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Implementation of Bayesian inference MCMC algorithm in phylogenetic analysis of Dipterocarpaceae family

Sinergi · Vol. 27 No. 1 (2023) · hlm. 23–30

DOI
10.22441/sinergi.2023..1.004
ISSN
2460-1217, 1410-2331
Terbit
2023-01-13
Penerbit
Universitas Mercu Buana
Bahasa
eng

Abstrak

Dipterocarpaceae is one of the most prominent plant families, with more than 500 members of species. This family mostly used timber plants for housing, making ships, decking, and primary materials for making furniture. In Indonesia, many Dipterocarpaceae species have morphological similarities and are challenging to recognize in the field. As a result, the classification process becomes difficult and even results are inconsistent when viewed only from the morphology. This research will analyze the phylogenetic tree of Dipterocarpaceae based on the chloroplast matK gene. The aim of the research is to classify the phylogenetics tree of Dipterocarpaceae family using Bayesian inference algorithm. This research used the chloroplast gene instead of morphological characters which has more accurate. The analysis steps are collecting data, modifying the structure sequence name, sequence alignment, constructing tree by using Markov Chain Monte Carlo (MCMC) from Bayesian Inference, and evaluating and analyzing the phylogenetic tree. The results showed that the tree constructed based on the gene is different from the tree based on morphology. Based on the morphological, Dipterocarpus should be in the Dipterocarpeae tribe but based on the similarity of its genes, Dipterocarpus is more similar to the Shoreae tribe.

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  • Mercu Buana University
  • Beijing Institute of Technology
  • Jakarta State Polytechnic
  • Universitas Esa Unggul
  • National University of Malaysia
  • Kigali Independent University
  • National Defence University of Malaysia
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Rekan penulisOrganisasiArtikel bersama
Trie Maya KadarinaMercu Buana University3
Arifiansyah ZodyUniversitas Esa Unggul2
Khoirul AzizMercu Buana University2
Inggis Kurnia TrisiawanMercu Buana University2
Kadek Dwi SuyasminiMercu Buana University2
Eko IhsantoMercu Buana University1
Dedik RomahadiMercu Buana University1
Aberham Genetu FelekeBeijing Institute of Technology1
Nur IndahNational University of Malaysia1
Dafit FeriyantoMercu Buana University1
Muhamad FitriMercu Buana University1
Hadi PranotoMercu Buana University1
Fina SupeginaMercu Buana University1
Muhammad Imam MuthahharMercu Buana University1
Asif KhanBeijing Institute of Technology1
Andi AdriansyahMercu Buana University1
Sabin HitimanaKigali Independent University1
Bugi Nur RohmanMercu Buana University1
Rahmat MuwardiMercu Buana University1
Asif KhanBeijing Institute of Technology1
Rinto PriambodoMercu Buana University1
Riandini RiandiniJakarta State Polytechnic1
Sulis SetiowatiJakarta State Polytechnic1
Rika Novita WardhaniJakarta State Polytechnic1
Mohd Taufik JusohNational Defence University of Malaysia1
Muhammad Fadhlillah Raisul AkbarMercu Buana University1
Muhammad Iqbal MaulanaMercu Buana University1
Ketty Siti SalamahMercu Buana University1
Arrival Dwi SentosaBandung Institute of Technology1

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Sumber metadata: OAI-PMH (metadata jurnal) https://publikasi.mercubuana.ac.id/index.php/sinergi/oai, pertama di-harvest 10 Nov 2026, terakhir terlihat 10 Nov 2026.
Metadata asli (oai_dc) 
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	<dc:title xml:lang="en-US">Implementation of Bayesian inference MCMC algorithm in phylogenetic analysis of Dipterocarpaceae family</dc:title>
	<dc:creator>Yunita, Mirna</dc:creator>
	<dc:creator>Muwardi, Rachmat</dc:creator>
	<dc:creator>Iklima, Zendi</dc:creator>
	<dc:subject xml:lang="en-US">Dipterocarpaceae</dc:subject>
	<dc:subject xml:lang="en-US">Phylogenetic</dc:subject>
	<dc:subject xml:lang="en-US">Bayesian inference</dc:subject>
	<dc:subject xml:lang="en-US">Markov Chain Monte Carlo</dc:subject>
	<dc:description xml:lang="en-US">Dipterocarpaceae is one of the most prominent plant families, with more than 500 members of species. This family mostly used timber plants for housing, making ships, decking, and primary materials for making furniture. In Indonesia, many Dipterocarpaceae species have morphological similarities and are challenging to recognize in the field. As a result, the classification process becomes difficult and even results are inconsistent when viewed only from the morphology. This research will analyze the phylogenetic tree of Dipterocarpaceae based on the chloroplast matK gene. The aim of the research is to classify the phylogenetics tree of Dipterocarpaceae family using Bayesian inference algorithm. This research used the chloroplast gene instead of morphological characters which has more accurate. The analysis steps are collecting data, modifying the structure sequence name, sequence alignment, constructing tree by using Markov Chain Monte Carlo (MCMC) from Bayesian Inference, and evaluating and analyzing the phylogenetic tree. The results showed that the tree constructed based on the gene is different from the tree based on morphology. Based on the morphological, Dipterocarpus should be in the Dipterocarpeae tribe but based on the similarity of its genes, Dipterocarpus is more similar to the Shoreae tribe.   </dc:description>
	<dc:publisher xml:lang="en-US">Universitas Mercu Buana</dc:publisher>
	<dc:date>2023-01-13</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
	<dc:type>info:eu-repo/semantics/publishedVersion</dc:type>
	<dc:type xml:lang="en-US">Peer-reviewed Article</dc:type>
	<dc:format>application/pdf</dc:format>
	<dc:format>application/msword</dc:format>
	<dc:format>application/msword</dc:format>
	<dc:identifier>https://publikasi.mercubuana.ac.id/index.php/sinergi/article/view/15164</dc:identifier>
	<dc:identifier>10.22441/sinergi.2023..1.004</dc:identifier>
	<dc:source xml:lang="en-US">SINERGI; Vol. 27 No. 1 (2023); 23-30</dc:source>
	<dc:source>2460-1217</dc:source>
	<dc:source>1410-2331</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>https://publikasi.mercubuana.ac.id/index.php/sinergi/article/view/15164/6473</dc:relation>
	<dc:relation>https://publikasi.mercubuana.ac.id/index.php/sinergi/article/view/15164/11279</dc:relation>
	<dc:relation>https://publikasi.mercubuana.ac.id/index.php/sinergi/article/view/15164/11280</dc:relation>
	<dc:rights xml:lang="en-US">Copyright (c) 2023 SINERGI</dc:rights>
</oai_dc:dc>