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All Journal Journal of Tropical Biodiversity and Biotechnology Biosaintifika: Journal of Biology & Biology Education
Agus Nuryanto
Faculty of Biology, Universitas Jenderal Soedirman
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Environmental Science Immunology & microbiology

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Diversity analysis of Rhacophorus margaritifer (Schlegel, 1837) in Baturraden based on RAPD markers Fajar Nur Sulistyahadi; I Gusti Agung Ayu Ratna Puspitasari; Agus Nuryanto
Journal of Tropical Biodiversity and Biotechnology Vol 5, No 1 (2020): April
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.49110

Abstract

Rhacophorus margaritifer is an endemic species of arboreal frog in Java. Previous studies found this frog in several locations of Baturraden, namely in primary forest of Ketenger area, along Pancuran Pitu tourism track, and Baturraden Botanical Garden. There were still limited studies of molecular diversity of R. margaritifer and no prior data from population in the southern slope of Mount Slamet. This study aimed to look at the genetic polymorphism and determine the locus diversity of R.margaritifer population in Baturraden by using the PCR-RAPD technique.  Frog tissue samples were taken from three populations in Kalipagu hiking trail (HPK 01), Baturraden hiking trail (HPK 02), and Baturraden Botanical Garden (KRB). DNA was extracted using the Chelex method. Molecular characterization was performed based on RAPD markers. The RAPD marker band pattern was changed to binary data 0-1 and analysed using Arlequin software ver.3.5. A total of 19 frog individuals were obtained during sampling at three locations. High genetic diversity had been observed in all populations with gene diversity range from 0.9643 in HPK 01 population to 1.0000 in both KRB and HPK 02 populations. A high locus variation was also observed for all populations with values of 0.159524 in KRB; 0.165816 in HPK 01; 0.192857 in HPK 02, respectively. AMOVA indicated no genetic difference among populations of R. margaritifer (p=0.50244). 
Molecular Barcoding Reveal the Existence of Mole Crabs Emerita emeritus in North Coast of Central Java Dian Bhagawati; Elly Tuti Winarni; Agus Nuryanto
Biosaintifika: Journal of Biology & Biology Education Vol 12, No 1 (2020): April 2020
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v12i1.20497

Abstract

The existence of mole crabs had been reported from the southern coast of Central Java. However, no mole crab data was available from the northern coast Central Java.  This study aimed to figure out the existence of mole crabs in the northern coast of Central Java as revealed from the cytochrome c oxidase 1 (COI) barcoding. Mole crabs samples collected in Sendang Sikucing Beach Kendal. Taxonomic status of the samples was inferred from sequences similarity test using basic local alignment search tool to conspecific sequence deposited in GenBank. Pairwise genetic distances were calculated based on the Kimura 2-parameter model. A phylogenetic tree had reconstructed in molecular evolution genetic analysis (MEGA) software based on neighbor-joining algorithm. Branching reliability was obtained from 1000 bootstraps replication while branching polarity was obtained from the out-group comparison. The mole crab samples from the northern coast of Central Java had unambiguously identified as Emerita emeritus based on high sequences similarities (98.27%-99.70%), low genetic distances (0.002-0.005), and their monophyly with Emerita emeritus (KR047035) in GenBank. Pairwise analysis among each possibility pair of samples had genetic distances ranged between 0.000 and 0.005, indicated that all sample belong to single species. The data provide the first record of the existence of Emerita emeritus in the northern coast of Central Java. Our data on the existence of E. emeritus in the northern coast of Central Java is among essentials information as a scientific basis in creating policy for the management of sustainable use of the mole crabs in the areas.
Phylogenetic Relationships among Ornamental Achanturid Fish from Ujunggenteng and Taman Manalusu, West Java Afra Nabila; Agus Nuryanto; Romanus Edy Prabowo; Dian Bhagawati; Kusbiyanto Kusbiyanto
Biosaintifika: Journal of Biology & Biology Education Vol 11, No 3 (2019): December 2019
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v11i3.20671

Abstract

Acanthuridae is a marine fish family with some members are known as ornamental species. Previous studies has been reported the diversity of Acanthuridae. However, there was no study on the phylogenetic relationship of the Acanthuridae from Ujunggenteng and Taman Manalusu southern coast of West Java. The purpose of this study was to provide information about the phylogenetic relationship among ornamental fishes under the Acanthuridae family of Ujunggenteng Beach Sukabumi and Taman Manalusu Beach Garut, West Java. The phylogenetic tree was reconstructed based on morphological characters using maximum parsimony algorithm in software PAUP with 1000 pseudoreplicates and with Halichoeres marginatus selected as an outgroup species. The phylogenetic tree had a consistency index of 0.6429. The value means that the tree was highly reliable due to its low homoplasy. Acanthuridae formed a monophyletic clade compared to the outgroup species by having seven synapomorphic characters. Acanthurid clade was divided into two subclades at generic levels by nine derived characters; three apomorphic characters in Acanthurus and six apomorphic characters in Naso. The tree indicates that Naso brevirostris and Naso lituratus represents basal group, while all species within genus Acanthurus are the most advanced species.  This study is the first to provide the data about the evolutionary relationship of ornamental acanthurid fish from the southern coast of West Java. Data on closely related species is one of the essential scientific basis on making policies regarding the sustainable use of those closely related species.
Molecular Characterization of Anguilla sp. with Special Notes on Its Population Genetic in the Rivers of Cilacap Central Java, Indonesia Agus Nuryanto; Sri Riani; Dian Bhagawati; Elly Tuti Winarni; Farida Nur Rachmawati
Biosaintifika: Journal of Biology & Biology Education Vol 14, No 1 (2022): April 2022
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v14i1.35421

Abstract

Taxonomic status of Anguilla species in the rivers of Cilacap is vital for further study, such as population genetics and evolutionary history. Taxonomic status, population genetic, and evolutionary histories of Anguilla can be assessed using single genetic marker, such as cytochrome oxidase 1 gene. This study aimed to determine taxonomic status, genetic diversity and connectivity, and evolutionary history of Anguilla populations in the rivers of Cilacap. Anguilla samples were collected from Doplang-Serayu and Segara Anakan watersheds.  Sequence homology test to the conspecific sequence in GenBank proved that all samples from Doplang-Serayu watershed were genetically identified as Anguilla bicolor (98.23 to 100% homology). The decision was supported by monophyly between samples and their conspecific references. Anguilla bicolor from both watersheds had high haplotype (gene) diversity. Amova and Fst analysis proved that no genetic difference (p=0.623) was observed between Doplang-Serayu and Segara Anakan watersheds, indicated panmixing.  Haplotype network proved that both populations were evolved from two primitive ancestors. This study concluded that Anguilla bicolor was the only freshwater eel observed in the rivers of Cilacap. Anguilla bicolor in the rivers of Cilacap has high genetic diversity but no genetic differentiation was observed among populations. Anguilla bicolor population in the rivers of Cilacap evolved from two primitive ancestors.
High Connectivity Among Synedrella nodiflora Populations in Java Island Based on Intergenic Spacer atpB-rbcL Agus Hery Susanto; Agus Nuryanto; Budi Setiadi Daryono
Biosaintifika: Journal of Biology & Biology Education Vol 10, No 1 (2018): April 2018
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v10i1.12038

Abstract

Synedrella nodiflora (L.) Gaertn has taxonomically been the only species of genus Synedrella, which spreads over many tropical countries. In spite of its wide range of distribution, the genus remains monospecific. This leads to assumption of the very low genetic diversity among S. nodiflora populations worldwide. It may also be the case in Java Island, though rapid changes in ecosystem condition occurs. Here we report our study on S. nodiflora population genetics in Java Island using intergenic spacer (IGS) atpB –  rbcL as a molecular marker, since it has been well known as one of the most variable chloroplast genome regions in a wide range of plant species so far. As many as 58 individuals were collected randomly from ten different locations in the island. Based on IGS atpB – rbcL sequences of 860 bp length, only two haplotypes were observed. Both show only one polymorphic site (0.12%) and one transversion, where T is substituted by G at position 790, indicating that high connectivity among populations of S. nodiflora in Java Island is observed. This results in a low genetic differences among the populations, which at the same time provides a fact of nearly no variation among the IGS atpB – rbcL sequences.
Molecular Characteristics of Batanghari, Tambago, Orange, and Mandiangin Giant Gourami Strains Agus Nuryanto; Anatasia Endang Pulungsari
Biosaintifika: Journal of Biology & Biology Education Vol 9, No 3 (2017): December 2017
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v9i3.12097

Abstract

Morphological variations among geographic and can be identified as different species. However, a lot of studies proved that morphological variations are also common in conspecific individuals. Therefore, precise identification using additional characters is vital, such as using a molecular marker. Here, we characterized Batanghari, Tambago, Orange, and Mandiangin gourami strains using the cytochrome b gene to evaluate their taxonomic status. Partial sequences of cytochrome b gene were sequenced for 40 individuals. Taxonomic status was checked for giant gourami sequences available in GenBank. Kimura 2-Parameter genetic distances were calculated in MEGA6 software. Haplotype and nucleotide diversity within population and Φst-value among populations were estimated in Arlequin software. Phylogenetic relationship was reconstructed using the neighbor-joining method in MEGA6 software based on Kimura 2-parameter model with 1000 pseudobootstraps. Taxonomic identification results in 99% sequences homology to Osphronemus goramy sequences (accession number KU984978.1 and AY763768.1), means that all strains belong to single species. Low genetic distances, medium haplotype and low-level nucleotide diversity were observed among strains. Pairwise Φst-comparison indicates no genetic differences among Sumatera strain, whereas strong genetic structures observed between Sumatera and Mandiangin strains. The phylogenetic tree showed that Mandiangin formed separate subclades from other strains with bootstraps value of 100%. This finding has important implication for breeding sciences and efforts.
Co-Authors Afra Nabila Agus Hery Susanto Anatasia Endang Pulungsari Budi Setiadi Daryono Dian Bhagawati Dian Bhagawati Elly Tuti Winarni Elly Tuti Winarni Fajar Nur Sulistyahadi Farida Nur Rachmawati I Gusti Agung Ayu Ratna Puspitasari Kusbiyanto Kusbiyanto Romanus Edy Prabowo Sri Riani