BIOSCI 109: Lecture 19 - Phylogenetic Trees & Tree-Thinking

Phylogenetic Trees

Populations, over generations, are divided up by various processes and can split into different species in speciation events. This tends to take many generations, but, phylogenetic trees help to simplify it, allowing us to focus on just the speciation events and the results.

Phylogenetic Tree Functions: Macroevolution

Similarly, macroevolution processes take a very long time to occur with multiple speciation events occuring across many different species. Phylogenetic trees help to condense these time frames and simplify the events.

Phylogenetic Tree Functions: Biogeography

Biogeography talks about where species are, how many, when, why, and how they got there.

Phylogenetic Tree Functions: Major Transitions

There are many “transitions” that have occured such as the transition to land from water, limbs from fins, and so on and so forth. Phylogenetic trees help to showcase the transitional steps from then to now and how long as well.

Phylogenetic Tree Functions: Testing Taxonomy

In taxonomy, it is a goal to have all the groups of a taxon (a clade) to be monophyletic, meaning that they are derrive from one common ancestor, making them a distinct group. Discovering a clade isn’t monophyletic typically means rivisions in the taxonomy (renaming species, regrouping them elsewhere, etc).

Monophyly

A clade in which they all derrive from one common ancestor

Paraphyly

A clade that includes a common ancestor for all the modern species grouped, but not all the descendants of the ancestor.

Polyphyly

A group of convergent descendants, but not their common ancestor

Phylogenetic Tree Functions: Showcasing Homology

Homology are shared characteristics. Phylogenetic trees help to show what species may share certain homologies and what species may not. If a common ancestor has a certain homology, it can be expected that all the descendants also have that homology (can be different form or function). This also lets us determine relative branching points.

Cladogram

Are similar to phylogenies but don’t show the time-scale, so, they tend to look a lot simpler and branch lengths are arbituary.

Since this is the case, the inversions and rotations of terminal branches at their internal nodes are arbituary as long as the same relationships are present.

Some parts of them include: terminal nodes (splitting point), terminal branches (the line after), root node (most recent common ancestor of all taxon), root branch (line before it), internal branches

Character Data

They are characteristics of species that can be objectively described and measured. They’re used to infer phylogenetic trees. These characters tend to be discrete (colour, digit of fingers, etc) or continuous (body size, etc). Some commonly used ones are bone structures, embryology, DNA and so on.

To infer phylogenetic trees, these characters have to be homologous so that we can compare it across organisms to identify the similarities and differences (or variations/character states).

From a character table of different characters and taxon, we should be able to infer a phylogeny. Species that have more similarities must have a common ancestor that split earlier than species that have less simialrities.