Topic 11 - Phylogenetics

Microevolution

Change in frequencies of traits in a population across generations

Macroevolution

The origin of species

Phylogenetic Tree

diagram representing the branching history of evolution • Pattern of branching indicates relationships between populations/species

Common Ancestor

Population found at a branching points, which gives rise to all descendent species

tree parts: tips

extant and sometimes extinct organisms being compared (Taxa or Individuals)

tree parts: branches

• Independently evolving lineages
• Could contain many species along the way
• Many branches are often excluded
• (e.g. leading to extinct species)

tree parts: nodes, branching points

Represent populations not individuals

tree parts: clades

All branches and tips derived from a given node

tree parts: Most Recent Common Ancestor (MRCA)

• Nearest node joining a clade together
• Represents an ancestor population which
was a distinct species from any of extant
species within the clade.
• Every node on a tree is the MRCA for a
different clade

tree parts: root

Node indicating the MRCA for all organisms on the tree

what are relationships on a tree defined by?

in terms of clades and common ancestors

How can we objectively decide which tree is right?

1. Gather data on the species in question
2. Draw all possible trees for all possible relationships (or as many as possible)
3. Map how each character may have changed along each tree to produce the data
4. Select the “best” tree as the most probable

Phylogenetic Inference Step 1: Data

1. Morphological
2. Behavioral
3. Fossil
4. Molecular
• DNA Sequences
• Protein Sequences
• Chromosome Structure
• RNA Folding Patterns
• Gene Duplications

Advantages of Molecular data

• Helps remove bias due to human perception
• Allows comparison of organisms with no morphological similarities (e.g. humans, apple trees, fireflies, bacteria, yeast, and mushrooms)

Phylogenetic Inference Step 2: Possible Trees

• To avoid bias, all possible trees should receive equal consideration as potentially representing evolutionary history.
• How many trees are possible for a given number of species?
• The number of unique rooted trees for

n taxa= [(2n-3)!] / [2n-2*(n-2)!]

Phylogenetic Inference Step 3: Map Characters

• Character evolution can be mapped to a tree by marking changes along the branches of the tree.
• Multiple histories are possible for each tree.

Principle of Parsimony

o Generally: the simplest solution which explains
all the data is preferred.
o In Phylogenetics: for any tree and character,
the preferred mapping is the one with the
fewest number of changes.

Phylogenetic Inference Step 4: Evaluate Trees, Maximum Parsimony

Criterion which says the best tree is the one which requires the fewest evolutionary changes for all characters

Tree Length

The total number of changes required for all characters on the tree

Homologous Structures

• Structures which evolved from the same feature in a common ancestor
• May be similar or very dissimilar in superficial appearance and function
• Similar embryonic development and underlying structure can be a clue that two structure are homologous

Homoplasious Structures

• Structures are similar in form and function that arose independently
• Convergent Evolution
• Do not arise from the same structure in their common ancestor
• Occurs when similar selective pressures act along two independent branches
• Will have different embryonic development and underlying structure
• Reveals physical principles relevant to form and function

Homology, requires at least 4

losses of camera eye

Homoplasy, requires only 2

“gains” of camera eyes

Homology/Homologous Structures

Different structures in two species that are derived from the same character found in a common ancestor

Homoplasy/Homoplasious Structures

Structures that are similar in form and function but have evolved independently in species due to common selective pressures.

Taxonomy

Classifying and naming organisms

Artificial Groups

rank assignments initially based only on similarity without concern for evolutionary relationships

• Domain
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus
• Species

Monophyletic

taxonomic group that includes the common ancestor and all descendants (i.e. a clade)

Paraphyletic

taxonomic group that includes the common ancestor but excludes descendants on one or more branches

Polyphyletic Groups

taxonomic group that does not include the common ancestor; often erroneously grouped due to homoplasy

Phylogeny

• Reconstruction of evolutionary
relationships vis-à-vis trees
• Clades represent natural groups due to
shared common ancestry without
regard for appearance

Monophyletic groups

groups reflect common ancestry and thus evolutionary history

Polyphyletic groups

groups do not reflect evolutionary history and should be re-organized

Paraphyletic

names may be helpful when discussing groups that share (or lack)
some key feature, but are avoided in strict taxonomical ranks.