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Molecular Phylogeny of Giant Clams Based on Mitochondrial DNA Cytochrome C Oxidase I Gene

HAYATI Journal of Biosciences Vol 14, No 4 (2007): December 2007
Publisher : Bogor Agricultural University, Indonesia

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Abstract

There is an uncertainty for the relationships among giant clam species of Tridacninae, in particular among species belongs to subgenus Chametrachea i.e. Tridacna crocea, T. maxima, and T. squamosa based on different genetic markers. This study examined the relationships among three species within subgenus Chametrachea compared to the previous studies. Neighbour Joining, Maximum Parsimony and Maximum Likelihood tree were constructed based on 455 bp of the mitochondrial DNA cytochrome c oxidase I gene from T. crocea, T. squamosa, T. maxima, T. gigas, and several sequences derived from Genbank for the outgroups. The results showed that giant clams formed a monophyletic group. Within Tridacna group, T. crocea was more closely related to T. squamosa than to T. maxima and they formed a monophyletic group. T. crocea and T. squamosa were sister taxa and sister group to T. maxima and T. gigas. Close affinity between T. crocea and T. squamosa was also supported by high similarity on nucleotide level (94.30%) and concordant with the results of the previous studies using mitochondrial 16S rRNA and nuclear 18S rRNA. Key words: phylogenetic relationships, Chametrachea, cytochrome c oxidase I

SEBARAN DAN KARAKTER MORFOLOGI RAYAP TANAH Macrotermes gilvus Hagen DI HABITAT HUTAN ALAM

Jurnal Ilmu dan Teknologi Hasil Hutan Vol 1, No 1 (2008): Jurnal Ilmu Teknologi Hasil Hutan
Publisher : Departemen Hasil Hutan, IPB

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Abstract

Subterranean termite, Macrotermes, play important role on plant nutritive cycles through disintegration and decomposition of organic matter processes.  In the other hand, subterranean termite can cause wooden damage in the nature and human dormitory as well. Therefore, Macrotermes are potential pest and need to be controlled.  Effective pest-control of subterranean termite can be made when their species status and distribution are well known. This research is aimed to identify the status of species and the dispersal of Macrotermes at their natural habitat in order to explore natural bio-resources richness and as an effort towards effective pest-control due to increasing risk of attack.  Survey method was used termite samples were collected at four different locations which are defined by global positioning system (GPS).  Nest classification is according to Meyer et al. (2003). The nest mapping is based on the elevations of their natural habitat in Gunung Halimun Salak National Park (900-1000 asl), and (600-700 asl), Yanlappa sanctuary (200-300 asl), and Ujung Kulon Nasional Park (0-100 asl). Phylogenetic relationships analysis showed that subterranean termite Macrotermes in the natural forest community are belongs to one big group Macrotermes gilvus Hagen. Based on nest size, the colony of Macrotermes can be classified into three different sizes: large, medium, and small nest.  Large and medium nest can be found in large amount in Yanlappa sanctuary (15 and 23 colonies, respectively) and the majority of small nest occurred in Gunung Halimun Salak National Park at 900 asl (78 colonies). Temperature and humidity is the most environmental factor that can influence on termite and other factor is rain fall, soil structure, and plant vegetation.   Keywords:  Distribution, identify, Macrotermes gilvus Hagen, nest

Karakteristik Morfologi, Perbedaan Jenis Kelamin, dan Pendugaan Umur Burung Weris (Gallirallus philippensis) di Minahasa, Sulawesi Utara (MORPHOLOGICAL CHARACTERISTICS, SEX DIFFERENCES, AND AGE ESTIMATION OF WERIS (GALLIRALLUS PHILIPPENSIS) FROM MINAHASA

Jurnal Veteriner Vol 14, No 2 (2013)
Publisher : Jurnal Veteriner

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Abstract

This study aim  to observeb Gallirallus philippensis  similarities between different sites in Minahasa,to detect sexual dimorphism, and to estimate the bird age based on morphological characteristics.  A totalof 35 birds  were collected  from four locations i.e. Tondano, Papontolan, Ranoyapo, and Wusa in MinahasaNorth Sulawesi.   The result showed that there were no differences in the length  of beak, wing, and shankbetween  birds from  the different locations.  Moreover, based on the Principle Component Analysis (PCA)the bird’s shank and tail’s length were the main component.  Based on cluster analysis, the birds from fourlocations had a close similarities.  The male bird’s body weight, beak length, and beak width were largercomponent to the female’s.  The bird’s age could be best predicted by their iris colour,  beak colour, feather colourof the neck and the growth of the wing feathers, respectively.

Tingkah Laku Menetas Piyik Burung Weris (Gallirallus philipensis) dan Burung Dewasa dalam Penangkaran (HATCHING BEHAVIOR AND BEHAVIOR IN CAPTIVITY OF GALLIRALLUS PHILIPPENSIS)

Jurnal Veteriner Vol 16, No 2 (2015)
Publisher : Jurnal Veteriner

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Abstract

The study of behavior has a very important role in wildlife management process both for cultivationand for preservation in nature. The purpose of this study was to observe and document behaviors and dailyactivities of weris. Observation of hatching process and behavior of juvenile weris used direct observationmethod, while the behavior of adult weris in captivity used scanning sampling method. The data wereanalyzed descriptively. Weris had six stages of hatching processes starting from the breakdown of the eggshell until the chick moved out from the shell. The placement of the eggs in hatching machine was byputting the dull part on upside. Weris is a diurnal bird that active in the morning until late afternoon.Young and adult weris birds had different activities, i.e., adult birds did bathing and flying activities,while the young birds just rest and sleep. Observation on behavior of adult weris (n = 10) showed that thehighest activity for 12 hours was moving (314,6 minutes), then followed by resting (283,1 minutes), eating(51,8 minutes), drinking (29 minutes), bathing (22,9 minutes), and the lowest was preening (18,6 minutes).Inherited behavior pattern, such as bathing, did not change, eventhough the environment changed.

Permodelan Kesesuaian Habitat Orangutan Kalimantan (Pongo pygmaeus pygmaeus) di Koridor Satwa Kapuas Hulu Kalimantan Barat

Jurnal Penelitian Hutan dan Konservasi Alam Vol 13, No 2 (2016): Jurnal Penelitian Hutan dan Konservasi Alam
Publisher : Pusat Penelitian dan Pengembangan Hutan

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Abstract

ABSTRACTKapuas Hulu, as conservation districts, established regional wildlife corridor that connected Betung Kerihun and Danau Sentarum National Park as a Strategic Area District which highlight aspects of the environment. This wildlife corridor holds a prominent role in the movement of animals, especially orangutans of both national parks. This research was conducted to identify the impact of land use policies on the distribution of orangutans in the corridor. Although it has been designated as a wildlife corridor, many land conversion disconnecting wildlife corridors such as road construction, large-scale plantations development, land clearing for settlement, cultivation, and deforestation. However, the two national parks still offers a secure place for orangutans. A remote sensing technology was used to map the distribution and habitat suitability for the orangutan in the wildlife corridor. Seven parameters were observed to study the habitat of orangutans. The results revealed that the habitat suitability level of wildlife corridor was 49.94%, 46.61% and 3.46% for high, moderate and low level of suitability respectively. The results were supported by validation of 32.29% and 67.71% for moderate and high suitability respectively.Key words : Corridor, habitat, orangutan, wildlife suitabilityABSTRAKKabupaten Kapuas Hulu sebagai kabupaten konservasi telah menetapkan daerah koridor satwa yang menghubungkan Taman Nasional Betung Kerihun dan Taman Nasional Danau Sentarum sebagai Kawasan Strategis Kabupaten yang menonjolkan aspek lingkungan. Koridor satwa ini memiliki peranan yang penting bagi pergerakan satwa terutama orangutan dari kedua taman nasional ini. Studi ini dilakukan untuk memahami dampak tata guna lahan terhadap sebaran orangutan, di koridor satwa. Pembukaan jalan, perkebunan skala besar, pembukaan lahan untuk pemukiman, perladangan serta penebangan hutan telah menjadi penyebab terputusnya habitat orangutan. Wilayah yang masih aman sebagai habitat orangutan adalah di dalam kawasan taman nasional. Penelitian ini dilakukan menggunakan teknologi penginderaan jarak jauh untuk memetakan sebaran dan kesesuaian habitat orangutan di kawasan koridor satwa. Tujuh parameter habitat orangutan digunakan dalam analisis spasial kesesuaian habitat. Dari hasil penelitian ini didapatkan bahwa kawasan koridor memiliki tingkat kesesuaian habitat yang tinggi sebesar 49.94%, tingkat kesesuaian sedang sebesar 46.61% dan kesesuaian yang rendah sebesar 3.46%. dan hasil ini ditunjang dengan besaran nilai validasi untuk kelas kesesuaian sedang sebesar 32.29% dan kelas kesesuaian tinggi sebesar 67.71%.Kata kunci : Habitat, kesesuaian, koridor, orangutan, satwa

Genetic Variability in the Indonesian Giant Clam (Tridacna crocea and Tridacna maxima) Populations: Implication for Mariculture and Restocking Program

Majalah Ilmiah Biologi BIOSFERA: A Scientific Journal Vol 24, No 2 (2007)
Publisher : Fakultas Biologi | Universitas Jenderal Soedirman

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Abstract

Tridacna crocea and T. maxima are relatively abundant in the Indonesian coral reef. These two species are, however, under high presure due to exploitation for food, industry, and aquarium trade.  It is, therefore, necessary to understand their biology, such as genetic variability within and between populations, before utilizing them for strain improvement and restocking, prior to the extinction of the populations of T. crocea and T. maxima.  Here we amplified a length of 456 bp of the mitochondrial DNA cytochrome c oxidase I gene from Tridacna crocea and of 484 bp from T. maxima to asses the genetic variability within and between populations of both species.  The results showed that both species have high genetic diversity and polymorphism within each local population. This provides a sufficient basis for selection of improved strain of T. crocea and T. maxima for mariculture. However, if the genetic variation led to genetic differentiation among populations due to the result of evolutionary adaptation, mixing genetically different populations may result in the break up of co-adaptation gene complexes.  This might result in the loss of the physiological capacities of the parental populations.

Molecular Phylogeny of Giant Clams Based on Mitochondrial DNA Cytochrome C Oxidase I Gene

HAYATI Journal of Biosciences Vol 14, No 4 (2007): December 2007
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Original Source | Check in Google Scholar | Full PDF (37.454 KB)

Abstract

There is an uncertainty for the relationships among giant clam species of Tridacninae, in particular among species belongs to subgenus Chametrachea i.e. Tridacna crocea, T. maxima, and T. squamosa based on different genetic markers. This study examined the relationships among three species within subgenus Chametrachea compared to the previous studies. Neighbour Joining, Maximum Parsimony and Maximum Likelihood tree were constructed based on 455 bp of the mitochondrial DNA cytochrome c oxidase I gene from T. crocea, T. squamosa, T. maxima, T. gigas, and several sequences derived from Genbank for the outgroups. The results showed that giant clams formed a monophyletic group. Within Tridacna group, T. crocea was more closely related to T. squamosa than to T. maxima and they formed a monophyletic group. T. crocea and T. squamosa were sister taxa and sister group to T. maxima and T. gigas. Close affinity between T. crocea and T. squamosa was also supported by high similarity on nucleotide level (94.30%) and concordant with the results of the previous studies using mitochondrial 16S rRNA and nuclear 18S rRNA. Key words: phylogenetic relationships, Chametrachea, cytochrome c oxidase I

Kode batang DNA ikan lais genus Kryptopterus asal Sungai Mahakam Kalimantan Timur [Barcoding DNA of catfish species genus Kryptopterus from Sungai Mahakam Kalimantan Timur]

Jurnal Iktiologi Indonesia Vol 14, No 3 (2014): Oktober 2014
Publisher : Masyarakat Iktiologi Indonesia (MII )

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Abstract

DNA barcoding of genus Kryptopterus catfish from Mahakam River, East Kalimantan by using mitochondrial DNA COI gene has been performed to obtain genetic marker (barcoding DNA), genetic characteristics and genetic tree. Amplification of mitochondrial COI gene regions was conducted by using COI Fish F1 and COI Fish R1 primers on the three catfish species consist of Kryptopterus apogon (N=3), K. micronema (N=6), and K. limpok (N=1). Based on partial COI mtDNA multiple alignment, we obtained three specific nucleotide site as genetic marker. Meanwhile, genetic characteristic analysis revealed 13.58% of nucleotide variation. Nucleotide substitution was greater at the third codon and transitional substitution was greater than transvertion. Genetic tree reconstruction based on p-distance separated the three catfish species with perfect bootstrap value. AbstrakPenelitian kode batang DNA spesies ikan lais genus Kryptopterus asal Sungai Mahakam Kalimantan Timur mengguna-kan gen COI DNA mitokondria dilakukan dengan tujuan untuk mengungkap penanda genetik (kode batang DNA), ka-rakterisasi genetik dan pohon genetik. Amplifikasi daerah gen COI DNA mitokondria dilakukan dengan menggunakan pasangan primer COI FishF1 dan COI FishR1 terhadap tiga spesies ikan lais yang terdiri atas Kryptopterus apogon (N=3), K. micronema (N=6), dan K. limpok (N=1). Hasil penelitian menunjukkan penyejajaran berganda pada gen par-sial COI DNA mitokondria antara spesies K. apogon, K. micronema, dan K. limpok diperoleh tiga situs nukleotida spe-sifik sebagai penanda genetik (kode batang DNA). Analisis karakterisasi genetik pada genus Kryptopterus berdasarkan gen parsial COI DNA mitokondria menunjukkan situs nukleotida yang bervariasi sebesar 13,58%, substitusi nukleotida lebih besar pada kodon ketiga dan bersifat transisi dari pada transversi. Konstruksi ulang pohon genetik berdasarkan ni-lai p-distance dapat memisahkan kelompok spesies K. apogon, K. micronema,dan K. limpok dengan nilai bootstrap sempurna.

Genetic Diversity and The Relationship Between The Indonesian Mangosteen (Garcinia Mangostana) and The Related Species Using Isozyme Markers

Jurnal Natur Indonesia Vol 13, No 01 (2010)
Publisher : Lembaga Penelitian dan Pengabdian kepada Masyarakat Universitas Riau

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Abstract

Indonesia was known to have high diversity of mangosteens (Garcinia mangostana) and the related species. Inorder to elucidate the genetics variability of the diversity, thirty three accessions were examined by using isozymeanalysis. The genetic diversity and relationships among several mangosteens and other Garcinia sp wereestablished by using four isozymes. The level of polymorphism as revealed by isoenzyme was 88%. Althoughmangosteen is believed to reproduce exclusively through apomixis, our result show that considerable geneticdiversity exists within G. mangostana and between other Garcinia species. Based on 27 bands there were 5-42%dissimilarity level among mangosteen accessions, while the other species has 75% dissimilarity. The dendrogramis built based on isozyme marker analysis to separate clusters of mangosteen and other Garcinia sp. The datashowed that G. mangostana is a close relative of G. malaccensis, G. porrecta, G. celebica, and G. hombroniana. Theconcurrence analysis on isozyme analysis result showed the very good fit of Rolf correlation value (0.914). Thisresult indicated that isozymes could group G.mangostana and the related species.

GENETIC VARIABILITY ANALYSIS ON APOMICTIC MANGOSTEEN (GARCINIA MANGOSTANA) IN INDONESIA AND ITS CLOSE RELATED SPECIES BY USING RAPD MARKERS

Floribunda Vol 3, No 3-4 (2007)
Publisher : PTTI

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Abstract

Analisis variabilitas genetik manggis apomiksis di Indonesia dan kerabat dekatnya dengan menggunakan penanda RAPD.