Efficiency assessment of regionally derived 16S rDNA and COI sequences for widescale detection of mangrove crab (Scylla serrata) (Forskål) population structure

• Main Author: Desuasido, Alexis Gwyneth P.
• Format: text
• Language: English
• Published: Animo Repository 2022
• Subjects: Scylla serrata; Scylla (Crustacea); Biotechnology; Molecular Biology
• Online Access: https://animorepository.dlsu.edu.ph/etdb_bio/17; https://animorepository.dlsu.edu.ph/cgi/viewcontent.cgi?article=1018&context=etdb_bio
• Institution: De La Salle University

Mangrove crabs or Scylla serrata is a commodity with increasing global market demand. Due to commercial importance, investigating the population genetic structure is necessary to determine population bottleneck used for planning on future management and conservation regulations in which previous studies have used different molecular markers. Among the markers, 16S ribosomal ribonucleic acid (rRNA) and cytochrome oxidase subunit I (COI) sequences are accessible through the public database. While this genetic study could also advance the understanding of the connectivity of mangrove crab populations across the Indo-West Pacific (IWP) in addition to known widespread clade, the efficiency assessment of the mitochondrial markers based on its consistency in detecting genetic diversity and structure remains necessary to establish the most appropriate marker for the species. In this study, a widescale detection of population structure was investigated using mitochondrial sequences 16S rRNA and COI with efficiency assessment based on consistency. A total of 21 16S rRNA sequences (436 bp) and 35 COI sequences (494 bp) had nine (9) and 33 unique haplotypes respectively. Phylogenetic analysis of 16S rRNA conforms with the analysis of molecular variance (AMOVA) of an overall genetic variation within populations of 88.32% with no discernable population structure due to significantly moderate value of ΦSC (0.32108) and significantly low pairwise value in Pakistan-India (0.08447) observing panmixia. Given the number of unique haplotypes from different locations, it was inconsistent with the pairwise difference values. In COI, high variance of 83.64% between populations agrees with the phylogenetic analysis while discernable population structures from significant high values of ΦSC (0.84430) and ΦST (0.83074) were found. Pairwise values were significant across all locations, aside from Kenya-Indian Ocean (-0.03478), ranging from 0.51890 to 0.95475 with Kenya and Pakistan of highest estimate and lowest in Indian Ocean and Australia. Investigating the efficiency of marker, COI marker detected population structure better with more consistent findings in which the number of v unique haplotypes were also reflected from significantly moderate to high pairwise difference values. Further assessment using Mayr’s central-peripheral population model (CCPM) is recommended using COI sequences as mitochondrial marker to establish sustainable market practices.