Lecture 2 - Phylogeny

What is Phylogeny?

The evolutionary history of a group of related species (or other taxonomic units)

What is a Phylogeny Tree?

Evolutionary tree which shows the evolutionary relationships between species

Which phylogenetic groups are considered valid?

Monophyletic

What is a Monophyletic group?

Includes all descendants of a most recent common ancestor

What is a Paraphyletic group?

Only some descendants included

What is a Polyphyletic group?

Only some descendants included + doesn't include most recent ancestor

How are branching points determined on a phylogenetic tree?

By shared derived character states

What are shared derived character states?

Traits evolved in common ancestor

What are the different types of shared derived characters?

- Molecular - genetic

- Morphological - phenotypic

What is the root of a phylogenetic tree?

The starting point, a common ancestor of all the species

What is an unrooted phylogenetic tree?

Unknown common ancestor

How are evolutionary relationships determined?

Comparing traits

What is required to define monophyletic groups by derived character states?

Compared characters should be homologous

What is a homologous character?

Similar traits inherited from a last common ancestor

What is convergent evolution?

Repeated evolution of similar traits

What is convergent evolution divided into?

Analogy and Homoplasy

What is Analogy Evolution?

Similar functional traits due to convergent evolution not inheritance from a lost common ancestor

What is Homoplasy Evolution?

Repeated evolution of the same state of the same character on a phylogenetic tree

How are Morphological Phylogenetic reconstructred?

• Matrix built

• Absence/Presence

• Inferrence

- Morphological character matrix built

- Records presence/absence of compared traits

- Matrix infers phylogeny

How does Phylogenetic Inference work?

Different optimality criteria used to search for the best tree

What is Neighbour Joining Phylogenetic Interference?

Join similar neighbours, simple calculation

What is Maximum Parsimony Phylogenetic Interference?

Best = least number of changes, requires all trees

What is Maximum Likelihood Phylogenetic Interference?

Best = most likely to produce most common in DNA-based phylogenetics

What is a Phylogenetic Molecular Clock?

- Dates divergence times

- Estimates absolute time of divergence based on a previouly estimated rate of mutation

What is required for a Phylogenetic molecular clock?

Constant rates of mutation

Phylogeny

Evolutionary history and relationships among species

Phylogenetic Tree

Diagram representing evolutionary relationships between species

Node

Point on a tree representing a common ancestor

Branch

Line representing evolutionary lineage

Root

Ancestral lineage from which all organisms in the tree descend

Sister Taxa

Groups that share an immediate common ancestor

Clade

Group consisting of a common ancestor and all its descendants

Monophyletic Group

Group including a common ancestor and all its descendants

Paraphyletic Group

Group including a common ancestor but not all descendants

Polyphyletic Group

Group that does not include the most recent common ancestor

Shared Derived Character (Synapomorphy)

Trait shared by a group due to inheritance from a common ancestor

Ancestral Trait (Plesiomorphy)

Trait present in the common ancestor but not unique to a group

Homology

Similarity due to shared ancestry

Analogous Traits

Similarity due to convergent evolution, not shared ancestry

Homoplasy

Similarity not due to common ancestry (e.g. convergence or reversal)

Convergent Evolution

Independent evolution of similar traits in unrelated species

Molecular Homology

Similarity in DNA or protein sequences due to shared ancestry

DNA Sequence Comparison

Method of comparing nucleotide sequences to determine relatedness

Protein Sequence Comparison

Method of comparing amino acid sequences to infer relationships

Genetic Similarity

Extent to which DNA sequences are alike between species

Evolutionary Distance

Measure of divergence between species over time

Mutation

Change in DNA sequence that contributes to evolutionary divergence

Molecular Clock

Method estimating divergence time based on mutation rate

Greater Similarity Interpretation

More similar DNA indicates more recent common ancestor

Less Similarity Interpretation

More differences indicate more distant relationship

Maximum Parsimony

Method choosing tree with fewest evolutionary changes

Maximum Likelihood

Method choosing tree with highest probability given data

Outgroup

A distantly related group used to root a phylogenetic tree

Rooting a Tree

Establishing direction of evolution using an outgroup

Character

Trait used in phylogenetic analysis

Character State

Form of a character (e.g. present/absent)

Derived Character

Trait that evolved in a lineage after divergence from ancestor

Cladistics

Method of classification based on shared derived characters

Cladogram

Tree showing relationships without branch length representing time

Phylogram

Tree where branch length reflects amount of change

Gene Tree

Tree representing relationships of a single gene

Species Tree

Tree representing relationships between species

Conflict Between Trees

Different genes may suggest different evolutionary histories

Horizontal Gene Transfer

Transfer of genes between unrelated species

Importance of Molecular Data

Provides quantitative and reliable evidence of relationships

Limitation of Morphology

Can be misleading due to convergent evolution

Limitation of Molecular Data

Different genes may evolve at different rates

Conserved Genes

Genes that change very little across species

Use of Conserved Genes

Useful for studying deep evolutionary relationships

Rapidly Evolving Genes

Genes that change quickly, useful for recent divergence

Parallel Evolution

Independent evolution of similar traits in related species

Reversal

Return to ancestral trait state

Importance of Homology in Phylogeny

Only homologous traits reflect true evolutionary relationships

Problem with Analogy

Analogous traits can mislead phylogenetic analysis

Interpretation of Nodes

More recent node = closer evolutionary relationship

Tree Rotation

Branches can rotate without changing relationships

Misconception About Trees

Adjacent species are not necessarily closely related without shared node

Evolution Not Goal-Directed

Phylogenies do not imply progress or direction

Common Ancestor Concept

All species in a tree trace back to a shared ancestor