Molecular phylogeography reveals multiple Pleistocene divergence events in estuarine crabs from the tropical West Pacific

Multigene Phylogenies of the Estuarine Sesarmid Parasesarma bidens Species Complex (Decapoda: Brachyura: Sesarmidae), with Description of Three New Species

S Parasesarma bidens (De Haan, 1835) is a common intertidal sesarmid crab that inhabits the estuarine and mangrove regions of East Asia, as well as Vietnam and the Philippines. Previous studies have suggested that P. bidens is a species complex composed of several species. Our findings indicated that the P. bidens species complex is monophyletic with six clades, as shown by reconstructed phylogenies based on mitochondrial 16S rDNA and cytochrome c oxidase subunit I, as well as nuclear 28S rDNA. Specimens of each clade exhibited different characters, including the morphology of the cheliped, anterior carapace, male gonopod 1, and female vulvae, as well as the coloration. Three species in this complex have been previously described: P. bidens (De Haan, 1835), P. cricotum (Rahayu & Davie, 2002), and P. sanguimanus Li, Shih & Ng, 2019. Here, we describe three additional species: P. continentale n. sp., P. insulare n. sp., and P. chiahsiang n. sp. Biogeographically, the range of P. bidens includes the southern margin of Korea, the main islands of Japan, and the Ryukyus, with a comparatively northern distribution. P. continentale is widely distributed from the continental coasts of southeastern and southern China (including northern Hainan Island) to southern Vietnam and is occasionally found in Penghu, Taiwan. Parasesarma insulare is an insular species distributed from Taiwan main island, the central Philippines, to northern Borneo. Finally, P. chiahsiang is mainly limited to the Penghu Islands (Pescadores) but is also sometimes found in Taiwan main island and the offshore Gueishan Island.

Linked selection, differential introgression and recombination rate variation promote heterogeneous divergence in a pair of yellow croakers

Understanding the mechanisms underlying heterogeneous genomic divergence is of particular interest in evolutionary biology. Highly differentiated genomic regions, known as genomic islands, often evolve between diverging lineages. These genomic islands may be related to selection promoting adaptation or reproductive isolation. Based on whole genome assembly and genome-wide RAD sequencing in a pair of yellow croakers (genus: Larimichthys), we investigated the evolutionary processes shaping genomic landscapes of divergence. Demographic modelling indicated that the two species diverged following a secondary contact scenario, where differential introgression and linked selection were suggested to be involved in heterogeneous genomic divergence. We identified reduced recombination rate in genomic islands and a relatively good conservation of both genetic diversity and recombination landscapes between species, which highlight the roles of linked selection and recombination rate variation in promoting heterogeneous divergence in the common ancestral lineage of the two species. In addition, we found a positive correlation between differentiation (F_ST ) and absolute sequence divergence (D_xy ), and elevated D_xy in genomic islands, indicating that the genomic landscape of divergence was not shaped by linked selection alone. Restricted gene flow in highly differentiated regions has probably remodelled the landscape of heterogeneous genomic divergence. This study highlights that highly differentiated genomic regions can also arise from a combination of linked selection and differential gene flow in interaction with varying recombination rates.