The Mitochondrial Markers Provide New Insights Into the Population Demographic History of Coilia nasus With Two Ecotypes (Anadromous and Freshwater)

Abstract

The Pleistocene climate oscillations have been proven to have profound influences in the evolutionary processes of marine species and left significantly tractable footprints in genomes of marine fauna. However, such history remains unknown for the Japanese grenadier anchovy Coilia nasus, a relatively large fish found in marine, freshwater and brackish water. In order to provide insight into the phylogeographic pattern and historical demography of C. nasus, we employed the mtDNA D-loop and Cyt b as molecular markers to estimate the genetic variation among populations of C. nasus. We took samples from 18 populations throughout the distribution of C. nasus. Partial sequences of mtDNA D-loop (n = 424) and Cyt b (n = 129) were obtained. Four phylogeographic lineages were revealed by the mtDNA D-loop analysis. Frequency changes of the four lineages throughout the species' distribution indicated limited genetic exchange among three major geographic regions. Patterns of isolation-by-distance were detected among the populations. Neutrality test, mismatch distribution, and network analyses consistently showed that all the four lineages had populations with relatively stable over time and then subjected to sudden expansion during the late-Pleistocene era (c. 20,000-75,000 years ago). The phylogeographic and demographic history of C. nasus was highly influenced by climatic fluctuations in the Pleistocene. Geographic isolation resulted from Pleistocene climatic fluctuations might have profound impacts on the distribution pattern of genetic variation of C. nasus. Our result also indicated that the population expansion event for C. nasus occured along with habitat continuous expansion during the inter-glacial period.

Genetic structure of the small yellow croaker (Larimichthys polyactis) across the Yellow Sea and the East China Sea by microsatellite DNA variation: implications for the division of management units

“…Low or not significant F ST was detected in most localities, revealing high flow among L. polyactis . This pattern was common for other marine organisms across this area ( Zhang et al, 2020a ; Gao et al, 2020 ). Zhang et al (2020a) ; Zhang et al (2020b) detected genetic variation in Engraulis japonicus in the northwestern Pacific based on restriction-site associated DNA (RAD) sequencing, suggesting high gene flow between the Bohai sea and the Yellow sea E. japonicus populations and no sign of local adaptation was found.…”

Genetic characterization of minor carp (Labeo gonius) from Indian rivers revealed through mitochondrial ATPase 6/8 and D-loop region analysis: implications for conservation and management

“…Among these markers, the D-loop is a non-coding region and exhibits generally higher genetic variations relative to coding regions. The D-loop control region is the marker of choice and has important value for investigating intraspecific genetic differentiation (Mandal et al, 2012;Sahoo et al, 2020;Zhang et al, 2020), and it has been the most widely used mtDNA marker in many phylogenetic genetic studies in fish (Xie et al, 2006;Paixão et al, 2018;Jiang et al, 2019;Gao et al, 2020;Sahoo et al, 2020). In addition, another important mitochondrial region ATPase 6/8 also mutates at a faster rate compared with the nuclear genes and is a potential marker analyzed for both phylogeny and phylogeography; hence, it is very useful in genetic diversity, population genetics, and evolution studies (Divya et al, 2015;Singh et al, 2016;Balasubramaniam et al, 2022).…”

A genetic assessment of the population structure and demographic history of Odontamblyopus lacepedii (Perciformes, Amblyopinae) from the northwestern Pacific

“…The complex interactions of post geological-history events, life history, and oceanographic condition as evolutionary processes played an important role in shaping population genetic structure and biodiversity of marine fishes ( Santos et al 2006 ; Hu et al 2011 ; Gao et al 2020 ). The East China Sea, including Yellow and Bohai seas, and South China Sea constitute the marginal oceanic regions of China.…”