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Sequence Polymorphism and Geographical Variation at a Positively Selected MHC-DRB Gene in the Finless Porpoise (Neophocaena phocaenoides): Implication for Recent Differentiation of the Yangtze Finless Porpoise?

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Abstract

Sequence polymorphism at the MHC class II DRB locus was investigated in three finless porpoise (Neophocaena phocaenoides) populations in Chinese waters. Intragenic recombination and strong positive selection were the main forces in generating sequence diversity in the DRB gene. MHC sequence diversity changed significantly along the study period. Significant decrease in heterozygosity and lost alleles have been detected in the Yangtze River population and South China Sea population since 1990. Furthermore, there is a trend of increasing population differentiation over time. Especially, the genetic differentiation between the Yangtze River population and the Yellow Sea population was very low prior to 1990 (F ST = 0.036, P = 0.009), but became very significant after 1990 (F ST = 0.134, P < 0.001), suggesting a recent augmentation of genetic differentiation between both populations probably in a relatively short-term period. Porpoises from the Yangtze River displayed divergent frequencies of shared and private alleles from those displayed by two marine populations, which suggest that the former riverine population has been under a different selection regime (characteristic of a fresh water environment) than that of its marine counterparts.

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Acknowledgments

We thank Dr. Anli Gao, Mr. Xin-Rong Xu, Mr. Hua Chen, and Dr. Qing Chang for their contribution in collecting samples for many years. A special thank-you is owed to Mr. Jun-Xiao Xu, for his assistance with the W–K analysis and positive selection analysis using the PAML 4 program suite. This research was financially supported by the key project of National Natural Science Foundation of China (NSFC) under grant nos. 30830016, and 30670294; the Program for New Century Excellent Talents in University (grant no. NCET-07-0445), the Ministry of Education of China; the Specialized Research Fund for the Doctoral Program of Higher Education (grant no. SRFDP 20060319002), the Ministry of Education of China; and the major project of the Natural Science Foundation of the Jiangsu Higher Education Institutions of China (grant no. 07KJA18016). Finally, a special thank-you is also due from the authors to anonymous referees and editors for their critical comments which greatly helped to improve this article.

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  1. Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210046, China

    Shixia Xu, Wenhua Ren, Xuming Zhou, Kaiya Zhou & Guang Yang

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Xu, S., Ren, W., Zhou, X. et al. Sequence Polymorphism and Geographical Variation at a Positively Selected MHC-DRB Gene in the Finless Porpoise (Neophocaena phocaenoides): Implication for Recent Differentiation of the Yangtze Finless Porpoise?. J Mol Evol 71, 6–22 (2010). https://doi.org/10.1007/s00239-010-9357-8

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