Hanoi 110403, Vietnam"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-2421-572X","authenticated-orcid":false,"given":"Tilo","family":"Nadler","sequence":"additional","affiliation":[{"name":"Three Monkeys Wildlife Conservancy , Nho Quan 08400, Vietnam"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0729-0322","authenticated-orcid":false,"given":"Hiroo","family":"Imai","sequence":"additional","affiliation":[{"name":"Center for the Evolutionary Origins of Human Behavior, Kyoto University , Inuyama 484-8506,","place":["Japan"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0190-4266","authenticated-orcid":false,"given":"Christian","family":"Roos","sequence":"additional","affiliation":[{"name":"Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research , 37077 G\u00f6ttingen,","place":["Germany"]},{"name":"Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research , 37077 G\u00f6ttingen,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5689-6270","authenticated-orcid":false,"given":"Ming","family":"Li","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences , 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