Phylogenetic tree and its construction and phylogeny of

Construction of phylogenetic trees , methods used for phylogenetic tree construction ,
Phylogeny of horse

1. Phylogenetic tree and its construction and phylogeny of horse NAME : SNEH LATA ROLL NO. CUHP18ZOO26 SUBMITTED TO . MS. EKTA GULERIA

2. PHYLOGENETIC TREE Phylogeny is the evolutionary history of a kind of organism . In phylogenetic studies , the most convenient way to study the evolutionary relationship among a group of organism is through the illustration of phylogenetic tree. DEFINITION –Phylogenetic tree is a two dimensional graph showing evolutionary relationship between organism , or genes from various organism .

3. Characteristics : Nodes can be internal or external . Each internal node represent the last common ancestor of the two lineage . External node (also termed as terminal node , leaves ) represent the tip of the tree . Node correspond to species , organism or sequences . Similarly, branches can be internal or external . Internal branches or internodes connect two nodes , whereas external branches connect a tip and a node .

4. A phylogenetic tree branches either be : - Scaled - Unscaled In scaled branches , their length are proportional to the evolutionary change . Example - phylogram . In unscaled branches , the branch length is not proportional to the number of changes . Example -cladogram

5. When constructing phylogenetic trees ,researcher identify homologous features that are share shared by some species but not by others. This allows them to group species based On their shared characterstics . Historically, comparison of morphological similarities and differences have been used to construct evolutionary trees. In this approach, species that share certain charactersticts (i.e.,homologous trait) tend to be placed closer together on the tree . In 1963,Linsus pauling and Emile Zuckerkandl were the first to suggest the use of molecular data to estabolish

6. Evolutionary relationship When comparing homologous genes in different species, the DNA sequences from closely related species are more similer to each other than are the sequences from distantly related species .

7. Phylogenetic tree based on homology Phylogenetic tress are now based on homology which refers to similarities among various species that occur because the species are derived from a common ancestor. Attributes that are the result of homology are said to be homologous. For eg.

8. Phylogenetic tree reconstruction Phylogenetic trees are constructed : - To reconstruct the evolutionary past. - To develop an understanding of when and which speciation event may have occurred to give rise to the organism exhibited today . A phylogenetic analysis consist of four steps and these are : SEQUENCE ALIGNMENT :- Sequence alignment is the essential preliminary to the tree reconstruction . The data used in reconstruction of a DNA –based phylogenetic tree are obtained by comparing nucleotide sequences.

9. These comparison are made by aligning the sequences so that nucleotide differences can be scored . DETERMINING THE SUBSITUTION MODEL TREE BUILDING TREE EVALUATION

10. Cladistic approach for the construction of tree

11. Cladogram

12. Steps involved in the construction of cladogram : Choose the species in whose evolutionary relationship you are interested . Choose characters for comparing different species . Determine the polarity of character states i.e. character state is ancestral or derived . Group species ( or higher taxa ) based on shared derived characters .

13. Build a cladogram based on following principles : All species are placed on the tip in the phylogenetic tree , not at branch points . A cladogram does not include ancestral species at branch points . Each cladogram branch point should have a list of one or more shared derived characters that are common to all species . All shared derived character appear together only once in a cladogram unless they independently arose during evolution .

14. Choose the best cladogram among possible option . When grouping species (or higher taxa) more than one cladogram may be possible . Therefore , analyzing the data and producing the best possible cladogram is a key aspect of this process .

15. Construction of phylogenetic tree 2 types of method Character based Distance based method method Maximum parsimony Maximum likelihood

16. Character based method : This method is also called as discrete method and are based directly on the sequence characters rather than on pairwise distances . The two most popular character based methods are : MAXIMUM PARSIMONY MAXIMUM LIKELIHOOD

17. Maximum parsimony Parsimony method is one of the pioneer method of phylogeny construction . Parsimony groups taxa together in way that minimize the number of changes . It assume that the best hypothesis is one that requires the fewest number of evolutionary changes hence it is also called as minimum evolution method . It also states that the preferred hypothesis is the one that is simplest .

18. EXAMPLE : If two species possess a tail then there are two hypothesis : First assuming that a tail arose once during evolution and that both species have descended from a common ancestor with a tail . Second hypothesis assuming that tails arose twice during evolution and that the tails in the two species are not due to descent from a common ancestor . So the first assumption is simplest one and is accepted .

19. Maximum parsimony example First we need sequence data than Start from the first nuclotide Construct a tree that represents minimum evolutionary change

20. Repeat this for the second nucleotide site . Calculate the number of substitution steps on each branch . The maximum parsimony tree is one with minimum total number of substitution . The maximum parsimony depends on the sequences of ancestral nodes so we need different algorithms to reconstruct the ancestral node . Algorithms used are : FITCH ALGORITHM Constructing maximum parsimony trees from protein /DNA sequence data using MEGA ( molecular evolutionary genetics analysis ) software .

21. Maximum likelihood approach The maximum likelihood method presents an additional opportunity to evaluate trees with variations in mutation rates in different lineage . The method can be used to explore relationship among more diverse sequences and condition that are not well handled by maximum parsimony methods .

22. Distance based method : Distance method are based on the amount of dissimilarity ( distance ) between two aligned sequences . Such method remain important when using fossil data to build phylogenies for extinct species and for living species it is more common to use DNA sequences from the two species . This method assume that all sequence involved are homologous and that tree branches are additive , meaning the distance between the two taxa equals the sum of all branch branch lengths connecting them .

23. Algorithms used in distance method UPGMA (Unweighted Pair Group method Using Arithmetic Average ) Neighbor joining

24. Pliohippus