Phylogeny

Phylogeny

• Evolutionary history of a species or a group of species

• Goal: Resulting phylogeny should match taxonomy (classification of an organism)

Phylogeny and Classification

Phylogenetic Tree

• Constructed using morphological similarities (homologies) of living or fossil species, DNA and protein sequences

• Show evolutionary history and relationships among groups of organisms

• Trees are dynamic (constantly being revised)

Understanding Phylogenies

• Click on the hyperlink above for an introduction to phylogenetic trees

• Read the first page and then click “next” at the bottom of the page for page 2 of Understanding Phylogenies

(Yes…I expect you to explore the link above – don’t ignore it)

Tree Terminology

Tree Terminology

• Sister taxa – groups of organisms that share an immediate common ancestor

• Node (branch point) – represents the most recent common ancestor of a group

• Root – single branch point from which all branches originate in the tree

Rooted versus Unrooted Trees

Clades

• Clade: a group of organisms that consists of a common ancestor and all of its descendants

Monophyletic Group

• A clade is also known as a monophyletic group

Phylogenetic Trees vs Cladograms

• Sometimes used interchangeably

• Branch lengths of trees may show evolutionary time and amount of genetic change

Character

• Characters are heritable traits that can be compared across organisms, such as physical characteristics (morphology), genetic sequences, and behavioral traits

• Example: wings shown below

Derived versus Ancestral Characters

• A derived character is one that evolved in one group but not in the other group (a new trait)

• An ancestral character is thought to have evolved in a common ancestor of both groups

Derived versus Ancestral Characters

• Identify a derived character for mammals

• Identify an ancestral character for mammals

Example of a Derived Trait

• Number of heart chambers in animals

• Tbx5 protein influences the formation of two ventricles in bird and mammalian hearts

Trees Show Speciation Events and Relatedness

• Examine common ancestry in order to determine relatedness

• Who is species 5 most closely related to?

Outgroup

• An outgroup is a group of organisms that serve as a reference group when determining the evolutionary relationship among a monophyletic group of organisms

• Used as a point of comparison for the ingroup

• Example:

- Chordates – Ingroup

- Echinodermata - Outgroup

Chordate Evolution

Another Outgroup Example

Trees May Show Time and Extinct Lineages

Extinct versus Extant

Phylogenetic Trees Based on Sequence Data

• Use of molecular (i.e. DNA, proteins) genetics to determine evolutionary relationships

• Disadvantages

–Need common genes

–Gene sequences need to be “aligned” first

Sequence Alignment

• Goal of Sequence Alignment: Maximize the number of matching nucleotides in all compared sequences

• Compare SNPs and Indels

SNPs and Indels

• SNPs – single nucleotide polymorphisms

• Indels – insertions and deletions

Maximum Parsimony

• Choosing a tree that requires the fewest evolutionary events (fewest amount of molecular changes)

• The simplest explanation that is consistent with the facts

Which is the most parsimonious tree?

Constructing a Phylogenetic Tree

• May require the use of a character table

• + or 1 indicates the presence of the character, - or 0 indicates the absence of the character

Now You Try It • Based on the shared characteristics in the

table below, build a tree of the most likely evolutionary history of these organisms

• + (present), - (absent)