Strong genetic differentiation of banana shrimp Penaeus merguiensis in Thai waters revealed by mitochondrial Cytochrome c oxidase subunit I polymorphism

Genetic diversity and population differentiation of wild and domesticated banana shrimp Fenneropenaeus merguiensis: Applications for development of its breeding program

Population genetic structure of Varuna litterata living along the coast of Thailand were examined in this study. The samples were collected from 3 coastal regions: The Andaman sea (Satun, Trang, Phang Nga), the lower Gulf of Thailand (Pattani, Songkhla, Nakhon Si Thammarat) and the upper Gulf of Thailand (Petchburi, Samut Songkram, Rayong, Trat). Intraspecific variation was determined based on partial sequences of the cytochrome oxidase subunits I gene. A total of 182 samples were collected but only 32 haplotypes were obtained from these samples. An excess of rare haplotypes indicated that the female effective population size of V. litterata living along the coast of Thailand is large. Estimated values of haplotype diversity and nucleotide diversity were 0.790 and 0.003, respectively. The AMOVA (analysis of molecular variance) and phylogenetic analysis results showed that based on genetic variation, the population of this organism was found to have 2 genetically different populations: The Andaman sea population and the Gulf of Thailand population. Genetic exchange of V. litterata among populations inhabiting along the coast of Thailand could be described by the stepping stone model. The results of neutrality tests, both Tajima’s D and Fu’s Fs statistics, yielded negative values (-1.992 and -26.877, respectively) and statistically significant deviation from the neutrality, indicating that the V. litterata living along the Thailand coast had experienced population expansion. Mismatch distribution analysis indicated that a possible expansion occurred 211,428 years ago during the Pleistocene glaciations period.

Genetic diversity and geographic differentiation of the giant tiger shrimp, Penaeus monodon, in Thai waters (Satun, Trang, Phangnga, and Ranong in the Andaman Sea and Chumphon and Trat in the Gulf of Thailand) were examined by COI polymorphism (N = 128). We observed 28 COI mitotypes across all investigated individuals. The sequence divergence between pairs of mitotypes was 0.00-20.76%. A neighbor-joining tree clearly indicated lineage separation of Thai P. monodon and large nucleotide divergence between interlineage mitotypes but limited divergence between intralineage mitotypes. High genetic diversity was found (mean sequence divergence = 6.604%, haplotype diversity = 0.716-0.927, pi = 2.936-8.532%). F-statistics (F(ST)) and an analysis of molecular variance (AMOVA) indicated that the gene pool of Thai P. monodon was not homogeneous but genetically differentiated intraspecifically (P < 0.05). Six samples of P. monodon could be allocated into three different genetic populations: Trat (A), Chumphon (B), and the Andaman samples Satun, Trang, Phangnga, and Ranong (C). Contradictory results regarding patterns of geographic differentiation previously reported by various molecular approaches were clarified by this study.

Ornate threadfin bream (Nemipterus hexodon) is an economically important fishery species in Southeast Asia. In Thailand, N. hexodon decreased dramatically due to overexploitation for commercial purposes. To construct an effective sustainable management plan, genetic information is necessary. Thus, in our study, the population genetic structure and demographic history of N. hexodon were investigated using 419 bp of the mitochondrial DNA sequence in cytochrome oxidase subunit I gene (mtDNA COI). A total of 142 samples was collected from nine localities in the Gulf of Thailand (Chonburi, Samut Songkhram, Surat Thani, Nakhon Si Thammarat, Songkhla), and the Andaman Sea (Satun, Trang, Krabi, Phang Nga). Fourteen polymorphic sites defined 18 haplotypes, revealing a high haplotype diversity and low nucleotide diversity among nine localities. The analysis of molecular variance (AMOVA) analysis, pairwise FST, and minimum spanning network result revealed that the genetic structure of N. hexodon was separated into two populations: the Gulf of Thailand and the Andaman Sea population. The genetic structure of N. hexodon can be explained by a disruption of gene flow from the geographic barrier and the Pleistocene isolation of the marine basin hypothesis. Neutrality tests, Bayesian skyline analysis, mismatch distribution, and the estimated values of population growth suggested that N. hexodon had experienced a population expansion. The genetic information would certainly help us gain insight into the population genetic structure of N. hexodon living on the coast of Thailand.

Short mackerel Rastrelliger brachysoma is an economical pelagic fish commonly found widely distributed along the coast of the Gulf of Thailand and Andaman Sea. The present study is to use Inter-simple sequence repeat (ISSR) and mitochondrial DNA sequencing methods to investigate genetic diversity, population genetic structure and phylogeographic relationships of R. brachysoma in Thai waters. ISSR method was used to investigate genetic diversity and population genetic structure of R. brachysoma. Forty-nine primers were screened, five reliable and polymorphic primers (HB13, HB15, UBC811, UBC840 and UBC841) were obtained and used. After the investigation on genetic diversity of two hundred and seventy-six R. brachysoma samples from eight sites (Chanthaburi, Rayong, Samut Songkhram, Prachuap Khiri Khan, Surat Thani, Songkhla, Satun and Krabi), fifty-two DNA bands can be scored, of which forty-two were polymorphic (80.77%). High genetic diversity at species level was found (PPB: 80.77%, H: 0.1485, I: 0.2373). The highest and lowest genetic diversity within population were detected in Satun (PPB: 46.15%, H: 0.1336, I: 0.2064) and Surat Thani (PPB: 28.85%, H: 0.0887, I: 0.1356) respectively. Pairwise genetic distances among populations ranged from 0.0061 to 0.1226. UPGMA dendrogram based on Nei’s genetic distances divided the populations of R. brachysoma into three groups, the upper area of Gulf of Thailand (Chanthaburi, Rayong, Samut Songkhram, Prachuap Khiri Khan, and Surat Thani), the southern area of the Gulf of Thailand (Songkhla) and Andaman Sea (Satun and Krabi). The hierarchical analysis of molecular variance tested by AMOVA showed highly significant genetic differences among populations (P&lt;0.001). When the populations divided into two regions (the Gulf of Thailand and Andaman Sea), which showed significant genetic differentiation among the regions (Fct: 0.1984, P=0.0342), among populations within regions (Fsc: 0.2223, P&lt;0.001) and within populations (Fst: 0.3766, P&lt;0.001). Mantel test showed correlation between genetic distances and geographic distances (r = 0.6925, P&lt;0.0003). The partial mtDNA control region and cytochrome b gene sequencing method was used to investigate phylogeographic relationships of 40 R. brachysoma samples in Thai waters. The sequences of partial mtDNA control region (549 base pairs) and the mitochondrial DNA cytochrome b gene (627 base pairs) were obtained. The variable sites of the two sequences were low. The 7 variable sites and 10 haplotypes of partial mtDNA control region sequences were identified and no distinct haplotype between the Gulf of Thailand and Andaman Sea. The 17 variable sites and 6 haplotypes of cytochrome b gene sequences and the 24 variable sites and 16 haplotypes of the combined sequence of the two regions showed unique haplotype for the Gulf of Thailand and Andaman Sea. Phylogeographic relationships were established using neighbor-joining and maximum parsimony methods. The partial mtDNA control region sequences did not showed population genetic structure between the Gulf of Thailand and Andaman Sea. Cytochrome b gene and the combined sequence of the two regions showed population genetic structure between the Gulf of Thailand and Andaman Sea. However, Songkhla population is likely to be separated from other populations of the Gulf of Thailand. The information obtained from this study will be useful for stock management and conservation plans of R. brachysoma in Thailand

Population genetics has been recognized as a key component of policy development for fisheries and conservation management and aquaculture development. This study aims to evaluate the genetic diversity and population structure of native cobia (Rachycentron canadum) in the Gulf of Thailand and Andaman Sea, establishing the existing population distributions and contributing information to aid in the development of policy, prior to extensive aquaculture development. Microsatellite analysis of natural cobia populations in these two ocean basins shows similar levels of gene diversity at 0.844 and 0.837, respectively. All populations and almost all microsatellite loci studied show significant heterozygote deficiency. Genetic differentiation between local populations is low and mostly not significant (R ST = −0.0109 to 0.0066). The population shows no marked structure over the long geographic barrier of the Thai–Malay peninsula, either when analyzed using pairwise genetic differences or evaluated without predefined populations using STRUCTURE. Additionally, a Mantel test shows no evidence of isolation by distance between the population samples. The significant heterozygote deficiency at most of the loci studied could be explained by the possibility of null alleles. Alternatively, given the behavior of forming small spawning aggregations, seasonal migration, and hitchhiking on large marine animals, the population genetics could be complex. The population of cobia at each location in Thai waters may be inbred, as a result of breeding between relatives, which would reduce heterozygosity relative to Hardy–Weinberg frequencies, while some of these populations could be making long distance migrations followed by admixture between resident and transient groups. This migration would cause population homogeneity in allele frequencies on a larger geographic scale. The results suggest that fisheries management for this species should be considered at both national and international levels, and until the possibility of local adaptation is fully investigated, policy development should apply the precautionary principle to ensure the preservation of genetic diversity and the sustainability of local and regional fisheries.

Anchored fish aggregating devices (AFADs) have been widely used for fishing in Thai waters. However, abandoned, lost, and discarded fishing gears (ALDFGs), including lost AFADs, may cause environmental impacts. Fishing gear marking (FGM) is considered as a tool to help identification of ALDFGs. The main objective of this study is to compare the durability represented by the percentage of remaining condition (R-value) of three material types of FGM applied for AFADs, i.e., stainless steel (SS), colored acrylic (CA), and polypropylene (PP). This study was carried out using 50 AFADs deployed in the Gulf of Thailand (GOT) and the Andaman Sea (ANS) between July and October 2020 in cooperation with 10 fishers. The AFADs were deployed in similar habitat (bottom depth and type) between the GOT and the ANS. The three material types of FGM were assumed to be sufficiently durable to last for the lifespan of the AFADs in both the GOT and the ANS (within 2 months and 3.5 months, respectively) though some FGMs in the ANS were detached from cable ties or broken before AFADs were lost. The loss of AFADs and FGMs was mainly caused by adverse weather condition (rough sea). Only data from the ANS was included in comparative analysis due to the insufficient variance data obtained from the GOT. The analysis revealed that SS had the higher durability than CA and PP when the AFADs lasted for less than 3.5 months. As a result of our study, some recommendations were made. For example, the cable ties can be replaced by ropes or threads to improve the installation method. This study serves as a basis to develop FGM and to support responsible fisheries. Beneficiaries of the study include fisheries policy makers, managers, and fishers.

Background and Aim:The International Union for the Conservation of Nature and Natural Resources lists the green turtle as endangered. Green turtle nesting behavior in the Gulf of Thailand has decreased to <50% of the 1995 level. The population structure of green turtles in the Gulf of Thailand has not yet been studied. This study aimed to characterize the genetic diversity of green turtles in the Gulf of Thailand based on comparisons of mitochondrial DNA (mtDNA) control region with sequences of Indo-Pacific management units (MUs) and rookeries, to investigate population structures, and to explore phylogeographic relationships.Materials and Methods:Blood samples (1 mL each) from 91 stranded green turtles were collected from four parts of the Gulf of Thailand (eastern, upper, central, and lower). The control mtDNA region was amplified by polymerase chain reaction using LCM15382 and H950 primer. The obtained 384-bp or 770-bp sequences were analyzed for haplotype, clade, and haplotype and nucleotide diversities and were used to construct a phylogenetic tree and haplotype network diagram, respectively. In addition, we analyzed genetic differentiation within and among populations of green turtles in the Gulf of Thailand and between green turtles in the Gulf of Thailand and other Indo-Pacific MUs and rookeries.Results:In total, 12 (based on 384 bp) or 13 (based on 770 bp) haplotypes and two clades (clades VII and VIII) were identified, with nine or 10 haplotypes belonging to clade VIII and three haplotypes belonging to clade VII. Of the new haplotypes, four or five were identified and classified as clade VII (two haplotypes, for both fragment lengths) and clade VIII (two or three haplotypes, for 384 bp or 770 bp fragments, respectively). The overall haplotype and nucleotide diversity of green turtles in the Gulf of Thailand were high (0.755 ± 0.039 and 0.01146 ± 0.00248, respectively). Based on the analysis of molecular variance, green turtles in the Gulf of Thailand could be divided into two subpopulations (UC-Eastern Gulf of Thailand [UC-EGT] and lower Gulf of Thailand [LGT]). Comparisons with other MUs and rookeries in the Indo-Pacific showed that UC-EGT was not genetically different from the Peninsular Malaysia and Eastern Taiwan (Lanyu) MUs and the Terrangganu and Mersing rookeries, and LGT were not genetically different from Peninsular Malaysia, Sipadan, Brunei Bay, Eastern Taiwan (Lanyu), Scott Reef and Browse Island, and Gulf of Carpentaria MUs and the Perak, Perhentain Island, Redang, Pahang, and Vietnam rookeries.Conclusion:To the best of our knowledge, this is the first report to identify the haplotypes and clades of green turtles in the Gulf of Thailand and to show that the populations in the Gulf of Thailand not only present high genetic diversity but also have haplotypic endemism. Longer mtDNA fragments (770 bp) increased the resolution of the stock structure. Clade VII is a unique clade not only for Japan but also for Thailand and Malaysia, and CmP82 is a unique haplotype for both the Gulf of Thailand and Malaysia. Conservation and management of these populations are important to preserve the genetic diversity, biological diversity, and evolutionary potential of green turtles in the Gulf of Thailand.

Mitochondrial genetic population structure and variation of the littoral earthworm Pontodrilus longissimus Seesamut and Panha, 2018 along the coast of Thailand

For long-term management and conservation of marine resources an understanding of their genetic diversity and geographic distribution is necessary. The red alga Gracilaria salicornia is widely distributed along the coasts of Thailand and has been used as food and as fertilizer. However, there have been no studies examining the genetic diversity of this alga. The present research aimed to employ two different genetic markers, mitochondrial (COI-5P) and chloroplast (RuBisCO spacer) for exploring the genetic diversity and phylogeography of G. salicornia in Thailand. Our analyses, inferred from both markers, revealed different levels of genetic diversity between the two coasts of Thailand, and the recognition of seven new COI haplotypes. Gracilaria salicornia in the Andaman Sea had higher genetic diversity than in the Gulf of Thailand. Significant genetic divergence was found between populations in the Andaman Sea and the Gulf of Thailand, likely due to the geographic barrier of the Thai-Malay Peninsula and the complex ocean currents. No genetic structuring was detected in the Gulf of Thailand, whereas low to moderate genetic differentiation was found between populations in the Andaman Sea, suggesting a possible break between the northern and southern Andaman Sea. This break could be explained by ocean circulation patterns around the Malacca Strait. These findings provide further evidence supporting the Thai-Malay Peninsula and oceanographic currents as strong barriers to dispersal, leading to genetic differentiation and population structuring of G. salicornia and other marine species. These results can be used to guide conservation management actions and exploitation of this marine resource.

This study examined numerical principal tidal constituents in the Gulf of Thailand and the Andaman Sea. The principal tidal constituents (K1, O1, M2 and S2) were calculated using a Harmonic method. These constituents were used to estimate the Form Factor (F). The simulated results from the Harmonic method were compared with the Moon phase in a 31-days cycle to verify our Harmonic model. We used observed water level data from 21 stations in the Gulf of Thailand and the Andaman Sea from both Hydrographic and Marine Departments. The tide types composed of (1) diurnal, (2) mixed with predominantly diurnal and (3) mixed with predominantly semidiurnal at 15 stations at the Gulf of Thailand coastline and semidiurnal at six stations of the Andaman Sea coastline. The Moon phase influenced tidal constituents in all stations, except the following 8 stations: Ko Prap (Surat Thani), Pakpanang (Nakhon Si Thammarat), Songkhla, Paknam Pattani (Pattani), Paknam Bangnara (Narathiwat), Paknam Ranong (Ranong), Ao Tublamu (Phangnga) and Paknam Krabi (Krabi) stations.

Genetic diversity and population differentiation of the blue swimming crab (Portunus pelagicus) in Thailand, originating from Ranong and Krabi located in the Andaman Sea (west) and Chanthaburi, Prachuap Khiri Khan, and Suratthani located in the Gulf of Thailand (east), were examined by AFLP analysis. High genetic diversity of P. pelagicus in Thai waters was found (N=72). The four primer combinations generated 227 AFLP fragments, and the percentage of polymorphic bands in each geographic sample was 66.19-94.38%. The mean genetic distance between pairs of samples was 0.1151-0.2440. Geographic heterogeneity analyses using the exact test and FST-based statistics between all pairwise comparisons were statistically significant (P<0.01), indicating a fine-scale level of intraspecific population differentiation of Thai P. pelagicus. The estimated number of migrants per generation (Nem) was 0.26-0.76, suggesting restricted gene flow levels of P. pelagicus in Thai waters.

Indo-Pacific bottlenose dolphins (Tursiops aduncus) are a coastal species found in Thai waters off the coasts of the Andaman Sea and the Gulf of Thailand. This species was recently re-listed as near-threatened by the IUCN Red List, though the population status in Thai seas is not known. Here, we investigated genetic diversity, population structure, maternal lineage, and demographics by analyzing skin tissue samples (n = 30) of T. aduncus stranded along the Andaman coastline of Thailand between 1990 and 2019. This study was based on 11 microsatellite loci and 265 bp mtDNA control regions compared to data available through the National Center for Biotechnology Information (NCBI). From microsatellites, the observed heterozygosity (Ho) ranged from 0.46 to 0.85. The mean fixation index (F) value for all loci was 0.10 ± 0.04, which suggests some degree of inbreeding. Two genetic clusters (the most likely K at K = 2) were observed in T. aduncus through the population structure analysis using multiple criteria. For the mtDNA control region, a total of 17 haplotypes were found for dolphins in Thai seas (14 haplotypes from our samples; three haplotypes from the NCBI database) with high levels of haplotype diversity (h) at 0.926 ± 0.027 and nucleotide diversity (π) at 0.045 ± 0.002. A decline in the effective population size from 0.05 million years ago also was observed in Thai T. aduncus through Bayesian Skyline Plots analysis. A unique set of haplotypes was identified in our samples, which may have originated from the Australian and Indian Oceans rather than the Western Pacific Ocean. These results improve our understanding of the maternal lineage of the Indo-Pacific bottlenose dolphin, which can be used for monitoring population status and establishing better conservation plans for this species in the Thai Andaman Sea.

Three genomic libraries were constructed for microsatellite isolation in the tropical abalone Haliotis asinina. The first genomic library was constructed from DNA fragments obtained from AluI digestion. The second library was from vortexed and sonicated genomic DNA. The third library was from mixed-enzyme (Alu I, Rsa I and Hinc II) digested genomic DNA. After screening with (GT)15-, it was found that the third library gave the highest percentage of positive clones (1.46%) whereas the first and the second libraries gave 0.2% and 0.43% of positive clones, respectively. Dot blot hybridization suggested that (GT)n -repeats were more abundant than (CT)n repeats. Nucleotide sequencing of positive clones revealed that perfect, imperfect and compound microsatellites were found in the same proportion. From 33 microsatellite loci, 10 pairs of specific primers were designed for microsatellie amplification. Preliminary analysis of polymophism of 10 loci (Has1-10) showed that numbers of alleles ranged from 3-26 alleles and observed heterozygosity were 0.27-0.85. Genotypes from these microsatellite were associated randomly (p &gt; 0.0031). All pairs of primers could not be used for cross-amplification in other tropical abalone species, H. ovina and H. varia. Sensitivity of PCR using 32P labeled primer indicated that genotyping of 2 week-old (spat) samples can be detected and only 50 pg of DNA is enough for detection.Three microsatellite loci, Has2, Has3 and Has8 were used for examination of genetic variation in natural and hatchery stocks of H. asinina. Three natural samples were collected from the Andaman Sea (Talibong Island) and the Gulf of Thailand (Samet Island and Cambodia). Hatchery samples were brought from 3 hatcheries where broodstocks originated from Samet Island, Cambodia and Philippines respectively. The effective number of alleles (ne) and observed heterozygosity (hobs) indicated that natural samples from the Gulf of Thailand (Semet: ne = 5.73, hobs = 0.78; Cambodia: ne = 7.65, hobs = 0.62) have higher genetic variation than that of the Andaman sea (Talibong: ne = 5.10, hobs = 0.58) and hatchery populations from Samet (ne = 6.16, hobs = 0.82) and Cambodia (ne = 6.63, hobs = 0.79) still have high genetic variation. Gene frequencies of each population conform to Hardy-Weinberg equilibrium (p &gt; 0.0027) except natural population from Cambodia (at Has2 loci (p &lt; 0.0001) and Has3 loci (P &lt; 0.0001)) and the Philippines samples (at Has8 locus (p &lt; 0.0001)). Analysis of geographic heterogeneity suggested that samples within the Gulf of Thailand did not showed significant heterogeneity to one another (p &gt; 0.0027) but significant heterogeneity was observed between the Gulf of Thailand, the Andaman Sea and hatchery stock from Philippines (p &lt; 0.0027). Phylogenetic reconstruction using the Neighbor-joining approach divided the 6 geographic samples to three different gene pools constituting of the Gulf of Thailand (A), the Andaman Sea (B) and the Philippines (C).

Sequence variation of the mitochondrial DNA 16S rRNA region of the Asian moon scallop, Amusium pleuronectes, was surveyed in seven populations along the coast of Thailand. A total of 16 unique haplotypes were detected among 174 individuals with a total 27 variable sites out of 534 bp sequenced. The mitochondrial haplotypes grouped into two distinct arrays (estimated to differ by about 2.62% to 2.99% nucleotide divergence) that characterized samples collected from the Gulf of Thailand versus the Andaman Sea. Low levels of intrapopulation variation were observed, while in contrast, significant divergence was observed between populations from the Gulf of Thailand and Andaman Sea. Results of AMOVA reveal a high F (ST) value (0.765) and showed that the majority of the total genetic variance (76.03%) occurred among groups (i.e., Andaman Sea and the Gulf of Thailand) and little among populations within the group (0.52%) and within populations (23.45%). The genetic differentiation between the populations recorded in the present study is similar to that observed in a variety of marine species in the Indo-Pacific. The implications of the findings for management of A. pleuronectes genetic resources in Thailand are discussed.