Effects of geological changes and climatic fluctuations on the demographic histories and low genetic diversity of Squaliobarbus curriculus in Yellow River

Population genetics and sympatric divergence of the freshwater gudgeon, Gobiobotia filifer, in the Yangtze River inferred from mitochondrial DNA

The ecosystem and Pleistocene glaciations play important roles in population demography. The freshwater gudgeon, Gobiobotia filifer, is an endemic benthic fish in the Yangtze River and is a good model for ecological and evolutionary studies. This study aimed to decode the population structure of G. filifer in the Yangtze River and reveal whether divergence occurred before or after population radiation. A total of 292 specimens from eight locations in the upper and middle reaches of the Yangtze River were collected from 2014 to 2016 and analyzed via mitochondrial DNA Cyt b gene sequencing. A moderately high level of genetic diversity was found without structures among the population. However, phylogenetic and network topology showed two distinct haplotype groups, and each group contained a similar proportion of individuals from all sampled sites. This suggested the existence of two genetically divergent source populations in G. filifer. We deduced that a secondary contact of distinct glacial refugia was the main factor creating sympatric populations of G. filifer, and climate improvement promoted population expansion and colonization.

Genetic structure of two sympatric gudgeon fishes (Xenophysogobio boulengeri and X. nudicorpa) in the upper reaches of Yangtze River Basin

BACKGROUND

Xenophysogobio boulengeri and X. nudicorpa are the only two species within the genus Xenophysogobio (Cyprinidae, Cypriniformes), and both are endemic to the upper reaches of the Yangtze River. In recent years, due to human activities, the natural resources available to both species have declined sharply. Sympatric species with overlapping niches inevitably compete for their habitats, and genetic structure and diversity can reflect population history and their potential for adaptation to changing environments, which is useful for management decisions.

METHODS

In the present study, microsatellite DNA and mitochondrial DNA (mtDNA) markers were used to investigate the patterns of population genetic structure for X. boulengeri and X. nudicorpa. Microsatellite DNA data, jointly with traditional summary statistics including F ST and F is, were used to assess the population genetic structure by structure analysis. The mtDNA sequences were then used to examine these patterns through time to detect demographic history.

RESULTS

Xenophysogobio boulengeri and X. nudicorpa exhibited high levels of genetic diversity in Yangtze River populations, except for two populations of X. nudicorpa in the Jinsha River, which were low in mtDNA diversity. X. boulengeri showed genetic homogeneity among populations, whereas X. nudicorpa appeared to have significant geographic genetic divergence. Both species experienced a late-Pleistocene sudden population expansion in Yangtze River populations, but not in the Jinsha River populations of X. nudicorpa.

DISCUSSION

The genetic homogeneity of X. boulengeri populations might result from similar population expansion events and environment features. The geographic genetic subdivision for X. nudicorpa between the Jinsha and Yangtze Rivers might be caused by the geographic isolation in the middle Pliocene, as well as climate and environmental heterogeneity.