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All Journal HAYATI Journal of Biosciences MEDIA PETERNAKAN - Journal of Animal Science and Technology Jurnal Ilmu Pertanian Indonesia MEDIA KONSERVASI Jurnal Ilmu dan Teknologi Kelautan Tropis Buletin Peternakan ILMU KELAUTAN: Indonesian Journal of Marine Sciences JBIO: jurnal biosains (the journal of biosciences) BIOTROPIA - The Southeast Asian Journal of Tropical Biology Jurnal Biologi dan Pembelajarannya (JBP) Jurnal Ilmu Ternak Veteriner Journal of the Indonesian Tropical Animal Agriculture Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (Journal of Natural Resources and Environmental Management) JITRO (Jurnal Ilmiah dan Teknologi Peternakan Tropis) BioCONCETTA Journal of Tropical Biodiversity and Biotechnology Aceh Journal of Animal Science JURNAL BIOLOGI INDONESIA ZOO INDONESIA Jurnal Biologi Tropis Majalah Ilmiah Biologi BIOSFERA: A Scientific Journal Bioma : Jurnal Biologi Indonesia AL-HAYAT: Journal of Biology and Applied Biology Zoo Indonesia Jurnal Sylva Lestari Treubia Biodiversitas Journal of Biological Diversity
ACHMAD FARAJALLAH
Departemen Biologi, Fakultas Matematika Dan Ilmu Pengetahuan Alam, Institut Pertanian Bogor, Kampus IPB Dramaga Bogor, 16680, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Decision Sciences, Operations Research & Management Earth & Planetary Sciences Education Energy Environmental Science Health Professions Immunology & microbiology Library & Information Science Materials Science & Nanotechnology Medicine & Pharmacology Veterinary Other

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Short Communication: Herpetofauna diversity, potential ecotourism in Mount Galunggung, West Java, Indonesia AWAL RIYANTO; TAUFAN NURZAMAN SULAEMAN; NUR RACHMAN; DIKI MUHAMAD CHAIDIR; WAHYU TRILAKSONO; ACHMAD FARAJALLAH
Biodiversitas Journal of Biological Diversity Vol. 20 No. 4 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200433

Abstract

Abstract. Riyanto A, Sulaeman TN, Rachman N, Chaidir DM, Trilaksono W, Farajallah A. 2019. Short Communication: Herpetofauna diversity, potential ecotourism in Mount Galunggung, West Java, Indonesia. Biodiversitas 20: 1173-1179. Here we provide a list of herpetofauna at Mount Galunggung, West Java, Indonesia as potential biodiversity for ecotourism. Data were collected from our observations in March 2013 and November 2018 using visual and acoustic encounter search methods in the three zones  (hot springs, craters, and foothills) on the nature tourism destination of the mount. We revealed 35 species of herpetofauna and their local distribution on these zones. Even though the diversity of herpetofauna has not been observed completely, we suggested that the biodiversity data from this zone should be used as the basic capital in turning nature tourism base into ecotourism base, so that it would provide more benefits to biodiversity conservation itself and to the local community.
The origin of pesisir cattle based on D-loop mitochondrial DNA Anzalia Eka Putri; ACHMAD FARAJALLAH; DYAH PERWITASARI
Biodiversitas Journal of Biological Diversity Vol. 20 No. 9 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200919

Abstract

Abstract. Putri AE, Farajallah A, Perwitasari D. 2019. The origin of pesisir cattle based on D-loop mitochondrial DNA. Biodiversitas 20: 2569-2575. Pesisir cattle is one of Indonesia's local cattle descended from Bos indicus which has small body characteristics. It was assumed due to crossbreeding between pesisir cattle and other cattle. Therefore this study aims to study the origin of pesisir cattle based on the D-loop mtDNA region and to find out the phylogenetic relationships between pesisir cattle and other cattle. Cattle blood samples were taken in two locations, Krui Way and Tanah Rekah. Amplification of the mitochondrial gene using the primary pair of collections of Dr. Achmad Farajallah, namely AF22 (forward) 5'-GCGTACGCAATCTTACGATCA-3' and AF23 (reverse) 5'-ATGCAGTTAAGTCCAGCTAC-3'. Reconstruction of phylogenetic trees was analyzed using the Neighbor-Joining Method based on Kimura 2 Parameters. The results of the mtDNA analysis in the D-loop region showed that there were two broods in pesisir cattle, namely Bos indicus and Bos javanicus. The closeness between these species is due to the close geographical distance between Bos indicus originating from Way Krui, Lampung and Bos javanicus from Java.
Short Communication: Insulin-like growth factor 1 (IGF-1) gene polymorphisms in Madura karapan and beef cattle breed Dyah Perwitasari-Farajallah; ROSE IDA UMMAH; REVA ADZANI NURJANNAH; ACHMAD FARAJALLAH
Biodiversitas Journal of Biological Diversity Vol. 20 No. 10 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d201041

Abstract

Abstract. Perwitasari D, Ummah RI, Nurjannah RA, Farajallah A. 2019. Short Communication: Insulin-like growth factor 1 (IGF-1) gene polymorphisms in Madura karapan and beef cattle breed. Biodiversitas 20: 3070-3074. Madura cattle breed is one of the four existing indigenous cattle breeds (Aceh, Pesisir, Madura, and Bali) in Indonesia. This Indonesian breed derived from crossbreeding between Bos indicus (zebu) and Bos javanicus (banteng). Cattle raising in Madura focused on three purposes i.e. bull race competition (karapan), beauty contest (sonok) and meat production. Insulin-like Growth Factor 1 (somatomedin-IGF-1) is a protein that plays a key role in cell differentiation, embryogenesis, growth, and regulation of metabolism. In cattle, the IGF-1 gene was localized on chromosome 5. Due to their role in the regulation of cell proliferation and animal growth, the IGF-1 and its gene are considered as candidate markers for growth rate and meat production traits. This research aimed to determine nucleotide variations in the IGF-1 gene among Madura karapan and beef cattle. PCR amplification of IGF-1 gene was conducted using a pair of primers. Amplicon was sent to commercial DNA sequencing company (1st Base) to perform DNA sequencing analysis. The size of IGF-1 gene was approximately 762 bp consisted of intron 3, exon 4, and intron 4. Sequence data were analyzed using MEGA 7 to identify the presence of nucleotide variation. Bos indicus (NC032654) was used as a reference sequence. The results showed no polymorphism was observed in intron 3 and exon 4 of Madura karapan and beef cattle breed. We determined G491A point mutation in intron 4. In conclusion, IGF-1 could not be able to be used as a genetic marker to differentiate karapan and beef cattle and furthermore morphological characteristics still can be applied as a standard for selection.
Short Communication: The mitochondrial cytochrome c oxidase subunit I (COI) for identification of batoids collected from landed sites in Medan, Indonesia MUFTI SUDIBYO; khairiza lubis; ACHMAD FARAJALLAH; NISFA HANIM
Biodiversitas Journal of Biological Diversity Vol. 21 No. 11 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d211149

Abstract

Abstract. Lubis K, Sudibyo M, Farajallah A, Hanim N. 2020. Short Communication: The mitochondrial cytochrome c oxidase subunit I (COI) for identification of batoids collected from landing sites in Medan, Indonesia. Biodiversitas 21: 5414-5421.  Batoids are member of Elsamoranch subclass which consist of many species. Most of batoids species are overexploited, especially in Medan Indonesia. Up to presents, the information about diversity of rays on the east coast of North Sumatra, Indonesia was very limited. Therefore, this research aimed to investigate the diversity of rays on the east coast of North Sumatra. We examined the morphological trait of 82 individuals of batoid from three landing sites on the east coast of North Sumatra, namely: Tanjung Balai, Belawan, and Percut, then identify its species based on determination key. After that, we collected pectoral muscle tissue from an individual in each species which successfully identified to extract its genomic DNA. Molecular based identification was carried out by using DNA fragment form COI gene. The successfully amplificated COI gene DNA fragment then was sequenced and analyzed. Based on morphological trait, we successfully identifying nine species of batoid, which is Maculabatis gerrardi, Gymnura poecilura, Dasyatis zugei, Brevitrygon heterura, Neotrygon kuhlii, Hemitrygon bennettii, Rhinobatos jimbaranensis, Rhinoptera javanica, and Taeniura lymma. The result of identification based on COI gene DNA fragment was in congruent with morphological-based identification based on data BLAST-N and genetic distance value within same species. The nucleotide diversity within same species ranged from 0-15 nucleotide variants.
Mitochondrial DNA suggests the existence of two distinct species in Moluccas and New Guinea within Nyctimystes infrafrenatus (Günther, 1867) Taufan Nurzaman Sulaeman; AMIR HAMIDY; ACHMAD FARAJALLAH; ANTOINE FOUQUET; AWAL RIYANTO; EVY ARIDA; MULYADI Mulyadi; WAHYU TRILAKSONO; MISBAHUL MUNIR
Biodiversitas Journal of Biological Diversity Vol. 22 No. 8 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220823

Abstract

Abstract. Sulaeman TN, Hamidy A, Farajallah A, Fouquet A, Riyanto A, Arida E, Mulyadi, Trilaksono W, Munir M. 2021. Mitochondrial DNA suggests the existence of two distinct species in Moluccas and New Guinea within Nyctimystes infrafrenatus (Günther, 1867). Biodiversitas 22: 3287-3297. Nyctimystes infrafrenatus is a widespread frog species distributed across northern Australia, New Guinea, Bismarck archipelago and in the eastern part of Indonesian archipelago. The species thus encompasses two biogeographic regions, Papua and Wallacea. We evaluated the phylogenetic relationships among the populations from Papua and Moluccas based on two mitochondrial loci (16S rRNA and Cytochrome Oxidase Subunit I). Two major subclades are recovered within Nyctimystes infrafrenatus with subclade A being represented by populations from New Guinea and northern Australia and subclade B by Moluccan populations (Halmahera and Tidore). Genetic distances (2.3-4.2% in 16S rRNA) between these subclades suggest they could belong to distinct species. Since New Guinea populations correspond to the nominal species and that Nyctimystes tennuigranulatus (Boettger 1895), currently considered as a junior synonym of Nyctimystes infrafrenatus, is available for the northern Moluccan populations, we proposed to remove this taxon from synonymy. However, samples used in this study come from northern Moluccas, further studies including samples from Ambon (where another synonym was described i.e. Calamita dolichopsis) is needed to determine the taxonomic status of the southern Moluccan population whether they are conspecific with northern Moluccan population or not.
Sexual dimorphism phenomenon of first record Macrobrachium lar (Fabricius, 1978) from the southern Sukabumi, West Java, Indonesia RISKA RISMAWATI; MAJARIANA KRISANTI; ACHMAD FARAJALLAH
Biodiversitas Journal of Biological Diversity Vol. 25 No. 5 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250509

Abstract

Abstract. Rismawati R, Krisanti M, Farajallah A. 2024. Sexual dimorphism phenomenon of first record Macrobrachium lar (Fabricius, 1978) from the southern Sukabumi, West Java, Indonesia. Biodiversitas 25: 1929-1937. Macrobrachium lar (Fabricius, 1798), commonly known as monkey river prawn, is a widely distributed amphidromous species found in various freshwater habitat, displaying adaptability to different salinities. This habitat diversity often leads to the emergence of cryptic species, particularly in freshwater shrimp. Notably, M. lar exhibits sexual dimorphism. The degree of sexual dimorphism can differ among decapod crustaceans. This study reports the first discovery of M. lar in Sukabumi, West Java, collected in January 2023 from a river tributary in the Cibitung Sub-district with insights into the sexual dimorphism phenomenon. We conducted species confirmation through molecular analyses. We use the Cytochrome Oxidase subunit 1 (COI) gene fragment for molecular analysis. Phylogenetic tree values revealed that the samples we found proved to be M. lar, forming a group with M. lar from the Indian-West Pacific region and M. lar from Pangandaran. However, they were distinct from the outgroups M. idae and M. Lepidactyloides. In this study, we only use the adult sample, which is already well-developed. Morphological analysis indicated that all morphological characters in males were larger than in females, with significant sexual dimorphism observed in the second pereiopod and its parts (ischium, merus, carpus, and palm). Although the body sizes of males and females are significantly different in a positive direction, the most distinguishing feature facilitating the identification of both as the same species is the pattern on the second pereiopod, which has irregular blotches of brownish coloration.
Diversity of freshwater shrimp species of the genus Macrobrachium (Decapoda: Caridea) in the big river of East Kalimantan, Indonesia MAULIDA NUR ANNISA; KANTHI ARUM WIDAYATI; JUSMALDI JUSMALDI; ACHMAD FARAJALLAH
Biodiversitas Journal of Biological Diversity Vol. 26 No. 3 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260348

Abstract

Abstract. Annisa MN, Widayati KA, Jusmaldi, Farajallah A. 2025. Diversity of freshwater shrimp species of the genus Macrobrachium (Decapoda: Caridea) in the big river of East Kalimantan, Indonesia. Biodiversitas 26: 1474-1484. Freshwater prawns are widely distributed in Indonesia, belonging to the subphylum Crustacea and order Decapoda. Freshwater shrimp commonly found in Indonesia belong to the families Atyidae and Palaemonidae. The Palaemonidae family is usually dominated by species of the genus Macrobrachium. Information on freshwater shrimp diversity in East Kalimantan, Indonesia, has never been reported, while water quality in East Kalimantan is declining due to increased exploitation of natural resources. This study was conducted to provide baseline information on freshwater shrimp species diversity for the future, before further changes occur in the East Kalimantan region and we provide Cytochrome Oxidase subunit I (COI) sequence data for molecular identification. Methods used for species identification based on morphological characters and species confirmation through molecular analysis using Cytochrome Oxidase subunit I (COI) gene fragments for molecular analysis. This study reports the diversity of freshwater shrimp in East Kalimantan, the results of morphological analysis showed confirmation of 7 species of freshwater shrimp. The family Palaemonidae consists of 7 species: Macrobrachium rosenbergii, M. lanchesteri, M. scabriculum, M. mammillodactylus, M. sintangense, M. equidens, and M. villosimanus. Molecular confirmation of species of the genus Macrobrachium using the COI gene showed genetic distance values ranging from 0 to 0.024. The species in this study have been confirmed based on genetic distance values and phylogenetic trees.
Reanalysis of Mitochondrial and Nuclear Markers (COI, 16S, 28S) in Coenobitidae, Diogenidae, and Paguridae for Species Delimitation Tazkiah Auliaputri; Tyani Fitrian; Achmad Alfiyan; Intan Ratu Pratiwi; Vendi Eko Susilo; Ali Mashar; Achmad Farajallah
Jurnal Ilmu dan Teknologi Kelautan Tropis Vol 18 No 1 (2026): Jurnal Ilmu dan Teknologi Kelautan Tropis
Publisher : Department of Marine Science and Technology, Faculty of Fisheries and Marine Science, IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jitkt.18.1.69987

Abstract

Public sequence repositories, such as GenBank, contain an extensive collection of molecular data that are widely used for phylogenetic inference and species identification. However, inconsistent annotation and potential misidentifications can obscure true genetic patterns, particularly in groups with complex morphology such as Paguroidea. This study reanalyzed 4,871 COI, 16S, and 28S sequences belonging to the families Coenobitidae, Diogenidae, and Paguridae retrieved from GenBank. Following rigorous quality filtering, 2,450 sequences were retained for downstream analyses to quantify intra and interspecific genetic distances for each family and each molecular marker. The results reveal substantial heterogeneity in genetic divergence across families, with COI and 16S exhibiting broad ranges and frequent overlap between intra and interspecific distances, whereas 28S displayed very low variation consistent with its slower evolutionary rate. Elevated intraspecific distances in several taxa suggest potential cryptic lineages, while unusually shallow interspecific values indicate possible synonymy or recent divergence. Rather than proposing taxonomic changes, this study provides a curated reference framework that establishes empirical distance thresholds for molecular species delimitation in Paguroidea. These findings offer a practical baseline for future research employing COI, 16S, and 28S markers in species identification, validation of public sequence data, and the refinement of hermit crab systematics.
Co-Authors A Anggraeni A Anggraeni A Anggraini A Batubara A. Anggraeni A. Anggraeni Achmad Alfiyan Achmad Alfiyan Achmad, Alfiyan AGUS A. HAKIM Agus Alim Hakim AKICHIKA MIKAMI ALFIYAN, ACHMAD Ali Mashar Ali Mashar Ali Suman AMIR HAMIDY Amir Hamidy AMIR HAMIDY Amir Hamidy Amir Hamidy ANIFA BINTAR Annawaty Annawaty, Annawaty ANTOINE FOUQUET Anzalia Eka Putri Arinana Arinana Arma Aditya Kartika Aron Batubara Aron Batubara Asri Febriana Asri Febriana, Asri AWAL RIYANTO AWAL RIYANTO 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 DEDY D. SOLIHIN Devi Sandriliana DEWI APRI ASTUTI DEWI PURNAMA DIAH IRAWATI DWI ARINI DIKI MUHAMAD CHAIDIR Dwi Sendi Priyono DWI SENDI PRIYONO DYAH PERWITASARI Dyah Perwitasari DYAH PERWITASARI -FARAJALLAH E Andreas E. Andreas E. Andreas Eric N. Smith Eric N. Smith Erni Sulistiawati Eryk Andreas EVY ARIDA Farid Akhsani Farjun Lahiaro Fauzan, Muhammad Fakhri Ferdy Saputra H. Nuraini HANIM, NISFA Hera Maheshwari Hermansyah, Alfandy I Inounu Imas Batubara Intan Ratu Pratiwi Irma Shita Arlyza Isdoni Bustaman J F Salamena Jarmuji Jarmuji Jeane Siswitasari Mulyana Joni Setiawan Jumadin, La Jusmaldi Jusmaldi Kaiin, Ekayanti Mulyawati KANTHI ARUM WIDAYATI Khairiza Lubis khairiza lubis Koekoeh Santoso KREY KREY Kuswati Kuswati Lora purnamasari, Lora Luthfia Nuraini Rahman M Doloksaribu M Karmita M. CHANDRA WIDJAJA M. Doloksaribu Mahendra, Arindina Majariana Krisanti Maria Ulfah MAULIDA NUR ANNISA Mennofatria Boer Meutiya Agustina Meutiya Agustina, Meutiya MISBAHUL MUNIR Moch. Syamsul Arifin Zein, Moch. Syamsul Arifin MUFTI SUDIBYO Mufti Sudibyo Muhammad Fakhri Fauzan Muhammad Khalid Yudhistiro MULYADI Mulyadi N Satriani NEVIATY PUTRI ZAMANI Nirmala Fitria Firdhausi NISFA HANIM Nisfa Hanim Nisfa Hanim Novita Anggraeni NUR RACHMAN Nurhayati D Nurlisa Alias Butet Nurulvadini Safrudin Paskah Partogi Agung Person Pesona Renta Pradana, Tengku Gilang Pristina Tuti Wijayanti 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 REVA ADZANI NURJANNAH RIKA RAFFIUDIN Riki Andika RISKA RISMAWATI Rissa Herawati Ginting Riyanto, Awal Riyanto, Awal Rose Ida Ummah ROSE IDA UMMAH RUDI A. WAHYUDIN 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 Taufan Nurzaman Sulaeman TAUFAN NURZAMAN SULAEMAN Tazkiah Auliaputri Tri Eko Susilorini Tsuji, Yamato Tyani Fitrian Ummahatul Mujahidah Vella Nurazizah Djalil Vendi Eko Susilo WAHYU TRILAKSONO WAHYU TRILAKSONO Wahyudin Abd. Karim, Wahyudin Abd. Widayat, Kanthi Arum i Widayati, Kanthi WINDRA PRIAWANDIPUTRA, WINDRA Windra Priawandputra Yanti Ariyanti Yanti Ariyanti YANTI ARIYANTI Yudhistiro Muhammad Khalid Yusli Wardiatno