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Parts of a phylogenetic tree
D
More recent
Taxon 6
Taxon 5
Taxon 4
Taxon 3
C
Time
Tips or
terminal nodes
Taxon 2
Taxon 1
sister taxa
Nodes
B
A
root
More ancient
Branches
“Reading” a phylogenetic tree
B
A
Time
More
recent
Taxon 6
Taxon 5
D
More
ancient
C
Taxon 4
Taxon 3
Taxon 2
Taxon 1
sister taxa
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
Often, a tree is
drawn on its side,
with time increasing
left to right.
Taxon 2
C
A
Branches are
drawn as “forks” on
cladograms. These
are trees drawn
using cladistic
methods.
sister taxa
B
Taxon 3
Taxon 4
D
Taxon 5
Taxon 6
More
ancient
Time
More
recent
Taxon 1
On cladograms,
only the relative
branching order is
important.
Taxon 2
So taxon 2 and 3
A
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.
sister taxa
C
B
Taxon 3
Taxon 4
D
Taxon 5
Taxon 6
More
ancient
Time
More
recent
Often the branches
are “squared off”
instead of drawn as
diagonal forks.
Taxon 1
Taxon 2
A
This is common for
phylogenies called
phylograms, in
which branch
lengths are scaled
to time (they
represent genetic
distance).
Phylograms are
generated by
phenetic methods.
sister taxa
D
Taxon 3
B
Taxon 4
C
Taxon 5
Taxon 6
Genetic distance = 10%
given a
molecular
clock of 2%
per million
years, 10% ≈
5 million
years
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!
images P. Gingerich
Basilosaurus isis skeleton
Fossil whale
ankle bones
Rhodocetis
Pronghorn
antelope
images P. Gingerich
Artiocetus
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.
A monophyletic group contains an
ancestor and all of its decendants
According to this field,
“valid” catagories are
monophyletic groups.
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
human
chimp
gorilla
orangutan
baboon
whales
sharks
skates
Pongidae
Hominidae
if this phylogeny is true,
the Pongidae is a
paraphyletic group (and
should be discarded?)
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
drift
H2N2
shift
H2*N2
H3N2
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 nonhuman 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