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All Journal Biodiversitas Journal of Biological Diversity
NOORHIDAYAH BINTI MAMAT
Institute of Biological Sciences, Faculty of Science, University of Malaya. 50603 Kuala Lumpur, Malaysia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology

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Genetic diversity and phylogenetic reconstruction of horseshoe crabs from East Java, Indonesia based on DNA barcode COI DWI ANGGOROWATI RAHAYU; RENI AMBARWATI; ULFI FAIZAH; ENDIK DENI NUGROHO; RUSDIANTO RUSDIANTO; PURITY SABILA AJININGRUM; NOORHIDAYAH BINTI MAMAT
Biodiversitas Journal of Biological Diversity Vol. 25 No. 10 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251041

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Abstract. Rahayu DA, Amarwati R, Faizah U, Nugroho ED, Rusdianto, Ajiningrum PS, Mamat NB. 2024. Genetic diversity and phylogenetic reconstruction of horseshoe crabs from East Java, Indonesia based on DNA barcode COI. Biodiversitas 25: 3789-3802. Horseshoe crabs or mimi mintuna (Indonesian) are an ancient arthropod with 4 species, but there are limited studies on the species from East Java. This indicates the need for the collection of more accurate genetic resources as an important step for its conservation. Therefore, this study aims to examine genetic diversity and phylogenetic reconstruction of horseshoe crabs from East Java using DNA barcode COI. A total of 20 samples were obtained from Beejay Bakau Resort, Probolinggo, Kenjeran Beach, Surabaya, Batah Timur Beach, Madura, and Lekok Beach, Pasuruan. The 621 bp CO1 gene sequence was used for genetic diversity analysis and phylogenetic tree reconstruction. Subsequently, muscle samples were preserved in pure-grade ethanol and subjected to DNA extraction, polymerase chain reaction (PCR), sequencing, and sequence analysis. The sequence data were analyzed using bioinformatics tools, Barcode of Life Data Systems (BOLD) Systems, the Automatic Barcode Gap Discovery (ABGD) web application, and haplotype network. Phenetic taxonomy was further applied using Ntysc to enhance the robustness of the genetic analysis. The results showed that the high haplotype diversity (Hd) of 0.957, 16 haplotypes, and nucleotide diversity (?) of 0.00097 indicated a wide range of genetic variations. The frequency of parsimony informative sites was 26.48%, with 19 polymorphic sites and an overall ts/tv ratio of 2.32. In addition, the phylogenetic trees showed a clear and unambiguous branching pattern for cluster Carcinoscorpius rotundicauda Latreille 1802 and Tachypleus gigas O.F.Müller 1785. This finding is a matter of concern for managing and conserving horseshoe crab species in East Java waters.
Morphological and genetic variation of local loach (Nemacheilus spp.) from Lumajang, East Java, Indonesia DWI ANGGOROWATI RAHAYU; WIDOWATI BUDIJASTUTI; SUNU KUNTJORO; WINARSIH WINARSIH; ENDIK DENI NUGROHO; RENI AMBARWATI; ULFI FAIZAH; CAHYA AJENG VALENTA TRESNA SULUNG; RUSDIANTO RUSDIANTO; NOORHIDAYAH BINTI MAMAT
Biodiversitas Journal of Biological Diversity Vol. 26 No. 6 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260632

Abstract

Abstract. Rahayu DA, Budijastuti W, Kuntjoro S, Winarsih, Nugroho ED, Ambarwati R, Faizah U, Sulung CAVT, Rusdianto R, Mamat NB. 2025. Morphological and genetic variation of local loach (Nemacheilus spp.) from Lumajang, East Java, Indonesia. Biodiversitas 26: 2896-2907. The genus Nemacheilus is a part of the family Nemacheilidae within the order Cypriniformes, comprising several morphologically similar fish species found in East Java, Indonesia. However, species identification in Lumajang remains unavailable. This study aimed to analyze morphological and genetic diversity of local loach species from Lumajang, East Java, contributing to the existing knowledge with new records. The experiment was carried out through diagnostic identification, meristic, and morphometric analyses, using Past.403 software for correlation assessments. Pectoral fin samples were preserved in high-purity ethanol for DNA extraction, followed by Polymerase Chain Reaction (PCR) targeting mitochondrial genomes, Recombinase-Activating Gene proteins 1 (RAG1), and mitochondrial Cytochrome C Oxidase I (COI) to explore phylogenetic relationships among Nemacheilidae species through maximum likelihood methods. Morphological identification showed two local loaches, Nemacheilus chrysolaimos (Valenciennes, 1846) and Nemacheilus fasciatus (Valenciennes, 1846) with two variants (dominant black color and yellow color). Several morphometric parameters showed high correlations, such as TL with SL, HL with Snout Length (SnL), and Dorsal Fin Length (DFL) with Anal Fin Length (AFL). The COI locus showed high genetic variation with 126 variable sites across 489 base pairs. Meanwhile, the RAG1 gene had a lower variation with 33 variable sites across 681 base pairs, with phylogenetic analysis showing two distinct clades. This comprehensive study enhanced the understanding of morphological and genetic variation in Nemacheilus species, related to conservation efforts and sustainable aquaculture.
Co-Authors CAHYA AJENG VALENTA TRESNA SULUNG DWI ANGGOROWATI RAHAYU DWI ANGGOROWATI RAHAYU ENDIK DENI NUGROHO ENDIK DENI NUGROHO PURITY SABILA AJININGRUM RENI AMBARWATI RENI AMBARWATI RUSDIANTO RUSDIANTO RUSDIANTO RUSDIANTO SUNU KUNTJORO ULFI FAIZAH ULFI FAIZAH WIDOWATI BUDIJASTUTI WINARSIH WINARSIH