Phylogenetic studies

Problems in Phylogenetics

Fossil records are sporadic and less reliable

Only available data is genetic data

How evolution operates is used in the tree construction

Phylogenetics

Study of evolutionary relatedness among various groups of organisms

Basis:Molecular sequencingMorphological data

*** Molecular data, protein and DNA sequences is the basis for present methods

Major assumptions

Sequences are homologous

Phylogenetic divergence is bifurcating

Each position in sequence evolved independently

Phylogenetic tree

Tree showing the evolutionary relationships among various biological species or other entities that are known to have a common ancestry

Types of Phylogenetic trees

Types of Phylogenetic trees

Types of Phylogenetic trees

Types of Phylogenetic trees

Rooted and Unrooted

Bifurcating & Multifurcating

Labeled & Unlabeled

Types of Phylogenetic trees

NR – No. of Rooted trees NU – No. of Unrooted treesn – No. of Taxa

Dendrogram

Cladogram

Phylogram

Chronogram or Ultrametric tree

Different representations

Cladogram

Monophyly

Paraphyly

Polyphyly

1. Choosing molecular markers

2. Performing multiple sequence alignment

3. Choosing a model of evolution

4. Determining a tree building method

5. Assessing a tree reliability

Steps

For very closely related organisms – Nucleotide sequences e.g., Noncoding regions of Mitochondrial DNA

For more divergent groups – Slowly evolving Nt sequences e.g., Ribosomal RNA Protein sequences

Choice of Molecular markers

Choosing a model of evolution

Distance-based methods – Based on distance (amount of dissimilarities) All sequences are homologous and tree branches are

additive

Character -based – Based on discrete characters (sequences) e.g., Ribosomal RNA Protein sequences

Tree building methods

Clustering-based – Based on a distance matrix starting from the most

similar sequences1. UPGMA (Unweighted Pair Group Method using

Arithmetic Average): Sequential clusteringAssumption: All taxa have constant evolutionary rates

2. Neibour-joining Taxa are not equidistant from the root Uses conversion step

Distance-based

Optimality based – Compare all possible tree topologies and select the best

1. Fitch-Margoliash: Sequential clusteringAssumption: All taxa have constant evolutionary rates

2. Neibour-joining Taxa are not equidistant from the root Uses conversion step

Distance-based

Distance methods:-e.g. Neighbor joining, UPGMA clustering

Character-based:-e.g. Maximum parsimony, Maximum likelihood

Methods

Efficiency

Power

Consistency

Falsifiability

Criteria for the selection