Mitochondrial DNA control region diversity and population structure of Pacific herring (Clupea pallasii) in the Yellow Sea and the Sea of Japan* LIU Ming () 1 , GAO Tianxiang (Ø)Ô) 1,** , SAKURAI Yasunori (1ðª) 2 , JIA Ning (>) 1 , ZHAO Linlin (u) 1 , DU Xiao (\S) 1 , JIANG Qun (ܤ) 1 , LU Zhichuang (×) 1 1 College of Fisheries, Ocean University of China, Qingdao 266003, China 2 Graduate School of Fisheries Sciences, Hokkaido University, Minato-cho, Hakodate, Hokkaido 041-8611, Japan Received Jan. 13, 2010; revision accepted Apr. 8, 2010 E Chinese Society for Oceanology and Limnology, Science Press, and Springer-Verlag Berlin Heidelberg 2011 Abstract To investigate the genetic variation and population structure of Pacific herring in the Yellow Sea and the genetic differentiation between the Yellow Sea and the Sea of Japan, fragments of 479-bp mitochondrial DNA control region were sequenced for 110 individuals collected from three different periods in the Yellow Sea and one locality in the Sea of Japan. High haplotype diversity and moderate nucleotide diversity were observed in Pacific herring. AMOVA and exact test of populationdifferentiationshowednosignificantgeneticdifferentiationsamongthethreepopulationsof the Yellow Sea and suggested the populations can be treated as a single panmictic stock in the Yellow Sea. However, a large and significant genetic differentiation (W ST 50.11; P50.00) was detected between thepopulationsintheYellowSeaandtheSeaofJapan.ThehighseawatertemperatureintheTsushima Strait was thought a barrier to block the gene exchange between populations of the two sea areas. The neutrality tests and mismatch distribution indicated recent population expansion in Pacific herring. Keyword: Clupea pallasii; mtDNA control region; genetic diversity; population genetics; the Yellow Sea; historical demography 1 INTRODUCTION The population structure of marine organisms is often poorly understood (Machado-Schiaffino et al., 2009). The absence of physical barriers and the mixing of ocean currents can facilitate gene exchange among marine fish populations (Palumbi, 1994). However, a number of studies have demonstrated that spatial and temporal genetic differentiation can occur among populations of marine fish, even in open marine areas that have no apparent barrier to migration. Researchers have hypothesized that historical climatic fluctuation and sea level changes, contemporary ocean currents, sea temperatures, salinity, and the life-history traits of marine fish (e.g. their potential for dispersal, homing to spawning zones, and larval retention) may have contributed to population differentiation (e.g. Santos et al., 2006; Liu et al., 2007a; Han et al., 2008a). Moreover, genetic differentiation has occurred among populations that live within the same region but at different times (Hsu et al., 2007), or within the same population but in different years (von der Heyden et al., 2007). Both these examples highlight the complexity of population structure in marine fish. Knowledge of population structure is particularly important for long-term fisheries management and conservation because consistent exploitation of mixed populations may result in declines of the least productive stocks (Hutchings, 2000). Pacific herring (Clupea pallasii) are commercially important in the *Supported by the National Natural Science Foundation of China (No. 31061160187), Special Fund for Agro-scientific Research in the Public Interest (No. 200903005), and Ocean University of China Students Innovation Trainning Program **Corresponding author: gaozhang@ouc.edu.cn Chinese Journal of Oceanology and Limnology Vol. 29 No. 2, P. 317-325, 2011 DOI: 10.1007/s00343-011-0008-8