Phylogenetic Analysis Of Genus Coilia In China And Molecular Phylogeography Of C. Nasus And C. Mystus

In the present study, morphological, mitochondrial DNA sequence and AFLP markerswere used for the phylogenetic and taxonomic analysis of Coilia in China. Thevalidity of naming species of C. brachygnathus and C. nasus taihuensis wasinvestigated. To elucidate the phylogeographic pattern of C. nasus, mitochondrialDNA sequence and ISSR markers were used to study the sample of C. nasus inYangtze River and Northwestern Pacific. To assess the genetic structure of C. mystus,we also examined the sample along the coastal regions of China by usingmorphological, mitochondrial DNA sequence and ISSR markers.1The phylogenetic and taxonomic analysis of Coilia in China:(1) The phylogeny and taxonomy of Coilia was studied by the morphological analysisin China. The results from the cluster analysis showed a close relationship among C.brachygnathus, C. nasus taihuensis, and C. nasus. C. brachygnathus and C. nasustaihuensis should be synonymized with C. nasus based on the results from the thecluster analysis, principal component analysis and the frequency distribution of themeristic characters in Coilia species.(2) To elucidate the phylogeny and taxonomy of Coilia, mitochondrial COI, ND5andCytb fragment were used for the combined analysis. C. brachygnathus, C. nasustaihuensis, and C. nasus did not form three separate monophyletic groups in the NJ,MP and BI trees. The average intraspecific genetic distance within C. brachygnathus,C. nasus, and C. nasus taihuensis approximates to their interspecific genetic distance.The mean pairwise Fst value obtained from C. brachygnathus, C. nasus, and C. nasus taihuensis comparisons was significantly lower than the mean pairwise Fst valueobtained between these species and the species of C. grayii and C. mystuscomparisons. Results of the AMOVA revealed that9.76%of the total molecularvariance can be attributed to the significant differences among species. The studyshowed no significant difference among C. brachygnathus, C. nasus, and C. nasustaihuensis. C. brachygnathus and C. nasus taihuensis should therefore besynonymized with C. nasus.(3) AFLP analysis was applied to study the phylogeny and taxonomy of Coilia inChina. The Gst value and the interspecific genetic distance among C. brachygnathus,C. nasus, and C. nasus taihuensis were significantly lower than those of Gst value andinterspecific genetic distance which were obtained between these species and thespecies of C. grayii and C. mystus. If C. brachygnathus and C. nasus taihuensis wereregarded as populations of C. nasus to investigate the genetic structures of the threespecies, C. nasus, C. grayii and C. mystus, most of the variance (P=0.00) was foundamong species and a small amount within species. In the neighbor-joining tree andUPGMA dendrogram, a close relationship was indicated among C. brachygnathus, C.nasus taihuensis, and C. nasus. Therefore, C. brachygnathus and C. nasus taihuensisshould be synonymized with C. nasus.2Molecular Phylogeography of C. nasus:(1) To elucidate the phylogeographic pattern of C. nasus, mitochondrial DNAsequences were used to study the sample of C. nasus in Yangtze River andNorthwestern Pacific. The BI tree constructed using the complete data set of113mitochondrial control region haplotypes identified three distinct lineages. The FStestsof three lineages were negative and highly significant, which indicated populationexpansion. Analyses of molecular variance and the population statistic Fst alsorevealed significant genetic structure among three lineages. As the base levels oferosion and ground water levels were lower as well, rivers in upland areas could formdeeply incised river valleys during the last Pleistocene glaciation. We conclude thatfreshwater populations of C. nasus could thereby have become isolated in the lakes ofYangtze River, resulting in a separate lineage observed in the mitochondrial genome. Strong genetic break was found between the Sea of Japan and the China Seapopulations, likely reflecting isolation of Ariake Bay in the Northwestern Pacificduring the late Pleistocene. A hypothetical scenario to explain the observedphylogeographic pattern is that genetic differentiation and homogeneity may beattributed to habitat and life-history characteristics.(2) Northwestern Pacific provides unique scenarios for studying the roles ofgeography and ecology in driving population divergence and speciation. Toinvestigate geographical patterns of genetic variation in the Japanese grenadieranchovy using ISSR markers we collected individuals from five locations throughouttheir distribution in the Northwest Pacific. Analyses of molecular variance showedthat genetic differentiation among groups is relatively high. Bayesian analysis of ISSRdata also revealed significant population structuring between Chinese and Japaneselocations. Phylogenetic reconstructions show reciprocal monophyly in populationsbetween China and the Ariake Bay of Japan. We conclude that the present-dayphylogeographic pattern is the result of genetic isolation between Japanese andChinese populations in the Northwestern Pacific following the glacial retreat, and thatlife-history traits and ecology may play a pivotal role in shaping the realizedgeographical distribution pattern of this species.(3) To investigate the phylogeographic pattern of C. nasus, ISSR markers were usedto study the sample of C. nasus in Yangtze River. Bayesian analysis of ISSR datarevealed significant population structuring between freshwater and anadromouspopulations (K=2). Analyses of molecular variance also revealed that geneticdifferentiation among groups is relatively high. Phylogenetic reconstructions showtwo distinct lineages in Yangtze River. We conclude that the present-dayphylogeographic pattern is the result of genetic isolation between freshwater andanadromous populations in Yangtze River during the last Pleistocene glaciation, andthat life-history traits and ecology may play a pivotal role in shaping the realizedgeographical distribution pattern of this species.3Phylogeography of C. mystus:(1) To investigate the genetic difference of C. mystus by the morphological analysis we collected individuals from five locations throughout their distribution alongChinese coastal waters. The results from the cluster analysis showed strong geneticbreak between Ningbo and the other populations. There were significant differencesbetween Ningbo and the other populations based on the results from the clusteranalysis, principal component analysis and the frequency distribution of the meristicand gill rakers characters in populations of C. mystus. Local populations may besufficiently locally adapted to the particular habitat to limit the dispersal amongpopulations of C. mystus. Habitat and life-history differences may play a pivotal rolein shaping morphological characteristics of this species.(2) To elucidate the phylogeographic pattern of C. mystus, mitochondrial DNAsequences were used to study the sample of C. mystus along Chinese coastal waters.The NJ tree constructed with mtDNA sequences identified two distinct lineages. Thecytochrome b and control region data suggests a divergence time of3.9MY betweenthe two lineages, indicating isolation in the middle Pliocene. A highest geneticdistance for COI gene was found between two lineages (5.6%). According to thebarcoding approach, species could be identified based on a ‘barcoding gap’ betweenintra-and interspecific genetic distances by using a threshold value of23%forspecies delimitation. The study indicated the presence of cryptic species within thepopulations of C. mystus. The neutrality tests indicated population expansion in thetwo lineages. Population range expansion must have occurred after the last glacialmaximum. Range contractions and expansions played a central role in shaping thegenetic diversity of the two lineages of C. mystus.(3) To investigate the phylogeographic pattern, ISSR markers were used to study thesample of C. mystus along Chinese coastal waters. Bayesian analysis of ISSR datarevealed significant population structuring between northern and southern groups(K=2). Analyses of molecular variance also revealed that genetic differentiationamong groups is relatively high. Phylogenetic reconstructions show reciprocalmonophyly in populations between northern (SH) and southern (NB, XM and DB)groups. The results showed strong genetic break northern and southern populations.Local populations may be sufficiently locally adapted to the particular habitat to limit the dispersal among populations of C. mystus. Life-history traits and ecology mayplay a pivotal role in shaping the realized geographical distribution pattern of thisspecies.