POPULATION GENETIC STRUCTURE OF SCALLOPED SPINY LOBSTER (PANULIRUS HOMARUS LINNAEUS, 1758) IN INDONESIAN WATERS BASED ON SNP-DARTSEQ MARKERS

• Main Author: Indriatmoko
• Format: Theses
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/67369
• Institution: Institut Teknologi Bandung

Several studies to assess the population structure of scalloped spiny lobster (Panulirus homarus Linnaeus, 1758) in Indonesia using mithocondrial DNA and microsattelite markers had been conducted but could not provide an accurate description of the lobster population structure. The study that utilizes SNP markers with whole-genome coverage is expected to provide a better description of the population structure of scalloped spiny lobster in Indonesia. This research was aimed at providing essential information regarding genetic population structure in Indonesia, such as genetic diversity, the evidence of population structure, and to identify environments factor contributed to the shape of scalloped spiny lobster population structure. This study involved 40 individuals of scalloped spiny lobster sample collected from five locations, i.e., Simeleu, Mandeh, Pangandaran, Trenggalek, and Makasar. Genotyping was conducted using DArTseq to gather Single Nucleotides Polymorphisms (SNP) information. Genetic diversity indices were analysed using Adegenet, hierfstat, pegas, and inbreedR. Phylogenetic tree constructed using RAxML (1000 bootstrap) while genetic distance was calculated according to Nei’s. Detection of population differentiation were conducted using pairwise-Fst followed by Analysis of Molecular Variance (AMOVA). Discriminant Analysis of Principal Components (DAPC) and STRUCTURE v2.3.4 were implemented to identify number of population cluster. Genotype-Environment Association (GEA) analysis was conducted by using outlier locus detected by Fst-outlier (Arlequin and BayeScan) and Environment-Association (LFMM and RDA) approach, and environment parameter extracted from raster layer data (Bio-Oracle.org). Initial DArTseq sequencing by using 2.5 million reads had successfully produced 143.638 SNP locus. Post-to SNP filtering processes to eliminate low quality data successfully to retained 31.798 SNP locus from 39 individuals. Genetic diversity indices analysis resulted in lower observed heterozygosity (Ho) value than expected heterozygosity (He) in all populations investigated. Genetic variation of scalloped spiny lobsters were ranged from 0.140-0.149. The relatively high Fis value showed indication of the structured scalloped spiny lobster population from Makasar population. The value resulted in g2 (0.002-0.014) and MLH (0.182-0.197) showed low inbreeding depression. Clearer evidence of structured population was shown by pairwise-Fst value (P < 0.001) in most of the population except from Mandeh-Pangandaran-Trenggalek and formation of monophyletic clade on constructed phylogenetic tree which were dominated by individuals from single population. Identification of optimum number of population cluster by DAPC and STRUCTURE resulted in 3 population cluster identified, i.e., Simeleu, Mandeh-Pangandaran-Trenggalek, and Makasar. AMOVA resulted significancy (P < 0.01) to all differentiated population except for Mandeh, Pangandaran, and Trenggalek, which was single population cluster. GEA analysis successfully identified 21 outlier locus and 31.777 neutral locus associated with 6 environment parameters. Sea surface temperature were showed the most significance (P < 0.01) as the main environment parameters affected by the scalloped spiny lobster population structure. Besides that, there was sea current-related parameter (velocity and primary productivity) which was also potentially affected the population structure formation. This research concludes the evidence of scalloped spiny lobster structured population in Indonesia and consisted by three population clusters affected by sea surface temperature and sea current-related parameters. This research provided information as the basis knowledge in developing better lobster fisheries enhancement and aquaculture.