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Zool."],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Inbreeding depression is a major threat to the long\u2010term viability of small populations. Although captive breeding and genetic rescue are the main alternative in conservation, their genomic impacts are largely unknown, and the unintended effects of these approaches may intensify the depression by introducing new deleterious mutations. Based on whole\u2010genome sequencing data from 247 critically endangered Chinese alligators, we constructed a high\u2010resolution genetic variation map and identified three distinct genetic populations, clarifying their demographic history and further supporting the independent origin of the American population. Comparisons between captive and semi\u2010wild populations revealed that captive management outperforms semi\u2010wild management in reducing inbreeding and increasing genetic diversity, while simultaneously elevating the accumulation of deleterious mutations, which may result from relaxed purifying selection. Although the inbreeding coefficient in this species is notably higher than in other endangered species, purging has likely played a significant role in reducing the amount of recessive deleterious mutations. Forward\u2010in\u2010time simulations indicated that mixing populations can mitigate the risk of demographic decline, yet current populations still remain vulnerable to future environmental changes. These findings provide valuable genomic evidence to guide balanced and effective conservation strategies for the Chinese alligator.<\/jats:p>","DOI":"10.1111\/1749-4877.70194","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T13:52:20Z","timestamp":1790085140000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Captive Breeding of the Chinese Alligator Reduces Inbreeding but Increases Genetic Load"],"prefix":"10.1111","author":[{"given":"Yihang","family":"Fan","sequence":"first","affiliation":[{"name":"College of Wildlife and Protected Area Northeast Forestry University  Harbin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9347-033X","authenticated-orcid":false,"given":"Tao","family":"Pan","sequence":"additional","affiliation":[{"name":"College of Life Sciences Anhui Normal University  Wuhu Anhui China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Dussex","sequence":"additional","affiliation":[{"name":"Department of Population Analysis and Monitoring Swedish Museum of Natural History  Stockholm Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianming","family":"Lan","sequence":"additional","affiliation":[{"name":"College of Wildlife and Protected Area Northeast Forestry University  Harbin China"},{"name":"Heilongjiang Key Laboratory of Complex Traits and Protein Machines in Organisms  Harbin China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,22]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2410945122","article-title":"Genetic Rescue of Florida Panthers Reduced Homozygosity but Did Not Swamp Ancestral Genotypes","volume":"122","author":"Aguilar\u2010G\u00f3mez D.","year":"2025","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.13797"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.094052.109"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msab032"},{"key":"e_1_2_9_6_1","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1007\/s44353-025-00053-z","article-title":"Reorienting Flagship Species Funding to Support Sustainable Conservation Efforts in Developing Countries","volume":"2","author":"Aryal A.","year":"2025","journal-title":"Discover Conservation"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.adx5842"},{"key":"e_1_2_9_8_1","first-page":"18","article-title":"Species Survival Plan for Chinese Alligator","volume":"12","author":"Behler J.","year":"1993","journal-title":"Crocodile Specialist Group Newsletter"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-022-00448-x"},{"key":"e_1_2_9_10_1","doi-asserted-by":"crossref","DOI":"10.3389\/fcosc.2021.814863","article-title":"The Disconnect Between Short and Long\u2010Term Population Projections for Plant Reintroductions","volume":"2","author":"Bialic\u2010Murphy L.","year":"2022","journal-title":"Frontiers in Conservation Science"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1111\/eva.12691"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13742-015-0047-8"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3002795"},{"key":"e_1_2_9_15_1","first-page":"80","article-title":"A Program for Annotating and Predicting the Effects of Single Nucleotide Polymorphisms, SnpEff: SNPs in the Genome of Drosophila melanogaster Strain w\n                  1118; 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