ORIGINAL PAPER Microsatellite variation and significant population genetic structure of endangered finless porpoises (Neophocaena phocaenoides) in Chinese coastal waters and the Yangtze River Lian Chen • Michael W. Bruford • Shixia Xu • Kaiya Zhou • Guang Yang Received: 20 May 2009 / Accepted: 2 March 2010 / Published online: 17 March 2010 Ó Springer-Verlag 2010 Abstract The finless porpoise (Neophocaena phocaeno- ides) inhabits a wide range of tropical and temperate waters of the Indo-Pacific region. Genetic structure of finless porpoises in Chinese waters in three regions (Yangtze River, Yellow Sea, and South China Sea) was analyzed, including the Yangtze finless porpoise which is widely known because of its highly endangered status and unusual adaptation to freshwater. To assist in conservation and management of this species, ten microsatellite loci were used to genotype 125 individuals from the three regions. Contrary to the low genetic diversity revealed in previous mtDNA control region sequence analyses, relatively high levels of genetic variation in microsatellite profiles (H E = 0.732–0.795) were found. Bayesian clustering analysis suggested that finless porpoises in Chinese waters could be described as three distinct genetic groups, which corresponded well to population ‘‘units’’ (populations, subspecies, or species) delimited in earlier studies, based on morphological variation, distribution, and genetic analyses. Genetic differentiation between regions was significant, with F ST values ranging from 0.07 to 0.137. Immigration rates estimated using a Bayesian method and population ancestry analyses suggested no or very limited gene flow among regional types, even in the area of overlap between types. These results strongly support the classifi- cation of porpoises in these regions into distinct evolu- tionarily significant units, including at least two separate species, and therefore they should be treated as different management units in the design and implementation of conservation programmes. Introduction A long-standing goal in evolutionary and conservation biology is to understand the extent to which current pat- terns of diversity in separated populations have been influenced by natural selection, genetic drift, gene flow coupled with their interactions (Palstra et al. 2007). Small, isolated populations are assumed to be vulnerable to local extinctions as a result of stochastic factors and more prone than large populations to lose genetic variation through random drift, resulting in a decrease in adaptive fitness (Frankham et al. 2003; Gilpin and Soule 1986; Lynch et al. 1995; Westemeier et al. 1998), which may further exac- erbate population decline. As predicted by population genetic theory, due to genetic drift and/or inbreeding, small populations should show lower levels of genetic variability than large populations (Hartl and Clark 1997). However, gene flow can counteract the potentially adverse effects of genetic isolation and the loss of genetic diversity in small populations while simultaneously limiting genetic differ- entiation between populations (Palstra et al. 2007; Van Rossum et al. 1997). Conversely, speciation may result from more limited gene flow and subsequent differentiation (e.g., Terry et al. 2000). In either case, knowledge of population structure and natural patterns of gene flow can contribute to a better understanding of species’s ecology and evolution, and to the implementation of informed Communicated by M. I. Taylor. L. Chen Á S. Xu Á K. Zhou Á G. Yang (&) Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210046 Nanjing, China e-mail: gyang@njnu.edu.cn M. W. Bruford Á G. Yang School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3TL, UK 123 Mar Biol (2010) 157:1453–1462 DOI 10.1007/s00227-010-1420-x