Phylogenetic Trees and Evolutionary Relationships

• Phylogenetics involves building phylogenetic trees to represent the evolutionary relationships between different organisms.
• The goals for this subject are to understand the inputs and outputs for phylogenetic reconstruction and to learn how to build a phylogeny.

Building a Phylogeny

• Data about the terminals, also called taxa, being studied needs to be collected.
• Morphological, DNA/RNA/Protein sequences, and behavioral traits can be collected.
• Homology: the same organ in different animals under every variety of form and function.
• Taxic homology is when homologue characters are located on the same body position.
• DNA, RNA, and Proteins are considered as molecular data.

Phylogeny Basics

• Phylogeny refers to the evolutionary history of organisms.
• Phylogenies are networks, generally represented as a tree diagram.
• OTUs (Operational Taxonomical Units) are equivalent to terminals on the tree.
• HTUs (Hypothetical Taxonomical Units) are equivalent to nodes, speciation events on the tree.
• A fully resolved tree is different than an unresolved tree.
• The unresolved tree can be a star tree.
• Partically resolved trees have polytomy.
• 'Hard' polytomy (simultaneous divergence) is different to 'Soft' polytomy (uncertainty).
• Parenthetical tree mode creates cladograms, or additive trees.
• ((A,B),C) is an example of the format found in the parenthetical tree mode.

Phylogenetic Analysis

• Maximum Parsimony refers model of evolutionary relationships.
• Maximum likelihood and Bayesian inference are other models.
• Parsimony involves choosing the simplest explanation which requires the fewest evolutionary changes.
• Parsimony produces cladograms.
• The tree obtained is the one that has the Maximum Likelihood given the data.
• Bayesian inference searches for the tree based on their posterior probability that the tree is true given the data, model of evolution, and prior information.

Bayesian Phylogenetics

• Pr (Tree | Data ) = (Pr (Data | Tree) x Pr (Tree)) / Pr (Data)

• Pr (Data | Tree ) = Likelihood (calculated as before but integrating the prior probability of all parameters)

• Pr (Tree ) = The probability that our tree is the correct among all trees

• Pr ( Data ) = Summation of over all trees

• Two types of homology are Orthology and Paralogy.

Molecular Evolution

• Sequence evolution involves changes in the nucleotides/amino acids at a particular position in that sequence.
• Substitution is a base change into a different base at the same position.
• Insertion is a base that appears in the sequence without a locally homologous position.
• Deletion is a base that disappeared in the sequence.

Sequence Alignment

• Pairwise alignment is different to multiple sequence alignment.
• Multiple sequence alignment (MSA) can be conducted via Progressive or Iterative methods.

Sequence Models

• Expected count of nucleotide substitutions per site can be transversions or transitions.
• JC69 (Jukes and Cantor 1969) assumes every nucleotide has the same rate of changing into another nucleotide.
• K80 (Kimura 1980) shows how transition and transversion rates are different.
• HKY85 (Hasegawa et al. 1985) = unequal base compositions and asymmetrical substitution rates.
• GTR (General reversible model) = each possible substitutions has its own probability.
• Dayhoff (Dayhoff et al. 1978) uses parsimony arugment to reconstruct ancestral sequences.
• JTT (Jones et al. 1992) defines another ancestral model.
• WAG (Whelan and Goldman 2001) defines another ancestral model.

Summary

• Phylogenies are built using morphological. molecular, and behavioral data.
• Homologue traits are taxic homology and molecular homology.
• Orthology and paralogy are types of homology.
• Parsimony or model-based methods (Maximum Likelihood or Bayesian Inference) are used to construct phylogenies.
• Parsimony yields cladograms only.
• ML searches for the tree based on probable evolution.
• BI searches for the tree based on posterior probability that the tree is true given the data, model, and prior information.
• Molecular data must be aligned using Multiple Sequence Alignments.
• Models of substitution accounts for the probability that one nucleotide will change for another.
• A tree that is less parsimonious than another requires more changes.
• The tree with 'jaws' is considered more parsimonious.

Learn about phylogenetics and building phylogenetic trees to represent the evolutionary relationships between organisms. Building a phylogeny requires collecting data about the terminals being studied, including morphological, DNA/RNA/Protein sequences, and behavioral traits. Phylogenies are networks, generally represented as a tree diagram.