phylogenetic studies
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Phylogenetic studies
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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
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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
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Major assumptions
Sequences are homologous
Phylogenetic divergence is bifurcating
Each position in sequence evolved independently
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Phylogenetic tree
Tree showing the evolutionary relationships among various biological species or other entities that are known to have a common ancestry
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Types of Phylogenetic trees
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Types of Phylogenetic trees
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Types of Phylogenetic trees
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Types of Phylogenetic trees
Rooted and Unrooted
Bifurcating & Multifurcating
Labeled & Unlabeled
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Types of Phylogenetic trees
NR – No. of Rooted trees NU – No. of Unrooted treesn – No. of Taxa
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Dendrogram
Cladogram
Phylogram
Chronogram or Ultrametric tree
Different representations
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Cladogram
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Monophyly
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Paraphyly
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Polyphyly
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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
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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
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Choosing a model of evolution
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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
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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
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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
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Distance methods:-e.g. Neighbor joining, UPGMA clustering
Character-based:-e.g. Maximum parsimony, Maximum likelihood
Methods
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Efficiency
Power
Consistency
Falsifiability
Criteria for the selection