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Phylogenetic studies
This document discusses phylogenetic studies and the construction of phylogenetic trees. It notes that fossil records are unreliable, so phylogenetic trees are primarily based on molecular sequencing data and morphological data. There are several assumptions made in phylogenetic analysis, including that sequences are homologous, phylogenetic divergence is bifurcating, and each position in a sequence evolved independently. The document outlines different types of phylogenetic trees, steps in phylogenetic analysis like choosing molecular markers and tree building methods, and criteria for assessing the reliability of phylogenetic trees.
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Phylogenetic studies
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- 2. Problems in Phylogenetics Fossilrecords are sporadic and less reliable Only available data is genetic data How evolution operates is used in the tree construction
- 3. Phylogenetics Study of evolutionaryrelatedness among various groups of organisms Basis: Molecular sequencing Morphological data *** Molecular data, protein and DNA sequences is the basis for present methods
- 4. Major assumptions Sequencesare homologous Phylogenetic divergence is bifurcating Each position in sequence evolved independently
- 5. Phylogenetic tree Tree showingthe evolutionary relationships among various biological species or other entities that are known to have a common ancestry
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- 9. Types of Phylogenetictrees Rooted and Unrooted Bifurcating & Multifurcating Labeled & Unlabeled
- 10. Types of Phylogenetictrees NR – No. of Rooted trees NU – No. of Unrooted trees n – No. of Taxa
- 11. Dendrogram Cladogram Phylogram Chronogram or Ultrametrictree Different representations
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- 16. 1. Choosing molecularmarkers 2. Performing multiple sequence alignment 3. Choosing a model of evolution 4. Determining a tree building method 5. Assessing a tree reliability Steps
- 17. For very closelyrelated 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
- 18. Choosing a modelof evolution
- 19. Distance-based methods – Basedon 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
- 20. Clustering-based – Based ona distance matrix starting from the most similar sequences 1. UPGMA (Unweighted Pair Group Method using Arithmetic Average): Sequential clustering Assumption: All taxa have constant evolutionary rates 2. Neibour-joining Taxa are not equidistant from the root Uses conversion step Distance-based
- 21. Optimality based – Compareall possible tree topologies and select the best 1. Fitch-Margoliash: Sequential clustering Assumption: All taxa have constant evolutionary rates 2. Neibour-joining Taxa are not equidistant from the root Uses conversion step Distance-based
- 22. Distance methods:- e.g. Neighborjoining, UPGMA clustering Character-based:- e.g. Maximum parsimony, Maximum likelihood Methods
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