Haplotype Diversity Values Research Articles

Genetic Variation and Population Structure of Clonorchis sinensis: An In Silico Analysis.

Clonorchis sinensis is an important zoonotic parasite that is mainly prevalent in China, Korea, Vietnam and the Russian Far East. To explore the genetic variation and population structure of C. sinensis, an in silico analysis was conducted based on mitochondrial cytochrome c oxidase subunit 1 (COX1), ribosomal internal transcribed spacer 1 (ITS1) and ribosomal internal transcribed spacer 2 (ITS2) sequences. The sequences obtained from NCBI were truncated for further analyses, including haplotype network, phylogenetic, gene flow, diversity and neutrality analyses. The results showed that there were 20, 11 and 4 haplotypes for COX1, ITS1 and ITS2, respectively. The results of both the haplotype network and phylogenetic analyses indicated that the haplotypes for each type of sequence from the same country were not all clustered together. Haplotype diversity values were all lower than 0.5. Values of nucleotide diversity were higher than 0.005, except for ITS2. Tajima's D and Fu's Fs values were all negative, and p-values showed significant differences, indicating that the population of C. sinensis is growing. Fst values were all lower than 0.05. In conclusion, this study found that there are specific variations of C. sinensis in different countries, and the population of this parasite is growing with less genetic variation. The findings provide a crucial foundation for understanding the molecular epidemiology and population dynamics of C. sinensis.

Microsatellite Markers & Mitochondrial D-Loop Based Phylogenetic And Diversity Analysis In Gabrali Cattle.

The Gabrali cattle is a multipurpose breed, native to Khyber Pakhtunkhwa, Pakistan. Despite its economic importance, scientific data about its phylogeny and genetic diversity is scarce. To address this issue, the present study was conducted on thirty (30) unrelated Gabrali male and female animals, from which blood samples were collected and DNA was extracted. Twelve (12) microsatellite loci and 1159bp of D-loop region were amplified via PCR and visualized on a 2% agarose gel. Sanger sequencing technique was used to sequence the D-loop amplicons. The microsatellite loci revealed 83 alleles with MNA (mean no of alleles per locus) = 8.8, the Ho (observed heterozygosity) and He (expected heterozygosity) of all loci were 0.58 and 0.50 respectively, mean PIC (Polymorphic Information content) = 0.59 and FIS (Inbreeding coefficient) = 0.056 using GeneAlEx® software. Microsatellite analysis revealed a normal allelic distribution across the breed, consistent with Hardy-Weinberg equilibrium. D-loop sequencing revealed eight haplotypes with 30 SNPs using DNA SP 6.0 software. High AT content was observed than GC content i.e. 55.9% and 44.1% respectively, while the transition to transversion ratio was R = 10:1. The value of Haplotype and Nucleotides diversity was Hd = 0.8601 ± SD = 0.0895 and Π = 0.0136 ± SD = 0.00197 respectively. Phylogenetic analysis done using Neighbor-joining method with bootstraps value of 1000, revealed the monophyletic clade of both Gabrali and Bos indicus haplotypes. Furthermore, the introgression of genes from national cattle breeds into Gabrali cattle was observed. It is concluded that Gabrali cattle have common ancestry with Bos indicus having no threats of genetic bottleneck having substantial genetic diversity.

Invisible dynamics: exploring the genetic diversity of peacock bass in Brazil

In Brazil, the introduction of non-native species into freshwater environments, such as peacock bass (Cichla spp.), was driven by aquaculture and sport fishing. These Amazonian fish possess phenotypic plasticity and resilience that facilitate their invasion and establishment in new habitats. Due to the taxonomic complexity of cichlids, studies on intraspecific variation are essential to mitigate the impacts of biological invasions. This study aimed to analyze the genetic diversity of peacock bass, assessing how invasive populations have diversified over time and across different regions in Brazil. Samples were collected from different invasive populations in Maranhão, São Paulo, Paraná, and Goiás. DNA was extracted and the 16S and COX1 genes were amplified. Ninety-seven specimens of the genus Cichla Schneider, 1801 were identified as Cichla monoculus Agassiz, 1831 (n=12); Cichla kelberi Kullander and Ferreira, 2006 (n=75); and Cichla piquiti (Kullander and Ferreira, 2006) (n=10). Sixteen 16S haplotypes (445bp) were identified, with haplotype diversity and nucleotide diversity values of Hd: 0.830 and Pi: 0.03777, respectively. The results showed proximity between the invasive populations from Maranhão and São Paulo, with haplotype sharing among Parque Nacional dos Lençóis Maranhenses, Baixada Maranhense, and Ilha Solteira. This highlights the fragility of species delimitation and definitions within the group, based solely on morphological data. By evaluating the set of morphological and genetic data, we found significant intraspecific variations, despite expecting population homogeneity due to the founder effect and bottleneck commonly observed in invasive populations. This underscores the adaptive potential of these cichlids.

Haplotype diversity of coastal horseshoe crab (Tachypleus gigas, Muller 1785) based on 16S rRNA gene markers as a basis for conservation

Abstract Tachypleus gigas is one of horseshoe crab species found in Indonesia, but does not have sufficient molecular biology information available. This study aims to predict the populations health of T. gigas from the waters of Langkat, Semarang, and Bintan; through analysis of haplotype diversity based on 16S rRNA gene markers. The observation was conducted from November 2022 until April 2023. Sample’s total DNA was isolated, extracted, amplified and then sequenced to obtain the nucleotide base sequence. The BLASTn results showed that the samples were validated as Tachypleus gigas and the genetic distance between locations showed a close kinship relationship between the three. The population health of the horseshoe crabs from Langkat and Semarang were indicated good with high haplotype diversity values, meanwhile the Bintan indicated poor health with low haplotype diversity values. This study of haplotype diversity provided the starting point to the conservation of horseshoe crab T. gigas

Population genetic structure of Culex tritaeniorhynchus in different types of climatic zones in China

BackgroundCulex tritaeniorhynchus is widely distributed in China, from Hainan Island in the south to Heilongjiang in the north, covering tropical, subtropical, and temperate climate zones. Culex tritaeniorhynchus carries 19 types of arboviruses. It is the main vector of the Japanese encephalitis virus (JEV), posing a serious threat to human health. Understanding the effects of environmental factors on Culex tritaeniorhynchus can provide important insights into its population structure or isolation patterns, which is currently unclear.ResultsIn total, 138 COI haplotypes were detected in the 552 amplified sequences, and the haplotype diversity (Hd) value increased from temperate (0.534) to tropical (0.979) regions. The haplotype phylogeny analysis revealed that the haplotypes were divided into two high-support evolutionary branches. Temperate populations were predominantly distributed in evolutionary branch II, showing some genetic isolation from tropical/subtropical populations and less gene flow between groups. The neutral test results of HNQH (Qionghai) and HNHK(Haikou) populations were negative (P < 0.05), indicating many low-frequency mutations in the populations and that the populations might be in the process of expansion. Moreover, Wolbachia infection was detected only in SDJN (Jining) (2.24%), and all Wolbachia genotypes belonged to supergroup B. To understand the influence of environmental factors on mosquito-borne viruses, we examined the prevalence of Culex tritaeniorhynchus infection in three ecological environments in Shandong Province. We discovered that the incidence of JEV infection was notably greater in Culex tritaeniorhynchus from lotus ponds compared to those from irrigation canal regions. In this study, the overall JEV infection rate was 15.27 per 1000, suggesting the current risk of Japanese encephalitis outbreaks in Shandong Province.ConclusionsTropical and subtropical populations of Culex tritaeniorhynchus showed higher genetic diversity and those climatic conditions provide great advantages for the establishment and expansion of Culex tritaeniorhynchus. There are differences in JEV infection rates in wild populations of Culex tritaeniorhynchus under different ecological conditions. Our results suggest a complex interplay of genetic differentiation, population structure, and environmental factors in shaping the dynamics of Culex tritaeniorhynchus. The low prevalence of Wolbachia in wild populations may reflect the recent presence of Wolbachia invasion in Culex tritaeniorhynchus.

Comparative Study of Two Himalayan Snow Trouts, Schizothorax esocinus and Schizothorax curvifrons Within the Schizothoracinae and Other Nearest Relatives of Cyprinidae, Inferred from Mitochondrial Sequences of Cytochrome b (Cyt-b) and Cytochrome Oxidase I (Co-I) Gene.

The Himalayan region encompasses varied aquatic ecosystems, characterized by the presence of diverse ichthyofauna, particularly represented by members of the Schizothorax genus, commonly referred to as snow trout. The primary objective of this work was to examine the molecular phylogeny of Schizothoracinae, specifically focusing on the two species, Schizothorax esocinus and Schizothorax curvifrons, which are known to inhabit the northern and north-eastern regions of the Himalayas. This investigation was conducted by analyzing the entire mitochondrial Cyt-b and Co-I gene sequences. The aligned Cyt-b and Co-I sequences for S. esocinus, S. curvifrons, and related members within the subfamily Schizothoracinae, spanned 1130 to 1141 and 1536 to 1551 base pairs, respectively. Using these gene, phylogenetic trees were created to compare Schizothoracinae species to other subfamilies of the family Cyprinidae (Barbinae, Alburninae, Leuciscinae, Xenocyprinae, Cyprininae, and Cultrinae). Genetic distances for Cyt-b and Co-I sequence at three hierarchical levels shows significant disparities in their average score. For Cyt-b, average p-distances for intraspecies, intragenus, and intrafamily were 2.13%, 4.1%, and 15.23%, respectively. Similarly, for Co-I, average p-distances were 1.19%, 3.6%, and 13.8% for intraspecies, intragenus, and intrafamily, respectively. Total number of haplotypes (h) based on Cyt-b and Co-I gene were 6 and 12 within the target Schizothorax spp. In the present study, the observed range of haplotype diversity (hd) for the Cyt-b gene varied from 0.00 to 0.847, with an average haplotype diversity of 0.847 ± 0.034. Similarly, for the Co-I gene, the observed haplotype diversity ranged from 0.00 to 0.931, with an average value of haplotype diversity estimated to be 0.931 ± 0.024. The results of the present study clearly shows that the representative species exhibited close affinities with members of Barbinae and Cyprininae, while other subfamilies formed distinct groups. The findings of the study also indicated that the Cyt-b and Co-I gene exhibits polymorphism and has the potential to serve as a marker for identifying genetic differentiation among populations based on ecological habitats. Mitochondrial Cyt-b and Co-I have been established as a universally accepted and validated genetic marker within a comprehensive bio-identification system at the species level.

Phylogeography of Clarias batrachus (Linnaeus, 1758) Inland Waters of Asia

Abstract Clarias batrachus is native species from the Clarias genus that has significant economic value in the world, including Indonesia. The genetic relationship between C. batrachus populations in Asia has not been intensively studied. This study used the mitochondrial COI gene as a marker to examine the phylogeography pattern of Clarias batrachus in Indonesia and other Asian nations. The samples were extracted, PCR and sequenced using a standard procedure for these purposes. Five C. batrachus samples in total were taken from Banda Aceh, Indonesia. The sequences from Aceh were compared with 39 samples from the Genbank were employed in this analysis. Of these, 10 samples from Thailand, 10 samples from India, 10 samples from Philippines and 9 samples from Java, Indonesia. The results showed that 15 haplotypes were produced from the sequences. All populations have a haplotype diversity (Hd) value of 0.892. With a genetic distance of 0.022, Thailand and the Philippines have the closest population, while Aceh and India have the furthest populations, separated by a genetic distance of 0.113. Within the population, the genetic distance varies between 0-0.005. Therefore, it is concluded that the C. batrachus population of Aceh is closer in genetic distance to the C. batrachus population of Thailand.

Determining the Matrilineal Origin of Indonesian Kerinci Duck Breed (Anas platyrhynchos) Based on MT-ND2 Gene Diversity

The Kerinci duck (Anas platyrhynchos), hailing from Jambi Province, represents one of the local duck breeds of Indonesia. This study aimed to ascertain the matrilineal origin of Kerinci ducks through analysis of the mitochondrial NADH Dehydrogenase subunit 2 (MT-ND2) gene. In this pursuit, forward sequences of the MT-ND2 gene (490 bp) were extracted from unsexed Kerinci ducks, totalling forty-eight (48) sequences, procured from blood samples. The findings demonstrated the identification of fifteen (15) distinct haplotypes within the MT-ND2 gene, with corresponding haplotype diversity (Hd) and nucleotide diversity (pi) values of 0.74 and 0.003, respectively. The resulting phylogenetic tree unveiled that Kerinci ducks exhibit two matrilineal origins: an Asian and an independent Kerinci lineage. Moreover, most Kerinci ducks were categorised within the H4 group (24 birds) of the Asian lineage. Nevertheless, this study also revealed the existence of an independent Kerinci lineage comprising eight (8) duck haplotypes. In conclusion, the analysis of the MT-ND2 gene underscored the genetic introgression of A. zonorhyncha and A. poecilorhyncha in Kerinci ducks.

Phylogeography of anabas testudineus bloch, 1792 (pisces: anabantidae) in asia

Anabas testudineus, the climbing perch, is a valuable and well-liked freshwater fish with significant commercial worth. This fish is found in Indonesia and other parts of Asia. Nonetheless, there hasn't been much research done on the genetic relationships across Asian populations of climbing perch. Thus, the aim of this work was to use the mitochondrial COI gene to examine the phylogeography of A. testudineus in freshwater Asia. The population sample was taken from South Aceh, Indonesia. The sample was extracted using a modified C-TAB protocol. In all, 48 sequences from the Genbank and three sequences from South Aceh were included in this investigation. Seven samples came from Indonesia, three from Malaysia, nine from Philippines, seven from Vietnam, eight from Thailand, ten from India, and four from Bangladesh. According to the findings, the sequences formed 17 different haplotypes. For every population, the haplotype diversity (Hd) value is 0.897. The genetic distance measuring the closest populations is 0.0007 between Indonesia and Philippines, whereas Indonesia and Vietnam populations are the furthest apart, at 0.0904. Between 0 and 0.0157 is the genetic distance within the population. Thus, the populations of A. testudineus in Aceh and Indonesia and the Philippines are genetically more similar.

Genetic Diversity and Phylogenetic Relationships of Mountain Papaya (Vasconcellea pubescens) in Dieng Plateau Based on Internal Transcribed Spacer Sequence

The Dieng Plateau is an area used to cultivate Mountain Papaya (&lt;em&gt;Vasconcellea pubescens&lt;/em&gt; A.DC.) as a food commodity in Indonesia. Research on diversity and relationships is vital as a first step in Mountain Papaya conservation in the Dieng Plateau. The study aims to determine the genetic diversity and relationship between Mountain Papaya accessions using Internal Transcribed Spacer (ITS) rDNA sequences. Fourteen accessions of Mountain Papaya with different sex distributions and altitudes are amplified using ITS1 and ITS4 primers. The genetic diversity is analyzed using the DnaSP 5.10.1 program. The Maximum Likelihood (ML) approach in MEGA 11 is utilized for assessing phylogenetic tree data based on ITS-rDNA regional sequences. With high haplotype diversity (Hd) values of 1.000 ± 0.027 and high nucleotide diversity (π) values of 0.09674 ± 0.00978, Mountain Papaya exhibits a high level of genetic diversity. Three main clades were identified in the phylogram tree based on the 14 ITS-rDNA sequences of Mountain Papaya. The results of this diversity data can support breeding programs intended to boost Mountain Papaya variety production.

Haplotype diversity of yellow-tail Rasbora population in Sundaland Hotspot based on COI Gene

Rasbora tornieri is known as a yellow-tail Rasbora because of its dark red tail. In Sundaland, R. tornieri is distributed in Sumatra and Kalimantan. The barrier caused by the life history between Sumatra and Kalimantan island can influence the genetic variation of yellow-tail Rasbora. Therefore, the necessary to conduct the haplotype diversity study of R. tornieri using the CO1 gene. Tissue samples of R. tornieri were collected from two populations representing upstream and downstream of Musi River in South Sumatra. A total of 633 bp of the CO1 gene were obtained for analysis. Three haplotypes were obtained from R. tornieri individuals in Sundaland, with the low haplotype diversity value of 0.28571. The value of nucleotide diversity R. tornieri was 0,00045. Overall, the values indicate the low genetic diversity and necessary to maintain also increase the genetic diversity of R. tornieri.

Haplotype diversity of Pangolin (Manis javanica Desmarest, 1822) based on the COI gene

The Pangolin (Manis javanica) is a unique scaly mammal with the IUCN status as a critically endangered species. In Indonesia, M. javanica is distributed in Java, Sumatra, and Kalimantan. The population of M. javanica has been declined due to the high poaching. M. javanica has been reported present in some locations in West Sumatra however, there is no biological data, especially molecular data. Therefore, it is necessary to conduct the haplotype diversity study of M. javanica using the CO1 gene. Hair samples of M. javanica were collected during the release of M. javanica in the Biology Education and Research Forest (HPPB) of Andalas University. The result of the study was obtained 601 bp of the CO1 gene for analysis. Two haplogroups were obtained from five sequences in West Sumatra and 15 Genbank sequences. The value of haplotype diversity was 0.995. The value of nucleotide diversity (π) in the haplogroup ranged from 0.042 to 0.047. The value of nucleotide diversity (π) between haplogroups ranged from 0.0148 to 0.0161. Overall, the values indicate the low genetic diversity of pangolin (M. javanica). Therefore, it is necessary to maintain and increase the genetic diversity of M. javanica within haplogroups.

Haplotype and phylogenetic diversity using mitochondrial 12S rRNA gene marker in Bali cattle

Bali cattle is one of Indonesia's original livestock genetic resources. The 12S rRNA can be used as a marker of genetic diversity, and until now, there has been no report on Bali cattle. The study was aimed to analyze the gene of mtDNA 12S rRNA to determine haplotype diversity and phylogenetics in Bali cattle populations of the eastern region of Indonesia. A total of 95 blood samples used consisted of three different populations which were Bali cattle, Ongole crossbred (PO) and Madura cattle as a comparison. This research was analyzed using PCR and sequencing methods. The data were analyzed using the cluster W method for estimating genetic distances, calculating diversity, and reconstructing phylogenetic trees using the MEGAX, DNAsP and Network. The genetic distance values ranged from 0.00200 to 0.01508, and the Haplotype diversity values ranged from 0.66000 to 0.91111. The nucleo-tide diversity values ranged from 0.00174 to 0.01673. There were 16 haplotypes found. The values of Gst, Nst and Fst were 0.00803, 0.07550, 0.07622; respectively. Based on the analysis, there were dif-ferences between Bali cattle from various populations, there were specific haplotypes. The 12S rRNA gene can be used as a genetic marker for diversity studies in Bali cattle and other cattle breeds although the diversity is low.

CKM intron: an appropriate marker for the determination of the genetic relationships among horse populations and breeds

To date, the origins, domestication, and genetic structure of Chinese Mongolian horses (CMH) are poorly understood. Furthermore, there have been sparse reports on the genetic differences between CMH and Thoroughbred. In order to determine their genetic structure, understand their genetic relationships, and explore their domestication processes, we performed an extensive survey of creatine kinase (muscle isoenzyme; CKM) variations among six populations of indigenous CMH, cultivated Sanhe horses, and imported Thoroughbred. Twenty-three single-nucleotide polymorphisms were found among the 343 horse sequences. From these, 40 haplotypes were inferred. Haplotype diversity (H) values differed from 0.6424 to 0.7881 and nucleotide diversity (π) values ranged from 0.00150 to 0.00211. The differences between Thoroughbred population and other Chinese horse populations were large, but only small differences were observed among Chinese horse populations with respect to CKM intron sequences suggesting that the domestication history, breeding measures, and origins of these horse populations are completely different. Results suggest that Sanhe and CMH are very closely related and the introgression (interbreeding) between them is serious. Our results suggest that Sanhe and Wushen require prompt and powerful protection. Overall, CKM intron was an appropriate marker for the determination of genetic relationships among horse populations and breeds.

Population genetic diversity in Nezara viridula by analysis of mitochondrial control region sequences

Abstract Here, we examine genetic diversity and dispersal patterns in populations of the agricultural pest Nezara viridula from Argentina using mitochondrial control region sequences. The DNA sequence comparisons of 1837 base pairs of the control region revealed 60 haplotypes determined by a total of 108 variable sites. The observed total haplotype diversity (Hd) value was 0.99, and the nucleotide diversity was 0.00423 and 0.00571 according to π and θW, respectively. The high haplotype diversity and low nucleotide diversity, as well as both neutrality tests and unimodal mismatch distributions, suggested a recent expansion in the populations of N. viridula from Argentina. The expansion of the populations of this insect is probably due to the recent agricultural expansion and intensification of soybean cultivation in this country. No significant levels of genetic differentiation were detected, suggesting that gene flow predominates over genetic drift. In addition, the Bayesian individual assignment analysis revealed that all populations share ancestry. It is probable that the growth in the area cultivated with soybean has generated stable and continuous habitats that allow gene flow among populations of N. viridula. The results of demographic history analysis suggest that the direction of migration of N. viridula would be associated with the growth pattern of soybean crops in Argentina.

Phylogeography pattern of Lutjanus kasmira in the Bengal Strait and the Arabian Sea

Lutjanus kasmira is one of the snappers occupying and commonly found in the Arabian Sea and the Bengal Strait. The purpose of this study was to examine the comparative phylogeography pattern of Lutjanus kasmira in the Bengal Strait and the Arabian Sea using the mitochondrial COI gene as a marker. The population sampled of Indonesia was taken from fish landing in Banda Aceh, Indonesia, while the population of India represented Bengal Strait, Oman, Yemen, Djibouti and Somalia respresented Arabian sea was retrieved from the NCBI Genbank. The extraction method was carried out using a modified C-TAB protocol. In this study at total of 47 sequences were analysed that produced 22 haplotypes where 18 haplotypes distributed in the Arabian Sea and 4 haplotypes from Bengal Strait. 10 samples of Oman population produced 6 haplotypes, 10 samples from Djibouti produced 5 haplotypes, 5 haplotypes from the population of Yemen, Somalia 2 haplotypes and India 1 haplotypes, respectively. Meanwhile, the Indonesian population, from 6 samples, produced 3 haplotypes. L. kasmira population from Arabian Sea and Bengal strait had no connectivity. The highest haplotype diversity (Hd) value was found in Oman population of 0.956 and the lowest found in Somalia population, while Indonesia population has a moderate genetic diversity.

Mitogenomic phylogeny reveals the predominance of the Nubian lineage of African wild ass in Indian donkeys

To contribute to the knowledge of maternal genetic diversity in domestic donkeys, this study investigated the mitochondrial DNA variations and analyzed the genetic structure in Indian donkeys based on 31 mitogenome sequences representing four breeds/populations (Agra, Halari, Kachchhi and Spiti). A total of 27 haplotypes with a haplotype diversity value of 0.989 were evident in the donkey genetic resources of India. The genetic differentiation between the investigated populations was evaluated using population pairwise FST values, which showed maximum differentiation between Kachchhi and Halari donkeys. The Neighbor-Joining (NJ) tree based on the whole mitogenome sequence and the Median-Joining (MJ) network for partial D-loop fragment showed clear demarcation of Indian donkeys into Nubian and Somali clades, substantiating African maternal origin of Indian domestic donkeys. The topology of the MJ network excluded the Asian wild asses as the possible progenitors of Indian donkeys. Halari and Agra donkeys showed conformity exclusively to the Nubian lineage of the African wild asses. However, representation of both the Nubian and Somali lineages was observed in Kachchhi and Spiti donkeys. Comprehensive analysis carried out by retrieving D-loop sequences from different countries representing Asia, Africa, Europe and South America revealed existence of shared haplotypes across geographically isolated regions of the globe. This observation is indicative of utility of donkeys as pack animals across inter-continental trading routes during development of human civilizations. Our results represent a valuable contribution to maternal genetic diversity of Indian donkeys and provide insights into the worldwide spread of the species following initial domestication in Africa.

Genetic diversity of bigeye thresher shark (Alopias superciliosus Lowe, 1841) landed in Palabuhanratu Fishing Port, Sukabumi, West Java, Indonesia

Abstract. Kanedi MM, Wijayanti DP, Widowati I, Malik MDA, Yusmalinda NLA, Sembiring A. 2023. Genetic diversity of bigeye thresher shark (Alopias superciliosus Lowe, 1841) landed in Palabuhanratu Fishing Port, Sukabumi, West Java, Indonesia. Biodiversitas 24: 3488-3494. The bigeye thresher shark Alopias superciliosus (Lowe, 1841) is a highly migratory marine shark, widely distributed globally in tropical and temperate seas. The bigeye thresher shark is listed as a Vulnerable/VU species on the red list of the International Union for Conservation of Nature (IUCN) and listed on Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Genetics is a substantial essential approach to conservation, management, and sustainability. This study investigates the bigeye thresher shark’s genetic diversity and structure populations A. superciliosus that landed in Palabuhanratu Fishing Port, Sukabumi, West Java, Indonesia. Samples were collected in Palabuhanratu (n=16) and secondary data from the Atlantic Ocean (n=212) and Indian Ocean (n=16) sequences were obtained from GenBank. A total of 16 sequences of A. superciliosus have been amplified using mitochondrial DNA control region (dloop) with 857 bp in size sequenced. The Genetic diversity result showed haplotype diversity value in Palabuhanratu (Hd=0.86667; ?=0.01048) considered a high value. Overall, AMOVA and FST results showed significant differences in population structure between Palabuhanratu, Atlantic, and Indian Ocean with an FST value of 0.04420 (p-value &lt;0.05). Based on the result, an effective strategy is needed to manage A. superciliosus sharks, both with the government and the private sector.

Bioinformatic Analysis of the Cytb Gene to Estimate the Domestication Potential of Mahseer Fish Genus Tor spp.

The purpose of this study is to estimate the population of fish of the genus Tor as a source of proper domestication. Bioinformatic analysis was carried out by extracting data from the NCBI gene bank and alignment of the Cytb gene sequences using the ClustalW program to further analyze the nucleotide characteristics using MEGA software, determining genetic variation using the dnasp5 software, and using median joining analysis to reveal the relationship between Tor fish haplotypes from different locations. The results obtained from this study show that the haplotype diversity values of fish of the genus Tor spp. in the domesticated farm population and the natural population are still high, namely 0.9 and 0.8, respectively, as well as the occurrence of haplotype groupings based on other population origins. Domestication of Tor genus fish can be sourced from domesticated farms, and the wild is still ideal because the haplotype diversity is still high.

Analysis of mutation rates and haplotypes of 23 Y-chromosomal STRs in Korean father–son pairs

Y-chromosomal short tandem repeats (Y-STRs) have been widely used in forensic genetics, and accurate knowledge of mutation rates at Y-STR loci is essential in kinship analysis. The main aim of this study was to estimate Y-STR mutation rates in Korean males. To obtain locus-specific mutations and haplotypes at 23 Y-STRs, we analyzed samples from 620 Korean father–son pairs. In addition, we also analyzed 476 unrelated individuals using the PowerPlex® Y23 System, with the aim of augmenting the available data for the Korean population. The PowerPlex® Y23 system facilitates analysis of the 23 Y-STR loci (DYS576, DYS570, DYS458, DYS635, DYS389 II, DYS549, DYS385, DYS481, DYS439, DYS456, DYS389 I, DYS19, DYS393, DYS391, DYS533, DYS437, DYS390, Y GATA H4, DYS448, DYS438, DYS392, and DYS643). Locus-specific mutation rate estimates varied from 0.00 to 8.06 × 10−3 per generation, with an average mutation rate of 2.17 × 10−3 (95% CI, 1.5–3.1 × 10−3). To obtain comprehensive genetic values for the Korean population, we combined data obtained in this study with previously reported values, thereby enabling us to estimate the locus-specific mutation rates regarding 22,711 allele transmissions. By combining these data, we obtained an overall average mutation rate of 2.91 × 10−3 (95% CI, 2.3–3.7 × 10−3). In addition, among the 476 unrelated Korean males, we detected 467 different haplotypes, with an overall haplotype diversity value of 0.9999. By extracting haplotypes of Y-STRs described in previous literature on 23 Y-STR reported in Korea, we obtained gene diversities for 1133 Korean individuals. We believe that the values and characteristics of the 23 Y-STRs analyzed in this study will contribute to establishing criteria for forensic genetic interpretation, including kinship analysis.