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Phylogenetic Study of Madura Cattle Based on Mitochondrial Cyt b and D-loop Sequences Nirmala Fitria Firdhausi; Achmad Farajallah; Dyah Perwitasari
Buletin Peternakan Vol 45, No 1 (2021): BULETIN PETERNAKAN VOL. 45 (1) FEBRUARY 2021
Publisher : Faculty of Animal Science, Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21059/buletinpeternak.v45i1.48557

Abstract

Madura Cattle is one breed of local cattle from Indonesia. Madura cattle are estimated to originate from a crossbreeding between Bos indicus and Bos javanicus. Another presumption is that Madura cattle are the result of a crossbreeding between B. indicus males and mixed B. javanicus or Bos taurus. Tracing the history of Madura cross and another cattle phylogenetic based on maternal lineage can be done by analyzing the variation of the mitochondrial genome (mtDNA). The purpose of this study was to determine the clarity of the origin of Madura cattle based on maternal lineage using mtDNA markers Cyt b and D-loop. This research is expected to provide genetic information and the origin of Madura cattle, so that it can be used to help improve the breeding and conservation program for Madura cattle. The results of the phylogeny tree reconstruction, using the Cyt b and D-loop genes showed that Madura cattle originated from Sampang region (Polagan, Golbung, and Komis) were grouped into two types of maternal origin. Madura cattle clade I are grouped with B. indicus and B. taurus, while Madura cattle clade II are grouped with B. javanicus. A crossbreeding between B. javanicus and B. indicus is estimated to have been carried out since the entry of Hindu culture brought by the India peoples to Indonesia around 1800 years ago. The crossing between B. javanicus and B. indicus was then more intensively carried out at the time of the government's promoting the development of Ongol cattles (B. indicus) in the days of the Dutch East Indies. The length segment of Cyt b that can be amplified is 230 bp and the D-loop segment of varying length, 577 bp for the Madura 41 and 29 samples, and 624 bp for sample 32.  
Phylogenetic Analysis of the Darkfin Hind, Cephalopholis urodeta (Serranidae) Using Partial Mitochondrial CO1 Gene Sequences (Analisis Filogenetik Cephalopholis urodeta (Serranidae) Menggunakan Runutan Gen CO1 Mitokondria Parsial) Yanti Ariyanti; Achmad Farajallah; Irma Shita Arlyza
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 20, No 1 (2015): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (309.879 KB) | DOI: 10.14710/ik.ijms.20.1.38-44

Abstract

Cephalopholis merupakan salah satu genera terbesar dalam subfamili Epinephelinae yang memiliki banyak species. Secara fenotip, C. urodeta dewasa mirip dengan juvenil C. sonnerati karena memiliki ciri mencolok yaitu garis yang menyudut pada sirip ekor. Untuk memahami hubungan genetik pada spesies ikan ini, maka dilakukan analisis molekuler menggunakan ruas gen CO1. Sejumlah spesies ikan (famili Serranidae) dikumpulkan dari wilayah Sulawesi Selatan seperti Sinjai dan Kepulauan Selayar. Karakter fenotip diidentifikasi menggunakan buku katalog spesies kerapu dunia FAO, kemudian sampel yang diduga C. urodeta secara morfologi dipisahkan. Jaringan yang digunakan sebagai sumber DNA adalah jaringan otot bagian dorsal. Berdasarkan sebagian runutan gen CO1, diyakini bahwa sampel tersebut adalah C. urodeta. Runutan basa nukleotida dari sampel dibandingkan dengan 22 runutan basa nukleotida C. urodeta dari GenBank. Berdasarkan rekonstruksi pohon filogeni, C. urodeta dari Sinjai dan Kepulauan Selayar mengelompok dengan C. urodeta dari berbagai tempat seperti Polynesia, Mariana Utara, Filipina, pulau-pulau di sekitar Madagascar (Ouest, St. Gilles, Canyon, Cimetiere, Jaune) dan Adaman, sedangkan sampel dari Laut Arab di lepas pantai India berada pada cabang yang terpisah. Penelitian ini menyatakan bahwa C. urodeta yang melibatkan beberapa tempat dari berbagai perairan seperti Samudera Pasifik bagian Selatan (Polynesia), Samudera Pasifik bagian Utara (Northern Mariana), Laut China Selatan (Filipina), Teluk Bengal (Andaman), Laut Laccadive (reunion of Ouest, St. Gilles and Cimetiere), Laut Arab dan Indo Pasifik Barat (Indonesia) memiliki perbedaan jarak genetik yang kecil. Hal ini berimplikasi pada pemahaman pola migrasi spesies tersebut dan sebagai bahan pertimbangan pengambilan kebijakan konservasi. Kata kunci: Cephalopholis urodeta, CO1, filogenetik, Serranidae, Sulawesi Selatan Cephalopholis is one of the largest genera belonging to Subfamilly Epinephelinae, which has various species. Phenotypically, an adult C. urodeta similar to a juvenile of C. sonnerati, since both of them have a striking trait, two white oblique stripes or bands on the caudal fins. This work was conducted to investigate the genetic relationships of this species using CO1 gene segment. Fish were collected from several sampling point in South Sulawesi areas such as Sinjai and Selayar Island. The phenotypic characterizations were identified using the FAO species catalogue of groupers of the world, and the species that seemed to have C. urodeta morphology then separated. Tissue samples from dorsal muscle tissue were used as the source of DNA. Using part of the CO1 gene sequence, it can be confirmed that our samples are exactly C. urodeta species. The 22 C. urodeta sequences from GeneBank compared with our sequences. Interestingly, because based on the phylogenetic tree, our sequences clustered with the other C. urodeta sequences from several part of the world except the Arabian Sea off the coast of India, which is a separate branch. The present study reveals less genetic distance in C. urodeta than some other parts of the ocean as follows; South Pacific Ocean (Polynesia), North Pacific Ocean (Northern Mariana), South China Sea (Philippines), Andaman, west coast of Réunion Island, Arabian Sea and Indo West Pacific (Indonesia). This has implications for understanding the migration pattern of the species and may affect conservation policy decisions. Keywords: Cephalopholis urodeta, CO1, phylogenetics, Serranidae, South Sulawesi
Redescription of Larval Development in Cultured Pearl Oyster Pinctada maxima Jeane Siswitasari Mulyana; Achmad Farajallah; Yusli Wardiatno
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 23, No 2 (2018): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (288.472 KB) | DOI: 10.14710/ik.ijms.23.2.109-112

Abstract

Larval development plays a major role in efficient pearl culture. The cultured larvae will be later used for recipient and donor oysters in cultured pearl production. Larval developmental stage of silver lip pearl oyster Pinctada maxima has been reported by several studies. Those studies used female and male oyster parents directly taken from natural habitat.This study aimed to redescribe larval development of P. maxima from commercial pearl oyster culture farm in Indonesia. Larval development of this species whose parents are originated from selected groups in the pearl culture farm has not been reported yet, thus it is necessary to be described. This species undergoes specific larval developmental stage. The larvae were observed under microscope, and then the average shell length (SL) and shell height (SH) were measured. D-shaped veliger larva (77.4±0.3 µm SL; 65.4±1.1 µm SH) appeared 20 h after fertilization. Tenday-old larva (156.2±2.8 µm SL; 149.5±5.6 µm SH) had developed umbo region so it was called umbonal larva. Umbonal larva then developed further into plantigrade larva (411.3±9.8 µm SL; 380.5±6.9 µm SH) in 25 days after fertilization. Developmental stage and larval sizein P. maxima is similar with those observed in P. fucata and P. margaritifera. Keywords: growth, larva, plantigrade, shell, umbo, veliger
Diversity and Abundance of Sand Crabs on the South Coast of Central Java (Diversitas dan Kelimpahan Kepiting Pasir di Pantai Selatan Jawa Tengah) Ali Mashar; Yusli Wardiatno; Mennofatria Boer; Nurlisa A. Butet; Achmad Farajallah
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 19, No 4 (2014): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (321.267 KB) | DOI: 10.14710/ik.ijms.19.4.226-232

Abstract

Kepiting pasir atau undur-undur laut merupakan biota bentik yang hidup di pantai berpasir yang mempunyai nilai ekologi dan nilai ekonomi cukup penting. Adanya tekanan penangkapan mengharuskan adanya pengelolaan yang bijak yang disesuaikan dengan karakteristik populasi kepiting pasir. Informasi tentang jenis dan kelimpahan kepiting pasir penting untuk diketahui terlebih dahulu sebagai langkah awal upaya pengelolaan lestari kepiting pasir. Penelitian ini bertujuan untuk mengetahui komposisi jenis dan kelimpahan setiap jenis kepiting pasir yang terdapat di dua lokasi penelitian, yaitu pantai Bocor, Kabupaten Kebumen, dan pantai Bunton, Kabupaten Cilacap. Hasil penelitian menunjukkan bahwa di kedua lokasi penelitian ditemukan tiga jenis kepiting pasir, yaitu Emerita emeritus, Hippa adactyla, dan Albunea symmysta. Kepiting pasir E. emerita ditemukan dengan persentase komposisi paling besar, 70,5%-75,3%; disusul H. adactyla 22,5%-24,7%; dan A. symmysta 2,2%-4,8%. Kepiting pasir betina dijumpai dengan persentase komposisi paling tinggi, yaitu 78,2% hingga 92,8%. Kepiting pasir E. emeritus juga ditemukan dengan kelimpahan rata-rata paling tinggi di kedua lokasi penelitian, yaitu 5 dan 34 ekor/100m2. Kepiting pasir E. emeritus dan H. adactyla yang ditemukan di pantai Bunton, Cilacap mempunyai kelimpahan lebih tinggi dari yang ditemukan di pantai Bocor, Kebumen, adapun kelimpahan rata-rata Albunea symmysta relatif sama di kedua lokasi penelitian, yaitu sekitar 1 ekor/100m2. Implikasi dari hasil penelitian ini adalah diversitas kepiting pasir di pesisir selatan Jawa Tengah relatif tinggi dengan kelimpahan yang berbeda-beda yang dipengaruhi oleh intensitas aktivitas manusia di wilayah pantai berpasir. Kata kunci: Albunea symmysta, Emerita emeritus, Hippa adactyla, kelimpahan, kepiting pasir, komposisi jenis  Sand crabs or mole crabs are benthic fauna that live in the sandy beaches. They have ecological and economic value. Because of fishing pressure to this organism, it requires wise management based on the characteristics of the sand crab population. Information on the type and abundance of sand crabs is important as an initial step in sustainable management of sand crabs. This study aims to determine the species composition and abundance of each species of sand crabs. Sand crab specimens were collected from two study sites, namely Bocor beach, Kebumen, and Bunton beach, Cilacap. The results showed that in both sites found three species of sand crabs, namely Emerita emeritus, Hippa adactyla, and Albunea symmysta. E. emerita found in greatest composition percentage, 70.5% -75.3%; followed by H. adactyla 22.5% -24.7%; and A. symmysta 2.2% -4.8%. Females sand crab found in highest composition percentage, which is 78.2% to 92.8%. E. emeritus were also found in highest abundance average in both sites, 5 and 34 ind.100m-2. E. emeritus and H. adactyla were found on Bunton beach, Cilacap have abundance higher than that found on Bocor beach, Kebumen, while average abundance ofAlbunea symmysta relatively similar in both study sites, which is about 1 ind.100m-2. Implication of this research is high diversity of sand crabs relatively on the southern coast of Central Java with varying abundance that affected by intensity of human activities in the sandy beach area. Keywords: abundance, Albunea symmysta, Emerita emeritus, Hippa adactyla, sand crab, species composition
Identification of Batoid Fishes from North Sumatra waters, Indonesia: Comparing between 12S and 16S rRNA gene as DNA marker Khairiza Lubis; Mufti Sudibyo; Achmad Farajallah; Nisfa Hanim; Person Pesona Renta
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 26, No 4 (2021): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.26.4.298-310

Abstract

Indonesia is one of the biodiversity hotspot areas for chondrichthyan fishes in the world, including batoid fishes. Nevertheless, some of the biological information of batoid fishes in Indonesia are still limited, such as batoid’s gene sequences for molecular identification. Two of those DNA marker for identifying batoid species, that it’s information still lacking in Indonesia is 12S and 16S gene. Therefore, this study aimed to identify batoid fishes species from North Sumatra using 12S and 16S rRNA gene fragments and comparing the identification result of those two markers. The genomic DNA was extracted from the pectoral fin muscle of eight batoid samples from eight different species. Amplification of both gene fragments was done by using two pairs of primers which were manually designed. The amplicon from both genes was sequenced and then were analyzed. In the present study successfully obtained eight good sequences of each 12S and 16S rRNA gene fragment. Five batoid samples were successfully identified to species level using both of gene fragments due to these identification results were matched with our previous morphological identification results. The identification result of Rhinoptera javanica sample based on 12S rRNA gene fragment was inaccurate due to several reasons. One of the possible reasons was due to the gene region that this work used did not contain sufficient information to differentiate Rhinoptera javanica until species level. The 3 remaining samples were unsuccessfully identified to species level using both genes due to the lack of conspecific targeted gene reference sequences in the database.
Exploration and prevalence of gastrointestinal worm in buffalo from West Java, Central Java, East Java and Lombok, Indonesia Wahyudin Abd. Karim; Achmad Farajallah; Bambang Suryobroto
Aceh Journal of Animal Science Vol 1, No 1: July 2016
Publisher : Syiah Kuala University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (900.172 KB) | DOI: 10.13170/ajas.1.1.3566

Abstract

The studies of parasites in buffaloes have not been widely explored. The aim of the present study was to explore the prevalence of gastrointestinal worm infection in buffaloes. The fresh faecal samples were collected from 89 buffaloes and observed by a modified McMaster technique. The faecal of buffaloes were collected in Bogor, Demak, East Java, and Lombok. The results of identification on gastrointestinal parasites show that there were one cestode and eight nematode. The total prevalence and infestation of cestodes and nematodes was found highest in Bogor. The prevalence and infestation of differences in geographical conditions were found highest in Bogor. The prevalence of gastrointestinal worm in males were highest than female, whereas for larger was found in females. The prevalence of gastrointestinal worms was found at age 1 year, whereas a larger infestation was found at the age of 1-5 years. The calculation of FEC in Bogor was 840 EPG, in Demak 375 EPG, in East Java 570 EPG and in Lombok 13 EPG. This study informed that there were nine genera of gastrointestinal worm found in Java and five genera in Lombok. Types larvae were found six i.e Strongyloides, Haemonchus, Cooperia, Oesophagostomum, Bunostomum and free living larvae.
MIGRASI Hemidactylus platyurus (Squamata: Gekkonidae) DI INDONESIA Devi Sandriliana; Rose Ida Ummah; Vella Nurazizah Djalil; Achmad Farajallah
ZOO INDONESIA Vol 27, No 1 (2018): Juli 2018
Publisher : Masyarakat Zoologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52508/zi.v27i1.3915

Abstract

Identifikasi Molekuler Microhyla, Tschudi 1839 dari Sumatera Berdasarkan Gen 16S rRNA Tengku Gilang Pradana; Amir Hamidy; Achmad Farajallah; Eric N. Smith
ZOO INDONESIA Vol 26, No 2 (2017): Desember 2017
Publisher : Masyarakat Zoologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52508/zi.v26i2.3717

Abstract

Penelitian ini bertujuan mengevaluasi posisi jenis Microhyla dari Sumatra berdasarkan sekuen data dari gen 16S rRNA di dalam pohon filogeni Microhyla secara umum. Pohon filogeni dihasilkan dengan menggunakan analisis Unweighted Pair Group Method with Aritmatic Means (UPGMA), Neighbor Joining (NJ), Maximum Likelihood (ML) dan Bayesian Inference (BI). Kami menggunakan Phrynella pulchra, Kaloula pulchra, Kalophrynus pleurostigma, Chalcorana chal-conota, dan Leptobrachium waysepuntiense sebagai anggota outgroup. Hasil pohon filogeni menunjukkan bahwa Micro-hyla terdiri dari sembilan kelompok utama, enam diantaranya merupakan Microhyla dari Sumatra. Microhyla dari Su-matra mengelompok dengan M. achatina, kelompok M. heymonsi, kelompok M. fissipes, kelompok M. palmipes, kelompok M. berdmorei dan kelompok M. superciliaris. Beberapa kelompok memiliki jarak genetik yang besar seperti pada M. achatina (3,1−3,4%), M. heymonsi (3,3−7,1%) dan M. palmipes (2,5−3,4%). Microhyla fissipes membentuk parafiletik dengan M. mukhlesuri, kemungkinan termasuk kedalam complex atau cryptic spesies. Hal ini membutuhkan kajian lebih lanjut secara morfologi dan suara guna menentukan status taksonomi dari masing masing populasi di dalam jenis-jenis tersebut.
EFEKTIVITAS JENIS ALAT TANGKAP DAN JENIS UMPAN YANG DIGUNAKAN UNTUK MENANGKAP UDANG AIR TAWAR DI DANAU KAMPUS INSTITUT PERTANIAN BOGOR Meutiya Agustina; Achmad Farajallah; Daisy Wowor
ZOO INDONESIA Vol 24, No 2 (2015): Desember 2015
Publisher : Masyarakat Zoologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52508/zi.v24i2.2337

Abstract

Studi mengenai penangkapan udang air tawar dengan metode eksperimental fishing telah dilakukan di Danau Kampus Institut Pertanian Bogor. Penelitian ini bertujuan untuk mengetahui efektivitas penangkapan udang air tawar dengan menggunakan alat tangkap Tray net dan bubu yang diberi tiga jenis umpan yang berbeda, yaitu terasi, pelet pakan ikan dan kelapa bakar. Alat tangkap tray net lebih efektif dibandingkan bubu dalam penangkapan udang, namun umpan terasi yang dimasukkan kedalam perangkap bubu adalah umpan yang paling efektif diantara ketiga jenis umpan yang diberikan. Udang air tawar yang diperoleh diidentifikasi dan didapatkan dua jenis udang yaitu Macrobrachium lanchesteri dan Caridina propinqua sebanyak 474 individu.
Hubungan Filogenetik Phrynella pulchra Boulenger, 1887 Berdasarkan Gen 16S rRNA Farid Akhsani; Amir Hamidy; Achmad Farajallah; Eric N. Smith
ZOO INDONESIA Vol 26, No 2 (2017): Desember 2017
Publisher : Masyarakat Zoologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52508/zi.v26i2.3721

Abstract

Phrynella merupakan marga monotipik yang sejauh ini hanya terdiri dari satu jenis, yakni Phrynella pulchra. Jenis ini terdistribusi di Semenanjung Malaysia, Sumatra dan Pulau Mentawai. Kami mengevaluasi status taksonomi populasi yang berasal dari Sumatra menggunakan data sekuen dari gen 16S rRNA mitokondria. Hubungan filogenetik dianalisis menggunakan Neighbour Joining (NJ), Maximum Likelihood (ML), Bayesian Inference Analisys (BI) dan Unweighted Pair Group Method with Arithmetic Means (UPGMA). Hasil penelitian menunjukkan bahwa P. pulchra adalah kelompok monofiletik terhadap anggota luar (Metaphrynella, Kaloula dan Micryletta). Kelompok monofiletik P. pulchra terbagi menjadi dua kelompok besar: Sumatra dan Semenanjung Malaysia. Kelompok Sumatra terdiri dari dua subkelompok: Aceh dan Sumatra Utara- Bengkulu. Jarak genetik (uncorrected p-distance) antara populasi Semenanjung Malaysia dan Sumatra berkisar antara 1,1 sampai 2,0%, sedangkan di dalam populasi Sumatra berkisar antara 0,0 sampai 1,1%. Rendahnya jarak genetik populasi Semenanjung Malaysia dengan Sumatra secara taksonomi menunjukkan populasi tersebut masih berada pada tingkat Jenis yang sama.
Co-Authors A Anggraeni A Anggraeni A Anggraini A Batubara A. Anggraeni A. Anggraeni Achmad, Alfiyan Agus Alim Hakim AKICHIKA MIKAMI ALFIYAN, ACHMAD Ali Mashar Ali Suman AMIR HAMIDY Amir Hamidy Amir Hamidy Annawaty Annawaty, Annawaty Arma Aditya Kartika Aron Batubara Aron Batubara Arum Widayati, Kanthi Asri Febriana Asri Febriana, Asri B Tiesnamurti B. Tiesnamurti Baiq Farhatul Wahidah Bambang Purwantara Bambang Suryobroto Burhanuddin Burhanuddin C Sumantri C Sumantri C. SUMANTRI C. Sumantri Cece Sumantri D Perwitasari D, Nurhayati D. Herdiana D. Rahmat Daisy Wowor Daisy Wowor Daisy Wowor, Daisy Dede Setiadi Devi Sandriliana DEWI APRI ASTUTI DEWI PURNAMA Dwi Sendi Priyono Dyah Perwitasari DYAH PERWITASARI -FARAJALLAH E Andreas E. Andreas E. Andreas Eric N. Smith Eric N. Smith Erni Sulistiawati Eryk Andreas Farid Akhsani Fauzan, Muhammad Fakhri Ferdy Saputra H. Nuraini HANIM, NISFA HERA MAHESHWARI Hermansyah, Alfandy I Inounu Imas Batubara Irma Shita Arlyza Isdoni Bustaman J F Salamena Jarmuji Jarmuji Jeane Siswitasari Mulyana Joni Setiawan Jumadin, La Kaiin, Ekayanti Mulyawati KANTHI ARUM WIDAYATI Khairiza Lubis koekoeh santoso KREY KREY Kuswati Kuswati Lora purnamasari, Lora Luthfia Nuraini Rahman M Doloksaribu M Karmita M. Doloksaribu Mahendra, Arindina Maria Ulfah Maria Ulfah Mennofatria Boer Meutiya Agustina Meutiya Agustina, Meutiya Moch. Syamsul Arifin Zein, Moch. Syamsul Arifin Mufti Sudibyo N Satriani NEVIATY PUTRI ZAMANI Nirmala Fitria Firdhausi Nisfa Hanim Nisfa Hanim Novita Anggraeni Nurhayati D Nurlisa Alias Butet Nurulvadini Safrudin Paskah Partogi Agung Person Pesona Renta Pradana, Tengku Gilang Pudji Achmadi Putri, Vinna Windy R Diyono R Misrianti R R Noor R R Noor R.R. Noor R.R. Noor Rarah Ratih Adjie Maheswari RIKA RAFFIUDIN Rissa Herawati Ginting Riyanto, Awal Riyanto, Awal Rose Ida Ummah Rudi Alek Wahyudin Sasmita, Annissa Nuridfi Silvia Puspitasari Siti Lutvaniyah Slamet Mulyanto Smith, Eric N. Soemarno, Suprayogo Soemarno, Suprayogo Syahruddin Said Tanaka, Hiroyuki TARUNI SRI PRAWAST MIEN KAOMINI ANY ARYANI DEDY DURYADI SOLIHIN TARUNI SRI PRAWASTI Tatewaki, Takafumi Tri Eko Susilorini Tsuji, Yamato Vella Nurazizah Djalil Wahyudin Abd. Karim Widayat, Kanthi Arum i Widayati, Kanthi Wijayanti, Pristina Tuti Yanti Ariyanti Yanti Ariyanti Yusli Wardiatno