Phylogenetics & Macroevolution

Lecture 10

Taxonomy

The theory and practice of classification & meaning

Systematics

The study of biodiversity and the evolutionary relationships among organisms

Taxon

A single named taxonomic unit at any level (plural = taxa)

Hierarchal system of classification

• Kingdom 

• Phylum

• Class

• Order

• Family

• Genus

• Species

Nodes

Historical lineage splitting events, when one lineage splits into two

Branches (aka “edges”)

Single ancestor-descendant lineages. All branches are connected by nodes

Tips (aka leaves, terminals, OTUs)

Do not have represented descendants

They can be:

• Individuals

• Species

• Clades

External branches

Connect tips and a node

Internal branches

Connects two nodes

Sister groups (aka sister taxa)

The immediate descendants of the same ancestor

Parents & daughters

“Parent” branches give rise to “daughters”

Roots

• A node representing earliest time point in the diagram

• Often represented by an unlabeled branhc

Ingroup

Focal species in a phylogenetic study

Outgroup

More distant relative of the ingroup taxa

MRCA

The youngest node that is ancestral to all lineages in a given group of taxa

Clade

Any piece of a phylogeny that includes an MRCA and all of its descendants

Monophyly

A group made up of an ancestor and all its descendants

Paraphyly

A group made up of an ancestor and some (but not all) of its descendants

Polyphyly

A group that does not contain the most recent common ancestor of all members

Ancestral

A trait that’s inherited in its present form from the MCRA of the clade

Derived

A trait that originated within the clade

Synapomorphy

A shared, derived trait for a clade. It is a trait that all species in the clade share, and that evolved on the branch leading to the clade

Homology

When structures observed in different taxa can be traced to a single structure present in a shared evolutionary ancestor

Homoplasy

When a character or character site aroses more than once on a phylogenetic tree

Paleontology

• Provides a direct record of past evolutionary change

• Inference is strongest for groups that fossilize well

Phylogenetics

• Provides an indirect record of past evolutionary change

• Inference is strongest for groups that have living representatives

Fosil records

• Provide only evidence for completely extinct clades

• Documents long-term patterns of global biodiversity

• Provides evidence for catastrophic extinctions during earth’s history

Mass extinction

Extinction of >75% of earth’s species in a geologically short period

Other features associated with increased diversification

• Herbivory

• Species with more sexual selection

• Animal pollination in plants

• Increased dispersal

• Increased range size