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

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.

Comparative Phylogeography and Phylogeny of Pennah Croakers (Teleostei: Sciaenidae) in Southeast Asian Waters

“…Our phylogeographic and population genetic surveys at cytb gene revealed a genetic homogeneity in P. macrocephalus and most P. anea L2 South China Sea populations ( Table 3 and Table 4 ). The same finding was also reported in the other marine fishes Thamnaconus hypargyreus [ 80 ]; Thunnus tonggol [ 81 ]; Pampus chinensis [ 82 ]; Decapterus maruadsi [ 83 ]. Population expansion that may facilitate wide distribution and present genetic exchange among the populations may explain this.…”

Genetic Structure and Diversity of the Yellowbelly Threadfin Bream Nemipterus bathybius in the Northern South China Sea

“…Previous studies have suggested that there were unlimited migrations between the South China Sea and the adjacent seas [7,16,55]. Within the South China Sea, previous studies also displayed unlimited migrations among populations [4,14,15,34,56].…”

Implication of single year seasonal sampling to genetic diversity fluctuation that coordinates with oceanographic dynamics in torpedo scads near Taiwan

“…We used the species from genus Trachurus ( T. declivis , T. japonicus , T. mediterraneus , T. novaezelandiae , T. picturatus , and T. trachurus ) as the distal outgroup. We set up three competing scenarios for time-calibration in the BEAST analyses, which are (1) the time-calibration based on the evolutionary rate, 3% to 10% per million years (My), of control region 33 , 34 ; (2) the divergence of M. cordyla populations occurred in the last glacial maximum (LGM) in ~ 250,000 years ago 35 ; (3) the divergence of M. cordyla populations occurred in the Pleistocene (~ 2.0 My ago, Mya). In the time-calibrated BEAST analyses, we applied an uncorrelated relaxed clock for independent branch rates, Yule model for speciation, and GTR + I + G model for nucleotide substation for all three BEAST analyses.…”

“…4). A molecular clock configured to a rate of 3-10% genetic divergence in the control region per million years (My) 33,34 revealed a split between the Singapore and Indonesia genotypes roughly 0.44 ± 0.287 My ago (Mya). The divergence date of M. cordyla populations calibrated using the time of the last glacial maximum (LGM) 35 was 0.012 ± 0.055 Mya.…”