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All Journal HAYATI Journal of Biosciences Journal of Tropical Biodiversity and Biotechnology Indonesian Fisheries Research Journal
Aji, Katon Waskito
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Environmental Science Immunology & microbiology

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Cryptic Diversity of Barred Mudskippers, Periophthalmus argentilineatus (Valenciennes, 1837), from the Southern Coast of Java and East Lombok, Indonesia inferred by COI Mitochondrial Gene Arisuryanti, Tuty; Aji, Katon Waskito; Herawati, Happy; Sari, Indah Paramita; Rha’ifa, Febrina Amaliya; Febriyanti, Diana; Priyono, Dwi Sendi
Journal of Tropical Biodiversity and Biotechnology Vol 9, No 3 (2024): September
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.84328

Abstract

The Barred Mudskipper (P. argentilineatus) is an amphibious fish species that displays fully terrestrial behaviour during low tides. Previous studies have indicated the existence of cryptic species of the barred mudskipper, leading to difficulties in taxonomic identification due to similarities in morphological characteristics. Therefore, this study aimed to generate DNA barcodes for Indonesian barred mudskipper populations. We collected ten specimens from Clungup Beach and Kondang Bandung Beach, representing our samples. Additionally, we incorporated 25 previously collected COI sequences from Indonesia into our analysis. The mitochondrial COI gene was amplified using PCR and analysed using various bioinformatics programs. This study provides evidence for the presence of three genetically distinct clades (A, B, and C) within the P. argentilineatus population in Indonesia, with a deep genetic divergence of 2.41% to 6.12%. Clade A showed a high genetic divergence of 5.51-6.12%, suggesting the presence of a cryptic species consistent with previous studies. The high level of haplotype diversity and low nucleotide diversity observed in each clade suggest a population bottleneck followed by a rapid expansion. The lack of geographical separation in the haplotype network analysis indicates that gene flow between populations may have been facilitated by glaciation events in the past. These findings contribute to a better understanding of the biodiversity of the barred mudskipper species in Indonesia and will aid in the accurate identification of cryptic species. This study highlights the importance of using molecular techniques to complement morphological identification in understanding the evolution and diversity of mudskipper fish species. 
Genetic Variation of Baram River Frog, Pulchrana baramica (Boettger, 1900), In Java, Sumatra, and Kalimantan based on 16S Mitochondrial Gene Fauzi, Luthfi; Arisuryanti, Tuty; Aji, Katon Waskito; Riyanto, Awal; Smith, Eric N.; Hamidy, Amir
Journal of Tropical Biodiversity and Biotechnology Vol 9, No 4 (2024): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.84814

Abstract

Baram River Frog (Pulchrana baramica) is a ranid species distributed in the Malay Peninsula, Borneo, Sumatra and represents the sole species from the genus Pulchrana on Java Island. Cryptic species are commonly encountered within the amphibian group which can cause confusion in the identification process. Due to the broad distribution range of P. baramica and the frequent occurrence of cryptic species within the amphibian group, it is important to evaluate the taxonomic status of P. baramica. Therefore, we investigated the taxonomic position of P. baramica from three populations (Kalimantan, Sumatra, and Java) and identified the interpopulation genetic variation based on molecular data of the 16S mitochondrial gene. We reconstructed phylogenetic relationships using Neighbour Joining, Maximum Likelihood, and Bayesian Inference. The research results revealed that Pulchrana baramica is a monophyletic group and nested within a group together with P. glandulosa and P. laterimaculata. The monophyletic group of P. baramica consisted of four distinct lineages that molecularly showed interspecific genetic variation. Clade 1 represents the population of Sumatra and Borneo (Kalimantan), clade 2 comprises the population from Borneo (Sarawak), clade 3 consists of population from Java, and clade 4 represents the population from Sumatra. Further research is required with the addition of morphological and acoustic data as supportive evidence to obtain more extensive comprehension of species identification.
Genetic Diversity of Mudskipper Species (Periophthalmus spp.) from the Southern Coast of Java, Indonesia, Based on the Mitochondrial 16S Gene Arisuryanti, Tuty; Nuraliyah, Tasya; Dwijayanti, Vindi; Aji, Katon Waskito; Priyono, Dwi Sendi; Daryono, Budi Setiadi
HAYATI Journal of Biosciences Vol. 32 No. 5 (2025): September 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.5.1352-1362

Abstract

The genus Periophthalmus (Bloch and Schneider, 1801) comprises a diverse group of mudskippers within the family Oxudercidae and subfamily Oxudercinae. It includes 20 verified species globally, with 11 of these species originating from Indonesia. Among them, P. kalolo and P. argentilineatus are prevalent across seven major islands. However, P. novemradiatus is less documented, with limited distribution records. The morphological similarities among Periophthalmus spp. complicate recognition, often leading to misidentification. To address this challenge, this study investigated the phylogenetic relationships and genetic diversity among these three species, utilizing the 16S rRNA gene as a marker. PCR amplification of the DNA from samples collected from seven regions along Java's southern coast employed primers 16Sar and 16Sbr. Phylogenetic analysis revealed three monophyletic clades corresponding to each species, with genetic divergences ranging from 3.66 to 5.40%. P. argentilineatus displayed a relatively high intraspecific divergence of 0.21-2.26%, suggesting the potential identification of cryptic species within this lineage, even with a conserved gene like 16S rRNA. We identified 47 variable sites within the 552-bp 16S rRNA sequence, including four singleton sites and 43 parsimony-informative sites. We discovered a unique marker at position 172 that could serve as a genetic identifier for distinguishing these species. These findings suggest that the 16S rRNA gene has potential as an alternative marker for species identification while also revealing genetic diversity, thereby complementing or even serving as an alternative to the commonly used COI gene in Periophthalmus spp.
Intraspecific Genetic Variation of Five Wild Indonesian Striped Snakehead (Channa striata (Bloch, 1793)) Populations Assessed Through 16S rRNA Sequences Suryani, Tuty Ari; Hastiwi, Titik Tri; Fitriani, Shentarya; Agiestina, Putri; Fajar, Ibnu; Aji, Katon Waskito
Indonesian Fisheries Research Journal Vol 29, No 1 (2023): (June) 2023
Publisher : Jakarta Technical University of Fisheries

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15578/ifrj.29.1.2023.%p

Abstract

The striped snakehead (Channa striata) belongs to the order Perciformes, suborder Channoidei, and the family Channidae. This fish is native to Sumatra, Java, and Kalimantan, but introduced to Sulawesi and Papua. Channa striata have potential as a food source, and pharmacological agent. However, the study on the genetic variation of snakehead fish in Indonesia is currently limited to specific areas, thus the genetic data obtained is insufficient. Therefore, the aim of this study was to examine the intraspecific genetic variation of the striped snakehead from five different locations in Indonesia using the 16S mitochondrial gene as a genetic marker. The PCR method was conducted with two primers, 16Sar and 16Sbr. The data obtained were then analyzed using DNASTAR, BLAST, Mesquite, MEGAX, BEAST, DnaSP, and NETWORK. The result revealed that all striped snakeheads investigated have 98.85-99.51% similarity to C. striata from the GenBank. The mtDNA 16S sequences generated 5 haplotypes with 5 variable sites and 4 parsimony informative sites. The mean of haplotype diversity and nucleotide diversity were 0.706 ± 0.088 and 0.00325 ± 0.00052 respectively with genetic divergence ranging from 0% to 0.73%. The phylogenetic tree revealed two distinct clades which were supported by a bootstrap value of 100% (NJ and ML), as well as a posterior probability value of 1.00 (BI). This finding suggests that there is intraspecific genetic variation of wild striped snakehead populations in Indonesia, with two distinct groups consisting of the western part of Indonesia (Sumatera) and the central to the eastern part of Indonesia (Kalimantan, West Nusa Tenggara, and Papua). This study will be helpful in efforts to conserve and cultivate the striped snakehead through breeding programs in Indonesia.
Co-Authors Agiestina, Putri AMIR HAMIDY BUDI SETIADI DARYONO Dwi Sendi Priyono Dwijayanti, Vindi Fauzi, Luthfi Febriyanti, Diana Fitriani, Shentarya Hastiwi, Titik Tri Herawati, Happy Ibnu Fajar Nuraliyah, Tasya Priyono, Dwi Sendi Rha’ifa, Febrina Amaliya Riyanto, Awal Sari, Indah Paramita Smith, Eric N. Suryani, Tuty Ari Tuty Arisuryanti, Tuty