Genetic Diversity And Population Structure Of Chinese Misgurnus Anguillicaudatus And Elopichthys Bambusa In The Yangtze River Basin As Revealed By Molecular Markers

The Yangtze River is the third longest river in the world that flows from west to east of China. The basin of the Yangtze River historically offered a potamo-lacustrine ecosystem to a wide variety of fishes. During last half century, anthropogenic interventions through construction of dams, irrigation works, and urbanization brought about huge alterations in the riparian ecosystems leaving drastic impact upon the ichthyofauna of the basin. The imperiled fish biodiversity in the region need be investigated at various scales. The present study was designed with the major focus at exploring the genetic diversity and existing population structure of Chinese loach and yellowcheek carp using microsatellite markers. Moreover, the mitochondrial gene Cytochrome b of yellowcheek carp was sequenced so as to reconstruct the phylogeographic structure in the studied populations.The loach Misgurnus anguillicaudatus is a small freshwater fish that is widely distributed in shallow water ecosystems of China. Despite major hydrological alterations in natural habitats, the population genetic structure of Chinese M. anguillicaudatus has not been disclosed yet. We investigated twelve loach populations originating from middle-lower mainstream sub-basin and the Hanjiang sub-basin of the Yangtze River. Total thirteen microsatellite loci with varying levels of polymorphism were employed to examine genetic differentiation and population structure of the species within sampling localities. The number of alleles per locus varied between 2 and 8 with an average of 4.6 alleles per locus. Observed heterozygosity varied from below 0.38 up to a maximum of 0.95; over all loci the average observed and expected heterozygosity was 0.57 and 0.56, respectively. Significant deviations from Hardy-Weinberg equilibrium (P < 0.01) were observed in about 50% of the total locus-population combination tests with apparent heterozygote deficits. This heterozygote deficit might be attributed to fishing pressure and migration-drift disequilibrium. AMOVA analyses indicated that most of the variance existed among the individuals (90.50%) rather than among populations within groups (9.03%). Based on pairwise F_ST and unbiased genetic distance, significant differentiation was found among the samples from scattered habitats with different connections to the Yangtze River. The UPGMA dendrogram clustered the populations onto two major branches, surprisingly following their ichthyogeographic distribution except ZIG and XGN populations which genetically departed from their geographical origin. The combined analyses showed a significant population genetic structuring at sub-basin level. Overall, the present study revealed that Chinese loach inhabiting the central China is genetically differentiated into two distinct geographical groups. The existing differentiation in loach populations is attributed to the current demographic configuration of the region, nonmigratory behavior of the loach and reduced flooding in the Yangtze River which restricted the gene flow among loach populations in riparian ecosystems.The second fish species, worthy of immediate concern, is yellowcheek carp Elopichthys bambusa. Despite rich ichthyofauna in the Yangtze River basin, the cyprinid E. bambusa is the only species of the genus Elopichthys reported to date. Added to the declining populations in face of growing anthropogenic and environmental perturbations, the scarce studies on the systematics, genetics and ecology of this species direly demand to evaluate the genetic diversity and phylogenetic structure of E. bambusa. The present study is the first effort to address the aforementioned issues. The genetic diversity, population structure and phylogeography of the E. bambusa in the Yangtze River were examined as inferred from microsatellite markers and mitochondrial gene, Cyt b sequences analyses. Total nine polymorphic microsatellite markers were employed to study five populations belonging to middle-and-lower reaches of the river. The results revealed low-to-moderate genetic diversity. The number of alleles per locus ranged between 3 and 8 with an average of 4.8. Observed heterozygosity ranged from 0.15 to a maximum of 1.00 whereas over all loci, the average observed and expected heterozygosity was 0.65 and 0.70, respectively. Significant deviations (P<0.01) from Hardy-Weinberg equilibrium were observed for all the tested locus-population combinations with clear heterozygosity deficits. AMOVA analysis indicated majority of the variance lies within populations (93.81%) than among the populations (7.05%). Pairwise F_ST and unbiased genetic distance pointed out significant differentiation among the samples from populations with different connections to the Yangtze River. In the UPGMA dendrogram, clustering pattern of populations was almost concordant with the ichthyogeographic distribution. The same five populations of E. bambusa were examined for mitochondrial divergence and phylogenetic structure using mitochondrial sequences. The complete mitochondrial Cyt b gene of 73 specimens was sequenced. The combined analyses revealed three distinct mtDNA lineages of E. bambusa showing high nucleotide divergence and haplotypes diversity. The sequence analysis of 73 samples revealed 39 haplotypes with haplotype diversity ranging from 0.8727 to 0.9777. The results of nucleotide divergence, Neighbor Joining tree and AMOVA indicate a historically restricted gene flow among the lineages. The populations of PYL, DTL and WHN gathered into one lineage where as the samples from both THL and DJR appeared as independent monophyletic lineages. As evident from the clustering pattern of UPGMA and NJ, the results of microsatellite and mitochondrial divergence reinforce each other. In addition to the old geological events, the hydrological alterations in the Yangtze River basin during the last century have contributed to the evolutionary process. The results point out an underestimated species diversity of the genus Elopichthys and that each of the mtDNA lineages may correspond to three distinct species.The study points out the factors involved in genetic differentiation and shaping the existing patterns of population structure of the M. anguillicaudatus and E. bambusa so as to provide guidelines for conservation strategies and management programs. The dwindling populations of both the species in natural ecosystems of China demand critical efforts to conserve the genetic diversity. The impact of human induced habitat fragmentation and hydrological alterations in terms of genetic diversity loss and differentiations through inbreeding and random genetic drift is profound. To avoid the threats of local extinction and reinforce conservation measures, investigations on morphology, reproduction and molecular genetic aspects of both the species in general and E. bambusa in particular are suggested. Employing more polymorphic markers and exhaustive sampling over a wide geographical scale may explore a fine-scale genetic structure of M. anguillicaudatus and E. bambusa populations.