Evolution Terms (from lectures after midterms)

Phylogeny

The evolutionary history of a group of organisms (or genes), showing how they are related through common ancestors.

Node

A point where a lineage splits (represents a common ancestor)

Outgroup

• A species closely related to the ingroup but not part of it

• Helps to determine evolutionary direction and relative timing of divergence

Clade & Sister taxa

Clade: a group that includes a common ancestor and all its descendants

Sister taxa: two groups that share the same immediate ancestor

Cladogram vs Additive Tree

a cladogram shows relationships only (no meaning to branch length), while an additive tree shows relationships and how much evolutionary change occurred (branch length matters)

Homoplasy

When character similarity is not due to common ancestry

Homoplasy examples

1. Convergent evolution: different species independently evolve similar traits (not from a common ancestor)

2. Secondary loss: a trait present in an ancestor is lost in some descendants

Advantages of molecular characters

• abundant data

• easy to compare between species (homology)

• strong models to study evolution

• heritable

Be careful:

• comparing the correct sequences

• model assumptions

• gene mixing (e.g. hybridization, gene transfer)

Phylogenetic methods

1. Distance

2. Maximum Parsimony

3. Maximum Likelihood

4. Bayesian (similar to likelihood in many

ways)

Maximum Likelihood

A method to find the evolutionary tree that most likely explains your data, using a model of sequence evolution, your data, and possible trees.

Why gene trees and species trees can differ

• Hybridization / introgression

• Horizontal gene transfer

• Ancestral polymorphism (incomplete lineage sorting)

Long branch attraction

Occurs when two fast-evolving lineages accumulate many mutations and independently evolve similar changes.

• phylogenetic methods may mistakenly group them together

What are key characteristics of animals (Metazoa)?

• obligate multicellular

• differentiated cell types

• epithelium

• development starts from fertilization

• regulated development (e.g. gastrulation)

What is synteny?

Genes being physically close or linked together on the same chromosome, often conserved across species.

What’s the sister group of animals

Choanoflagellates

Key features of prokaryotic evolution

• Good at acquiring and/or exchanging DNA

• Prokaryotic cells are typically haploid

• Most have very big population sizes- low genetic drift, higher natural selection

What are myxobacteria?

• saprophytic, soil-dwelling, gram-negative bacteria

• produce many complex compounds

• show complex behaviors (gliding motility, aggregation, fruiting bodies)

Smallest known bacteria

Vidania (symbiont)

How do prokaryotes exchange DNA?

• conjugation (plasmid transfer)
• transduction (via viruses/phages)
• transformation (uptake from environment)

What is recombination in prokaryotes?

• homologous recombination → similar to gene flow/sexual recombination
• nonhomologous recombination → introduces new DNA (horizontal gene transfer)

What is horizontal gene transfer (HGT)?

transfer of genes between organisms; major source of adaptation, detectable by unusual sequences or phylogeny, and can involve many gene types (e.g. antibiotic resistance)