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)