Lecture 2 - Phylogenetic Reasoning

Remember: These are not verbatim lecture notes. Instead, what follows is a kind of summary with some interpretation / additions / deletions (in blue).

You are not responsible for everything you see on this and subsequent web pages. We will provide you with a study guide prior to the first examination (a series of questions that will help focus your studying). Only concepts covered on that study guide will be asked on the exam, but keep in mind that examination questions often require you to synthesize across topics.


Brief history of evolutionary thought

 Questions King of France JB Lamarck AR Wallace TH Huxley  C Darwin
 1) extinction?  N Y Y Y Y
 2) species descended from other species? N Y Y Y Y
 3) single common ancestor? N N Y Y Y
 4) NS account for 'fit' between organism and environment? N N Y Y Y
 5) NS explain speciation? N N Y N Y
 6) sky blue? Y Y Y Y Y

you can click on all figures to open them in a new window (sometimes better resolution)


Darwin / Wallace "Tree of Life" = branching with a single common ancestor

vs. Lamarck "Chain of Being" = not branching, multiple common ancestors



Phylogeny = genealogy of a group of taxa; a kind of "family tree"

The goal of cladistics is to provide a phylogeny that reflects evolutionary history. Essentially we seek to make hierarchical groups.

Minimum Essential Terms (also see pg 437)

1) Monophyletic Group = a group that contains all descendants of a common ancestor

The motivation for creating these can be kind of confusing. You're probably familiar with taxonomy (Kingdom, Phylum, Class, etc.) though. Imagine we have a bunch of squid-like things that Frank wants to put into the same genus and Curt does not. We can do a phylogenetic analysis to reveal the evolutionary relationships among these squid-like things. If they indeed form a monophyletic group, Frank has support for placing them in the same taxonomic group. If not, then these squid-like things are not closely related and probably should not be in the same taxonomic group alone.

2) Cladistics = methods for identifying monophyletic groups on the basis of shared derived characters.

More on this will follow in the lab Friday

3) Synapomorphy = a shared derived character states

Syn (synthesis / together) - apo (derived) -morphy (morphological feature)

Synapomorphies define clades (all descendants of a recent common ancestor) --> monophyletic groups are recognized because they share uniquely derived traits

Other words you may hear in the lab on Friday and as you enter other fields:

Sympleisiomorphy = shared primitive character state

Autapomorphy = derived trait that is unique to a particular taxon. A species is defined by the presence of an autapomorphy

Homoplasic character states = shared but independently derived (evolved) character states

Paraphyletic group = a group that contains some but not all the descendants of a common ancestor

Polyphyletic group = a group where most members do not share a common ancestor (this is a very useless group!)

4) Parsimony = a method of cladistics. Phylogenetic hypotheses are constructed by assembling trees which require the least number of character state changes.

This method assumes several things:

mutations are infrequent and random

traits are inherited from parents to offspring

it is more likely that shared characters are passed on through inheritance than independently evolved


Things to notice about this tree:

A, B, & C form a monophyletic group

A, B, C, & E do not form a monophyletic group

The group ABCE is actually paraphyletic

The group AE is polyphyletic

Character state x is a shared-derived character for AB (synapomorphy)

Character state y is a shared-derived character for ABC (synapomorphy)

Character state y is a shared-ancestral character for AB (sympleisiomorphy)

At the right is cladogram for the major animal phyla.

Here are a few of the things we noticed in class

1. Pharyngeal gill slits is a synapomorphy for the sister groups sea squirts & Fish/mammals.

2. Segmentation is a synapomorphy for the sister groups earthworms and lobsters.

3. Bilateral symmetry is a synapomorphy for the sister groups flatworms/squids/earthworms/lobsters & starfish/sea squirts/fish

4. Bilateral symmetry is a shared ancestral character (sympleisiomorphy) for the sister groups starfish & sea squirts/fish

5. A complete gut evolved twice, but the origin of the mouth during embryogenesis is different.

6. The goal of parsimony is to minimize the number of multiple origins of triats in the construction of the cladogram. For example, it is more parsimonious to have gill slits evolve once, and thus have sea squirts and fish as sister taxa, than to put the sea squirts near the clams, and have the gill slits evolve at least twice. (the larvae stage of the sea squirts have the gill slits.)

More on cladistics will follow in lab on Friday. Frank.