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.

To understand the spatial and seasonal variations of fish communities in Taiwanese estuaries, this study collected environmental DNA (eDNA) water samples and assessed environmental parameters from four estuaries in northeastern, southeastern, northwestern, and southwestern Taiwan between February and December 2023. The 12S rRNA genetic marker was used as a mini-barcode to detect fish compositions in 16 samples. Assessment of environmental parameters revealed that (1) there were significant differences between estuaries but no differences between seasons; (2) the northwestern estuary exhibited the greatest seasonal variation; and (3) the greatest spatial variation was exhibited in summer. Fish community analysis revealed that (1) fish diversity was highest in the northeastern estuary and lowest in the southeastern estuary; (2) fish compositions significantly differed among the estuaries; (3) fish compositions in the southeastern estuary exhibited the greatest seasonal variation, and those in the northeastern estuary exhibited the smallest seasonal variation; (4) fish compositions in winter slightly differed from those in the other seasons; and (5) invasive fish species were present in all estuaries. In summary, the fish compositions in Taiwanese estuaries were influenced by local environmental variables and ocean currents.