Complete Cladist -Chapter 2

Chapter 2 is all about basic phylogenetic techniques.

Some notes:
-Hennig's Auxiliary Principle=always assume homology in the absence of contrary evidence.
-convergence and parallelism are both homoplasies
-it is not always true that the outgroup has plesiomorphic characters
-isomorphic=topologically identical -I've never heard this term used for this before
-"there is only 1 true phylogeny" -is there? what about cases with reticulating speciation or horizontal gene transfer? what evidence do we have to make this assumption? are there any other scenarios where this might not be the case?
-I think it is odd that the entire internode is supposed to be the ancestor, but then we plot character states/transformations on the internode. Isn't this a bit misleading?
-I found the exercises in chapt. 2 to be too time consuming! They should have put just 1 or 2 simple examples in to get their point across. Then, in the answers, they don't even give you a diagram of the tree. If we are going to put all that work in to do the exercises, the least they could do is make the answers as clear as possible. Jeesh.

Complete Cladist -Chapter 1

I'm a bit behind but here are some of my comments for Chapter 1 of 'The Complete Cladist'.

-taxon= a group of organisms given a name. Is there a term for a group of organisms not given a name? :)
-I have to remember that an ancestor is not represented by a node, but by the internodes between branches!
-I've never seen a Venn diagram used to depict relationships before. Interesting!
-something I would like to discuss further with the group would be conditions of homologous characters
-transformation series=a group of homologous characters
-I think their character/character state philosophy is odd
-I'd like to go over the answer to question 1 of the quick quiz on characters. I didn't quite get that.
*note -try to run own dataset without a root just to see what it looks like

Chapter 4

Today we discussed chapter 4. I was only present for half the meeting, but this is what happened:

• Nobody seemed to have any trouble with Tree Lengths, and Consistency indices.

• We discussed whether or not bootstrap and bremer analysis can actually compare trees. It is not the same as saying two p values are the same (or comparable)

• Apparently molecular phylogenetists are more cocky with their data.

Today's meeting

Today we went over chapter three of Cladistics: A practical primer.

Questions that arose concerned:
Semi-Strict Consensus: what exactly does this mean? How is it different from the others?
Ghost Lineages: why the box representation?
Outgroups: "How to pick an outgroup if you aren't sure what the outgroup should be" and "what sorts of qualities should be included to make a quality outgroup?"

And that's all I remember!

Great idea!

This is a great idea!