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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