Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa...
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Transcript of Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa...
![Page 1: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/1.jpg)
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
![Page 2: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/2.jpg)
“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...
![Page 3: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/3.jpg)
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.
![Page 4: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/4.jpg)
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.
![Page 5: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/5.jpg)
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.
![Page 6: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/6.jpg)
Phenetic methods
• Group taxa based on their overall similarities and
differences
• No explicit evolutionary hypothesis
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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
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Phenetic methods
“neighbor-joining”: the most popular method for building trees from distance data
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Cladistic methods
• cladistics: the branch of systematics that builds phylogenies based on hypotheses for evolutionary relationships
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Cladistic methods
• cladistics and cladograms are based on clades—monophyletic groups defined by shared, derived homologous characters: synapomorphies
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Shared derived homologous characters
amniotic egg
homologous = similar due to common descent
derived = evolved later, in a recent common ancestor
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Cladistic methods
• a synapomorphy for the artiodactyl mammals is the trochleated astragulus
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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
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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
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Synapomorphies appear in a nested fashion that “naturally” produces hierarchical ancestor-descendant relationships. You can see this by tracing the tree upwards in (b).
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Synapomorphies in tetrapods
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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
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A problem
Modern whales lack ankles, so presence/absence of astragulus is
impossible to evaluate
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Solution: fossil whales have ankle bones!
Image from Thewissen lab (Kent State Univ.)
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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
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Fossil whale ankle bones
Rhodocetis ArtiocetusPronghorn antelope
images P. Gingerich
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Independent analyses of DNA sequences agree
Milk protein (-casein) DNA sequences from Gatesy et al. (1999)
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Using parsimony to distinguish
homology from convergence
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“Reading” trees to determine branching order
Does the “subtree” in (b) show the same relationships as the tree in (a)?
Figure 14.19
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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
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Applications of phylogenies in systematics
sister taxon relationships
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Issues in systematics: identifying sister taxa
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Phylogenetic analysis of mitochondrial cytochrome oxidase II sequences by Ruvolo et al. (1994) revealed that chimps were the sister taxon to humans.
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Applications of phylogenies in systematics
identifying monophyletic groups
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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
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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
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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
![Page 35: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/35.jpg)
Reptiles are a paraphyletic group
• Reptilia includes its
common ancestor and
most descendents,
but not the birds
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Another famous paraphyletic group…
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Applications for testing
hypotheses for speciation
Sister taxa and branching order
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Allopatric speciation• The Isthmus of Panama
closed ~ 3.1 MYA
• About 150 “geminate” (twin) species now exist
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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
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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
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A phylogeny of Hawaiian Drosophila
D. heteroneura
D. silvestris
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Hawaiian Laupala crickets
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Applications to studies of pathogen evolution and
disease outbreaks
Sister taxa, branching order, monophyletic groups
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Influenza pandemics
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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
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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
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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
![Page 48: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/48.jpg)
HA• Antibodies to HA
neutralize virus
infectivity
• But variability in HA
amino acid
sequence helps
overcome this
immune response
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Neuraminidase (NA)
• Involved in replication
and virus “spreading”
• Enzymatically digests
cell receptors and
releases new virions
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Neuraminidase (NA)
• 9 known serotypes in influenza A
– e.g. H5N1 “bird flu”
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Nucleoprotein (NP)
• RNA-binding protein, a component of viral transcriptase complex
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Nucleoprotein (NP)• Involved in
nuclear/ cytoplasmic transport of vRNA
• A major determinant of host specificity
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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”)
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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
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Origin of influenza pandemics inferred from phylogenies
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Nucleoprotein phylogenetic tree
from Gorman et al. (1991)
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1968 pandemic strains (bolded):
NPs, and strains, are each other’s closest relatives...
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And while NAs are
closely related
(both N2), HAs are
distantly related
(H3 and H2)
![Page 59: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/59.jpg)
H3 was new to
human
populations,
suggesting a
“reassortment”
caused the
epidemic
![Page 60: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/60.jpg)
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
![Page 61: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/61.jpg)
Human H3 genes branch from within the avian H3 clade
![Page 62: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/62.jpg)
And the 1968 pandemic strain is at the base of the human clade
![Page 63: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/63.jpg)
Implies that human influenza got its H3 gene from a bird flu
![Page 64: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/64.jpg)
Back to the
nucleoprotein
phylogeny....
![Page 65: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/65.jpg)
It shows flu transmission from birds to pigs
![Page 66: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/66.jpg)
from humans to pigs
and from pigs to humans
![Page 67: Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 A B C More ancient More recent Time sister taxa Nodes Branches Tips or terminal nodes Parts of a phylogenetic.](https://reader037.fdocuments.net/reader037/viewer/2022102616/56649d0b5503460f949df0cd/html5/thumbnails/67.jpg)
One popular hypothesis
• Bird flus and human flus simultaneously infect pigs
• Swap genes
• Move from pigs back to people, initiating pandemic