Tax

on 1

Tax

on 2

Tax

on 3

Tax

on 4

Tax

on 5

Tax

on 6

A

B

C

Mor

e an

cien

tM

ore

rece

ntT

ime

sister taxa

NodesBranches

Tips or

terminal nodes

Parts of a phylogenetic tree

D

root

“Reading” a phylogenetic tree

Tax

on 1

Tax

on 2

Tax

on 3

Tax

on 4

Tax

on 5

Tax

on 6

A

B

C

Mor

e an

cien

tM

ore

rece

ntT

ime

sister taxa

D

Start at the bottom and work up. A is the common ancestor of all taxa 1-6. It split into two groups. One evolved into taxon 1, and the other into the population indicated by node B. This is the common ancestor of taxa 2-5...

Taxon 1

Taxon 2

Taxon 3

Taxon 4

Taxon 5

Taxon 6

A

B

D

More ancient

More recentTime

sister taxaC

Often, a tree is drawn on its side, with time increasing left to right.

Branches are drawn as “forks” on cladograms. These are trees drawn using cladistic methods.

Taxon 1

Taxon 2

Taxon 3

Taxon 4

Taxon 5

Taxon 6

A

B

D

More ancient

More recentTime

sister taxaC

On cladograms, only the relative branching order is important.

So taxon 2 and 3 split from their ancestor (C) earlier than taxon 4, 5, and 6 did from (D), but the tree does not show how much earlier.

Branches are not scaled to time on cladograms.

Taxon 1

Taxon 2

Taxon 3

Taxon 4

Taxon 5

Taxon 6

A

C

sister taxaD

B

Often the branches are “squared off” instead of drawn as diagonal forks.

This is common for phylogenies called phylograms, in which branch lengths are scaled to time (they represent genetic distance).

Genetic distance = 10%

given a molecular clock of 2% per million years, 10% ≈ 5 million years

Phylograms are generated by phenetic methods.

Phenetic methods

• Group taxa based on their overall similarities and

differences

• No explicit evolutionary hypothesis

Phenetic methods

• Often used for DNA data, from which genetic distances are calculated

• The preferred tree is the one that minimizes the total distance along the tree

Phenetic methods

“neighbor-joining”: the most popular method for building trees from distance data

Cladistic methods

• cladistics: the branch of systematics that builds phylogenies based on hypotheses for evolutionary relationships

Cladistic methods

• cladistics and cladograms are based on clades—monophyletic groups defined by shared, derived homologous characters: synapomorphies

Shared derived homologous characters

amniotic egg

homologous = similar due to common descent

derived = evolved later, in a recent common ancestor

Cladistic methods

• a synapomorphy for the artiodactyl mammals is the trochleated astragulus

The ungulates or hoofed mammals• Perissodactyla

– odd-toed ungulates, e.g. rhino and horse

– 1 or 3 toes

• Artiodactyla– even toed ungulates,

e.g. hippo and deer– most 2, some 4 toes

Synapomorphies arise from independent evolution after speciation (branching events). When gene flow stops, populations evolve shared derived characters by selection and drift.

Fig. 4.2

Synapomorphies appear in a nested fashion that “naturally” produces hierarchical ancestor-descendant relationships. You can see this by tracing the tree upwards in (b).

Synapomorphies in tetrapods

Selection between alternative cladistic trees is often based on parsimony. Parsimony is a logical criterion that prefers the tree with the fewest evolutionary changes.

trochleated astragulus: gained lost

A problem

Modern whales lack ankles, so presence/absence of astragulus is

impossible to evaluate

Solution: fossil whales have ankle bones!

Image from Thewissen lab (Kent State Univ.)

Philip Gingerich: fossil whale research in Egypt and Pakistan

Univ. of MI camp in Egypt, source of > 400 fossil whales!

Basilosaurus isis skeleton

images P. Gingerich

Fossil whale ankle bones

Rhodocetis ArtiocetusPronghorn antelope

images P. Gingerich

Independent analyses of DNA sequences agree

Milk protein (-casein) DNA sequences from Gatesy et al. (1999)

Using parsimony to distinguish

homology from convergence

“Reading” trees to determine branching order

Does the “subtree” in (b) show the same relationships as the tree in (a)?

Figure 14.19

Applications of phylogenies in biology

• tests of hypotheses often are based on the following features of a tree

– sister taxon relationships – identity of monophyletic groups– branching order

Applications of phylogenies in systematics

sister taxon relationships

Issues in systematics: identifying sister taxa

Phylogenetic analysis of mitochondrial cytochrome oxidase II sequences by Ruvolo et al. (1994) revealed that chimps were the sister taxon to humans.

Applications of phylogenies in systematics

identifying monophyletic groups

The goal of phylogenetic systematics is to produce taxonomic categories that accurately depict evolutionary history.

According to this field, “valid” catagories are monophyletic groups.

A monophyletic group contains an ancestor and all of its decendants

The goal of phylogenetic systematics is to produce taxonomic categories that accurately depict evolutionary history.

Paraphyletic groups are not valid categories.

A paraphyletic group contains an ancestor and some but not all of its decendants

Resolving human-chimp relationships produced a paraphyletic group

skat

es

shar

ks

wha

les

babo

on

oran

guta

n

chim

p

hum

an

Hominidae

Pongidae

if this phylogeny is true, the Pongidae is a paraphyletic group (and should be discarded?)

goril

la

Reptiles are a paraphyletic group

• Reptilia includes its

common ancestor and

most descendents,

but not the birds

Another famous paraphyletic group…

Applications for testing

hypotheses for speciation

Sister taxa and branching order

Allopatric speciation• The Isthmus of Panama

closed ~ 3.1 MYA

• About 150 “geminate” (twin) species now exist

Proof for allopatric speciation in snapping shrimps

Knowlton et al.(1993): a phylogeny of Pacific (P) and Carribean (C) species pairs of Alpheus

In 6 out of 7 cases, the closest relative of a species was in the other ocean

Proof for allopatric speciation in snapping shrimps

The phylogeny suggests that the ancestor of P1/C1, P2/C2, P3/C3, P4/C4, P5/C5, and P6/C6 was split into descendant species when the Isthmus of Panamá closed

A phylogeny of Hawaiian Drosophila

D. heteroneura

D. silvestris

Hawaiian Laupala crickets

Applications to studies of pathogen evolution and

disease outbreaks

Sister taxa, branching order, monophyletic groups

Influenza pandemics

Influenza biology and evolution•RNA virus (Orthomyxoviridae)

•Genome of 8 single stranded RNA molecules

•Key to infection and to immunity are viral envelope proteins hemagglutinin and neuraminidase

Hemagglutinin (HA)*• Controls attachment to host cell

(by binding to a receptor)

• Mediates membrane fusion

*Origin of its name: HA binds to red blood cells, causing agglutination

HA• 15 known serotypes in influenza

A (e.g. H1, H5)

• A single amino acid in HA

position 226 determines host

species (mostly)

– HA226Gln Bird flu

– HA226Leu Human flu

HA• Antibodies to HA

neutralize virus

infectivity

• But variability in HA

amino acid

sequence helps

overcome this

immune response

Neuraminidase (NA)

• Involved in replication

and virus “spreading”

• Enzymatically digests

cell receptors and

releases new virions

Neuraminidase (NA)

• 9 known serotypes in influenza A

– e.g. H5N1 “bird flu”

Nucleoprotein (NP)

• RNA-binding protein, a component of viral transcriptase complex

Nucleoprotein (NP)• Involved in

nuclear/ cytoplasmic transport of vRNA

• A major determinant of host specificity

Immune response

• antibodies recognize amino acids in antigenic sites of HA and NA

– immunity is used to sort virus strains into subtypes (e.g. H1N1: the 1918 “Spanish flu”)

Evading immune response

• Antigenic drift: amino acid substitutions in antigenic sites, leading to epidemics

• Antigenic shift: reassortment or swapping of HA and NA genes (e.g H2N2 H3N2) leading to pandemics

H2N2

H2*N2

H3N2

drift

shift

Origin of influenza pandemics inferred from phylogenies

Nucleoprotein phylogenetic tree

from Gorman et al. (1991)

1968 pandemic strains (bolded):

NPs, and strains, are each other’s closest relatives...

And while NAs are

closely related

(both N2), HAs are

distantly related

(H3 and H2)

H3 was new to

human

populations,

suggesting a

“reassortment”

caused the

epidemic

Source of the new H3 gene in human flu populations

Bean et al. (1993): a phylogeny of H3 genes from human and non-

human influenza

Human H3 genes branch from within the avian H3 clade

And the 1968 pandemic strain is at the base of the human clade

Implies that human influenza got its H3 gene from a bird flu

Back to the

nucleoprotein

phylogeny....

It shows flu transmission from birds to pigs

from humans to pigs

and from pigs to humans

One popular hypothesis

• Bird flus and human flus simultaneously infect pigs

• Swap genes

• Move from pigs back to people, initiating pandemic