Phylogeography Of Boleophthalmus Pectinirostris (Teleostei:Gobiidae) In Marginal Seas Of The Northwestern Pacific

Marginal seas in the northwestern Pacific are the perfect research areas to explore effects of cyclical sea level fluctuations during the Quaternary on spatial genetic structure and demographic history of organisms. Intertidal mudflats are dominant habitats along the continental coast of the marginal seas. However, studies on animal phylogeography in the habitats are limited. Boleophthalmus pectinirostris is a common fish in intertidal mudflats, previous studies on spatial genetic structure and historical biogeography of this species only contain the East China Sea populations and did not consider the South China Sea populations. Therefore, range-wide sampling is needed to reveal phytogeographical patterns of B. pectinirostris. In addition, the Malaysia populations are needed to be validated if they are B. pectinirostris.This study samples multiple populations across the entire distribution range of B. pectinirostris. The Cyt b (Cytochrome b) and ND5(NADH dehydrogenase subunit5) genes are chosen as molecular markers. The aims of this study are1) to compare the genetic divergence between Malyasia and East Asia populations;2) to reveal the phylogeographical pattern of East Asia populations,3) to discuss the possible evolutionary mechanism for spatial genetic structure and demographic history. This study will also provide scientific knowledge for the conservation of genetic diversity in marginal seas of the northwestern Pacific.The phylogeographical analyses were conducted based on510specimens from25populations of East Asia and Malaysia. Major results are listed as follows:1. Phylogeography of East Asia Boleophthalmus pectinirostris1) Phylogenetic relationships among haplotypesThe data set of1511bp mitochondrial fragments of498species from23East Asia populations yielded255haplotypes. Among them,215haplotypes were private. Three clades were revealed based on the minimum spanning haplotype network. Part of haplotypes from the Beibu Gulf and northern South China Sea consists of Clade I; Clade Ⅱ include haplotypes from the Beibu Gulf and northern South China Sea, all haplotypes from Taiwan Strait, southern East China Sea, and most haplotypes from the southern Yellow Sea; the other haplotypes from southern Yellow Sea and all haplotypes from northern Yellow Sea and Ariake Sea in Japan form Clade Ⅲ.2) Genetic diversity Overall haplotype diversity was high (h=0.97). Haplotype diversities of most populations were also high (0.89-1.00), but haplotype diversities of Jiaozhou and Rokkaku populations were relative low (0.54and0.40). Overall nucleotide diversity was low (π=0.0048). Nucleotide diversity of the Rokkaku population was the lowest (0.0003) and nucleotide diversities of Dangjiang and Qinzhou population was the highest (0.0057and0.0051).3) Spatial genetic structurePairwise ΦST analyses revealed that there were no significant genetic divergences among populations within a region and genetic divergence to a certain extent among populations in different regions. Jiaozhou and Rokkaku populations in the edge of species distribution range exhibited significantly genetic divergences with other populations. The Spatial Analysis of Molecular Variance divided23populations into three groups:a) populations along the Chinese coastal populations; b) the Suncheon population in Korea; c) Ariake Bay populations in Japan. Excluding the populations with less than10specimens, the Principal Coordination Analysis divided the East Asia populations to four groups:A) Ariake Bay populations; B) Jiaozhou population; C) Beibu Gulf populations; D) other remaining populations. Isolation with Migration analyses revealed low gene flow between Dangjiang population and Zhanjiang population, which indicates the isolation between Beibu Gulf and northern South China Sea. Low gene flow between Jiaozhou and Yancheng populations revealed the existence of edge effects. Gene flow among populations of the Ariake Bay, Yellow Sea and East China Sea was also limited, which indicates the isolation between islands and continent.4) Demographic historyNeutrality tests showed significant negative values of Tajima’s D and Fu’s Fs in most populations, which indicate historical population expansion of B. pectinirostris. The timing of population expansion in the South China Sea was from60to200ka before present. The timing of population expansion in the Taiwan Strait, southern East China Sea and the Yancheng were later than those in the South China Sea, which ranges from16to51ka before present. The timing of population expansion in the Rokkaku was only7ka. Population expansion in the Jiaozhou might be a very recent event. The Bayesian Skyline Plot revealed the expansion of Clade Ⅰ and Ⅱ began at30to50ka before present, and the expansion of Clade Ⅲ began at13ka before present. 2. Population genetic divergence between Malaysia and East Asia1) PhylogenyThe12specimens from Malaysia generate8haplotypes. Bayesian phylogenetic inference revealed monophyly of East Asia or Malaysia populations with strong support (100%posterior probability). The minimum spanning haplotype network revealed156mutations between East Asia and Malaysia haplotypes.2) Genetic distance and divergence timeThe uncorrected p-distances of ND5gene within East Asia populations were0.13～1.58%, those within Malaysia populations were0.13～0.79%, and those between East Asia and Malaysia were8.96～10.28%. The uncorrected p-distances of Cyt b gene within East Asia populations were0.13～2.13%, those within Malaysia populations were0.13～1.06%, and those between East Asia and Malaysia were11.17～12.90%. The net average K2P distance between East Asia and Malaysia was9.86±1.20%. The divergence time between East Asia and Malaysia was estimated to be2.53±0.38Ma before present using the divergence rate of3.89±0.33%per Ma.In conclusion, this study on phylogeographical pattern of Boleophthalmus pectinirostris in northwestern Pacific revealed:Ⅰ) Boleophthalmus pectinirostris only distributed in East Asia, and the Malaysia population was a cryptic species which needs further morphological description; Ⅱ) phylogeo graphical patterns of East Asia B. pectinirostris include:a) high haplotype diversity and low nucleotide diversity; b) strong phylogeographical structure, especially the monophyly of the Japanese Ariake Bay populations; c) secondary contact of Clade Ⅰ and Ⅱ along the Chinese coastal line; d) rapid population expansion at the Late Last Glacial Period; e) a founder effect in the Jiaozhou population.