The South China landmass has been characterized by a complex geological history, including mountain lifting, climate changes, and river capture/reversal events. To determine how this complexity has influenced the landmass’s phylogeography, our study examined the phylogeography of Garra orientalis, a cyprinid widely distributed in South China, using sequences from the mitochondrial DNA control region and cytochrome b gene (1887 bp) and polymorphisms of thirteen microsatellite loci. In total, 157 specimens were collected from eight populations. All 88 mtDNA haplotypes were identified as belonging to three major lineages, and these lineages were almost allopatric in their distributions. The results of a statistical dispersal-vicariance analysis suggested that the ancestral populations of G. orientalis were distributed south of the Yunkai Mountains, including on Hainan Island. The mtDNA data revealed a strong relationship between phylogeny and geography. In the microsatellite analysis, a total of 339 alleles with an average of 26 alleles per locus were observed across thirteen microsatellite loci. A clustering algorithm for microsatellite data revealed an admixture-like genetic structure. Although the mtDNA and microsatellite data sets displayed a discordant population structure, the results of an approximate Bayesian computation approach showed that these two markers revealed congruent historical signals. The population history of G. orientalis reflects vicariance events and dispersal related to the complex geological history of South China. Our results (i) found that the discordances between mtDNA and microsatellite markers were accounted for by admixtures; (ii) showed that the Wuzhishan and Yinggeling mountain ranges and Qiongzhou Strait were important barriers limiting gene exchange between populations on both sides; (iii) indicated that during glaciation and inter-glacial periods, the strait and continental shelves were exposed and sank, which contributed with the dispersion and differentiation of populations; and (iv) displayed that the admixtures between lineages took place in coastal populations and then colonized the tributaries of the Pearl River.

Background: The freshwater species on Taiwan Island have been documented to have originated from mainland China and the Japanese islands from multiple events and by multiple colonization routes. Moreover, the sequences from the mitochondrial DNA cytochrome c oxidase subunit I (COI) have been used for DNA barcoding to identify the species. This study used the COI sequences to identifyNeocaridinaspecies in Taiwan and to examine their geographical and temporal origins.Results: In total, 479 specimens were collected from 35 localities, which covered almost all rivers in Taiwan. In addition, some sequences were downloaded from GenBank. The maximum likelihood (ML) tree displayed that all sequences were sorted into 13 taxa (clades), and all sequences in Taiwan were sorted into four clades. The Bayesian skyline plots revealed that these fourNeocaridinaspecies have declined recently in Taiwan.Conclusions: All results support that (1) there are fourNeocaridinaspecies in Taiwan, which areN. davidi,N. saccam,N. ketagalanand an undescribedNeocaridinaspecies (N.sp.); (2) these four species colonized Taiwan Island in four colonization events; (3)N.sp. colonized Taiwan first; (4) after the island reached its shape,N. ketagalanandN. saccamcolonized Taiwan from the Japanese islands and mainland China, respectively; (5)N. davidicolonized northern Taiwan last; and (6) the cyclic glacial and landform changes in East Asia shaped the colonization events and population structures of theNeocaridinaspecies.

The genetic structure of four populations of Pararasbora moltrechti, an endemic species of the Cyprinidae in Taiwan, was investigated based on the genetic variation of mtDNA Cyt b gene and five microsatellite loci. High haplotype diversity (h = 0.92) but low nucleotide diversity (0.004) in mtDNA was detected in this endangered species. In total, 33 haplotypes and four clusters were identified in its mtDNA. Nevertheless, low correspondence was found between geographical division and mtDNA clusters. In contrast, Bayesian cluster analysis of the microsatellite data identified four genetic groups and revealed highly structured populations. Significantly negative Tajima's D statistics and mismatch distribution analyses suggest that P. moltrechti populations may have experienced a demographic expansion. In light of the results of a nested clade analysis of mtDNA haplotypes, we conclude that recent population fluctuations and restricted gene flow played major roles in shaping the spatial genetic structure of P. moltrechti populations.

The genetic structure and demography of the yellowbelly threadfin bream, Nemipterus bathybius, in the northern South China Sea were examined using the mitochondrial DNA cytochrome b gene (1141 bp). High levels of haplotype and nucleotide diversities (0.98 and 5.26 × 10⁻³, respectively) showed that all populations exhibited a high level of genetic diversity. Analysis of molecular variance (AMOVA), F_ST statistics, and haplotype networks suggested the absence of significant genetic differentiation along the coast of the northern South China Sea. Although the results suggested that the lack of differentiation within the population structure of N. bathybius was shaped by ocean currents, our results also showed that the Qiongzhou Strait limited their migration between Beibu Gulf and the northern South China Sea. Neutrality tests and mismatch distributions indicated population expansion, but the Bayesian skyline plots and approximate Bayesian computation approaches suggested that the population sizes recently contracted. The diversification of multiple stocks, which were induced by two ocean current systems, contributed to these discordant results. Although these analyses of demographic history revealed no evidence for recent population bottlenecks, the population demography needs to be evaluated further.