LUCA & Tree of LIfe

What happens when a lineage splits?

• daughter lineage shares many traits

• homology: sharing of traits via common ancestry

• analogy: sharing traits that DO NOT have common ancestry; evidence of independent origins

• divergence: daughter lineages resemble each other less over time

Features of Phylogenetic Tree

branches: distinct line in tree that represent evolution over time

nodes: points where branches join represent separation of one lineage into multiple distinct lineages

tips/terminal nodes/leaves: represent end points for each branch

Monophyletic group (clade)

ancestor and all its descendents

paraphyletic group

only some of species share common ancestor within the group

polyphyletic group

species are treated as a group because of some shared biological feature even though they DO NOT share common ancestor

Phylogram

a type of phylogenetic tree that indicates the amount of evolution in addition to the branching order, branch lengths are variable

• quantify rate of change

polytomy

3 branches emerge from single node

• represent starburst-like evolutionary patterns

• used to represent ambiguity in a model

Rooted v. Unrooted trees

Unrooted trees assume that all organisms represented in the tree have a shared ancestor, but the position of that ancestor is unknown.

What do Bootstrap Values measure?

measure how strongly the data support a clade/grouping

• Higher values = greater confidence/support for that relationship.

What can make phylogenetic trees difficult to construct?

Relationships are often inferred, evolutionary rates vary among lineages, and analogous traits can be misleading

What is convergence?

Similar traits evolve independently due to similar environments.

• Only homologous traits should be used to build trees.
  Example: Gliding evolved independently in lemurs, flying foxes, squirrels, and marsupials.

What is parallel evolution?

• Similar traits arise independently from the same ancestral feature.

LUCA importance

most likely not first living organism but most distant common ancestor

What is the Principle of Parsimony, and how is it applied to LUCA?

Choose the simplest explanation. If a trait is shared by all organisms, the simplest explanation is that it was present in LUCA.

• ex: Since all species have homologous small-subunit rRNA, LUCA likely had small-subunit rRNA.

What is an ancestral character state?

A trait state that was present in an ancestral organism and was inherited by its descendants.

What is a derived character state?

A trait state that evolved from the ancestral state and differs from it.

Why can determining ancestral vs. derived character states be complicated?

Because a trait may have different states in different species, making it difficult to determine which state was ancestral.

Why is rooting the Tree of Life challenging?

All organisms are thought to be related, so there is no obvious outgroup to determine where the tree's root should be placed.

What is an outgroup?

An organism or lineage that is outside the group being studied and is used to help determine relationships and root a phylogenetic tree.

How has molecular analysis helped with rooting the Tree of Life?

Molecular data, including the evolution of certain genes, can provide clues about ancestral relationships and the root of the tree.

What are paralogs?

Genes that arise when a gene duplication event produces two or more copies of a gene.

What is the difference between paralogs and orthologs?

• Paralogs: Homologous genes that arise through gene duplication, usually within a species.

• Orthologs: Homologous genes that diverge due to speciation, occurring in different species.

What does it mean that paralogs undergo parallel evolution?

After duplication, the duplicated genes can evolve independently within the same species.

How can paralogs help root a phylogenetic tree?

If a gene duplication occurred before LUCA, the two resulting paralogs can be used as outgroups for each other to help determine the ancestral state and root the tree.

What are EF-Tu and EF-G, and why are they useful?

EF-Tu and EF-G are paralogous genes that likely arose from a gene duplication before LUCA. Since both are found in all species, one can be used as an outgroup to construct a tree for the other.