Apomorphy - n. a derived state apomorphic - adj.

Plesiomorphy - n. an ancestral state plesiomorphic - adj.

Synapomorphy - n. shared derived state

Symplesiomorphy - n. shared ancestral state

Mark SiddallAMNH

2005

rootroot node nodes

hypothetical ancestors

branches or edges

terminal taxaterminals

I

II

III

IV

V

Tree Think

Mark SiddallAMNH

2005

I II III IV V I IIIII IVV I IIIIIIVV

these trees are all identical

I II III IV V

cladogram

I

II

IIIIV

VI

II

IIIIV

V

phylograms

Mark SiddallAMNH

2005

I II III IV V ((I (II III)) (IV V))

((I, (II, III)), (IV, V))

((I:0.1, (II:0.3, III:0.07):0.06):0.2, (IV:0.1, V:0.4):0.08)I

II

IIIIV

V

parenthetical notation (TNT)

newick / altnexus

newick / altnexus with branch lengths

Mark SiddallAMNH

2005

Mark SiddallAMNH

2005

I II III IV V I II III IV VFully resolved Not fully resolved

a polytomya trichotomy

I III IV V

BalancedI II III IV V

Pectinate

I II III IV V

Mark SiddallAMNH

2005

Monophyly - descended from a common ancestor,including all descendents of that ancestor

(this tree has 4 monophyletic groups)Synapomorphy defines monophyly (e.g., mammary glands and mammals)

I II III IV V Paraphyly - descended from a common ancestor,fails to include all descendents of that ancestor

Symplesiomorphy defines paraphyly (e.g., reptiles are paraphyletic)

I II III IV V Polyphyly - not descended from a common ancestor

Convergence defines polyhyly (e.g., homeotherms are polyphyletic)

Mark SiddallAMNH

2005

Remember this?

How is the plesiomorphic state determined?

internal atrial two temporal pedicillateTaxon amnion legs scales blood nostrils septum fenestrations hemipenes gizzard teeth feathers wings vertebraeperch no no yes cold no no no no no no no no yes

coelocanth no no yes cold yes yes no no no no no no yessalamander no yes no cold yes yes no no no yes no no yes

frog no yes no cold yes yes no no no yes no no yesturtle yes yes yes cold yes yes no no no no no no yes

human yes yes no warm yes yes no no no no no no yesgecko yes yes yes cold yes yes yes yes no no no no yessnake yes no yes cold yes yes yes yes no no no no yes

alligator yes yes yes cold yes yes yes no yes no no no yesbudgy yes yes no warm yes yes yes no yes no yes yes yes

Define group of interest = INGROUPINGROUP = TETRAPODA (assumed to be monophyletic)

Find other taxa, not in the ingroup, probably closely related, possessing traits of some ingroup taxa = OUTGROUPOUTGROUP = LOBED-FIN-FISHES AND RAY-FIN-FISHES

A state present in the OUTGROUP and the INGROUPis plesiomorphic for the ingroup

Mark SiddallAMNH

2005

I IIIIIba

III

III b

a

Rooted UnrootedIIIIIIb

a

Analyses are always done on unrooted trees, including someoutgroup(s), then rooted on theoutgroup(s) a posteriori.

I IIIIIba

Mark SiddallAMNH

2005

Number of starsin the known

universe

Number of treesFor 25 taxa<<

(2t-3)!2t-2(t-2)!

5102050

1053 x 107

8 x 1021

3 x 1076

Number of rearrangements PAUPcan do on my G5 in 1 second 2500

Number of millenia PAUP wouldtake to examine all trees for 20 taxa 4 x 1021

Mark SiddallAMNH

2005

Multiple Equally Parsimonious Trees

I II III IV V I II III IV V I II III IV V

I II III IV V I II III IV V

100

66 66

STRICT CONSENSUS MAJORITY RULE CONSENSUS

Mark SiddallAMNH

2005

Multiple Equally Parsimonious Resolutions

I II III IV V I II III IV V I II III IV V

I II III IV V

DELTRAN ACCTRAN ACCTRAN

Mark SiddallAMNH

2005

Multiple Equally Parsimonious Resolutions

I II III IV V I II III IV V