Title: Origin and population structure of major prawn and shrimp species in Bangladesh

The Indo-Pacific region possesses the world’s largest biodiversity, with a unique ecosystem. Origins and population structures of six commercially and ecologically important prawn and shrimps in Bangladesh are the subject of this thesis. The species are five penaeid shrimps: Fenneropenaeus indicus, Penaeus monodon, Penaeus semisulcatus, Metapenaeus monoceros, Parapenaeopsis sculptilis, and the palaemonid prawn Macrobrachium rosenbergii. The species were studied at different depth, using mitochondrial DNA markers, microsatellites, single nucleotide polymorphisms (SNPs) and short DNA sequences from restriction sites sampled randomly from the genome. Analysis of the genetic variation allows in addition to an assessment of the phylogenies, the diversity and the demographic history of the species. Mitochondrial DNA based phylogeny of the genus Fenneropenaeus and Metapenaeus showed polyphyletic relationships within the genus and revealed three distinct lineages which indicate cryptic species in F. indicus, one in Bangladesh and India, the second in India, Sri Lanka and Australia, and the third in south-eastern Africa, Iran and Oman. A further support for cryptic species were obtained within P. monodon. The phylogeographic analyses revealed a match between the genetic divergence and the known biogeographic barriers in the western Indian Ocean, between the Bay of Bengal and the south-eastern Africa, and across the Sunda-Shelf and the Isthmus of Kra. Mitogenomic variation revealed population structure in P. semisulcatus from Sri Lanka and in M. rosenbergii from Bangladesh. Microsatellites and SNPs revealed clear genetic patterns in P. monodon sampled along the coast in Bangladesh from west to southeast. Similarly, at least three distinct populations were observed in M. rosenbergii, sampled from four watersheds in Bangladesh, based on SNPs and alleles obtained from double digest restriction-site associated DNA sequencing (ddRADseq). The high genetic variation of the Bangladesh prawn and shrimps, but shallow mitochondrial genealogy, were in accordance with expectation of sudden expansion model for population changes, dating back to 74 kyr ago in P. sculptilis to 466 kyr in M. monoceros. The expansion of the Bangladesh F. indicus population started more recently (~78 kyr ago) than the population in Sri Lanka (~120 kyr ago). The phylogeographic lineages identified in this study should be considered as evolutionary significant units (ESUs) or conservation units and should be considered in the management of these valuable species, both in aquaculture and fisheries in order to maintain the large diversity within the species in the Indo-Pacific region. The populations detected in Bangladesh P. monodon and M. rosenbergii should be considered as separate management units. The use of gravid and ovigerous females of wild P. monodon and M. rosenbergii in hatcheries should consider the population structures for the quality postlarva production. The sequences from this study have been deposited in GenBank and can be used to trace an unknown catch and control illegal fishing of shrimps from different lineages.