Mitogenomic variation of Bangladesh Penaeus monodon (Decapoda, Panaeidae) and reassessment of its phylogeography in the Indo-West Pacific region

Abstract

Large variation in the mtDNA control region (CR) in Penaeus monodon has been reported from the Indo-West Pacific region, characterizing three distinct lineages, A, B and C. This diversification has been explained by geographic barriers but may also be due to paralogous duplication events. Here we evaluate the diversity, origin and population patterns of this species in Bangladesh based on mtDNA, and reconsider the evidence for paralogous duplication. MtDNA variation revealed high diversity with almost all individuals carrying a unique haplotype, indicating a large effective population size and a single reproductive pool. The Bangladesh haplotypes cluster within lineage C, found mainly west of the Sunda Shelf. This lineage, which diverged from lineages A and B around 6.6 Mya, has diverged further into several lineages in the western Indian Ocean. Sequences of mitochondrial CR, 16S rRNA gene and a combined fragment of the 16S rRNA and tRNA Val genes from Bangladesh did not reveal any duplication or heteroplasmy. Further, phylogenies based on the three markers, including samples from different areas in the Indo-West Pacific region, support the occurrence of three distinct lineages. Thus, the variation in CR appears to result from segregation of orthologous variants rather than diversification following a paralogous duplication.

Mitochondrial DNA variation reveals distinct lineages in Penaeus semisulcatus (Decapoda, Penaeidae) from the Indo‐West Pacific Ocean

“…Variation among the three mtDNA markers varied from the least in the 16S rRNA to the highest in the noncoding region (as expected) of CR , where almost all individuals carried a unique haplotype. Such a high degree of genetic variation in CR has also been reported for Penaeus monodon from Bangladesh (Alam et al., ). A single population based on mtDNA variation was also observed in Fenneropenaeus indicus and P. monodon from Bangladesh (Alam et al., , ), which may reflect a random mixing of pelagic larval stages and/or migration of adults as there are no obvious oceanographic or geographic barriers along the coast.…”

“…Such a high degree of genetic variation in CR has also been reported for Penaeus monodon from Bangladesh (Alam et al., ). A single population based on mtDNA variation was also observed in Fenneropenaeus indicus and P. monodon from Bangladesh (Alam et al., , ), which may reflect a random mixing of pelagic larval stages and/or migration of adults as there are no obvious oceanographic or geographic barriers along the coast. In Sri Lanka, the western population differed from the northwestern and southern populations and low genetic diversity was observed in the southern sample.…”

“…These phylogeographic patterns may have resulted from restricted genetic connectivity of populations across the Sunda Shelf during periods of low sea level in the glacial periods of the Pleistocene Ice Age (Voris, ). A further split has been observed in the Western Indian Ocean, between the coast of Africa and the Bay of Bengal (Alam et al., , ). Information about genetic variation of P. semisulcatus is scarce, and no molecular studies have been conducted on this species in Bangladesh and Sri Lanka.…”

“…Such diversification has also been observed within species including Penaeus monodon (Fabricius 1798) and Fenneropenaeus indicus (H. Milne‐Edwards 1837), whereby populations living east and the west of the Sunda Shelf are characterized by distinct mitochondrial DNA (mtDNA) lineages, which may even constitute cryptic species ( e.g . Alam, Westfall, & Pálsson, , ; Benzie et al., ). Similar patterns within the Indo‐West Pacific region have also been observed within various marine species (Gaither et al., ; Keyse et al., ).…”

Historical demography and genetic differentiation of the giant freshwater prawn Macrobrachium rosenbergii in Bangladesh based on mitochondrial and ddRAD sequence variation

“…Genetic diversity facilitates further evolution given environmental change and may in addition play a key ecosystem function (Reusch & Hughes, ). Information of genetic variation in M. rosenbergii in Bangladesh has until recently been mostly unexplored, but recent studies on Penaid shrimps in Bangladesh have uncovered high levels of genetic diversity (Alam, de Croos, & Pálsson, ; Alam & Pálsson, ; Alam, Westfall, & Pálsson, , ; Hurwood et al., ). Several genetic studies have been applied to M. rosenbergii including allozymes (reviewed in Agarwal et al., ), mtDNA (De Bruyn et al, ; Hurwood et al., ), microsatellites (Hurwood et al., ; Khan et al., ), and more recently identification of single nucleotide polymorphisms (SNPs) (Agarwal et al., ; Jung et al., ).…”