Genetic structure and diversity of Nodularia douglasiae (Bivalvia: Unionida) from the middle and lower Yangtze River drainage

Abstract

The Yangtze River drainage in China is among the most species rich rivers for freshwater mussels (order Unionida) on Earth with at least 68 species known. The freshwater mussels of the Yangtze River face a variety of threats with indications that species are declining in abundance and area of occupancy. This study represents the first analyses of the genetic structure and diversity for the common and widespread freshwater mussel Nodularia douglasiae based on microsatellite DNA genotypes and mitochondrial DNA sequences. Phylogenetic analysis a fragment of the COI mitochondrial gene indicated that N. douglasiae collected from across the middle and lower Yangtze River drainage are monophyletic with N. douglasiae from Japan, Russia, and South Korea. The results of the analysis of both the mtDNA and microsatellite datasets indicated that the seven collection locations of N. douglasiae in the middle and lower Yangtze River drainage showed high genetic diversity, significant genetic differentiation and genetic structure, and stable population dynamics over time. Moreover, we found that the connections among tributaries rivers and lakes in the Yangtze River drainage were important in maintaining gene flow among locations that N. douglasiae inhabits. An understanding of the genetic structure and diversity of a widespread species like N. douglasiae could be used as a surrogate to better understand the populations of other freshwater mussel species that are more rare in the Yangtze River drainage. At the same time, these results could provide a basis for the protection of genetic diversity and management of unionid mussels diversity and other aquatic organisms in the system.

Fig 1. Collection locations for N. douglasiae in the middle and lower Yangtze River drainage.

LZ: Liangzi Lake; DT: Dongting Lake; PY: Poyang Lake; GJ: Gan River; XN: Xiannv Lake; HZ: Hongze Lake; TH: Taihu Lake. Collection location symbol colours correspond to Fig 6 (K = 3).

Fig 2. Phylogenetic tree of the COI fragment for Nodularia obtained using Bayesian Inference (BI).

Support values represent BI posterior probabilities. Only support values above 0.50 are shown.

Fig 3. Haplotype network for N. douglasiae populations in the middle and lower reaches of Yangtze River.

Each cross-hatched line represents one base-pair difference between haplotypes, black dots are inferred missing haplotypes, and haplotype frequency is relative to the size of the circle. Collection location codes as in Table 1. Colours used are in similar hues (blue, green, red) corresponding to the results of the STRUCTURE analysis (K = 3, Fig 6).

Fig 4. Mismatch distribution analysis (MDA) for N. douglasiae collection locations in the middle and lower reaches of Yangtze River.

Fig 5. Bayesian skyline plot for N. douglasiae from the middle and lower Yangtze River drainage reconstructing the population size history using an evolutionary rate of 2.0 × 10⁻⁸ substitutions/site/year.

Fig 6. STRUCTURE bar plots for seven N. douglasiae collection sites in the middle and lower reaches of Yangtze River.

STRUCTURE runs were completed without a priori populations assigned, admixture and correlated alleles were assumed, The most probable number of populations was K = 2 using the Evanno et al.^[33] method, but K = 3 had slightly higher ln likelihood scores. Collection location codes are as in Fig 1.

Fig 7. Principal Coordinates Analysis (PCoA) based on multilocus genotypes of individuals of N. douglasiae from seven collections sites in the middle and lower reaches of Yangtze River.

Collection location codes and colours are as in Fig 1.