Fisheries and Aquatic Sciences

Biomonitoring and environmental impact assessment of marine ecosystems are important for the effective management of petroleum platform activity. Eukaryote biodiversity in water and sediment near petroleum platforms in the Gulf of Thailand was surveyed using environmental DNA (eDNA) based on 18S ribosomal DNA variable region 4 (18S rDNA-V4), the full-length 18S rDNA gene (18S rDNA-FL), and cytochrome c oxidase subunit 1 (COI). Water and sediment samples were collected from three platforms. The water sample was also collected from a reference site located farther south, away from the platforms. Both 18S rDNA markers outperformed COI. A total of 1144 and 889 species were found in water and sediment when analyzed by 18S rDNA-V4, and 519 species were found in sediment when analyzed by 18S rDNA-FL. Only 99 species were found in water samples when analyzed by COI. Alpha-diversity (Shannon and Simpson Evenness) indices were significantly different in water (p < 0.05), but not in sediment (p > 0.05). Beta-diversity (PCoA and NDMS) revealed significant species components between different petroleum platforms (p < 0.01). Species distribution revealed biological connectivity between eukaryotes from different platforms suggesting the importance of platforms on ecological impacts. This study also illustrates the possible application of eDNA for monitoring ecological toxicity around petroleum platforms.

A breeding program of Asian seabass (Lates calcarifer, also called barramundi) was established for sustainable aquaculture in Thailand. Estimated breeding values (EBVs) for growth of the base population (G0, 51 families, N = 1655) were evaluated. Fish exhibited either high (HEBV, averaged body weight = 1036.80 ± 250.80 g, N = 133) or low (LEBV, averaged body weight = 294.50 ± 167.20 g, N = 147) growth EBVs, and their parental fish (N = 26) were analyzed by Specific Locus Amplified Fragment Sequencing (SLAF-Seq). An average of 159,769 SLAF tags/sample was generated, covering 13.79-fold of the genome size, and 225,498 SNPs were applied for population genomics. Observed (H_o) and expected (H_e) heterozygosity values were 0.224 and 0.308, 0.178 and 0.246, and 0.184 and 0.305, respectively. Polymorphic information content (PIC) ranged from 0.205–0.251. A selective sweep was performed based on Fst, and nucleotide polymorphism (π) revealed significant differences between allelic contents of growth- and immune-related genes in HEBV and LEBV populations. Kinship analysis revealed that 84.38% of examined fish showed r values < 0.2, and population admixture analysis revealed three subpopulations in HEBV and four subpopulations in LEBV groups. Fish that possessed a single cluster were found in each subgroup of both populations, along with those exhibiting mixed ancestral clusters. This information is critically important for further applications in our ongoing seabass improvement breeding program.

Genetic diversity and population connectivity of brownstripe red snapper (Lutjanus vitta) from different petroleum platforms located in the north (N1, N2, N3, and N4), central, and south regions and two coastal locations, Songkhla and Samaesarn (Gulf of Thailand), were examined using the control region (CR) polymorphism. In total, 59 haplotypes of CR were found, and 42 of these were private haplotypes (found in only one geographic location). The haplotype no./sample size (N_H/N) found in the central (0.800), south (0.741), and north (0.733) platforms was greater than that in the coastal populations (0.643 in Samaesarn and 0.682 in Songkhla). Haplotype diversity of north, central, and south platforms and coastal populations were comparable (Hd = 0.943–0.982). Nucleotide diversity within populations was estimated. The lowest and highest nucleotide diversity was observed in the north (1.293%) and south (2.850%) platforms. Larger genetic divergence was found between north–central (0.096%) and north–south platforms (0.069%) than between coastal populations (0.007%). A lack of nucleotide divergence was found between central–south platforms and between platforms and coastal populations (north–Samaesarn, central–Songkhla, and south–Songkhla). The F_ST estimate did not reveal significant population differentiation between all pairwise comparisons (p > 0.01 after the sequential Bonferroni’s adjustment). AMOVA confirmed a lack of intraspecific population structure of L. vitta in the Gulf of Thailand (p > 0.05). Genetic connectivity between fish from different sampling sites was noticed based on haplotype network, phylogenetic analysis, and population structure analysis. Demographic statistics revealed that L. vitta went through a sudden population expansion.

Genetic diversity and population differentiation of an aquaculture population of Banggai cardinalfish (Pterapogon kauderni) introduced and maintained in Phang Nga province, Southern Thailand (A1, N = 45) was examined using control region (CR) polymorphism in comparison with three wild transplanted populations from Gilimanuk Bay (Bali), collected in 2019 (W1, N = 25), Banyuwangi (East Java), collected in 2024 (W2, N = 22), and Gilimanuk Bay (Bali), collected in 2024 (W3, N = 39). In total, 14 haplotypes were identified. Haplotype 3 was found in all populations, while haplotype 4 was found in wild transplanted but not in aquaculture populations. The remaining (12) haplotypes were private haplotypes. Of these, five private haplotypes (H5, H6, H7, H8 and H9) were found only in the A1 population. Moreover, genome-wide single nucleotide polymorphisms (SNPs) in P. kauderni from A1 (N = 21), W2 (N = 15) and W3 (N = 15) populations were also analyzed by Specific Locus Amplified Fragment-Sequencing (SLAF-Seq). In total, 648,378 SNPs were identified. By analyzing both mitochondrial DNA and SNP markers, significant genetic differences were clearly found between farmed and wild transplanted populations of P. kauderni. Reduced genetic diversity was found in a farmed population from genome-wide SNPs but not mtDNA analyses.