Apomorphy 

Derived character state

Synapomorphy

Shared character state

Plesiomorphism

ancestral/primitive state

Automorphism

Derived character state

¨

Homoplasy

Similarity in derived characters

Consistent character

Congruent character

Conflicting / Homoplastic character

Compatible or not compatible?

Compatible

Monophyletic vs paraphyletic

A paraphyletic group is a group of any size and systematic rank that originated from a single common ancestor, but does not – as opposed to a monophyletic group – contain all descendants from this ancestor. The ancestral species of this group is thus also the ancestor of one or more other groups.

What does CI value equal to one describe?

CI = M / S

No homoplasy

RI -  retention index

RI = observed steps / possible steps

[image]

Hvilken er derived og hvilken ancestral?

Hvem gjør hva? og hvilke leder til gaps?

1) Substitution

2) insertion

3)deletion

1) A blir G

2) AT blir A GG T

3) AAATG blir ATG

2) og 3)

hva kan vi gjøre i TNT?

Tree searching algorithm

Measure of character fit

Consensus tre

Branch support

How do you root a tree in parsimony?

Ad an outgroup!

Branch and bound...

start: unrooted tree with three taxa, add one taxa and choose the best and so on?

Heuristic method is what?

Istedenfor exact, så bygger vi på og fortsetter kun på det beste treet tilgjengelig ved et gitt steg. Dette garanterer ikke at det beste treet blir funnet, da kan vi gjøre flere tilfeldig startpunkt og dermed utforske landskapet bedre.

RAS

Branch swapping

NNI
SPR

TBR

Consensus tree

strict vs semi strict vs majority rule

strict - continue only with the groups that occur in all the MTP´s

semistrict - same as strict, but

majority rule - include clades that are represented more than a given percentage

Cladorgam

Phylogram

Chronogram