High levels of genetic variability and differentiation in hilsa shad, Tenualosa ilisha (Clupeidae, Clupeiformes) populations revealed by PCR-RFLP analysis of the mitochondrial DNA D-loop region

Abstract

The hilsa shad, Tenualosa ilisha (Clupeidae, Clupeiformes) is an important anadromous clupeid species from the Western division of the Indo-Pacific region. It constitutes the largest single fishable species in Bangladesh. Information on genetic variability and population structure is very important for both management and conservation purposes. Past reports on the population structure of T. ilisha involving morphometric, allozyme and RAPD analyses are contradictory. We examined genetic variability and divergence in two riverine (the Jamuna and the Meghna), two estuarine (Kuakata and Sundarbans) and one marine (Cox's Bazar) populations of T. ilisha by applying PCR-RFLP analysis of the mtDNA D-loop region. The amplified PCR products were restricted with four restriction enzymes namely, XbaI, EcoRI, EcoRV, and HaeIII. High levels of haplotype and gene diversity within and significant differentiations among, populations of T. ilisha were observed in this study. Significant FST values indicated differentiation among the river, estuary and marine populations. The UPGMA dendrogram based on genetic distance resulted in two major clusters, although, these were subsequently divided into three, corresponding to the riverine, estuarine and marine populations. The study underlines the usefulness of RFLP of mtDNA D-loop region as molecular markers, and detected at least two differentiated populations of T. ilisha in Bangladesh waters.

Genetic Diversity in the mtDNA control region and population structure of Chrysichthys nigrodigitatus from selected Nigerian rivers: Implications for conservation and aquaculture

“…nigrodigitatus excluding any Nigerian population revealed high levels of genetic variability comparable to marine species (Kotoulas et al 1991). In this study, the pattern of genetic polymorphism in the C. nigrodigitatus mtDNA control region is high and similar to those described for Plecoglossus altivelis (Temminck & Schlegel) (Iguchi et al 2002), Lutjanus argentimaculatus (ForsskDl) (Ovenden and Street 2003), Brachyplatystoma rousseauxii (Castelnau) (Batista and Alves-Gomes 2006), Sicyopterus japonicus (Tanaka) (Watanabe et al 2006), Colossomma macroponum (Cuvier) (Santos et al 2007), some cichlids of Lake Tanganyika (Koblmüller et al 2007, Sefc et al 2007, and Tenualosa ilisha (Hamilton) (Mazumder and Alam 2009). The high genetic variability of the control region in C. nigrodigitatus could derive in part from a combination of the high mutation rate of the region, active dispersal of juveniles and adults, and the existence of many rare or private haplotypes (about 86%), that is, population-specific haplotypes.…”

Population Genomics of an Anadromous Hilsa Shad Tenualosa ilisha Species across Its Diverse Migratory Habitats: Discrimination by Fine-Scale Local Adaptation

“…The lack of genetic structure in the neutral loci indicates that all Hilsa shad individuals from different collection sites are connected via high levels of gene flow between the marine water and freshwater environments, which is consistent with previous studies using allozyme [14,15], restriction fragment length polymorphism (RFLP) [16,17], random amplification of polymorphic DNA (RAPD) markers [54][55][56][57], and mitochondrial DNA cytochrome b gene nucleotide sequencing [18,19]. The genetic divergence depicted by the outlier loci dataset suggests that dispersion may likely happen in the foraging ground in marine and brackish water habitats, allowing for a substantial gene flow among distant locations.…”

“…However, only neutral genetic markers have been extensively used in the Hilsa shad in recent decades. The limited number of neutral markers used, and their insufficient power to discriminate fine-scale genetic structures due to the recent divergence in their large population size, has caused the results concerning the structuring pattern of Hilsa shad populations to be inconclusive [14][15][16][17][18][19]. Moreover, assessing the fish population structure by the simultaneous use of both neutral and adaptive markers is yet to be common along the Bay of Bengal regions [20,21].…”

Unraveling the Limits of Mitochondrial Control Region to Estimate the Fine Scale Population Genetic Differentiation in Anadromous FishTenualosa ilisha

“…F statistics ( F ST ) and AMOVA could not clearly demarcate the population structure among populations from Bay of Bengal. Mazumder and Alam [ 10 ] used RFLP of mitochondrial D-loop region to differentiate riverine, estuarine, and marine stocks and observed significant differentiation between the riverine and marine (Cox's Bazar) populations, but not between the marine and one of the estuarine populations as electrophoretic analysis of PCR-RFLP has lower resolving power than sequencing of the same PCR product. They suggested sequencing of D-loop region and faster evolving molecular markers for population structure studies, such as microsatellite loci.…”

“…So, the baseline information on genetic stocks needs to be authenticated. However several morphometric and molecular studies (RAPD, RFLP) were conducted in Bangladesh and India but no study was done using mitochondrial D-loop to understand population genetic structure and patterns of gene flow of T. ilisha [ 10 ].…”