Abstract
The kuruma shrimp (Marsupenaeus japonicus) includes two cryptic species, which are distributed mostly allopatrically but co-occur in the northern South China Sea (from Huilai to Beihai). To obtain a better understanding of the fine-scale genetic structure and parapatric diversification of these two varieties in the northwestern Pacific region, we used a genotyping-by-sequencing (GBS) and comparative transcriptomics approach to establish their phylogenetic relationships. Using the GBS technique, we genotyped 28891 SNPs in 160 individuals in the Northwest Pacific. The results supported two highly diverged evolutionary lineages of kuruma shrimp (var. I and II). The ND and XM populations showed complex genetic patterns, which might be affected by the complex environment of the Taiwan Strait. In addition, the migration rates and inbreeding coefficients of XM and BH were much lower than those of the other populations, which might be related to the land-sea changes and complex ocean currents in the Taiwan Strait and Qiongzhou Strait. Based on the synonymous substitution rates (ds) of 2,491 candidate orthologs, we estimated that the divergence time between the two varieties was 0.26~0.69 Mya. Choice and no-choice interbreeding experiments provided support for the biological species concept, by showing the existence of reproductive isolation or incompatibility. In view of these differences between the two Marsupenaeus species, we believe that it is essential and urgent to establish a genetic database for each and reevaluate their ecological suitable conditions in order to improve species-specific culturing techniques. Moreover, this research can serve as a case study for future research on speciation and hybridization.
Highlights
The northwestern (NW) Pacific marginal seas comprise approximately 75% of the world’s marginal seas (Tamaki, 1991)
We investigated the areas of sympatry and whether there is hybridization among the wild populations by sampling from a narrow sympatric zone
We conclude the occurrence of prezygotic reproductive isolation between the two varieties, which prevents natural hybridization
Summary
The northwestern (NW) Pacific marginal seas comprise approximately 75% of the world’s marginal seas (Tamaki, 1991). Due to climatic fluctuations associated with Pleistocene glaciation-interglaciation, the shoreline and configuration of these marginal seas changed dramatically (Wang, 1999; Ni et al, 2014). Repeating drastic changes and complex ocean currents together shape the abundant geographic variation and ecological adaptation of marine animals. Due to ubiquitous cryptic and sibling species, the geographical distribution of marine biodiversity is often underestimated (Bickford et al, 2007; Taylor et al, 2017; Jorde et al, 2018). Cheng et al revealed the allopatric speciation and recent hybridization of two Oratosquilla oratoria cryptic species using the mtDNA COI and nrDNA ITS genes (Cheng and Sha, 2017). Shen et al documented no gene flow among three cryptic species of Mugil cephalus in the NW Pacific, indicating complete speciation (Shen et al, 2011)
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