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Teknik molekuler untuk identifikasi spesies ordo Cetartiodactyla menggunakan DNA barcode Zein, Moch. Syamsul Arifin; Fitriana, Yuli Sulistya
ZOO INDONESIA Vol 21, No 2 (2012): Desember 2012
Publisher : Masyarakat Zoologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar

Di Indonesia banyak terjadi kasus produk makanan yang berasal dari ternak tidak jelas identitasnya. Sebagian besar kasus yang terjadi berasal dari ordo Cetartiodactyla yang banyak dikonsumsi sebagai sumber protein hewani. Oleh sebab itu diperlukan alat identifikasi spesies yang akurat dari organ tubuh/daging atau produk olahan yang berasal dari hewan tersebut untuk menyelesaikan berbagai kasus yang dapat merugikan konsumen. Keragaman urutan sekuen gen sub unit cytochrome c oxidase subunit I (COI) telah terbukti menjadi alat yang efektif untuk identifikasi spesies hewan. Studi ini menganalisis 112 spesimen terdiri dari 4 Famili, 10 Genus dan 15 spesies dari ordo Cetartiodactyla yang dikumpulkan dari berbagai lokasi di Indonesia. Hasil yang didapat dari studi ini menunjukkan bahwa gen ini sangat cocok untuk mengidentifikasi tingkat spesies pada hewan tercermin pada pohon filogeni yang terbentuk. Jarak genetik dalam spesies berkisar antara 0-0,7% (rata-rata 0,13ÃÂ±0,05%) dan antar spesies berkisar antara 2-28%, dalam genus berkisar antara 8,8-27,4% (rata-rata1,36ÃÂ±0,037%) dan antar genus berkisar antara 8,8-27,4%, sedangkan dalam famili berkisar antara 5,8-11,9% (rata-rata 7,8ÃÂ±2,85%) dan antar famili berkisar antara 18,6-26,3%. Hasil konstruksi pohon filogeni Cetartiodactyla menunjukkan semua spesies membentuk sebuah cluster kohesif yang jelas berbeda.

Aplikasi Kajian DNA Molekuler dan Fenotipik Pada Program Pelepasliaran Burung Kakatua Zein, Moch Syamsul Arifin; Haryoko, Tri; Fitriana, Yuli Sulistya; Sulistyadi, Eko; Prawiradilaga, Dewi Malia
JURNAL BIOLOGI INDONESIA Vol 13, No 1 (2017): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

ABSTRACTThere are six species of cockatoos in Indonesia which are well known as exotic, smart, and they can be trainedÂ in a variety of attractions. Thus, many people want to keep those birds as pets. All of pets which have been keptÂ by community should be evaluated from various aspects before being reintroduced to their natural habitat. TheÂ examination of sex and species of illegal cocktoos play as a key role for the reintroduction programme. Theobjective of this study was to evaluate the reliability and effectivity of evaluation technique of morphometricÂ and molecular for reintroduction programme of cockatoos. We used the COI gene sequences from 68individuals of cockatoos from pet communities in and around Jakarta and four sequences from GenBank. TheÂ phylogenetic analysis used the neighbor-joining method, in which the genetic distance matrix calculations withÂ Kimura 2-parameter models that are implemented on a pairwise distance calculation in the MEGA programÂ version 6:05. The result of the genetic variation of the cockatoo species which shows intraspecific divergenceÂ was Cacatua alba (n=4)= 0%, C. galerita (Australia n=9)= 0.6%, C. galerita (Indonesia n=53)= 0.3%,Â C .goffiniana (n=3)= 0%, C. moluccensis (n=7)= 0.1%, and C. sulphurea (n=2)= 0.3%, with a range of 0-0.6%.Â The results indicate that the average of intraspecific of COI in the cockatoos community was 0.25Â±0.055%, andÂ interspecific divergences ranged from 3.1 to 11.6%. The phylogenetic tree shows the monophyletic clade ofÂ cockatoo species in Indonesia. In addition, DNA barcode analysis and molecular sexing could correct the errorÂ and doubts the result of five individual species identification and two individual sexing identification of C.galerita by morphological identification. The results of morphological examanation base on body weight, bodyÂ length and head-bill length of C. galerita triton were not significantly different (P?0,5). Finally, 19 individualsÂ C. galerita triton and two individuals P. aterrimus were reintroduced to their natural habitat.Keywords: cockatoo, barcodes DNA, reintroduction

Barcoding DNA pada Komunitas Kelelawar Pemakan Buah di Indonesia Zein, Moch Syamsul; Fitriana, Yuli Sulistya
JURNAL BIOLOGI INDONESIA Vol 11, No 1 (2015): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v11i1.2156

Family Pteropodidae known as fruit bats which has ecological services as seed dispersers, pollinator, and plays important role in the forest regeneration. Identification of bat species frequently encountered problems, i.e.,ÃÂ criptic morphology and behaviour. Therefore it is necessary to confirm its identity using DNA barcodes. Cytochrome c oxidase subunit I (COI) mitochondrial DNA is representative of the protein coding mitochondrial DNA and has been used extensively as a means of animal species identification. This study evaluated 141 specimens consist of 42 species and 17 genera which were collected from Java, Nusa Tenggara, Sumatra, Kalimantan, Sulawesi, Maluku, and Papua. Phylogenetic analysis using the neighbor-joining method, in which the genetic distance matrix calculation by Kimura-2 parameter models are implemented on the pairwise distance calculation in the program MEGA version 6:05. The results of the analysis showed variation intraspecific ranging from 0 to 7.9% (0.9 ÃÂ±0.014%) and there were 4 species with very high intraspecific average sequence divergence, i.e., Penthetor lucasi (3.2%), Thoopterus nigrescens (3.7%), and Chironax melanocephalus (8.7 %). Average interspecific of genetic distanceÃÂ of fruit bats in Indonesia was 20% (1.3-26.1%). These results produce a phylogeny tree construction to form a clearly different cohesive cluster, except in the genus Dobsonia ( D. moluccensis, D. viridis, and D. crenulata), Cynopterus (C. brachyotis C. minutus, and C. luzoniensis), and Macroglossus (M. minimus and M. sobrinus ), because this did not correspond with currently recognized species boundaries based on morphology.ÃÂ Keywords: DNA barcoding, COI, PteropodidaeÃÂ

KAJIAN GENETIKA UNTUK KONSERVASI BADAK SUMATERA (DICERORHINUS SUMATRENSIS GLOGER, 1841) Zein, Moch Syamsul Arifin; Fitriana, Yuli Sulistya; Kurniawan, Yuyun; Chaerani, Kurnia; Sirupang, Meriam
JURNAL BIOLOGI INDONESIA Vol 15, No 1 (2019): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v15i1.3767

ABSTRACTThe Sumatran rhinoceros is one of the most critically endangered species of large mammals due to habitat loss, fragmentation and illegal hunting so that the population of this species drastically decreased. At present, reproductive problems with a limited population are also a threat and require an appropriate solution. Therefore, data on molecular genetic information is very important as a basis for conservation management in maintaining long-term persistence of this species. Phylogenetic analysis based on sequences of CO1, 12SrRNA, and Cytochrome b gen from mitochondrial DNA genomes using neighbor-joining and genetic distance matrix calculations with the Kimura 2-parameter model (K2P) were implemented in pairwise distance calculations in the Mega (Molecular Evolutionary Genetics Analysis) program version 6.05. The study results show the genetic distance of Sumatran Rhinos from Sumatra and Kalimantan respectively 0.2 ± 0.00%, 0.8 ± 0.4%, and 0%. These results were reconfirmed that the Sumatran Rhino species in Sumatra and Kalimantan were taxonomy is no different. The study of genetic diversity based on D-loop of mitochondrial DNA contained 5 haplotypes, namely haplotypes 1 and 2 originating from the island of Sumatra and haplotypes 3, 4, and 5 originating from the island of Borneo. The genetic distance between individuals in this study ranged from 2.54 ± 1.4%, haplotype diversity (Hd) was 0.8 ± 0.172, nucleotide diversity (Pi) was 0.02269, Fu?s Fs value was 2.523, and Tajima?s test was 0.69497. The positive value (Fu?s Fs and Tajima?s test) indicated low genetic diversity and population expansion in the Sumatran rhino. In the study using 10 microsatellite loci, where the average number of allel/loci in Kalimantan (1.68) was higher than in Sumatra (1.22). Data from this study show that genetic variation between Sumatran rhinoceros from Sumatra and Kalimantan can be used as a basis for alternative that the populations of Sumatra and Borneo be considered as a single management unit. Keywords: Sumateran Rhinoceros, Mitochondrial DNA, Microsatellite

KAJIAN GENETIKA UNTUK KONSERVASI BADAK SUMATERA (DICERORHINUS SUMATRENSIS GLOGER, 1841) Zein, Moch Syamsul Arifin; Fitriana, Yuli Sulistya; Kurniawan, Yuyun; Chaerani, Kurnia; Sirupang, Meriam
JURNAL BIOLOGI INDONESIA Vol 15, No 1 (2019): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v15i1.3767

ABSTRACTThe Sumatran rhinoceros is one of the most critically endangered species of large mammals due to habitat loss, fragmentation and illegal hunting so that the population of this species drastically decreased. At present, reproductive problems with a limited population are also a threat and require an appropriate solution. Therefore, data on molecular genetic information is very important as a basis for conservation management in maintaining long-term persistence of this species. Phylogenetic analysis based on sequences of CO1, 12SrRNA, and Cytochrome b gen from mitochondrial DNA genomes using neighbor-joining and genetic distance matrix calculations with the Kimura 2-parameter model (K2P) were implemented in pairwise distance calculations in the Mega (Molecular Evolutionary Genetics Analysis) program version 6.05. The study results show the genetic distance of Sumatran Rhinos from Sumatra and Kalimantan respectively 0.2 ± 0.00%, 0.8 ± 0.4%, and 0%. These results were reconfirmed that the Sumatran Rhino species in Sumatra and Kalimantan were taxonomy is no different. The study of genetic diversity based on D-loop of mitochondrial DNA contained 5 haplotypes, namely haplotypes 1 and 2 originating from the island of Sumatra and haplotypes 3, 4, and 5 originating from the island of Borneo. The genetic distance between individuals in this study ranged from 2.54 ± 1.4%, haplotype diversity (Hd) was 0.8 ± 0.172, nucleotide diversity (Pi) was 0.02269, Fu?s Fs value was 2.523, and Tajima?s test was 0.69497. The positive value (Fu?s Fs and Tajima?s test) indicated low genetic diversity and population expansion in the Sumatran rhino. In the study using 10 microsatellite loci, where the average number of allel/loci in Kalimantan (1.68) was higher than in Sumatra (1.22). Data from this study show that genetic variation between Sumatran rhinoceros from Sumatra and Kalimantan can be used as a basis for alternative that the populations of Sumatra and Borneo be considered as a single management unit. Keywords: Sumateran Rhinoceros, Mitochondrial DNA, Microsatellite

APLIKASI KAJIAN DNA MOLEKULER DAN FENOTIPIK PADA PROGRAM PELEPASLIARAN BURUNG KAKATUA Zein, Moch Syamsul Arifin; Haryoko, Tri; Fitriana, Yuli Sulistya; Sulistyadi, Eko; Prawiradilaga, Dewi Malia
JURNAL BIOLOGI INDONESIA Vol 13, No 1 (2017): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v13i1.3105

ABSTRACTThere are six species of cockatoos in Indonesia which are well known as exotic, smart, and they can be trained in a variety of attractions. Thus, many people want to keep those birds as pets. All of pets which have been kept by community should be evaluated from various aspects before being reintroduced to their natural habitat. The examination of sex and species of illegal cocktoos play as a key role for the reintroduction programme. Theobjective of this study was to evaluate the reliability and effectivity of evaluation technique of morphometric and molecular for reintroduction programme of cockatoos. We used the COI gene sequences from 68individuals of cockatoos from pet communities in and around Jakarta and four sequences from GenBank. The phylogenetic analysis used the neighbor-joining method, in which the genetic distance matrix calculations with Kimura 2-parameter models that are implemented on a pairwise distance calculation in the MEGA program version 6:05. The result of the genetic variation of the cockatoo species which shows intraspecific divergence was Cacatua alba (n=4)= 0%, C. galerita (Australia n=9)= 0.6%, C. galerita (Indonesia n=53)= 0.3%, C .goffiniana (n=3)= 0%, C. moluccensis (n=7)= 0.1%, and C. sulphurea (n=2)= 0.3%, with a range of 0-0.6%. The results indicate that the average of intraspecific of COI in the cockatoos community was 0.25±0.055%, and interspecific divergences ranged from 3.1 to 11.6%. The phylogenetic tree shows the monophyletic clade of cockatoo species in Indonesia. In addition, DNA barcode analysis and molecular sexing could correct the error and doubts the result of five individual species identification and two individual sexing identification of C.galerita by morphological identification. The results of morphological examanation base on body weight, body length and head-bill length of C. galerita triton were not significantly different (P?0,5). Finally, 19 individuals C. galerita triton and two individuals P. aterrimus were reintroduced to their natural habitat.Keywords: cockatoo, barcodes DNA, reintroduction

BARCODING DNA PADA KOMUNITAS KELELAWAR PEMAKAN BUAH DI INDONESIA Zein, Moch Syamsul; Fitriana, Yuli Sulistya
JURNAL BIOLOGI INDONESIA Vol 11, No 1 (2015): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v11i1.2156

Family Pteropodidae known as fruit bats which has ecological services as seed dispersers, pollinator, and plays important role in the forest regeneration. Identification of bat species frequently encountered problems, i.e.,Â criptic morphology and behaviour. Therefore it is necessary to confirm its identity using DNA barcodes. Cytochrome c oxidase subunit I (COI) mitochondrial DNA is representative of the protein coding mitochondrial DNA and has been used extensively as a means of animal species identification. This study evaluated 141 specimens consist of 42 species and 17 genera which were collected from Java, Nusa Tenggara, Sumatra, Kalimantan, Sulawesi, Maluku, and Papua. Phylogenetic analysis using the neighbor-joining method, in which the genetic distance matrix calculation by Kimura-2 parameter models are implemented on the pairwise distance calculation in the program MEGA version 6:05. The results of the analysis showed variation intraspecific ranging from 0 to 7.9% (0.9 Â±0.014%) and there were 4 species with very high intraspecific average sequence divergence, i.e., Penthetor lucasi (3.2%), Thoopterus nigrescens (3.7%), and Chironax melanocephalus (8.7 %). Average interspecific of genetic distanceÂ of fruit bats in Indonesia was 20% (1.3-26.1%). These results produce a phylogeny tree construction to form a clearly different cohesive cluster, except in the genus Dobsonia ( D. moluccensis, D. viridis, and D. crenulata), Cynopterus (C. brachyotis C. minutus, and C. luzoniensis), and Macroglossus (M. minimus and M. sobrinus ), because this did not correspond with currently recognized species boundaries based on morphology.Â Keywords: DNA barcoding, COI, PteropodidaeÂ

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