Phylogenetic Trees

Phylogenetic Trees

• Phylogenetic trees can be unrooted or rooted, and rooted trees can be constructed using statistical tools, such as mid-point rooting.
• Rooting involves assumptions, and the choice of the outgroup is crucial in normalizing the branches of the unrooted tree.

Rooting Trees

• Mid-point rooting involves finding the midpoint of the sum of the distances between two sequences.
• Example: if the distance between sequences A and D is 18, the midpoint would be 9.

Number of Possible Trees

• The number of rooted trees (NR) and unrooted trees (NU) for n sequences can be calculated using formulas:
  • NR = (2n-3)!/2n-2(n-2)!
  • NU = (2n-5)!/2n-3(n-3)!

Tree Construction Methodology

• The steps involved in constructing a phylogenetic tree are:
  1. Consider the set of sequences to analyze.
  2. Align the sequences properly.
  3. Apply phylogenetic tree construction methods.
  4. Evaluate the obtained phylogenetic tree statistically.

Alignment

• Alignment is a crucial step in constructing a phylogenetic tree.
• Errors in indel placement can lead to incorrect tree reconstruction.

Phylogenetic Tree Construction Methods

• There are three main classes of phylogenetic methods:
  1. Methods directly based on sequences:
     • Maximum Parsimony: find a tree that explains the data with as few evolutionary changes as possible.
     • Maximum Likelihood: find a tree that maximizes the probability of the genetic data given the tree.
  2. Methods indirectly based on sequences:
     • Distance-based methods (Neighbour Joining): find a tree such that branch lengths of paths between sequences fit a matrix of pairwise distances.
• Character-based methods assume that each character substitution is independent of its neighbors.
• Validation methods include bootstrapping and jackknifing.

Reconstructing Phylogenies

• The rules for reconstructing a phylogeny include:
  1. Maximum likelihood states that when considering multiple phylogenetic hypotheses, one should take into account the one that reflects the most likely sequence of evolutionary events given certain rules about how DNA changes over time.

Maximum Likelihood

• Maximum likelihood is a statistically-based method that creates all possible trees and calculates the probability of each tree reflecting the sequence data.
• The tree with the best probability is shown as the maximum likelihood tree.

Phylogenetic Software

• PHYLIP (Phylogeny Inference Package) is a software package that offers parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees.
• Other software packages include MEGA, PAML, and Clustalw.

Choosing a Phylogenetic Method

• The choice of phylogenetic method depends on the strength of similarity between sequences:
  • Strong similarity: Maximum Parsimony.
  • Distant similarity: Distance-based methods.
  • Very weak similarity: Maximum Likelihood.

Distance-Based Clustering Methods

• Examples include:
  • Neighbor-Joining (unrooted tree).
  • UPGMA (rooted tree).

UPGMA

• UPGMA is a distance-based clustering method that builds a guide tree by clustering distances.
• The steps involved in UPGMA are:
  1. Multiple alignments based on all-against-all pairwise comparisons.
  2. Building a distance matrix of all compared sequences.
  3. Disregarding the actual sequences.
  4. Constructing a guide tree by clustering distances iteratively.

Evaluating Phylogenetic Methods

• None of the phylogenetic reconstruction methods guarantee a single true tree.
• There is currently no statistical method to compare trees obtained from different phylogenetic methods.

This quiz covers the basics of phylogenetic trees, including the difference between unrooted and rooted trees. Learn about the structure and representation of these trees.