Demographic history and population genetic analysis of Decapterus maruadsi from the northern South China Sea based on mitochondrial control region sequence.

Su-Fang Niu,Ren-Xie Wu,Zhong-Lu Li,Zhen-Bang Liang,Yu-Hang Chen,Hao-Ran Zhang,Yun Zhai

doi:10.7717/peerj.7953

Abstract

Late Pleistocene climate oscillations are believed to have greatly influenced the distribution, population dynamics, and genetic variation of many marine organisms in the western Pacific. However, the impact of the late Pleistocene climate cycles on the demographic history and population genetics of pelagic fish in the northern South China Sea (SCS) remains largely unexplored. In this study, we explored the demographic history, genetic structure, and genetic diversity of Decapterus maruadsi, a typical pelagic fish, over most of its range in the northern SCS. A 828–832 bp fragment of mitochondrial control region were sequenced in 241 individuals from 11 locations. High haplotype diversity (0.905–0.980) and low nucleotide diversity (0.00269–0.00849) was detected, revealing low levels of genetic diversity. Demographic history analysis revealed a pattern of decline and subsequent rapid growth in the effective population size during deglaciation, which showed that D. maruadsi experienced recent demographic expansion after a period of low effective population size. Genetic diversity, genetic structure, and phylogenetic relationship analysis all demonstrated that no significant genetic differentiation existed among the populations, indicating that D. maruadsi was panmictic throughout the northern SCS. Periodic sea-level changes, fluctuation of the East Asian Monsoon, and Kuroshio variability were responsible for the population decline and expansion of D. maruadsi. The demographic history was the primary reason for the low levels of genetic diversity and the lack of significant genetic structure. The life history characteristics and ocean currents also had a strong correlation with the genetic homogeneity of D. maruadsi. However, the genetic structure of the population (genetic homogeneity) is inconsistent with biological characteristics (significant difference), which is an important reminder to identify and manage the D. maruadsi population carefully.

Highlights

Late Pleistocene climate oscillations drastically altered the sea-level and nutrient inputs into the western Pacific marginal seas
The present study reveals that LGM-Holocene climate oscillations had an important impact on the demographic history, genetic structure, and genetic diversity of D. maruadsi in the northern South China Sea (SCS)
The demographic history is considered to be responsible for the low levels of genetic diversity for D. maruadsi in the northern SCS

Summary

Introduction

Late Pleistocene climate oscillations drastically altered the sea-level and nutrient inputs into the western Pacific marginal seas This is believed to have greatly influenced the population distribution, genetic variation, and demographic history of marine organisms (Hewitt, 2000; Lambeck, Esat & Potter, 2002; Liu et al, 2007; Xue et al, 2014; He et al, 2015). The cyclic changes during the Late Pleistocene era in the sea-level and nutrient inputs likely led to expansions and contractions in the populations of marine organisms (Grant & Bowen, 1998; Liu et al, 2006; He et al, 2014) These historic processes are thought to have greatly influenced the evolutionary patterns of the populations of several coastal organisms in the northern SCS, such as genetic differentiation caused by population contraction or genetic homogeneity resulting from population expansion (Liu et al, 2007; He et al, 2010; He et al, 2015). The impact of late Pleistocene climatic cycles on the demographic history and population genetics of pelagic fish in the northern SCS remains largely unexplored

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