Lecture 10 - Phylogenies (continued)

included on exam 2

how to form maximum likelihood values (with bootstrapping)

when several trees are made via bootstrapping, count how many times a certain relationship appears

turn that number into a decimal, then multiply by 100 to get a percentage without the % sign

cladogram

any type of phylogenetic tree where the tips all line up with each other

branched lengths are irrelevant, don’t convey any information

phenogram

a phylogenetic tree where the tips don’t all align

still shows the relationships between species, but also tells more information

branch lengths are informative, typically the number of nucleotide differences between species

i.e. shorter branches have fewer base pair differences than long branches

(note: branch lengths are in comparison to each other, not just to the MRCA)

ultrametric tree

a phylogenetic tree that dates a phenogram

uses a molecular clock to calibrate the dating (e.g. establish that 1 nucleotide change happens every 1 million years)

tips of extant taxa are aligned, but not extinct species

consensus

a tree that summarizes a collection of data or other phylogenetic trees

generally not illustrated on node supports

how genetic trees and species trees may differ

gene duplication

gene loss

horizontal gene transfer

how to date a phylogenetic tree

calibrate the molecular clock with: fossils, geographical activity (e.g. volcanic activity or island formation), real-time data

(note: fossils are the most common method)

a fossil can be found that looks like an ancestor to a species

we know the age of the fossil with uniform distribution or log normal

the speciation event can be placed based on that fossil

log normal

a method of dating a phylogeny based on a fossil

a time window is given for the fossil’s age, with a definite youngest age and a most likely older age

but it is possible that the fossil could be older than that window, with decreasing probability

better than uniform distribution