{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T01:54:30Z","timestamp":1789696470081,"version":"4.0.1"},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,7,17]],"date-time":"2017-07-17T00:00:00Z","timestamp":1500249600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2017,7,17]],"date-time":"2017-07-17T00:00:00Z","timestamp":1500249600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Chinese alligator (<jats:italic>Alligator sinensis<\/jats:italic>) is an endangered freshwater crocodilian endemic to China, which experienced a severe bottleneck about 30 years ago. In this study, we developed locus-specific primers to investigate the polymorphism of 3 major histocompatibility complex (MHC) loci in 3 Chinese alligator populations, in combination with 6 neutral microsatellite markers as a contrast. We found the genetic trace for the bottleneck effect on the endangered Chinese alligator: the low allelic diversity (2 alleles at each locus), the low nucleotide substitution rate (no more than 0.009) at all sites, the deviation from Hardy-Weinberg Equilibrium\/heterozygote deficiency, and the significant Tajima\u2019s D values, indicating the MHC class I and class II loci being at different stages of bottleneck. We also obtained 3 pieces of evidence for balancing selection on this severely bottlenecked reptile: an obvious excess of nonsynonymous substitutions over synonymous at the antigen-binding positions, the mean synonymous substitution rate of MHC exons significantly higher than mean nucleotide substitution rate of introns, and the differentiation coefficient <jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub> of MHC loci significantly lower than that of microsatellite loci. Consequently, we emphasize that the Chinese alligator holds a pretty low adaptive ability and requires scientific conservation strategies to ensure the long-term population development.<\/jats:p>","DOI":"10.1038\/s41598-017-05640-2","type":"journal-article","created":{"date-parts":[[2017,7,11]],"date-time":"2017-07-11T09:42:56Z","timestamp":1499766176000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Effects of Population Bottleneck and Balancing Selection on the Chinese Alligator Are Revealed by Locus-Specific Characterization of MHC Genes"],"prefix":"10.1038","volume":"7","author":[{"given":"Teng","family":"Zhai","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hai-Qiong","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui-Can","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li-Ming","family":"Fang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guo-Heng","family":"Zhong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheng-Guo","family":"Fang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,7,17]]},"reference":[{"key":"5640_CR1","unstructured":"Thorbjarnarson, J. & Wang, X. M. The Chinese Alligator: Ecology, Behavior, Conservation and Culuture. (The Johns Hopkins University Press, 2010)."},{"key":"5640_CR2","doi-asserted-by":"publisher","first-page":"2586","DOI":"10.1007\/s11434-011-4615-8","volume":"56","author":"ZH Wang","year":"2011","unstructured":"Wang, Z. H., Yao, H., Ding, Y. Z., John, T. & Wang, X. M. Testing reintroduction as a conservation strategy for the critically endangered Chinese alligator: movements and home range of released captive individuals. Chin Sci Bull \n                           56, 2586\u20132593 (2011).","journal-title":"Chin Sci Bull"},{"key":"5640_CR3","doi-asserted-by":"publisher","first-page":"725","DOI":"10.1093\/czoolo\/59.6.725","volume":"59","author":"L Zhao","year":"2013","unstructured":"Zhao, L. et al. The sex ration of wild Chinese alligators Alligator sinensis. Current Zoology \n                           59, 725\u2013731 (2013).","journal-title":"Current Zoology"},{"key":"5640_CR4","doi-asserted-by":"publisher","first-page":"1902","DOI":"10.1111\/j.0014-3820.2002.tb00116.x","volume":"56","author":"PW Hedrick","year":"2002","unstructured":"Hedrick, P. W. Pathogen resistance and genetic variation at MHC loci. Evolution \n                           56, 1902\u20131908 (2002).","journal-title":"Evolution"},{"key":"5640_CR5","first-page":"415","volume":"25","author":"Y Shi","year":"2004","unstructured":"Shi, Y., Wu, X. B., Yan, P. & Chen, B. H. Cloning and sequences analysis of the second exon of MHC class IIB genes in Chinese alligator (Alligator sinensis). Zool Res \n                           25, 415\u2013421 (2004).","journal-title":"Zool Res"},{"key":"5640_CR6","doi-asserted-by":"publisher","first-page":"918","DOI":"10.1016\/S1673-8527(07)60103-9","volume":"34","author":"H Liu","year":"2007","unstructured":"Liu, H., Wu, X. B., Yan, P. & Jiang, Z. G. Polymorphism of exon 3 of MHC class IIB gene in Chinese alligator (Alligator sinensis). J Genet Genomics \n                           34, 918\u2013929 (2007).","journal-title":"J Genet Genomics"},{"key":"5640_CR7","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1007\/s11033-012-2061-6","volume":"40","author":"CP Nie","year":"2013","unstructured":"Nie, C. P., Zhao, J., Li, Y. Y. & Wu, X. B. Diversity and selection of MHC class IIb gene exon3 in Chinese alligator. Mol Biol Rep \n                           40, 295\u2013301 (2013).","journal-title":"Mol Biol Rep"},{"key":"5640_CR8","first-page":"86","volume":"91","author":"CP Nie","year":"2012","unstructured":"Nie, C. P., Li, Y. Y., Zhao, Z. & Wu, X. B. Extremely high MHC class IIb gene intron 2 variation and population structure in Chinese alligator. J Genet \n                           91, 86\u201391 (2012).","journal-title":"J Genet"},{"key":"5640_CR9","doi-asserted-by":"publisher","first-page":"1254449","DOI":"10.1126\/science.1254449","volume":"346","author":"RE Green","year":"2014","unstructured":"Green, R. E. et al. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science \n                           346, 1254449 (2014).","journal-title":"Science"},{"key":"5640_CR10","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1186\/gb-2012-13-1-415","volume":"13","author":"JA St John","year":"2012","unstructured":"St John, J. A. et al. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol \n                           13, 415 (2012).","journal-title":"Genome Biol"},{"key":"5640_CR11","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1038\/cr.2013.104","volume":"23","author":"QH Wan","year":"2013","unstructured":"Wan, Q. H. et al. Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator. Cell Res \n                           23, 1091\u2013105 (2013).","journal-title":"Cell Res"},{"key":"5640_CR12","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1007\/s00251-012-0637-x","volume":"64","author":"W Jaratlerdsiri","year":"2012","unstructured":"Jaratlerdsiri, W., Isberg, S. R., Higgins, D. P. & Gongora, J. MHC class I of saltwater crocodiles (Crocodylus porosus):polymorphism and balancing selection. Immunogenetics \n                           64, 825\u201338 (2012).","journal-title":"Immunogenetics"},{"key":"5640_CR13","doi-asserted-by":"publisher","first-page":"e87534","DOI":"10.1371\/journal.pone.0087534","volume":"9","author":"W Jaratlerdsiri","year":"2014","unstructured":"Jaratlerdsiri, W., Isberg, S. R., Higgins, D. P., Miles, L. G. & Gongora, J. Selection and trans-species polymorphism of major histocompatibility complex class II genes in the order Crocodylia. PLoS One \n                           9, e87534 (2014).","journal-title":"PLoS One"},{"key":"5640_CR14","doi-asserted-by":"publisher","first-page":"e114631","DOI":"10.1371\/journal.pone.0114631","volume":"9","author":"W Jaratlerdsiri","year":"2014","unstructured":"Jaratlerdsiri, W. et al. Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC. PLoS ONE \n                           9, e114631 (2014).","journal-title":"PLoS ONE"},{"key":"5640_CR15","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1016\/j.gene.2012.06.035","volume":"507","author":"K He","year":"2012","unstructured":"He, K. et al. A bacterial artificial chromosome library for the Chinese alligator (Alligator sinensis). Gene \n                           507, 74\u201378 (2012).","journal-title":"Gene"},{"key":"5640_CR16","unstructured":"Ye, Q. Construction of genomic BAC library of Chinese alligator and contigs of MHC class II and OR gene. (Zhejiang University, 2011)."},{"key":"5640_CR17","unstructured":"Ma, M. Y. The development of high resolving microsatellite markers in Chinese alligator. (Zhejiang University, 2015)."},{"key":"5640_CR18","doi-asserted-by":"publisher","first-page":"958","DOI":"10.1073\/pnas.86.3.958","volume":"86","author":"AL Hughes","year":"1989","unstructured":"Hughes, A. L. & Nei, M. Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proc Natl Acad Sci USA \n                           86, 958\u2013962 (1989).","journal-title":"Proc Natl Acad Sci USA"},{"issue":"3","key":"5640_CR19","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1093\/genetics\/123.3.585","volume":"123","author":"F Tajima","year":"1989","unstructured":"Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics \n                           123(3), 585\u2013595 (1989).","journal-title":"Genetics"},{"key":"5640_CR20","doi-asserted-by":"publisher","first-page":"3709","DOI":"10.1111\/j.1365-294X.2004.02368.x","volume":"13","author":"HC Miller","year":"2004","unstructured":"Miller, H. C. & Lambert, D. M. Genetic drift outweighs balancing selection in shaping post-bottleneck major histocompatibility complex variation in New Zealand robins (Petroicidae). Mol Ecol \n                           13, 3709\u20133721 (2004).","journal-title":"Mol Ecol"},{"key":"5640_CR21","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1007\/PL00006211","volume":"45","author":"AL Hughes","year":"1997","unstructured":"Hughes, A. L. & Yeager, M. Comparative evolutionary rates of introns and exons in murine rodents. J Mol Evol \n                           45, 125\u201330 (1997).","journal-title":"J Mol Evol"},{"key":"5640_CR22","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1146\/annurev.genet.32.1.415","volume":"32","author":"AL Hughes","year":"1998","unstructured":"Hughes, A. L. & Yeager, M. Natural selection at major histocompatibility complex loci of vertebrates. Annu Rev Genet \n                           32, 415\u2013435 (1998).","journal-title":"Annu Rev Genet"},{"key":"5640_CR23","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1098\/rspb.1992.0099","volume":"249","author":"RW Slade","year":"1992","unstructured":"Slade, R. W. Limited MHC polymorphism in the southern elephant seal: implications for MHC evolution and marine mammal population biology. Proc R Soc London B \n                           249, 163\u2013171 (1992).","journal-title":"Proc R Soc London B"},{"key":"5640_CR24","doi-asserted-by":"publisher","first-page":"8150","DOI":"10.1073\/pnas.90.17.8150","volume":"90","author":"H Ellegren","year":"1993","unstructured":"Ellegren, H., Hartman, G., Johansson, M. & Andersson, L. Major histocompatibility complex monomorphism and low levels of DNA fingerprinting variability in a reintroduced and rapidly expanding population of beavers. Proc Natl Acad Sci USA \n                           90, 8150\u20138153 (1993).","journal-title":"Proc Natl Acad Sci USA"},{"key":"5640_CR25","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1111\/j.0014-3820.2002.tb01395.x","volume":"56","author":"TM Hambuch","year":"2002","unstructured":"Hambuch, T. M. & Lacey, E. A. Enhanced selection for MHC diversity in social tuco-tucos. Evolution \n                           56, 841\u2013845 (2002).","journal-title":"Evolution"},{"key":"5640_CR26","unstructured":"Sambrook, J., Fritsch, E. & Maniatis, T. Molecular cloning: a laboratory manual 2nd. (Cold Spring Harbor Laboratory Press, 1989)."},{"key":"5640_CR27","doi-asserted-by":"publisher","first-page":"e14518","DOI":"10.1371\/journal.pone.0014518","volume":"6","author":"QH Wan","year":"2011","unstructured":"Wan, Q. H. et al. A novel HURRAH protocol reveals high numbers of monomorphic MHC class II loci and two asymmetric multi-locus haplotypes in the P\u00e8re David\u2019s Deer. PLoS ONE \n                           6, e14518 (2011).","journal-title":"PLoS ONE"},{"key":"5640_CR28","doi-asserted-by":"publisher","first-page":"2731","DOI":"10.1093\/molbev\/msr121","volume":"28","author":"K Tamura","year":"2011","unstructured":"Tamura, K. et al. MEGA5: Molecular evolutionary genetics analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol \n                           28, 2731\u20132739 (2011).","journal-title":"Mol Biol Evol"},{"key":"5640_CR29","doi-asserted-by":"publisher","first-page":"1451","DOI":"10.1093\/bioinformatics\/btp187","volume":"25","author":"P Librado","year":"2009","unstructured":"Librado, P. & Rozas, J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics \n                           25, 1451\u20131452 (2009).","journal-title":"Bioinformatics"},{"key":"5640_CR30","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1093\/bioinformatics\/15.9.763","volume":"15","author":"JM Comeron","year":"1999","unstructured":"Comeron, J. M. Bioinformatics \n                           15, 763\u2013764 (1999).","journal-title":"Bioinformatics"},{"key":"5640_CR31","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1006\/smim.1994.1050","volume":"6","author":"J Kaufman","year":"1994","unstructured":"Kaufman, J., Salomonsen, J. & Flajnik, M. F. Evolutionary conservation of MHC class I and class II molecules\u2014different yet the same. Semin Immunol \n                           6, 411\u2013424 (1994).","journal-title":"Semin Immunol"},{"key":"5640_CR32","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1111\/j.1755-0998.2010.02847.x","volume":"10","author":"L Excoffier","year":"2010","unstructured":"Excoffier, L. & Lischer, H. E. L. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Res \n                           10, 564\u2013567 (2010).","journal-title":"Mol Ecol Res"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-05640-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-05640-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-05640-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,23]],"date-time":"2022-12-23T06:48:47Z","timestamp":1671778127000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-05640-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,7,17]]},"references-count":32,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,12]]}},"alternative-id":["5640"],"URL":"https:\/\/doi.org\/10.1038\/s41598-017-05640-2","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,7,17]]},"assertion":[{"value":"14 January 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 June 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 July 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}],"article-number":"5549"}}