Phylogenetic trees

Phylogenetics describes

The history of descent from common ancestry

Phylogenetics is used to

1) Determine which organisms are more closely related

2) Estimate when species formed

Node

Taxonomic unit

Rooted trees

Show common ancestor, direction of each path to each node corresponds to time

Unrooted trees

Only specifies relationship, not evolutionary path between nodes, they do not depict time or a common ancestor

Clades

Parts of the phytogenic tree including an ancestral node and all their descendants

Monophyletic group

A clade that contains a single common ancestor and all of their descendants

Paraphyletic group

A monophyletic group that excludes one or more descendants of the common ancestor

Cladogram

Illustrates evolutionary relationships among different species or groups

Phylogram

Type of phylogenetic tree that represents evolutionary relationships with branch lengths proportional to the amount of evolutionary change

Orthology

The relationship of 2 homologous genes that both descended from the same gene in their most recent common ancestor.

Paralogy

The relationship of 2 homologous genes that have arisen from a duplication event

Xenology

The relationship of 2 homologous genes whose history involves an interspecies (horizontal) transfer.

Bootstrap

A statistical method used to estimate the reliability of phylogenetic trees by resampling data and assessing how often specific clades appear

Multiple Sequence Alignment (MSA)

Aligns a set of homologous DNA/protein sequences so each column derives from a common ancestor. It relies on:

→ Scoring (sum-of-pairs score using substitution matrices)

→ Optimization Heuristics (tools use progressive alignment/iterative refinement)

Basic Principle of Pairwise Distance Methods

1. Compute a distance matrix: For every pair of taxa, calculate a genetic distance (e.g. percent differences, corrected substitutions).

2. Cluster taxa: Iteratively join the closest pairs (smallest distances) into nodes, updating distances as you go (e.g. UPGMA, Neighbor-Joining).

3. Output: A tree whose branch lengths reflect the original pairwise distances.

Coping with Multiple Substitutions

Problem: Over long times, the same site may mutate more than once (“hidden” changes), leading raw differences to underestimate true divergence.

Solutions:

• Correction models (e.g. Jukes–Cantor, Kimura 2‐parameter) that mathematically adjust observed differences to estimate actual substitutions.

• Maximum likelihood or Bayesian methods that incorporate explicit substitution models and account for rate variation among sites.

Orthologs, Paralogs and Xenologs

Orthologs → Genes in different species that diverged by a speciation event. (E.g. human haemoglobin α vs. mouse haemoglobin α.)

Paralogs: Genes within the same (or different) species that arose by a gene‐duplication event. (E.g. human hemoglobin α vs. hemoglobin β.)

Xenologs: Genes related by horizontal (lateral) gene transfer between species.

Bootstrapping a Phylogenetic Tree

1. Resample alignment columns (sites) with replacement to create many “pseudo‐datasets.”

2. Reconstruct a tree for each pseudo‐dataset using the same method.

3. Calculate support: For each clade in your original tree, count the percentage of bootstrap trees where that clade appears.