Lecture 17

Update Warning! This page has not been revised yet for the 2007 Fall term. Some of the slides may be reused, but please consider the page as a whole out of date as long as this warning appears here.

 

 

(Previous lecture) ... (Next lecture)

Phylogenetic Analysis

...

Add:

• Summary points
• Exercises
• Further reading

Lecture Slides

Slide 001

Lecture 17, Slide 001

Slide 002

Lecture 17, Slide 002

Slide 003

Lecture 17, Slide 003

Slide 004

Lecture 17, Slide 004

Slide 005

Lecture 17, Slide 005

Slide 006

Lecture 17, Slide 006

Slide 007

Lecture 17, Slide 007

Slide 008

Lecture 17, Slide 008

Slide 009

Lecture 17, Slide 009

Slide 010

Lecture 17, Slide 010

Slide 011

Lecture 17, Slide 011

Slide 012

Lecture 17, Slide 012
Usually, analysis of confidence implies a "bootstrapping" procedure: rerun the analysis many times with partial data and analyze which features of the tree (branching order -> topology!) are well conserved, and which ones depend critically on unreliable features of the input data.

Slide 013

Lecture 17, Slide 013

Slide 014

Lecture 17, Slide 014
Note that distance methods first reduce the explicit molecular data into a matrix of pairwise distances, then operate on that "summary" to construct the most plausible tree. They are fast, but less accurate than some alternatives.

Slide 015

Lecture 17, Slide 015

Slide 016

Lecture 17, Slide 016

Slide 017

Lecture 17, Slide 017

Slide 018

Lecture 17, Slide 018

Slide 019

Lecture 17, Slide 019

Slide 020

Lecture 17, Slide 020

Slide 021

Lecture 17, Slide 021

Slide 022

Lecture 17, Slide 022

Slide 023

Lecture 17, Slide 023
Genomes are and always have been exquisitly plastic, malleable entities. That we have long thought this not to be the case is a consequence of our limited personal experience and anthropocentric world view.

Slide 024

Lecture 17, Slide 024

Slide 025

Lecture 17, Slide 025

Slide 026

Lecture 17, Slide 026

Slide 027

Lecture 17, Slide 027