Use of RAPD Fingerprinting for Discriminating Two Populations of Hilsa shad (Tenualosa ilisha Ham.) from Inland Rivers of Bangladesh

Shifat, Rehnuma; Begum, Anwara; Khan, Haseena

doi:10.5483/bmbrep.2003.36.5.462

Cited by 14 publications

(11 citation statements)

References 6 publications

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“…However, this conclusion may be contradicted through the presence of some private haplotypes in the Balashi and Chandpur populations. These results also run counter to those of Shifat et al (2003), who reported that the two river populations of T. ilisha , the Meghna and the Padma were different stocks, though they observed certain alleles shared by some individuals of these two river samples. The presence of private haplotypes indicates the extent of mixing between populations.…”

Section: Discussioncontrasting

confidence: 99%

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

Mazumder

Alam

2009

Genet. Mol. Biol.

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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.

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Section: Discussioncontrasting

confidence: 99%

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

Mazumder

Alam

2009

Genet. Mol. Biol.

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“…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.…”

Section: Discussionsupporting

confidence: 90%

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

Asaduzzaman

Igarashi

Wahab³

et al. 2019

Genes

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The migration of anadromous fish in heterogenic environments unceasingly imposes a selective pressure that results in genetic variation for local adaptation. However, discrimination of anadromous fish populations by fine-scale local adaptation is challenging because of their high rate of gene flow, highly connected divergent population, and large population size. Recent advances in next-generation sequencing (NGS) have expanded the prospects of defining the weakly structured population of anadromous fish. Therefore, we used NGS-based restriction site-associated DNA (NextRAD) techniques on 300 individuals of an anadromous Hilsa shad (Tenualosa ilisha) species, collected from nine strategic habitats, across their diverse migratory habitats, which include sea, estuary, and different freshwater rivers. The NextRAD technique successfully identified 15,453 single nucleotide polymorphism (SNP) loci. Outlier tests using the FST OutFLANK and pcadapt approaches identified 74 and 449 SNPs (49 SNPs being common), respectively, as putative adaptive loci under a divergent selection process. Our results, based on the different cluster analyses of these putatively adaptive loci, suggested that local adaptation has divided the Hilsa shad population into two genetically structured clusters, in which marine and estuarine collection sites were dominated by individuals of one genetic cluster and different riverine collection sites were dominated by individuals of another genetic cluster. The phylogenetic analysis revealed that all the riverine populations of Hilsa shad were further subdivided into the north-western riverine (turbid freshwater) and the north-eastern riverine (clear freshwater) ecotypes. Among all of the putatively adaptive loci, only 36 loci were observed to be in the coding region, and the encoded genes might be associated with important biological functions related to the local adaptation of Hilsa shad. In summary, our study provides both neutral and adaptive contexts for the observed genetic divergence of Hilsa shad and, consequently, resolves the previous inconclusive findings on their population genetic structure across their diverse migratory habitats. Moreover, the study has clearly demonstrated that NextRAD sequencing is an innovative approach to explore how dispersal and local adaptation can shape genetic divergence of non-model anadromous fish that intersect diverse migratory habitats during their life-history stages.

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“…12), OPH-13 gave 9 fragments from150 to 680 bp (Table 14 & Fig. 13), (same primer OPH-13 gave 48 bands, 9 of them polymorphic in Tenualosa ilisha Ham of the Clupeidae family (Shifat et al, 2003), OPM-11 gave 13 fragments in the four species of Cephalopholis ranged in size between 120 and 580 bp (Table 15 & Fig. 14) and primer OPM-12 generated 10 fragments from150 to 600 bp (Table 16 & Fig.…”

Section: Resultsmentioning

confidence: 95%

RAPD –PCR analysis of four coral reef fish species, genus cephalopholis (Family: serranidae) in the Red sea.

A.M.

2014

Egypt. J. of Aquatic Biolo. and Fish.

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The genetic relationships between four species of groupers: Cephalopholis oligosticta, C. sexmaculata, C. hemistiktos and C. argus, common coral reef fish in the Red Sea of family Serranidae were studied by using Random Amplified Polymorphic DNA (RAPD) technique. Twenty random primers were used. Each primer was individually tested with the four fish species. Amplification products were resolved on agarose gel electrophoresis and visualized under UV light, then photographed. The number and size of amplified DNA fragments showed a wide range of variation. Tabulation and analysis of the data using the genetic similarity coefficient were carried out. The highest genetic similarity observed was between C. hemistiktos and C argus and the lowest was between C. oligosticta and C. sexmaculata. Dendrogram analysis revealed three clusters: first, comprises C. hemistiktos and C. argus; second, contains C. oligosticta and (C. hemistiktos and C. argus); the third incompasses C. sexmaculata and (C. oligosticta, C. hemistiktos and C. argus).

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Use of RAPD Fingerprinting for Discriminating Two Populations of Hilsa shad (Tenualosa ilisha Ham.) from Inland Rivers of Bangladesh

Cited by 14 publications

References 6 publications

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

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

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

RAPD –PCR analysis of four coral reef fish species, genus cephalopholis (Family: serranidae) in the Red sea.

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