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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Bioma : Berkala Ilmiah Biologi TREUBIA BERITA BIOLOGI JURNAL BIOLOGI INDONESIA ZOO INDONESIA Biosaintifika: Journal of Biology & Biology Education
AMIR HAMIDY
Bidang Zoologi Pusat Penelitian Biologi-Lembaga Ilmu Pengetahuan Indonesia, Bogor
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Education Environmental Science Other

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GENETIC DIVERGENCE AND GEOGRAPHIC DISTRIBUTION OF FROGS IN GENUS FEJERVARYA FROM INDONESIA INFERRED FROM MITOCHONDRIAL 16S rRNA GENE ANALYSIS Igawa, Takeshi; Sumida, Masayuki; Kurniawan, Nia; Djong, Tjong Hon; Maideliza, Tesri; Hamidy, Amir; Hasan, Mahmudul
TREUBIA Vol 41 (2014): Vol. 41, December 2014
Publisher : Research Center for Biology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/treubia.v41i0.361

Abstract

The Indonesian archipelago is an ideal setting for the study of speciation and biogeography. This archipelago is divided into three island groups based on zoogeography: Sundaland, Wallaceaand the Australian region. In this paper we used frogs in genus Fejervarya (Bolkay) to study biogeography and examine patterns of gene flow across proposed zoogeographic boundaries. Severalmolecular studies on Fejervarya species from Indonesia have been carried out, but comparative studies among members of the genus Fejervarya have yet to be performed. In order to elucidate genetic divergence and geographic distribution of these frogs, we conducted a molecular analysis of the mitochondrial 16S rRNA gene using 179 frogs from five Fejervarya species. In total we collected from 32 localities in Sumatra, Kalimantan (Indonesian part of Borneo), Java, Bali, Sulawesi and Lesser Sunda Islands in Indonesia. Molecular phylogenetic analysis recovered 35 haplotypes and showed that frogs in the genus Fejervarya were divided into two well-supported clades. The first group were of three species, F. limnocharis, F. iskandari and F. cf. verruculosa and the other group clade consisted of Fejervarya cancrivora and Fejervarya sp. (Sulawesi-type). The average sequence divergence among these four species ranged from 1.09 to 16.03% (mean = 11.29±2.83%). The present results clearly show that there are five Fejervarya species in the Indonesian archipelago. Fejervarya limnocharis and F. cancrivora are widely distributed and sympatric in Sumatra, Borneo and Java. Fejervarya iskandari is not endemic to Java and also occurs in the Lesser Sundas. Fejervarya cf. verruculosa and Fejervarya sp. (Sulawesi-type) are endemic to Lesser Sunda and Sulawesi Island, respectively. Key words: Fejervarya, genetic divergence, geographic distribution, 16S rRNA gene
PHYLOGENETIC RELATIONSHIPS OF LEPTOBRACHIUM HASSELTII TSCHUDI, 1838 (AMPHIBIA, ANURA, MEGOPHRYIDAE) - DETECTION OF A POSSIBLE CRYPTIC SPECIES Hamidy, Amir; Matsui, Masafumi
TREUBIA Vol 44 (2017): Vol. 44, December 2017
Publisher : Research Center for Biology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/treubia.v44i0.3286

Abstract

By examining mitochondrial DNA phylogeny using 2424bp of sequence data 12S rRNA, tRNAval, and 16S rRNA genes, we evaluated the taxonomic relationships among Javan litter frogs Leptobrachium hasseltii from southern Sumatra, Java, and Bali. Leptobrachium hasseltii formed a well-supported monophyletic group, which comprised two major clades. One major clade represented the southern Sumatran and Javan populations and the other consisted of the population from Bali. The Javan and southern Sumatran clade included two subclades: the West Javan-southern Sumatran group and the Central Javan group. The genetic divergence between the two major clades (Bali vs. Java-Sumatra) suggested their separation happen at species level. Further studies using morphological and acoustic data are needed to determine the taxonomic status of Bali population.
Variasi Suara Panggilan Kodok Hylarana nicobariensis (Stoliczka, 1870) Dari Lima Populasi Berbeda di Indonesia (Anura: Ranidae) Kurniati, Hellen; Hamidy, Amir
JURNAL BIOLOGI INDONESIA Vol 12, No 2 (2016): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (932.382 KB) | DOI: 10.14203/jbi.v12i2.2877

Abstract

Hylarana nicobariensis (Stoliczka, 1870) is a very common frog, which has a wide distribution, covering the southern part of Thailand, Peninsular Malaysia, Sumatra, Borneo, Java, Bali and Palawan in the Philippines. The presence of this frog is very easy to be recognized by listening its shrill call that is sounded loudly all day. Detailed descriptions of H. nicobariensis’s calls from Ulu Gombak in Peninsular Malaysia and Danum Valley in Sarawak have been published by Jehle and Arak (1998), which are some call characters of the frog from the two locations are significantly different. To determine the call characters that can distinguish among populations of this frog, advertisement calls of five different populations (Batukaru, Curup, Limau Manis, Curug Nangka and Lake Ecology Park) were analyzed. The characters of the call waves on the five populations are different in the structure of sub-pulses, dominant frequency and lower frequency. Among the five populations, the population from Lake Ecology Park is the most different in the terms of the dominant frequency (3996.95 ± 124.74 Hz) and lower frequency (1692.51 ± 80.77 Hz), of this population both these characters occupy the highest level compared to four other populations; however individuals from Curup occupy the lowest level on dominant frequency (2919.67 ± 67.76 Hz) and lower frequency (832.96 ± 32.42 Hz).Key words: Ranidae, Hylarana nicobariensis, bioacoustics
Karakteristik Suara Kelompok Kodok Microhylidae Bertubuh Kecil Asdal Bali (Anura: Microhylidae) Kurniati, Hellen; Hamidy, Amir
JURNAL BIOLOGI INDONESIA Vol 10, No 2 (2014): Jurnal Biologi Indonesia
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (300.455 KB) | DOI: 10.14203/jbi.v10i2.2099

Abstract

Advertisement calls of Microhyla palmipes and Oreophryne monticola have never been described before; howevercharacteristics of M. orientalis’s calls has been described just to support new species publication. The advertisement calls oftwo individual males of M. orientalis and M. palmipes which originated from Wongaya Gede, Bali were recorded in July2010 at air temperatures of 26.0°C. Three individuals males of O. monticola were recorded in Eka Karya Botanical Garden,Bali at air temperature of 25.0°C. Call components were obtained from 65 calls of M. orientalis, consisting of 95 pulses; 10calls of M. palmipes, consisting of 113 pulses; 3 calls of O. monticola, consisting of 127 pulses, which were then analyzed toobtain the characteristics of sound waves by using software of Adobe Audition 3.0. Sound waves of M. orientalis mainlyconsists of two dominant frequencies raging from 1873-2062 Hz and 3375-3562 Hz; however sound waves of M. palmipesand O. monticola mainly consist of only one dominant frequency that ranges of the frequency is the same, i.e. 3000-3937Hz. Although M. palmipes and O. monticola have the same range on dominant frequency, but the two species have significantlydifferent on number of period per pulse, pulse duration, pulse interval, pulse period, call duration and call interval.Key words: frog call, Microhylidae, Bali Island
VARIASI DAN DEGRADASI SUARA PANGGILAN KODOK JANGKRIK [HYLARANA NICOBARIENSIS (STOLICZKA, 1870)] ASAL PULAU ENGGANO (ANURA: RANIDAE) [Variation and degradation on advertisement calls of Cricket Frog, Hylarana nicobariensis (Stoliczka, 1870) from Enggano Island] Kurniati, Hellen; Hamidy, Amir
BERITA BIOLOGI Vol 15, No 3 (2016)
Publisher : Research Center for Biology-Indonesian Institute of Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (3468.466 KB) | DOI: 10.14203/beritabiologi.v15i3.2293

Abstract

Frog’s group of Hylarana nicobariensis (Stoliczka, 1870) is a complex species that has diverse genetic populations and variations on advertisement calls. Variations on advertisement calls among populations have been reported in Sumatra, Java and Bali. The population of frog in Enggano has different phenomenon that was not found in Sumatra and Java.  Enggano population was genetically identical, but the advertisement calls were very diverse. There were four types of advertisement calls on the population in Enggano Island, namely: (1) advertisement call type 1 which has pulse wave with the dominant frequency of 2855.13 ± 135.22 Hertz; (2) advertisement call type 2 which has pure tone wave with the dominant frequency of 2720.29 ± 97.69 Hertz; (3) advertisement call type 3 which has pulse wave with dominant frequency 2634.61 ± 292.81 Hertz; (4) advertisement call type 4 which has pure tone wave with dominant frequency 1618.79 ± 83.05 Hertz. The degradation of the dominant frequency and the lower frequency was likely due to the increase of snout to vent length (SVL) of adult male that were followed by increasing the size of the head.
On Skeletochronology of Asian grass frog Fejervarya limnocharis (Gravenhorst, 1829) from Java to support management conservation Phadmacanty, Ni Luh Putu Rischa; Hamidy, Amir; Semiadi, Gono
TREUBIA Vol 45 (2018): Vol. 45, December 2018
Publisher : Research Center for Biology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/treubia.v45i0.3109

Abstract

Asian grass frog Fejervarya limnocharis is being utilized as pets, for laboratory experiments, for a mixture of traditional medicine and for cuisine. The harvest of F. limnocharis in high volume can threat its population. Biological data such as the age when the specimens are harvested is valuable information to manage the harvesting system in sustainable way. We conducted the skeletochronology technique using paraffin methods and hematoxylin staining from 69 samples (46 males, 21 females, 2 juveniles). The results showed that the age harvested male ranged from 1 to 3 years old, while the female ranged from 2 to 3 years old. The snout-vent length (SVL) of harvested specimens ranges between 39.84−52.37 mm for both sexes. We propose an intervention in the harvesting system by limitation of the size for harvested specimens to at least 46 mm. In this minimum size, individuals of F. limnocharis have reproduced several times and have contributed to the  population in the wild.
A new species of Microhyla (Anura: Microhylidae) from Sumatra, Indonesia Atmaja, Vestidhia Yunisya; Hamidy, Amir; Arisuryanti, Tuty; Matsui, Masafumi; Smith, Eric N.
TREUBIA Vol 45 (2018): Vol. 45, December 2018
Publisher : Research Center for Biology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/treubia.v45i0.3625

Abstract

A new species of frog in the genus Microhyla is described from Sumatra, Indonesia based on molecular and morphological characters. This new species was previously confused with M. achatina, a Javan endemic. This new species is diagnosable from its congeners by possessing a medium size (SVL in adult males 18.20–21.32 mm, in adult females 20.37–25.51 mm), a stout body, a nostril–eyelid length being about half of the snout length, having a single outer palmar tubercle, a tibiotarsal articulation reaching the center of the eye (when the hindlimbs are stretched and adpressed to the body), having finger and toe tips dilated, having the dorsum with medial longitudinal grooves, and excibiting a very thin and short dark stripe on the temporal region above a wider cream stripe, extending from the postorbital area to insertion of forelimb. Additionally, the new species is characterized by possessing relatively little foot webbing. Uncorrected 16S rRNA sequence divergences between the new taxon and sequences for other congeneric species available ranged from 4.8 to 15.0%.
Hubungan Filogenetik Phrynella pulchra Boulenger, 1887 Berdasarkan Gen 16S rRNA Akhsani, Farid; Hamidy, Amir; Farajallah, Achmad; Smith, Eric N.
ZOO INDONESIA Vol 26, No 2 (2017): Desember 2017
Publisher : Masyarakat Zoologi Indonesia

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

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

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (2201.609 KB)

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.
Karakter Suara Limnonectes modestus (Boulenger, 1882) Asal Suaka Margasatwa Nantu, Gorontalo, Sulawesi Bagian Utara Kurniati, Hellen; Hamidy, Amir
JURNAL BIOLOGI INDONESIA Vol 14, No 2 (2018): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1315.381 KB) | DOI: 10.14203/jbi.v14i2.3728

Abstract

ABSTRACTCall characteristics of Limnonectes modestus (Boulenger, 1882) which is endemic to Sulawesi have never been described before.  The advertisement calls of two individual males collected from Nantu Wildlife Sanctuary, Gorontalo, northern Sulawesi were recorded in December 6, 2014 at air temperatures of 26°C.  Adobe Audition 3.0 software was used to visualize sound waves.  Advertisement call of L. modestus is very simple, which only has one type of call containing 1-6 pulses.  Pulse duration, pulse rate and call rate of the two individual males are very diverse, ranged between 21-56 milli seconds, 2.58 to 7.87 pulses/second and 0.09-1.16 call/second; but the frequency variation of call is very low, the lower frequency range between 515.6 to 593.0 Hertz (CV=3.1%), whereas the upper frequency range between 2179.0 to 2859.0 Hertz (CV=5.4%); the band width of the frequency range between 1616.5 to 2320.0 Hertz (CV=7.1%). Key words: vocalization, Limnonectes modestus, Nantu Wildlife Sanctuary, North Sulawesi 
Co-Authors ACHMAD FARAJALLAH Akhsani, Farid Ardiantoro, Ari Atmaja, Vestidhia Yunisya Bambang Agus Suripto Djong Hon Tjong Donan Satria Yudha Fathoni, M Fauzi, Muhammad Alif GONO SEMIADI Haekal, Muhammad Hanifa, Berry Fakhry Hellen Kurniati, Hellen Karyadi Baskoro Mahmudul Hasan, Mahmudul Margareta Rahayuningsih Nugroho Edi K Masayuki Sumida, Masayuki Matsui, Masafumi Matsui, Masafumi Mediyansyah Mediyansyah Misbahul Munir Mochamad Hadi Mumpuni Mumpuni Ni Luh Putu Rischa Phadmacanty Nia Kurniawan Pradana, Tengku Gilang Riyanto, Awal Rury Eprilurahman Septiadi, Luhur Smith, Eric N. Takeshi Igawa, Takeshi Tesri Maideliza Tuty Arisuryanti, Tuty Vera Budi Lestari Sihotang, Vera Budi Lestari Winda Rahmawati Wiradarma, Huda