Lecture 21: Phylogenetics & Comparative Genomics

What was Darwin’s central idea in 1859?

Descent with modification — species evolve over time through common ancestry

Phylogeny

Evolutionary history or “tree of life”

Phylogenetics

Study of evolutionary model and inference of phylogenetic trees 

Phylogenomics 

Using whole-genome data for phylogenetic analysis 

What does population genetics study?

Genetic variation to infer population history and evolution

What is a “node” in a phylogenetic tree?

A common ancestor

What is a “branch”? 

Evolutionary lineage 

What is a “root”?

The most recent common ancestor of the tree

What does the Out of Africa hypothesis state? 

Modern humans originated in Africa around 200,000 years ago 

How is phylogeny applied to cancer?

Tumor evolution can be traced through phylogenetic trees of mutations

What are phylogenies inferred from?

Traits and characters, including physiological and molecular data

How does traditional phylogenetics differ from modern? 

Traditional uses few stable traits (i.e., horns, teeth) while modern uses large-scale DNA/protein data 

What complicates modern phylogenetics?

Frequent back-mutations and noisy traits

What data can be used to infer trees?

Nucleotide or peptide sequences

What method can be used for tree reconstruction? 

Hierarchical clustering 

What does comparative genomics study?

Comparing genomes across species to reveal evolutionary relationships and functional elements

How do functional & non-functional regions evolve differently?

Non-functional accumulate mutations; functional regions are conserved due to selective pressure

What can conservation patterns reveal? 

Functional elements like exons and regulatory regions 

How do selective pressures help?

Different pressures leave distinct mutations patterns that indicate function.