Nugraha, Fitra Arya Dwi (2017) Filogenetik Dan Zoogeografi Ular Colubridae Di Jawa Dan Sumatera Berdasarkan Gen 12s Rdna. Magister thesis, Universitas Brawijaya.
Abstract
Sejarah geologi mulai pembentukan hingga dinamika perubahan topografi wilayah paparan sunda telah berdampak pada distribusi Colubridae di pulau Jawa dan Sumatera. Penelitian ini bertujuan untuk menganalisis profil filogenetik, zoogeografi dan waktu divergensi Colubridae di pulau Jawa dan Sumatera. Isolasi DNA, amplifikasi gen 12S rDNA dan sequencing dilakukan pada 5 genus Colubridae yang terdiri dari 10 spesies dari 11 lokasi. Sebelas data tambahan diambil dari genbank terdiri dari 8 Colubridae dan 3 outgroup. Total 28 sequence digunakan dalam analisis p-distance, pohon filogenetik maximum parsimony (MP); maximum likelihood (ML); bayesian inference (BI); dan waktu divergensi. Nilai p-distance intra-genus Boiga (5,6-6,8%, rata-rata 6,2±0,6); Coelognathus (0,3-9%, rata-rata 6,40±3,4), Ptyas (0-9,6%, rata-rata 6,4±4,8) dan Dendrelaphis (0-12,1%, rata-rata 6,5±3,9). Rata-rata jarak inter-genus terendah adalah antara Ptyas dengan Coelognathus (6,2-11,2%, rata-rata 9,2%±1,5); tertinggi adalah antara Lycodon dengan Dendrelaphis (11,2-16,5%, rata-rata 13,7%±1,7). Rata-rata jarak antara subfamily Colubrinae dengan Ahaetulinae adalah 12,2%± 1,5 (9-16,5). Nilai p-distance intraspesies <3,7%, intragenus <12,1% dan intergenus <16,5%. Semua pohon filogenetik memisahkan subfamily Colubrinae dengan Ahaetulinae. Kelompok Ptyas tidak membentuk satu clade, sedangkan D. pictus Sumatera dan Jawa Barat terpisah dari Jawa Tengah dan Jawa Timur serta didukung dengan nilai p-distance yang tinggi. Colubridae mulai memisah pada akhir Eocene (37,6 juta tahun lalu) sejalan dengan fosil Colubridae tertua di Wai Lek, Thailand. Colubrinae dan Ahaetulinae mulai memisah pada akhir Oligocene, berturut-turut pada 25,1 dan 24,8 juta tahun lalu. Pemisahan antara D. pictus Sumatera-Jawa Barat dengan Jawa Tengah-Jawa Timur dimulai pada akhir Miocene (9 juta tahun lalu). Penyebaran dan pemisahan didalam satu genus menjadi spesies berbeda pada Colubrinae semuanya terjadi pada akhir Miocene (20,9 hingga 9,2 juta tahun lalu), sedangkan pada Ahaetulinae pada akhir Oligocene hingga akhir Miocene (24,8 hingga 6 juta tahun lalu).
English Abstract
A geological history in the region of Sundaland, which started by the assembling and the changing of the topogaprhy, influenced the Colubrid snakes distribution in Java and Sumatera. This study addressed to analyze the phylogenetic, zoogeography and divergence time of Colubridae in Java and Sumatera. The extraction of DNA, amplification of 12S rDNA gene, sequencing were conducted for 5 genera of Colubridae consisting of 10 species taken from 11 localities. Eleven additional sequences were taken from genbank including 8 data of Colubridae and 3 data of outgroup. A total of 28 sequences was used for p-distance analysis; construction of maximum parsimony, maximum likelihood and bayesian inference phylogenetic tree; and divergence time estimation. The value of pdistance of intra-generic level for Boiga (5,6-6,8%, mean 6,2±0,6); Coelognathus (0,3-9%, mean 6,40±3,4), Ptyas (0-9,6%, mean 6,4±4,8) and Dendrelaphis (0-12,1%, mean 6,5±3,9). The lowest value for intra-generic level was performed among Ptyas with Coelognathus (6,2-11,2%, mean 9,2%±1,5) and the highest was showed among Lycodon with Dendrelaphis (11,2-16,5%, mean 13,7%±1,7). The value of p-distance between Colubrinae and Ahaetulinae was 9-16,5 (mean 12,2%± 1,5). The treshhold of 12S for intraspecies was <3,7%, intrageneric <12,1% and intergeneric <16,5%. All of phylogenetic tree supported the separation of Colubrinae from Ahaetulinae. The group of Ptyas was not nested in one clade while D. pictus from Sumatera-West Java separated from D. pictus Central-East Java which was supported by the value of p-distance. The colubrid snakes begin to diverge in the late Eocene (37,6 mya) which is corroborated by the earliest fossil of colubrid in Wai Lek pit, Thailand. Colubrinae and Ahaetulinae diverged in the late Oligocene at approximately 25,1 mya and 24,8 mya, respectively. The divergence between D. pictus Sumatera-West Java and Central-East Java was estimated to have occurred in the late Miocene at about 9 mya. The radiation and divergence in the level of intrageneric became a different species within Colubrinae was all occurred in the late Miocene from 20,9 mya through 9,2 mya, while within Ahaetulinae was estimated in the late Oligocene through late Miocene (24,8
| Item Type: | Thesis (Magister) |
|---|---|
| Identification Number: | TES/597.962/NUG/f/2017/041705512 |
| Uncontrolled Keywords: | COLUBRIDAE, ZOOGEOGRAPHY, PHYLOGENY, INDONESIA - JAVA, INDONESIA - SUMATRA, RIBOSOME, DNA, SNAKES - ECOLOGY |
| Subjects: | 500 Natural sciences and mathematics > 597 Cold-blooded vertebrates > 597.9 Reptilia (Reptiles) > 597.96 Serpentes (snakes) > 597.962 Colubridae |
| Divisions: | S2/S3 > Magister Biologi, Fakultas MIPA |
| Depositing User: | Nur Cholis |
| Date Deposited: | 26 Jul 2017 02:58 |
| Last Modified: | 25 Nov 2020 15:26 |
| URI: | http://repository.ub.ac.id/id/eprint/635 |
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