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Systematics:
1) Taxonomy: Classification and naming of organisms
a.
Hierarchical nomenclature with taxonomic categories
(kingdom, phylum, class, order, family, genus, and species)
2) Phylogenetic analysis: The study of evolutionary relationships among
species
a. Under common decent, hierarchical classification reflects true
genealogical relationships
Tree of Life
http://tolweb.org/tree/phylogeny.html
Phylogenetic Terms
Species 2
Species 1
i1
e1
d1
f1
h1
g1
Species 3
Species 4
j1
Ancestor 3
Ancestor 2
b1
a1
c1
Ancestor 1
monophyletic group: set of species that share
a common ancestor.
synapomorphy: shared derived character
state.
autapomorphy: uniquely derived character
state.
Phylogenetic Analysis
Species 1
Species 2
Species 3
a b c d e f g h i j
0 0 1 1 1 0 0 0 0 0
a b c d e f g h i j
0 0 1 0 0 1 1 1 1 0
a b c d e f g h i j
0 0 1 0 0 1 1 0 0 1
i1
h1
e1
d1
g1
Species 4
a b c d e f g h i j
1 1 0 0 0 0 0 0 0 0
j1
Ancestor 3
(node)
f1
b1
shared
characters
a1
Ancestor 2
(node)
1
2
3
4
c1
Ancestor 1
a b c d e f g h i j
0 0 0 0 0 0 0 0 0 0
1
1
1
0
2
4
3
0
3
5
7
0
4
5
3
4
-
shared derived
characters
The identification of synapomorphies help define
nested series of monophyletic groups.
Phylogenetic Analysis
Species 1
Species 2
Species 3
a b c d e f g h i j
0 1 1 0 0 0 1 1 0 1
a b c d e f g h i j
0 1 1 1 1 1 0 1 0 0
a b c d e f g h i j
0 1 1 1 1 1 1 0 1 1
j0
h1
h1
f1
g1
d1
g1
Species 4
a b c d e f g h i j
1 0 0 0 0 0 0 0 0 0
i1
Ancestor 3
e1
shared
characters
a1
Ancestor 2
j1
c1
b1
Ancestor 1
1
2
3
4
1
3
4
0
2
5
5
0
3
5
6
0
4
4
3
4
-
shared derived
characters
Phylogenetic Terms
Species 1
h1
g1
Ancestor 2
Species 2
Species 3
Species 4
i1
j0
h1 g1
f1 Ancestor 3
e1
d1
j1
c1
b1
a1
Ancestor 1
homoplasy: when two species share a
derived character state because of convergent
evolution or evolutionary reversal, but not
because of common descent.
convergent evolution: independent evolution
of a derived character state in two or more
taxa.
Types of Homoplasy
Convergence: Shared derived similarities, that are not based on
common origin (i.e. homology ), but on an independent origin in
different taxa.
Example: Wings in insects, birds, and bats
Reversal : The secondary presence of an apparently ”ancestral”
character state.
Example: Aquatic mode of life for fish, terrestriality
for tetrapods, reversal to aquatic life in whales
Homoplasy: Common in DNA sequence data. Each nucleotide
position defines a separate character
Homoplasy - independent evolution
• Loss of tails evolved independently in humans and frogs - there
are two steps on the true tree
Lizard
Human
TAIL (adult)
Frog
Dog
absent
present
Homoplasy: Misleading evidence of phylogeny
• If misinterpreted as a synapomorphy, the absence of tails would be
evidence for a wrong tree: grouping humans with frogs and lizards
with dogs
Human
Lizard
TAIL
Frog
Dog
absent
present
Homoplasy: Reversal
• Reversals are evolutionary changes back to an ancestral condition
• As with any homoplasy, reversals can provide misleading evidence of
relationships
1
True tree
2 3 4
5 6 7 8
Wrong tree
9 10 1
2
7 8 3 4
5 6
9 10
So how do we construct trees with a sample of homologous
characters?
• How do we sort out phylogeny from a mixture of signal
(synapomorphies) and noise (homoplasy).
• Cladistic methodology (Willi Hennig) utilizes the principle of
parsimony.
• Parsimony= The tree that requires the fewest number of
evolutionary changes or steps to explain the data is preferred.
Tree Reconstruction with Parsimony
Tree Reconstruction with Parsimony
Tree 1
Nucleotide substitution
= evolutionary step
Tree 2
Tree 3
Tree Reconstruction with Parsimony
Tree Reconstruction with Parsimony
Character 2
I(A)
Tree 1
II(G)
III(A) I(A)
Tree 2
IV(G) III(A)
II(G) I(A)
IV(G)
Tree 3
IV(G)
or
I(A)
II(G)
II(G)
III(A)
or
III(A)
I(A)
II(G)
IV(G)
IV(G)
III(A)
What to do when some characters tell you one
thing and others tell you something else
(Homoplasy)?
Parsimony with Multiple Characters
1
The most parsimonious pattern of character change is
noted for each character separately, for each tree.
2
The number of changes is summed across characters
for each tree.
3
The preferred tree is the one that implies the fewest
overall character changes.
Tree 1
Tree 2
Tree 3
Tree 1 is favored under the criterion of Parsimony
Parsimony
• Advantages:
– Simple method - easily understood operation
– Does not seem to depend on an explicit model of evolution
– Should give reliable results if the data are well structured and
homoplasy is either rare or widely (randomly) distributed on the
tree
• Disadvantages:
– Doesn’t always provide the best estimate of phylogeny
• Maximum likelihood
• Bayesian analysis
Parsimony is Computationally Intensive
• The number of possible
trees increases
exponentially with the
number of species, making
exhaustive searches
impractical for many data
sets.
• Need to utilize a way to
search for the best tree
without evaluating all
possible trees.
A
D
E
F
B
G
E
A
C
• Tree bisection and
reconnection
C
A
B
G
F
D
F
B
G
D
C
E
What if there is a large amount of
homoplasy in the data?
• Sequence data may have
multiple, “hidden”
substitutions.
• Use a model of evolution to
correct for different rates of
substitutions or unequal base
frequencies or other
parameters.
• Maximum-likelihood
phylogenetic analysis
Seq 1
Seq 2
Seq 1
Seq 2
C
C
T
C
AGCGAG
GCGGAC
A
A
Plot of base pair
differences between
pairs of mammalian
species for a
representative gene.
L = P (DT, M)
C
A
A
Example: Model of sequence evolution
• Simplest Model = JukesCantor - Assumes all
substitutions are equally likely
(a
a
A
a
a
a
a
C
G
a
T
Example: What is the total number of substitutions?
Expected Difference
AGATCG CAACGC CCGGAC TTCTTA ATCGGG
K = - 3 ln ( 1 4
4
p
3 )
= 0.27
total observed = 7 ; p = 7/30 = 0.23
Total expected = 0.27 x 30 = 8.24
Sequence Difference
AGGTCG CATTGC CCCGAT CTCTTG ATCGGG
Correction
Observed
Difference
Time
Phylogenetic Inference Using Maximum Likelihood
• Model of sequence evolution and the estimation of its parameters allows
the placement of probabilities on different types of substitutional change.
• Likelihood analysis focuses on the data, not the tree. It is the Probability
of the Data given a Tree and a Model of evolution.
Seq 1
Seq 2
ATATC
CTAGC
L = P (DT, M)
The Likelihood (i.e. the probability of observing the data)
is a sum over all possible assignments of nucleotides to
the internal nodes
Phylogenetic Inference Using Maximum
Likelihood
• Calculate the Likelihood for each base position in the sequence
and summarizes across all base positions.
• The ML tree is the tree that produces the highest likelihood.
• Evaluates the branching structure of the tree, and also the branch
length, using similar tree-searching strategies as used in parsimony
analysis.
– This is important, because by using a model-based approach,
mutational change is more probable along longer branches than
on shorter branches.
• Can be extremely computationally intensive.
Phylogenetic Inference Using Maximum
Likelihood
• Important point about ML: The model you choose to use can
have a large impact on the resulting ML tree.
• If you flip a coin and get a head, what is its likelihood?
– If it’s a 2 sided and fair coin (your model), the likelihood is 0.5
– If it’s a two-headed coin (your model), the likelihood is 1.0
Assessing the Robustness Of Trees
• We can use a number of methods to assess the robustness of
particular branches in our trees
– Bootstrapping (Jackknifing, Decay-Index)
•Bootstrapping:
• Multiple new data sets are made by re-sampling from the
original data set.
–Bootstrapping: Sampling done with replacement
• The resampled data sets are subjected to phylogenetic analysis.
• The proportion of times a clade appears in the trees across all
replicate data sets is called its bootstrap proportion.
Taken from Baldauf, S. L. Phylogeny for the faint of heart: a tutorial. Trends in Genetics 19:345-351.
Bootstrapping
• Clades that receive a high bootstrap are considered to be more
supported by the data than clades with a lower bootstrap.
– 70% or greater is good, but many phylogeneticists will only consider
branches with ≥90% as being strongly supported.
Bootstrap
• Can perform with any type of phylogenetic analysis: parsimony, ML, distance-based
• Important to emphasize that a bootstrap does not reveal the probability that a
particular clade is true, but only how well it is supported by the particular dataset.
Molecular Clocks
• The mutation rate for some genes may be relatively constant across
species.
• This idea is based on neutral theory (this will be introduced later in
the course) - nucleotide or amino acid substitutions occur at a rate
equal to the mutation rate.
• Generally in applying a molecular clock, you assume that the
mutation rate for a gene does not differ among species.
Molecular Clocks
1) Construct A Tree
2) Date a Node in the Tree
Outgroup
Outgroup
Species 1
Species 1
Species 2
Species 2
Species 3
Species 3
Species 4
Species 4
Fossil for Species 4
~1 MY
3) Calculate Divergence
Species 3
Species 4
2% Sequence
Divergence
}
You know that the most recent
possible divergence between 3 and 4 is
at least 1 MY
4) Calculate a Rate
R= 2%/1MY
Molecular Clocks
5) Apply Rate to Other Nodes in Tree
Outgroup
Species 1
Species 2
Species 3
5MY
Species 4
2MY
1MY
• Best applied when dates available for multiple nodes.
• Can utilize solid geological information as well as fossil
information.
• Must be aware of possible non-clock behavior of genes.
Phylogeny of North American Black Basses
Near et al., 2003. Evolution 57:1610–1621.
Previous hypothesis that speciation within the genus Micropterus occurred during
the Pleistocene.
Micropterus has a very good fossil record.
Calibration of a molecular clock
and calculation of divergence
times among species reveals that
most species diverged well
before the Pleistocene
Bayesian Inference of Phylogeny
Pr[Tree | Data] =
Pr[Data | Tree] x Pr [Tree]
Pr[Data]
Generates a posterior probability
distribution of trees
The tree with the highest posterior probability
provides the best estimate of phylogeny
Species Delimitation in Rapidly Radiating Systems
• Accumulation of species diversity over short periods of time.
• Adaptive radiations
• Often of very recent origin
• Difficult to resolve monophyletic species-level lineages.
Salzburger, W. and A. Meyer. 2004. Naturwissenschaften 91:277-290.
Ambystoma tigrinum species complex
A. californiense
Shaffer & McKnight 1996 Evolution 50:417-433
Gerald and Buff Corsi © California Academy of Sciences
Species Delimitation in Rapidly Radiating Systems
(Species trees vs gene trees)
Lineage sorting and the retention of ancestral alleles or allelic lineages
Species Delimitation in Rapidly Radiating Systems
Lineage sorting and the retention of ancestral alleles or allelic lineages
Darwin’s Finches
East African
Cichlid Fish
Moran and Kornfield. 1993. Mol. Biol. Evol. 10:1015-1029.
Takahashi et al. 2001. Mol. Biol. Evol. 18:2057-2066.
Sato et al. 1999. PNAS. 96:5101-5106.
Species Delimitation in Rapidly Radiating Systems
Limited reproductive isolation leads to hybridization and introgression
Ambystoma tigrinum species complex
A. californiense
Shaffer & McKnight 1996 Evolution 50:417-433
Gerald and Buff Corsi © California Academy of Sciences
An early study found that
A. ordinarium was not a
monophyletic group (when
using mtDNA as the source
of characters).
Indeed, more data shows
extensive mtDNA nonmonophyly with respect to A.
ordinarium.
Polyphyly: A. ordinarium does not form a monophyletic group.
Paraphyly: A. ordinarium does form a monophyletic group but
other species should also be included in this group, based on the
character that is used to reconstruct relationships.
Nuclear Genes Summary
• 4 genes yield A. ordinarium monophyly.
• 3 genes yield A. ordinarium paraphyly. (2 are nearly monophyletic.)
• 1 gene yields A. ordinarium polyphyly.
• Nuclear data strongly suggests that A. ordinarium is a monophyletic
lineage.
Signatures of Rapid Lineage Diversification
Poe, S., and A. L. Chubb. 2004. Syst. Biol. 58:404-415.
Short Internal Branches
Phylogenetic Discordance
Among Loci
A. dumerilii
Shared and minimally divergent mtDNA haplotypes strongly indicate
recent hybrid introgression.