Phylogeny

Concept of phylogeny , history of phylogeny, phylogenetic tree

1. PHYLOGENY PHYLOGENETIC TREE,CLADISTICS AND PHYLOGENETIC TREE CONSTRUCTION NAME- NIKITA ROLL NO. – CUHP18ZOO18 SUBMITTED TO – MISS EKTA GULERIA

2. PHYLOGENY is the study of the evolutionary history and relationships among individuals or group of organisms. Evolutionary history for understanding life through time. Over long periods of past time. The connections between all groups of organisms as understood by ancestor or descendent relationships. It represents tree of life . Phylogeny is diagrammatically represented by phylogenetic trees. Phylogenetic analysis have become central to understanding biodiversity, evolution and genomes.

3. HISTORY OF PHYLOGENY The term ‘’PHYLOGENY’’ derives from the German word ‘’PHYLOGENIE’’ introduced by Ernst Haeckel in 1866 and Darwinian approach to classification become known as ‘’Phyletic approach’’. Ernst Haeckel’s recapitulation theory was widely accepted during late 19 th century It was often expressed as ‘’ontogeny recapitulates phylogeny’’ i.e. the development of single organisms during its lifetime , from germ to adult , successively mirrors the adult stages of successive ancestors of species to which it belongs. But in modern world this theory has been rejected.

4. PHYLOGENETIC TREE - It is a two dimensional graph showing evolutionary relationships between organisms or genes from various organisms. Phylogenetic tree or evolutionary tree is a branching diagram or tree showing evolutionary history of organisms. All life on the Earth is a part of single phylogenetic tree,indicating common ancestory . T YPES OF PHYLOGENETIC TREE Phylogenetic trees are of two types : Rooted tree Unrooted trees

5. ROOTED TREE :-- has a root that denotes commom ancestory . The root node does not have parent node, but serves as parent of all other nodes in the tree. UNROOTED TREE :- only specifies the degree of kinship among taxa but not the evolutionary path. Unrooted trees can always be generated from rooted ones simply omitting the root. A PHYLOGENETIC TREE BRANCHES either be:- Scaled branches – their length are proportional to the evolutionary change. Example: Phylogram . Unscaled branches – the branch length is not proportional to the number of changes. Example: Cladogram.

6. Rooted tree Unrooted tree

7. CHARACTERISTICS:- Nodes can be internal or external. External node represent the last common ancestor of the two lineage. Each internal node represents the last common ancestor of two lineage. Branches can be internal or external. Nodes correspond to species , organisms or sequences. Internal branches or internodes connect two nodes, whereas external branches connect a tip and a node.

8. CLADISTICS:- Cladistics is an approach to biological classification in which organisms are categorized in groups [clade] based on the most recent common ancestors. Cladistics in the original sense refers to a particular set of methods used in phylogenetic analysis. Cladistics reflects an organism’s evolutionary history. It shows evolutionary relationships based on ‘’shared derived characters’’. Cladistic relationship illustrated through the use of cladogram.

9. CLADOGRAM :- A cladogram is a phylogenetic tree with a series of splits and can trace back to a common ancestor of two species. In cladistics ,common descendent is the primary criteria used to classify organisms. Group of species is called ‘’clade’’ ,each of which includes an ancestral species and all of its descendents .

10. Clade is divided into three types :- Monophyletic Clade – a monophyletic taxon of a clade is a taxon that includes all descendents of an inferred ancestor. A monophyletic clade is characterized by one or more apomorphies : derived character states present in first member of taxon , inherited by its descendents and not by any other taxa. Paraphyletic Clade - a paraphyletic assemblage is one that is constructed by taking a clade and removing one or more smaller clades. It is characterized by one or more plesiomorphies : character states inherited from anestors but not present in all of their descendents . Polyphyletic Clade - a polyphyletic assemblage is one which is neither monophyletic nor paraphyletic. It is characterized by one or more homoplasies : character states which have converged or reverted so as to be the same but which have not been inherited from a common ancestor.

11. COMPARISON BETWEEN CLADOGRAM AND PHYLOGENETIC TREE :-

12. SIMILARITIES :- Both cladogram and phylogenetic tree are two types of evolutionary tree that shows relationships between a group of organisms called taxa. Each branch of both evolutionary trees represents descending taxa from common ancestor. The nodes on both represents the cmmon ancestors of the descendents . The descendents separated from same node called sister groups. tn both , sister groups are close relatives of each other.

13. DIFFERNCES :- The main difference between cladogram and phylogenetic tree is that ‘cladogram ia an evolutionary tree with branches with equal distane showing relationships between a group of clades’ whereas ‘phylogenetic tree is an evolutionary tree showing an estimate of phylogny where the distance of each branch is proportional to the amount of inferred evolutionary change’. Relatedness – The shape of cladogram shows the relatedness among a group of organisms whereas the distance of phylogenetic tree branch depends on amount of inferred evolutionary change. Genetic distance – In cladogram, it does not represent evolutionary time or genetic distance while phylogenetic tree represents the evolutionary time and the genetic distance between group of the organisms. Evolutionary history – cladogram represents a hupothesis about actual evolutionary history whereas phylpgenetic tree represents true evolutionary history of some extent.

14. CONSTRUCTION OF PHYLOGENETIC TREE :- It involves two types of methods : Character based method . Distance method . 1. CHARACTER BASED METHOD -> Also known as discrete method and are based directly on the sequence characters rather than on pairwise distances . The two most common and popular character based methods are : Maximum parsimony –> P arsimony method is one of the pioneer method of phylogeny construction . - Parsimony groups taxa together in a way that minimize the number of changes. - It assume that the best hypothesis is one that requires the fewest no. of evolutionary changes ,hence it is also called as minimum evolution method. Maximum likelihood method -> The maximum likelihood method represents an additional opportunity to evaluate trees with variations in mutation rates in different linerage . -The method can be used to explore relationships among more diverse sequences and condition that are not well handled by maximum parsimony methods.

15. 2. DISTANCE BASED METHOD :-> Distance based methods are based on the amount of dissimilarity 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 two species. Algorithms used in distance method are ::- UPGMA [unweighted pair group method using arithmetic average ] Neighbour joining method .

16. 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 organisms exhibited today. A phylogenetic analysis consist of 4 steps and are :-> 1. Sequence alignment  It is essential preliminary to the tree reconstruction . The data used in reconstruction of DNA based phylogenetic tree are obtained by comparing nucleotide sequences. These comparisons are made by aligning the sequences so that nucleotide differences can be scored. 2. Determining the substitution model. 3.Tree building. 4.Tree evaluation.

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