The South China Sea and beyond: A genome-wide phylogeographical study of macrobenthos in the chemosynthesis-based ecosystems of the subtropical to temperate Northwestern Pacific Ocean

Research on deep-sea chemosynthetic ecosystems including hydrothermal vents and cold seeps has advanced our understanding of the formation of mineral resources, origin of life, and biological adaptations in extreme environments. Nevertheless, for many macrobenthic organisms in chemosynthetic ecosystems, their phylogeography – the processes responsible for the contemporary geographic distributions – has not been studied. Given the intensified threats of human activities such as trawling and mining, it is imperative to study their phylogeography to enable scientific basis of management of these deep-sea resources. The discovery of two cold seeps in the South China Sea has provided us a unique opportunity to study their phylogeographic position, specifically the connectivity of their macrobenthos with other known populations in the subtropical to temperate Northwestern Pacific. As a large marginal sea, the South China Sea can potentially act as a source and/or sink of larvae for other regions. Previous phylogeographic studies of deep-sea animals have mainly relied on DNA sequences from one to several genes, which suffer from the lack of sensitivity required to resolve their fine genetic structure, especially for animals with a long pelagic larval period. We propose a highly sensitive approach to study the genetic connectivity between chemosynthetic ecosystems in the South China Sea and other regions of the subtropical to temperate Northwestern Pacific. Specifically, we will use a genome-wide restriction site–associated DNA genotyping method to analyze the genetic make-up of four species of representative macrobenthos (1 species of mussel, 1 species of limpet, and 2 species of squat lobsters). These animals have contrasting life-history strategies that are known to influence genetic structure. Using these data, we will calculate the amount of genetic exchange between populations, determine the source/sink of these populations, trace the history of their population expansion, and determine the genes and genomic regions that may have undergone positive selection. Our study will unveil the position of the South China Sea in the subtropical to temperate Northwestern Pacific chemosynthesis-based ecosystems, and contribute to the designation of a global network of chemosynthetic ecosystem reserves in the deep-sea.