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

Abstract

Macrobrachium rosenbergii, the giant freshwater prawn, is an important source of high quality protein and occurs naturally in rivers as well as commercial farms in South and South‐East Asia, including Bangladesh. This study investigated the genetic variation and population structure of M. rosenbergii sampled from four rivers in Bangladesh (sample size ranged from 19 to 20), assessing sequence variation, both in the mitochondrial cytochrome oxidase subunit 1 (CO1) gene and in 106 single nucleotide polymorphisms (SNPs) sampled randomly from the genome with double digest RAD sequencing (ddRADseq). The mitochondrial variation presented a shallow genealogy with high haplotype diversity (h = 0.95), reflecting an expansion in population size for the last ~82 kyr. Based on the CO1 variation the current effective population size (N e) was 9.7 × 106 (CI: 1.33 × 106 – 35.84 × 106) individuals. A significant population differentiation was observed with the mitochondrial CO1 sequence variation and based on the ddRADseq variation, which could be traced to the divergence of the population in the Naf River in the South‐East border with Myanmar from the other populations. A differentiation in mtDNA haplotype frequencies was also observed between the Biskhali River and the Karnaphuli Rivers in eastern Bangladesh. This study demonstrated the use of high‐throughput genotyping based on the ddRADseq method to reveal population structure at a small geographical scale for an important freshwater prawn. The information from this study can be utilized for management and conservation of this species in Bangladesh.

A new approach to molecular biosurveillance of invasive species using DNA metabarcoding

“…Each PCR pool was purified prior to library preparation using Ampure XP PCR purification magnetic beads at a 3:1 bead to sample ratio. Subsamples from each purified pool were stained with SYBR Green and quantified with a Tecan Infinite M200Pro fluorescence reader using a standard concentration curve generated from serial dilutions of lambda DNA (for protocol see Alam, Westfall, & Pálsson, ). Average concentrations were calculated from duplicate sample dilutions of 1:200 and 1:400.…”

Targeted Next Generation Sequencing of environmental DNA improves detection and quantification of invasive European green crab (Carcinus maenas)

“…PCR replicates of all water and zooplankton samples, blanks, and standard curve concentrations (see next paragraph) were pooled at equal volumes into two sequencing pools and cleaned twice with SPRI beads at 0.9x ratio. Libraries were quantified using a SYBR-Green fluorometric assay read on the Tecan Infinite Pro (Alam et al, 2017) and 15 pmoles of each library were loaded on two runs of MiSeq v2 300 cycles (150bp paired end).…”

Mitochondrial DNA variation of Metapenaeus monoceros (Decapoda, Penaeidae) reveals high genetic variation within Bangladesh with distinct lineages in the Indian Ocean

“…For proper management and conservation of these species greater understanding of penaeid, it is important to study its diversity, that is taxonomy, phylogeography, population differentiation and demographic history is needed.. Several studies (cf. Alam & Pálsson, 2018) have assessed genetic variation and population structure of some of the major prawn and shrimp species along the Bangladesh coastline and analysed their phylogeographic patterns in the Indo‐West Pacific region (IWP), that is Macrobrachium rosenbergii (De Man 1879) (Alam et al., 2017), Penaeus indicus (H. Milne‐Edwards 1837) (Alam et al., 2015), Penaeus monodon (Fabricius 1798) (Alam & Pálsson, 2016; Alam et al., 2016b) and Penaeus semisulcatus (De Haan, 1844) (Alam et al., 2016a). These studies revealed high genetic variation in all studied species, population structures in M. rosenbergii and P. monodon along the coast of Bangladesh and distinct phylogeographic lineages or even cryptic species in P. indicus , P. monodon and P. semisulcatus in the IWP region.…”