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All Journal Jurnal Biologi Udayana ILMU KELAUTAN: Indonesian Journal of Marine Sciences Biotropika Journal of Innovation and Applied Technology Jurnal Kelautan Tropis Jurnal Sumberdaya Akuatik Indopasifik Jurnal Perikanan Universitas Gadjah Mada Jurnal Iktiologi Indonesia (Indonesian Journal of Ichthyology) Musamus Fisheries and Marine Journal Bioscientist : Jurnal Ilmiah Biologi Nekton
Muhammad Dailami
Program Studi Budidaya Perairan, Fakultas Perikanan Dan Ilmu Kelautan, Universitas Brawijaya
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Computer Science & IT Earth & Planetary Sciences Economics, Econometrics & Finance Education Environmental Science Immunology & microbiology Social Sciences

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Analisis Pola Pertumbuhan dan Pendekatan DNA Barcoding untuk Identifikasi Turbo stenogyrus P. Fischer, 1873 (Mollusca: Gastropoda) Dandi Saleky; Simon P.O Leatemia; Thomas F. Pattiasina; Isma Isma; Rosa D. Pangaribuan; Marius A. Welliken; Edy H.P. Melmambessy; Muhammad Dailami
Biotropika: Journal of Tropical Biology Vol 8, No 2 (2020)
Publisher : University of Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.biotropika.2020.008.02.03

Abstract

Pengelolaan dan pelestarian keanekaragaman hayati berawal dari pengetahuan tentang ketersediaan sumberdaya, identifikasi, dan sistematika spesies. Banyaknya spesies Turbinidae dengan berbagai bentuk morfologi dan transformasi bentuk menjadikan identifikasi dengan gen COI sangat penting dalam mempercepat pengungkapan identitas spesies. Penelitian ini dilakukan dengan tujuan menganalisis pola pertumbuhan dan mengidentifikasi gastopoda Turbinidae dengan pendekatan DNA barcode. Hasil identifikasi berdasarkan karakter morfologi menunjukkan bahwa genus Turbo yang diamati adalah dari spesies Turbo stenogyrus. Analisis pola pertumbuhan menunjukkan bahwa pola pertumbuhan T. stenogyrus adalah allometrik negatif. Amplifikasi DNA dengan gen COI menghasilkan panjang sekuen DNA 650 bp dengan hasil identifikasi sesuai dengan pengamatan morfologi yaitu Turbo stenogyrus. Berdasarkan analisis filogenetik dan jarak genetik, sekuen DNA yang dianalisis membentuk clade yang sama dengan spesies Turbo stenogyrus dengan jarak genetik terdekat 4,2%. Analisis genetik melalui gen COI sangat baik dan memberi kemudahan dalam identifikasi spesies gastropoda
Improvement Of Teaching Material And Capacity Building On Laboratory Of Aquaculture, Fish Disease Division, Faculty Of Fisheries And Marine Science, Universitas Brawijaya Maftuch Maftuch; Sri Andayani; Yenny Risjani; Muhammad Musa; Asus Maizar Suryanto Hertika; Febriyani Eka Supriatin; Muhammad Dailami
Journal of Innovation and Applied Technology Vol 6, No 2 (2020)
Publisher : Lembaga Penelitian dan Pengabdian Kepada Masyarakat Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jiat.2020.006.02.15

Abstract

The laboratory is one of the effective learning places for students to develop scientific knowledge and skills. FPIK has 6 laboratories and 4 UPTs that can be used by students and lecturers. In practice, there are still limitations in this laboratory, including the malfunction of the equipment in the laboratory, due to damage to the equipment and the lack of mastery in operating the tools. This community service is intended to help solve problems that exist in the Aquaculture Laboratory of the Fish Disease Division of FPIK UB by increasing the capacity of human resources and laboratories in testing services. The form of service activities carried out includes organizing online workshops on fish hematology and histology testing, making learning videos for practicum analysis of fish hematology, developing collaboration networks with other laboratories, adding laboratory testing instruments and packages and cooperation in scientific publications.
DNA barcoding pada invertebrata laut Agus Mohammad Hikam; Nurul Jadid Mubarakati; Muhammad Dailami; Abdul Hamid A. Toha
Jurnal Biologi Udayana Vol 25 No 1 (2021): JURNAL BIOLOGI UDAYANA
Publisher : Program Studi Biologi, Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas Udayana

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24843/JBIOUNUD.2021.v25.i01.p06

Abstract

A large number of species of marine invertebrates that have similar morphology cause misidentification very possible. Molecular species identification is important in taxonomy study accurately. This study aims to determine the identity of Aquatic Papua marine invertebrates with DNA barcoding technique using markers COI gene (Cytochrome c oxidase I). The study identified 29 individuals of marine invertebrates, which came from sea cucumbers (6 samples), lobsters (6 samples), octopus (6 samples), chitons (5 samples), and sea urchins (6 samples). Molecular identification methods consist of DNA isolation, PCR COI gene fragments, sequencing, and DNA sequence analysis using bioinformatics software. The results showed that the sea cucumber came from the Bohadschia marmorata species, the lobster came from the Panulirus versicolor species, the octopus came from the Octopus cyanea species, the chiton came from the Ischnochitonaustralis species, and the sea urchins came from the Tripneustesgratilla species. The similarity of samples and references are in the range of 84.58 to 100.00%. The disparity index, genetic distance, and phylogenetic tree supported this result.
Cryptic Species from Biodiversity Hotspot: Estimation of Decapoda on Dead Coral Head Pocillopora in Raja Ampat Papua Eka Maya Kurniasih; Andrianus Sembiring; Ni Putu Dian Pertiwi; Aji Wahyu Anggoro; Ni Kadek Dita Cahyani; Muhammad Dailami; Ambariyanto Ambariyanto; Diah Permata Wijayanti; Christopher P. Meyer
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 25, No 1 (2020): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (404.259 KB) | DOI: 10.14710/ik.ijms.25.1.1-6

Abstract

Cryptic organisms that live within the interstices of reef habitats contribute significantly to coral reef biodiversity. One example of this cryptic biodiversity is the high abundance of decapods in dead coral heads that associated with various biota. However, this diversity poorly studied especially species identification and species richness. This study aims to estimate the decapods diversity in Raja Ampat, Papua, using Pocillopora dead coral head method as semi-quantitative sampling approach. Raja Ampat in Papua is chosen because it situated in the center of Coral Triangle marine hotspot. Data were collected from 10 dead coral heads of genus Pocillopora from 10-meter depth near the islands of Kri and Misool. This study observed a total of 205 individuals Decapoda from Kri Island and 672 Individual from Misool Islands. Species richness observation (Chao1 and ACE) of the total samples reports only 11 families of decapoda detected in this study. Rarefaction curve reach an asymptote after all after all ten dead coral were analyzed; indicating that additional sample collection would not change estimates of diversity found in this study. The Shannon-Wiener index diversity on the Kri Island showed lower diversity value (2.09) compared to Misool Island (2.18). In the future, this research can be used as a basis for understanding the diversity of coral reefs as well as for management and conservation of coral reef ecosystems.
Pola Pertumbuhan dan Identifikasi Genetik Turbo setosus Gmelin, 1791 [Turbinidae, Gastropoda] Dandi Saleky; Febriyani Eka Supriyatin; Muhammad Dailami
Jurnal Kelautan Tropis Vol 23, No 3 (2020): JURNAL KELAUTAN TROPIS
Publisher : Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jkt.v23i3.7514

Abstract

Morphological dan genetic identification is an essential part of biology and ecological study. Environmental degradation, physical and chemical facto in water, and utilization of gastropod by society will give impact in distribution pattern, population size, morphology and genetic characteristic of the snail. This research aims to analyze the growth pattern and molecular aspect of Turbo setosus. The variable that examined is total weight and length, and cytochrome oxidase subunit one gene sequence. The growth factor of T. setosus is negative allometric, which means weight growth is slower than the length growth. The total length of cytochrome oxidase subunit 1 of these samples were 650 base pairs. Based on the DNA barcoding analysis, the sequence is 96.92% identic with the sequence of T. setosus in GenBank. The phylogenetic tree was reconstructed with neighbour-joining methods and 1000 replication bootstrap, show the clade grouping based on the similarity and genetic distance of the species. The sequence data is vital for species identification fast and accurately.    Identifikasi morfologi dan genetik menjadi bagian penting dari setiap studi biologi maupun ekologi, degradasi lingkungan, faktor fisik-kimia lingkungan dan pemanfaatan gastropoda secara terus menerus akan mempengaruhi penyebaran, penurunan populasi, karakteristik morfologi dan juga karakter molekuler spesies. Penelitian ini bertujuan untuk menganalisis pola pertumbuhan dan karakter molekuler Turbo setosus. Variabel yang diukur adalah berat total dan panjang total serta identifikasi molekuler dengan menggunakan gen sitokrom oksidase I. Pola pertumbuhan T. setosus adalah allometrik negatif yang berarti pertambahan berat lebih lambat dari pertambahan panjang. Hasil identifikasi dengan DNA barcoding diperoleh spesies T. setosus dengan panjang sekuen DNA 650 bp. Rekonstruksi filogenetik dengan metode Neighbor-Joining boostrap 1000x memperlihatkan pengelompokan sekuen berdasarkan kimiripan dan jarak genetik antar spesies. penting dalam identifikasi spesies secara cepat, tepat dan akurat.
Konservasi Genetik Ikan Kakap Putih (Lates calcarifer, Bloch, 1790) Melalui Pendekatan DNA Barcoding dan Analisis Filogenetik di Sungai Kumbe Merauke Papua Dandi Saleky; Muhammad Dailami
Jurnal Kelautan Tropis Vol 24, No 2 (2021): JURNAL KELAUTAN TROPIS
Publisher : Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jkt.v24i2.10760

Abstract

Genetic data is very important as the basis for fisheries management and conservation related to connectivity between regions and population structure. White snapper Fish is one of the fish that has high economic value which is utilized either by its meat or by its swim bladder. This research was aimed to identify the species of white snapper fish were collected from the Kumbe River, Merauke Regency, Papua using the Cytochrome Oxidase I gene. The results shows that this sample is a species of Lates calcarifer, Bloch, 1790 with 100% similarity. The haplotype of white snapper fish from Merauke has similarities with the haplotype from Australia, Malaysia and China, this indicating that there is gene flow and connectivity among those locations. The phylogenetic tree explains the grouping of species based on genetic distance and the level of DNA Sequences similarities. Molecular approach can be used in the management and conservation of fish with high economic value.
Sizing and scarring of whale shark (Rhincodon typus Smith, 1828) in the Cenderawasih Bay National Park Yusup A Jentewo; Roni Bawole; Tresia S Tururaja; Mudjirahayu Mudjirahayu; Zeth Parinding; Hendrikus R Siga; Muhammad Dailami; Abdul Hamid A Toha
Jurnal Iktiologi Indonesia Vol 21 No 3 (2021): October 2021
Publisher : Masyarakat Iktiologi Indonesia (Indonesian Ichthyological Society)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.32491/jii.v21i3.587

Abstract

This study aims to determine the total length and scar condition of the body of whale sharks (Rhincodon typus) in Cendrawasih Bay National Park (TNTC), Papua-Indonesia. Photo-identification was used to identify individuals of the whale shark R. typus based on spot patterns behind the last gill slit of each individual. Photo-identification was also used to determine the scar of the whale shark. The total length of whale sharks were estimated based on the length of a snorkeller (assumed to be 1.6 m) swimming alongside the whale shark. We identified 21 individuals of R. typus. Of these 21 individuals, 14 were new sightings and seven were re-sightings that have been recorded in the previous photo collection database. R. typus ranged in size from 2 to 5 m total length (average 3.78 m, ±0,86, N= 21). Based on their size, all individuals of whale shark were categorized as juvenile. 52% of R. typus identified had scars and 38 % were not and 10% were unknown. The majority of whale sharks had amputation (12 individuals) and abrasion (7 individuals) scars. Scars occurred most often on the caudal fin and dorsal fin, five and four individuals respectively. This information is useful for understanding potential threats and designing better management programmes for R. typus conservation in TNTC. Abstrak Penelitian ini bertujuan untuk menganalisis panjang total dan kondisi luka hiu paus (Rhincodon typus) di Taman Nasional Teluk Cendrawasih (TNTC), Papua-Indonesia. Identifikasi foto digunakan untuk menentukan identitas individu hiu paus berdasarkan pola bintik di balik celah insang terakhir masing-masing individu. Identifikasi juga menggunakan foto berdasarkan luka hiu paus. Panjang tubuh total hiu paus diperkirakan berdasarkan panjang seorang perenang snorkel (diasumsikan 1,6 m) yang berenang bersama hiu paus. Kami mengidentifikasi 21 individu hiu paus, 14 individu diantaranya adalah hiu paus baru, sedangkan tujuh individu lainnya merupakan hiu paus yang pernah tercatat dalam database koleksi foto sebelumnya. Hiu paus berukuran panjang total 2 sampai 5 m (rata-rata 3,78 m, ± 0,86, N = 21). Berdasarkan ukurannya, semua individu hiu paus termasuk dalam kategori yuwana. Sebanyak 52% dari hiu paus yang diidentifikasi memiliki luka, 38% tidak memiliki luka dan 10% tidak teridentifikasi. Mayoritas hiu paus memiliki bekas luka potong (12 individu) dan luka lecet (tujuh individu). Lokasi luka paling sering terjadi pada sirip ekor dan sirip punggung, masing-masing lima dan empat individu. Informasi ini berguna untuk memahami potensi ancaman dan untuk merancang program pengelolaan yang lebih baik untuk konservasi R. typus di TNTC.
Identifikasi dan Analisis Filogenetik Ikan Ekonomis Penting Oreochromis sp. dengan Pendekatan DNA Barcoding Reny Sianturi; Muhammad Dailami; Dandi Saleky
Bioscientist : Jurnal Ilmiah Biologi Vol 9, No 2 (2021): December
Publisher : Department of Biology Education, FSTT, Mandalika University of Education, Indonesia.

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33394/bioscientist.v9i2.4027

Abstract

Species identification is one of the most basic and important factors in fisheries management. Oreochromis sp., such as tilapia (Oreochromis mosambicus) and tilapia (Oreochromis niloticus) are introduced species of fish originating from outside Merauke which are now the dominant fish and are commonly found in inland waters of Merauke. The purpose of this study was to identify the economically important fish species Oreochromis sp. which landed at Merauke Traditional Market with DNA Barcoding approach. DNA amplification with the COI gene resulted in a DNA sequence length of 655 bp with the identification result being Tilapia (Oreochromis niloticus). Based on the phylogenetic tree data and genetic distance, the DNA sequences of the samples formed the same clade as the Oreochromis niloticus sequences from GeneBank with 0% genetic distance and it was estimated that these species came from the same parents. Identification with DNA Barcoding makes it easy to identify species quickly and accurately.
Identifikasi Genetik Ikan Teri dari Teluk Cenderawasih dengan pendekatan DNA Barcoding Muhammad Dailami; Yuni Widyawati; Abdul Hamid A. Toha
Musamus Fisheries and Marine Journal Volume 3 Number 2, April 2021
Publisher : Faculty of Agriculture Musamus University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.35724/mfmj.v3i2.3521

Abstract

The Cenderawasih Bay is a marine habitat for whale sharks (R. typus) which appear almost all year round. The appearance of this whale shark is triggered by various factors, including the food. Anchovy is one of the attractions for the emergence of whale sharks, so it is necessary to conduct genetic, biological and ecological studies. Anchovy has a small in size, making it difficult to identify morphologically. The purpose of this study was to genetically identify anchovy samples obtained from Cenderawasih Bay and compare the sequences with the GenBank database. The COI gene fragments were amplified by PCR method, using primer jg-LCO and jg-HCO. Sequencing is carried out from two directions, forward and reverse with the sanger termination dideoxy method. The resulting DNA sequence has a length of 669 base pairs encoding 223 amino acids. The results of homological comparisons with the NCBI and BOLD System databases show that this sample has similarities to the COI sequence of Spratelloides gracilis with a similarity number up to 99%. The results of the phylogenetic tree analysis showed that the anchovy samples from Cenderawasih Bay were in one clade with S. gracilis from Japan and separated from the clade of S. gracilis from the Red Sea, with a distance between clades is 0.104. This result is in line with the identification by homological comparison in the NCBI and BOLD System.
Kajian Molekuler Ikan Oreochromis spp. dari Perairan Daratan Merauke-Papua, Berdasarkan DNA Mitokondria Fragmen Gen Sitokrom Oksidase Subunit I Dandi Saleky; Reny Sianturi; Muhammad Dailami; Aradea Bujana Kusuma
Jurnal Perikanan Universitas Gadjah Mada Vol 23, No 1 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jfs.61026

Abstract

Pemanfaatan perikanan secara lestari sangat diperlukan agar sumberdaya perikanan yang ada saat ini bisa terus dimanfaatkan dan juga dalam rangka pemulihan stok perikanan yang telah rusak. Ikan nila (Oreochromis niloticus) dan ikan mujair (Oreochromis mossambicus) secara luas telah dikenal sebagai salah satu spesies ikan air tawar yang penting dalam perikanan budidaya. Penelitian ini dilakukan dengan tujuan identifikasi spesies ikan Oreochromis spp. dari perairan daratan Merauke dengan menggunakan marka gen COI. Amplifikasi DNA dengan gen COI menghasilkan panjang sekuen DNA 656 bp dengan hasil identifikasi adalah O. niloticus dan O. mussambicus dengan tingkat kemiripan 100 % pada masing-masing spesies. Berdasarkan analisis filogenetik dan jarak genetik, sekuen DNA yang dianalisis membentuk clade sesuai dengn hasil indentfikasi dengan jarak genetik 0,000 - 0,002 pada ikan nila dan 0,000 pada ikan mujair. Analisis keragaman genetik ditemukan hanya 1 haplotype dari kedua jenis ikan tersebut. DNA barcode dan filogenetik dapat digunakan dalam mengidentifikasi spesies dalam pengelolaan dan konservasi.
Co-Authors Abdul Hamid A. Toha Abraham Welliam Manumpil Agus Mohammad Hikam Aji Wahyu Anggoro Ambariyanto Ambariyanto Andrianus Sembiring Aradea Bujana Kusuma Asus Maizar Suryanto H Buana Insan Kamil Christopher P. Meyer Condro Puspo Nugroho Dandi Saleky Dandi Saleky Dandi Saleky Dandi Saleky Dandi Saleky Dandi Saleky Dean Rama Prayoga Delvira Riska Ananta Dewa Gede Raka Wiadnya Diah Permata Wijayanti Dyah Kinasih Wuragil EDY H.P. MELMAMBESSY Eka Maya Kurniasih Elsa Syafi’ul Umma Febriyani Eka Supriyatin Fitri Nur Azizah Hardoko Hardoko Hariati, Anik Martinah Heder Djamaludin Hendrikus R Siga Indria Graha Hayuningtyas Isma Isma Jemmy Manan Maftuch Maftuch Marius Agustinus Welliken Mudjirahayu Mudjirahayu Muhammad Musa Ni Kadek Dita Cahyani Ni Putu Dian Pertiwi Nurul Jadid Mubarokati Putri Nur Azizah Reny Sianturi Roni Bawole Rosa D. Pangaribuan Simon P.O Leatemia Sri Andayani Supriatin, Febriyani Eka Surya Dewa Ramadhan Thomas F. Pattiasina Tresia S Tururaja Vivi Nurhadianty Yenny Risjani Yuni Widyawati Yusup A Jentewo Zeth Parinding