Computational protocol: High levels of genetic diversity in Penaeus monodon populations from the east coast of India

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Protocol publication

[…] A total of 81 sequences, each 562 bp in length (on average) from the mtDNA control region, were obtained for analysis. Nine of the original samples with incomplete sequence reads were not included in analysis. The usable sequences were aligned using Bio-edit sequence editor package (Hall ), and data analysis was performed using ARLEQUIN version 3.0 (Excoffier et al. ) and MEGA 4. The mean nucleotide composition, number of transitions, transversions, indels, number of haplotypes, haplotype diversity (h) and nucleotide diversity (pi) values (Nei ) were calculated for all the populations. The haplotype data were analysed phylogenetically by the neighbour-joining (NJ) method using MEGA 5.0 and the genetic distance by the Jukes and Cantor (). Support for the tree nodes was assessed by the bootstrap method (1000 replicates). The geographical structuring of population was examined by performing analysis of molecular variance (AMOVA) to partition the total genetic variation into its variance component and to produce FST statistics (Weir and Cockerham ). […]

Pipeline specifications

Software tools Arlequin, MEGA
Application Population genetic analysis
Organisms Penaeus monodon
Diseases Substance-Related Disorders