Proceedings of the 2nd International Conference on Natural and Environmental Sciences (ICONES)September 9-11, 2014 , Banda Aceh, Indonesia

ISSN 2407-2389

36

Phylogenetic Analysis of Dipterocarpaceae Using NeighborjoiningAlgorithm

Ulfi Maulida1, Muhammad Subianto1, and Essy Harnelly2

1Department of Informatics, Syiah Kuala University, 2Department of Biology, Syiah Kuala University, Banda Aceh,Indonesia

Abstract. Phylogenetic analysis of family Dipteriocarpaceae using neighbor joining algorithm is aimed to analyze geneticrelationship of some species of family Dipterocarpaceae and comparing analysis results based on bootstrap value and timespent to construct phylogenetic tree using substitute of Jukes and Cantor method and type of Kimura model. As for analysisstep is consist of data collection, modification of sequence name structure, sequence collimation, construction of tree,evaluation of tree and analysis of tree. Analysis results of genetic relationship of both mpdels of substitution shows thatphylogenetic tree resulted is identic where, genus Dipterocarpus is not to forming group monophyletic with other genusfrom tribe Dipterocarpaceae time required to construction is not indicated a significant difference.

Keywords: Phylogenetic, neighbor-joining, Jukes and Cantor, Kimura.

INTRODUCTION

Indonesia is an archipelago country consisting of 17,508 islands. It has land area of 1,9 million squarekilometers and 3,1 millions square kilometers of ocean area. Indonesia lies between 6o North Latitude – 11o

South Latitude and 95o – 141o Longitude East. Thereby, Indonesia is located in the tropical season area andpassed by equatorial line. This location causes Indonesia a high biodiversity [1]. Indonesia has the mostcomplete biodiversity source called Megabiodiversity Country. Biodiversity in Indonesia consists ofmicroorganism diversity, animal and plant. Plant diversity in Indonesia has approximated amount 25,000species or more of 105 from flora of world [1]. In case of plant diversity, Indonesia assumed as one of the worldeconomic plant diversity centers, one of them is wood types of family Dipterocarpaceae. Wood of familyDipterocarpaceae has high economic value, so that it got the best of international wood trading, in particular inSouth-East Asian [2]. Based on Flora Malesiana [3] in Indonesia, family Dipterocarpaceae spreads best inKalimantan for 57,5% (200 species) and in Sumatera for 31,9% (111 species), while in the east is around 4%and Nusa Tenggara has least family type of Dipterocarpaceae. The diversity of family Dipterocarpaceaetraditionally has been classified based on morphological characteristics. Together with rapid developmenttechnology, in particular the development of molecular biology, developmental rate of molecular biology wasincreasingly developed supported by booming of Bioinformatics, a science to learn the application ofcomputation technique to manage and analyze biological information. This field is covered the application ofmathematics, statistics, and informatics methods to solve biology problems, particularly related to use of DNAand amino acids sequence. One sample of main topic in this field is including phylogenetic analysis [4].

Phylogenetics is the study of evolutionary relationships. Phylogenetic analysis is the means of inferring orestimating these relationships. The evolutionary history inferred from phylogenetic analysis is usually depictedas branching, treelike diagrams that represent an estimated pedigree of the inherited relationships amongmolecules, organisms, or both. The basic concept behind phylogenetics is that members of a group share acommon evolutionary history and are more related to each other than to members of another group. A givengroup is recognized by sharing unique features that were not present in distant ancestors. Usually, phylogeneticanalysis is performed by comparing multiple characteristics or ‘‘characters’’ at once, either multiple phenotypiccharacters or multiple base pairs or amino acids in a sequence. The methods for building phylogenetic trees inthis case is distance-based methods. Distance methods compute pairwise distances according to some measureand then discard the actual data, using only the fixed distances to derive trees.

Phylogenetic distance-based method in this case using neighbor-joining algorithm. Where the NJ algorithm iscommonly applied with distance tree building, regardless of the optimization criterion. The fully resolved tree is‘‘decomposed’’ from a fully unresolved ‘‘star’’ tree by successively inserting branches between a pair of closest(actually, most isolated) neighbors and the remaining terminals in the tree. The closest neighbor pair is thenconsolidated, effectively reforming a star tree, and the process is repeated. The method is comparatively rapid[5]. When estimating phylogenetic relationships among DNA sequences, the use of a model of nucleotidesubstitution. A model of evolution is necessary. Distance methods explicitly estimate the substitution rateparameters according to the model of evolution specified. Models of evolution are used in phylogenetic analysesto describe changes in character state, i.e., the rate of change from one nucleotide to another. The first model

Proceedings of the 2nd International Conference on Natural and Environmental Sciences (ICONES)September 9-11, 2014 , Banda Aceh, Indonesia

ISSN 2407-2389

37

developed for molecular evolution was that of Jukes and Cantor (1969) (JC), who considered all possiblechanges among nucleotides to occur with equal rates. The other models is Kimura (1980). The Kimura (1980)two-parameter model (K80) proposed a model that accounts for different transition and transversion rates.Substitutions between the two pyrimidines (T ↔ C) or beetween the two purines (A↔ G) are called transition,while those between a pyrimidine and purine (T, C ↔ A,G) are called transversions [4].

METHODS

The sequence data of molecular of family Dipterocarpaceae obtained from NCBI (GenBank). Furthermore, wesearched homolog sequence using Basic Local Alignment System Tools (BLAST) program in NCBI database.The collection data are species’ of subfamily Dipterocarpoideae especially species from tribe Shoreae andDipterocarpeae and one species from subfamily Monotoidea as an outgroup. Total species used in this study was38 species. Sequence name of each species collected from the database of GenBank consist of database genbankcode, sequence base length, species name, type of gene chloroplast and coding sequence information. Thestructures of sequence name is modified by erasing the database gene code and the sequence base length andadd the underscore mark “_” as separator between genus name and species using language of java programming.It is to facilitate identification for species in results of construction phylogenetic tree. To build the phylogenetictree, those sequences need to be aligned to maximize resemblance inter-sequence by checking off the order ofresemble DNA bases. Sequence alignment is done using software clustal W [6] which called by software R [7].Phylogenetic tree was constructed to visualize evolution relationship among of various species. Phylogenetictree in form of branches diagram was constructed based on similarity or difference of genetic from DNAsequence. The phylogenetic tree in this study built using neighbor-joining algorithm using DNA substituionJukes and Cantor 1969 model and Kimura 1980 and calculate required time to construction by adding code tocalculate time. Phylogenetic construction with this neighborjoining algorithm using library ape[8] in language ofprogramming R. The phylogenetic which have been built then examined for reliability using bootstrap methods.A bootstrap method is a re-sampling-based method of sample data that represent true population data tocomplete statistical one sample measurement. Bootstrap value be node label each branch of evolution tree.

RESULTSGenetic relationship of family Dipterocarpaceae from construction result using Neighbor-joining indicatedoccur outgroup separation (M..madagascariensis) with group of Dipterocarpaceae which is one of tribe infamily Dipterocarpaceae. Based on Neighbor-joining algorithm genus Dipterocarpus was making group withtribe Shoreae. It was different with grouping morphologically [3].

FIGURE 3. Phylogenetic tree using neighborjoining algorithm.

Proceedings of the 2nd International Conference on Natural and Environmental Sciences (ICONES)September 9-11, 2014 , Banda Aceh, Indonesia

ISSN 2407-2389

38

Neighbor-joining method is a method based on distance, where the smaller sequence distance inter-pairs thecloser its genetic relationship [5]. In this case, the difference of such grouping caused the Neighbor-joiningmethods suggested that genus Dipterocarpus has a closer distance with tribe Shoreae, which calculated fromnumber of mutation occur in sequence pair of genus Dipterocarpus and tribe Shoreae was smaller than tribeDipterocarpaceae (Figure 1).

Construction results phylogenetic tree of this family Dipterocarpaceae is identical to both substitution modelused. Either Jukes and Cantor 1969 model or Kimura 1980 model and the difference of required time forconstruction of phylogenetic tree from both models were only 0, 0159 seconds difference. Such case states thateither substitution model of Jukes and Cantor or Kimura model were not showed a significant difference.

CONCLUSION

Genetic Relationship of neighbor-joining algorithm indicated that genus Dipterocarpus was not form groupmonophyletic with other genus from tribe Dipterocarpaceae. Based on required time for construction and resultsof construction phylogenetic tree both using Jukes and Cantor model and Kimura is same.

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REFERENCES

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Cambridge university press, 2009, pp. 212-213.5. A.D. Baxevanis and B. F. F. Ouellette, Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. 3nd

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7. R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna,Austria. 2014. URL http://www.R-project.org/.

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