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All Journal JURNAL BIOLOGI INDONESIA ZOO INDONESIA Biosaintifika: Journal of Biology & Biology Education
Hidayat Ashari, Hidayat
Zoology Division, Research Centre for Biology, Indonesian Institute of Sciences Cibinong Science Centre, Jl. Jakarta- Bogor KM 46, Cibinong, West Jawa, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Other

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Analisis Gen Cytochrome Oxydase-1 (CO1) untuk Konfirmasi Status Taksonomi Burung Srigunting Sumbawa (Dicrurus, Dicruridae) Astuti, Dwi; Ashari, Hidayat; Irham, Mohammad; Sulandari, Sri
ZOO INDONESIA Vol 26, No 1 (2017): Juli 2017
Publisher : Masyarakat Zoologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (620.941 KB)

Abstract

Sekuen DNA dari gen cytochrome oxydase-1 (COI) diadopsi untuk membangun pengelompokan dan kekerabatan dari burung-burung srigunting (Dicrurus; Dicruridae). Tujuannya adalah untuk mengkonfirmasi apakah srigunting dari Sum-bawa merupakan spesies tersendiri atau merupakan bagian dari superspesies D. hottentotus. Sekuen DNA sepanjang 795-bp pada gen COI diambil dari delapan burung srigunting dari Sulawesi Tenggara (D. hottentotus leucops), enam srigunting dari T.N. Gn. Halimun, Jawa Barat (D. remifer), dan dua srigunting dari Sumbawa. Analisis Neighbor-joining (NJ) dilakukan untuk mengkonstruksi pohon filogeninya dengan mengkalkulasi semua substitusi basa (transisi dan trans-verse) pada software MEGA-5. Pohon NJ menunjukkan bahwa dua individu yang berasal dari Sumbawa jelas-jelas terpisah dari Dicrurus asal Sulawesi Tenggara (D. hottentotus) dengan didukung nilai bootstrap sebesar 100 % dan dipisahkan oleh nilai divergensi sekuen > 3,5%. Sedangkan D. remifer memisah jauh dari keduanya. Penelitian ini cenderung mendukung pendapat bahwa srigunting dari Sumbawa merupakan populasi yang berbeda dan tidak termasuk dalam grup D. hottentottus, tetapi termasuk dalam grup D. densus dari Nusa Tenggara dan kemungkinan besar adalah spesies monopiletik tersendiri sebagai D. bimaensis.
Study on Phylogenetic Status of Javan Plover Bird (Charadrius, Charadriidae, Charadriiformes) through DNA Barcoding Analysis Ashari, Hidayat; Astuti, Dwi
Biosaintifika: Journal of Biology & Biology Education Vol 9, No 1 (2017): April 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.v9i1.9195

Abstract

Javan Plover named Charadrius javanicus is taxonomically under controversy and phylogenetically unresolved yet. Through an analysis of DNA barcode, this study aims (1) to confirm whether Javan Plover is separated species named Charadrius javanicus or a subspecies of C. alexandrinus which named C. a. javanicus and (2) to determine a relationship within this genus. Totally 666 bp DNA sequences of COI barcode gene were analyzed. The results showed that a sequence divergence between Javan Plover and C. alexandrinus alexandrinus was only 1.2%, while sequence divergences between C.a.alexandrinus and others species, or between Javan Plover and others species were ranged from 9-12%. Neighbour-joining (NJ) and maximum-parsimony (MP) analyses showed that all individuals of both Javan Plover and Kenith Plover were clustered together, and supported by 99 % and 100 % of bootstrap value in NJ and MP, respectively. This study tends to support the previous findings that Javan Plover was not a separated species named C. javanicus, but it was as a subspecies of C. alexandrinus; named C. a. javanicus. There were two groups of Plover in this study; (C. leschenaultii and C. javanicus + C.a.alexandrinus), and (C.dubius and C. melodus + C. semipalmatus). DNA barcoding analysis can give certainty taxonomic status of the bird. Then, this study has implication as a basic data that can be used to provide and support the planning of Javan plover conservation programs.
Variasi nukleotida gen COI pada Burung Sempidan (Genus Lophura) Astuti, Dwi; Irham, Mohammad; Ashari, Hidayat
JURNAL BIOLOGI INDONESIA Vol 14, No 1 (2018): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v14i1.3668

Abstract

ABSTRACTGallopheasant birds (Genus Lophura) belonging to Phasianidae family. L. inornata and L.ignita were 2 of 5 species in Indonesia. This study was aimed to determine the genetic variation and diversity of those two bird species based on DNA sequences of COI gene. Total genomic DNA was extracted from blood samples and wet meat from 5 individuals (4 individuals L.inornata hoogerwerfi and 1 individual L. Ignita). Amplification of COI gene by PCR produced a single fragment of about 860 bp. The 785 bp of DNA sequence data from 5 birds were analyzed to determine its genetic variation and diversity, both of at intra and inter-species levels using MEGA 5 software. Genetic distance between individual bird (intraspecific) of L.i. hoogerwerfii ranged from 0.00 to 0.0013 ± 0.0012, whereas between 2 species (L. hoogerwerfii vs L. ignita) ranged from 0.0467 ± 0.0078 to 0.0481 ± 0.0080. Three individuals of L. i. hoogerwerfii have the same DNA sequence haplotype (HLh1) and one individual has one haplotype that was very different from the other 3 individuals (HLh2), so from 4 indi-vidual birds there were only 2 haplotypes with 0.400 ± 0.237 haplotype diversity (Hd) value. Nucleotide substi-tution / differences occured in 4 nucleotide sites (site 320, 711, 738, and 779) and nucleotide diversity (Pi) was 0.00204 ± 0.00121. Between two species (L.i.hoogerwerfii and L. ignita) occured 39 - 404 nucleotide subsitu-tion sites. The average number of codon encoding amino acid was 261 with a value of codon bias was 0.314. The existence of a nucleotide substitution indicated that there were genetic variations in both intraspecies and interspesies levels. Genetic variation and diversity of L.i. hoogerwerfii were low. Information from this re-search is useful for conservation of this bird.Keywords: DNA sequence, COI, genetic variation, Lophura inornata hoogerwerfii, L. ignita.
VARIASI NUKLEOTIDA GEN COI PADA BURUNG SEMPIDAN (GENUS LOPHURA) Astuti, Dwi; Irham, Mohammad; Ashari, Hidayat
JURNAL BIOLOGI INDONESIA Vol 14, No 1 (2018): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v14i1.3668

Abstract

ABSTRACTGallopheasant birds (Genus Lophura) belonging to Phasianidae family. L. inornata and L.ignita were 2 of 5 species in Indonesia. This study was aimed to determine the genetic variation and diversity of those two bird species based on DNA sequences of COI gene. Total genomic DNA was extracted from blood samples and wet meat from 5 individuals (4 individuals L.inornata hoogerwerfi and 1 individual L. Ignita). Amplification of COI gene by PCR produced a single fragment of about 860 bp. The 785 bp of DNA sequence data from 5 birds were analyzed to determine its genetic variation and diversity, both of at intra and inter-species levels using MEGA 5 software. Genetic distance between individual bird (intraspecific) of L.i. hoogerwerfii ranged from 0.00 to 0.0013 ± 0.0012, whereas between 2 species (L. hoogerwerfii vs L. ignita) ranged from 0.0467 ± 0.0078 to 0.0481 ± 0.0080. Three individuals of L. i. hoogerwerfii have the same DNA sequence haplotype (HLh1) and one individual has one haplotype that was very different from the other 3 individuals (HLh2), so from 4 indi-vidual birds there were only 2 haplotypes with 0.400 ± 0.237 haplotype diversity (Hd) value. Nucleotide substi-tution / differences occured in 4 nucleotide sites (site 320, 711, 738, and 779) and nucleotide diversity (Pi) was 0.00204 ± 0.00121. Between two species (L.i.hoogerwerfii and L. ignita) occured 39 - 404 nucleotide subsitu-tion sites. The average number of codon encoding amino acid was 261 with a value of codon bias was 0.314. The existence of a nucleotide substitution indicated that there were genetic variations in both intraspecies and interspesies levels. Genetic variation and diversity of L.i. hoogerwerfii were low. Information from this re-search is useful for conservation of this bird.Keywords: DNA sequence, COI, genetic variation, Lophura inornata hoogerwerfii, L. ignita.
Co-Authors Baveja, Pratibha Dewi M. Prawiradilaga, Dewi M. Dewi Malia Prawiradilaga, Dewi Malia Dwi Astuti Eaton, James A. Frank E Rheindt Gwee, Chyi Yin Mohammad Irham Ng, Nathaniel Sheng Rong Peter R Wilton, Peter R Philippe Verbelen, Philippe Rheindt, Frank E. Rheindt, Frank Erwin Siswahyudianto SRI SULANDARI