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Dendrogram, Cladogram and

Chapter · January 2015

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Jyoti Prasad Gajurel

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Jyoti Prasad Gajurel Central Department of Botany, Tribhuvan University, Kirtipur, Kathmandu, Nepal. Email: [email protected]

1.Introduction A phylogenetic analysis starts with a careful analysis of number and choice of character in the taxa, coding of characters in taxa, making of data matrix and then analyzing the data and interpreting the results (http:// www.ucmp.berkeley.edu/IB181/VPL/Phylo/Phylo3.html). help in finding of the branching pattern of the while phenetics classify the overall similarity among taxa without evolutionary studies but the phylogenetic analysis use all the information based on phylogeny (Li, 1993). The method based on share derived characters which is useful in the grouping of the taxa is known as cladistics or phylogenetic systematics (Lipscomb, 1998). The phylogenetic analysis which use the evolutionary history as well as studies to make relation of the taxa and the graphical representation is called as Cladogram or . The simple representation of the relationship between the taxa under the study in the graphical form is called dendrogram. Cladogram is the graphical representation of the phylogentic relationship in the taxa under study (Lipscomb, 1998). It differs from dendrogram as dendrogram does not show phylogentic relationship in the taxa. However, the taxa under study can be compered based on the character states from the specimens studied from the dendrogram (Lipscomb, 1998). During the construction of cladogram, those taxa whose evolutionary relationships needed to be tested needs to be selected. All the taxa need to be monophyletic (with common recent ancestor). The homologous characters need to be selected as they are inherited from a common ancestor. This will be important for the reconstructing phylogenies among the taxa. Another important step in the construction of phylogeny is to find out the order of the evolution which is called polarity of the characters. The character states which are present in the outgroup can be considered as the ancestral character states. Sometimes

-177 - the records from the fossils can be used for the comparison with ancestral character states. The taxa are grouped by shared derived characters called synapomorphies. Then the cladogram constructed can be tested with simple principles of parsimony (fewest steps in the evolutionary history) or by checking synapomorphies (Lipscomb, 1998). Therefore, this paper attempts in presenting the simple method of using the information from the study of the taxa and using them in the construction of dendrogram or phylogenetic tree and using it in the study of the taxa. The method can be used by free software or other software available in the market.

2.Construction of Dendrogram and Cluster The modern electronic data-processing techniques like MS EXCEL (Microsoft 2010) can use in the storage of morphological characters in the form of data matrix in the columns and rows as in Table 1 (Gajurel, 2008). Table 1: Character and Character States

Taxa Leaves Stamen Carpel Seed

Out glabrous all fertile without swelling below tip uniseriate Taxa1 pubescent all fertile with swelling below tip bisseriate Taxa2 glabrous all not fertile with swelling below tip bisseriate Taxa3 pubescent all not fertile without swelling below tip bisseriate Taxa4 pubescent all not fertile with swelling below tip bisseriate

Then next step would be preparing the character state codes as in table 2. Table 2: Character Code S. N. Characters Coding 1. Leaves 0=glabrous; 1=pubescent 2. Stamen 0=all fertile; 1=all not fertile 3. Carpel 0=without swelling below tip; 1=with swelling below tip 4. Seed 0=uniseriate; 1=bisseriate

The characters in table 1 need to be converted into character state codes which can be used for construction of the phylogenetic tree or the dendrogram as in Table 3

-178 - Table 3. Character Coding Taxa Leaves Stamen Carpel Seed Out 00 0 0 Taxa 1 10 1 1 Taxa 2 01 1 1 Taxa 3 11 0 1 Taxa 4 01 1 1

For the construction of the dendrogram SPSS Program. The cluster can also be constructed with R package pvclust (Suzuki and Shimodaira, 2004) in freeware R (R Development Core Team, 2013) using the above mentioned data. This results in the following figures.

Figure 1. Dendrogram (from SPSS) based on characters in Table 1.

-179 - Figure 2. Cluster based on characters in Table 1 constructed from R software.

The dendogram thus obtained from the SPSS can be analyzed and used in various ways. From figure 1, it is understood that the taxa 1 and taxa 3 are more closely related as compared to others. They have more ancestral characters as compared to other taxa. This can also be used for classifying the taxa as well as looking the most important characters state separating the species. Similarly, it can also be used in checking the relationship between the taxa.

References Gajurel, J.P. 2008. of the family Commelinaceae in Nepal.Master’s dissertation submitted to Central Department of Botany, Tribhuvan University, Kathmandu, Nepal. Li, G. 1993. A review on Cladistics. Acta Phytotaxonomica Sinica 31 (1): 80- 99. Lipscomb, D. 1998. Basics of Cladistic Analysis. George Washington University Washington D.C. Microsoft. 2010. Microsoft Excel [computer software]. Redmond, Washington: Microsoft. RDevelopmentCoreTeam. 2013. R: A language and environment for statistical computing. R Foundation for Statistical Computing. Vienna, Austria. Suzuki, R. and Shimodaira, H. 2004. An application of multiscale bootstrap resampling to hierarchical clustering of microarray data: How accurate are these clusters?. The Fifteenth International Conference on Genome Informatics 2004.

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