Dan Graur

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Molecular Phylogenetics

• Dan Graur

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Objectives of molecular phylogenetics

• Reconstruct the correct evolutionary
  relationships among biological entities
• Estimate the time of divergence between
  biological entities
• Chronicle the sequence of events along
  evolutionary lineages

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Evolutionary relationships are illustrated by
means of a phylogenetic tree or a dendogram.
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Ernst Heinrich Haeckel 1834-1919
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July 2007
July 1837
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November 1859
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The routes of inheritance represent the passage
of genes from parents to offspring, and the
branching pattern depicts a gene tree.
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Different genes, however, may have different
evolutionary histories, i.e., different routes of
inheritance.
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The routes of inheritance are confined by
reproductive barriers, i.e., gene flow occurs
only within a species. A species tree is a
representation of splitting of species lineages.
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Terminology
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A phylogenetic tree or dendrogram is a graph
composed of nodes and branches, in which only one
branch connects any two adjacent nodes.
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Internal
External or Peripheral Branch
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Assumptions Bifurcation Real speciation
event Multifurcation Lack of resolution
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Binary tree
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Rooted and unrooted trees
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How many unrooted topologies are here?
a
b
d
d
2
1
b
a
e
e
c
c
a
c
e
e
4
3
a
b
d
d
b
c
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In an unrooted tree with four external nodes, the
internal branch is referred to as the central
branch.
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Cladograms Phylograms(collectively Dendograms)
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Unscaled phylogram
Scaled phylogram
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The Newick format   In computer programs, trees
are represented in a linear form by a string of
nested parentheses, enclosing taxon names (and
possibly also branch lengths and bootstrap
values), and separated by commas. This type of
representation is called the Newick format. The
originator of this format in mathematics was
Arthur Cayley.
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The Newick format   The Newick format for
phylogenetic trees was adopted on June 26, 1986
at an informal meeting at Newick's Lobster House
in Dover, New Hampshire. The Newick format
currently serves as the de facto standard for
representing phylogenetic tree and is employed by
almost all phylogenetic software tools.
Unfortunately, it has never been described in a
formal publication the first time it is
mentioned in a publication is in 1992.
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The Newick format   In the Newick format, the
pattern of the parentheses indicates the topology
of the tree by having each pair of parentheses
enclose all members of a monophyletic group. A
phylogenetic tree in the Newick format always
ends in a semicolon ().

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The Newick format   One can use the Newick format
to write down rooted trees, unrooted trees,
multifurcations, branch lengths, and bootstrap
values.
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3 OTUs
1 unrooted tree 3 rooted trees
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4 OTUs
3 unrooted trees 15 rooted trees
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The number of possible bifurcating rooted trees
(NR) for n ? 2 OTUs
The number of possible bifurcating unrooted trees
(NU) for n ? 3 OTUs
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¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾ Number of OTUs Number
of possible rooted tree ¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾
2 1 3 3 4 15 5 105 6
954 7 10,395 8 135,135 9 2,0
27,025 10 34,459,425 15 213,458,046,67
6,875 20 8,200,794,532,637,891,559,375 ¾¾¾¾¾
¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾
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Evolution is an historical process. Only one
historical narrative is true. From
8,200,794,532,637,891,559,375 possibilities, 1
possibility is true and 8,200,794,532,637,891,559,
374 are false. Truth is one, falsehoods are many.
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How do we know which of the 8,200,794,532,637,891,
559,375 trees is true?
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We dont, we infer by using decision criteria.
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True and inferred trees The sequence of
speciation events that has led to the formation
of a group of OTUs is historically unique. A tree
representing the true evolutionary history is
called the true tree. A tree that is obtained
by using a certain set of data and a certain
method of tree reconstruction is called an
inferred tree. An inferred tree may or may NOT
be the true tree.
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Cladogenesis the splitting of an evolutionary
lineage into two genetically
independent lineages.
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Anagenesis changes occurring along an
evolutionary lineage.
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In molecular phylogenetics, we assume that
species are only created by cladogenesis.
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A gene tree may differ from a species tree
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Gene trees and species trees
A
a
Species tree
Gene tree
B
b
D
c
It is often assumed that gene trees always equal
species trees. This may be not be true.
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Orthologs and paralogs
paralogous
A
C
b
orthologous
orthologous
A
c
B
C
a
b
A mixture of orthologs and paralogs is sampled
Duplication yields 2 copies (paralogs) on the
same genome
Ancestral gene
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Taxon (singular) Taxa (plural)
A taxon is a species or a group of species that
has been given a name, e.g., Homo sapiens (modern
humans), or Lepidoptera (butterflies), or herbs.
There are codes of biological nomenclature
which seek to ensure that every taxon has a
single and stable name, and that every name is
used for only one taxon.
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Clades

• Strictly A clade is a group of all the taxa that
  have been derived from a common ancestor plus the
  common ancestor itself.
• In molecular phylogenetics A clade is a group of
  taxa under study that share a common ancestor,
  which is not shared by any other species outside
  the group.

also monophyletic groups, natural clades
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Paraphyletic Taxa

• A taxon whose common ancestor is shared by any
  other taxon is called a paraphyletic taxon or an
  invalid taxon.

Reptiles are paraphyletic.
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• A named taxon that lacks phylogenetic validity,
  but is nonetheless used, is called a convenience
  taxon.

Fish (Pisces)
a convenience fish
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Sister Taxa

• If a clade is composed of two taxa, these are
  referred to as sister taxa.

Birds and crocodiles are sister taxa.
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Which of the following groups are not
monophyletic?
E. coli
mouse
baboon
rat
human
chimp
a. human, chimpanzee, baboon b. mouse,
chimpanzee, baboon c. rat, mouse d. human,
chimpanzee, baboon, rat, mouse e. E. coli, human,
chimpanzee, baboon, rat, mouse
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Which of the following groups are not
monophyletic?
E. coli
mouse
baboon
rat
human
chimp
a. human, chimpanzee, baboon b. mouse,
chimpanzee, baboon c. rat, mouse d. human,
chimpanzee, baboon, rat, mouse e. E. coli, human,
chimpanzee, baboon, rat, mouse
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A character provides information about an
individual OTU. A distance represents a
quantitative statement concerning the
dissimilarity between two OTUs.
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A character is a well-defined feature that in a
taxonomic unit can assume one out of two or more
mutually exclusive character states.
Mutually exclusive If David is tall, David
cannot be short.
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Character
Continuous
Discrete
Binary
Multistate
Unordered
Ordered
Unpolar
Polar
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A character is unordered if a change from one
character state to any other character state can
occur in one step.
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A character is ordered if there exists a unique
symmetrical path of change from one character
state to another.
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A character is polar if there exists a unique
asymmetrical (irreversible) path of change from
one character state to another.
Polar
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In partially ordered characters the number of
steps varies for the different pairwise
combinations of character states, but no definite
relationship exists between the number of steps
and the character-state. Amino-acid sites are
partially ordered characters. An amino acid
cannot change into all other amino acids in a
singe step, as sometimes 2 or 3 steps are
required. For example, a tyrosine may only
change into a leucine through an intermediate
state, i.e., phenylalanine or histidine.
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The number of steps in partially ordered
characters is specified by a step matrix, the
elements of which indicate the number of steps
required between any two character states
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Assumptions about character evolution Methods of
phylogenetic reconstruction require that we make
explicit assumptions about (1) the number of
discrete steps required for one character state
to change into another. (2) the probability
with which such a change may occur.
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Temporal Polarity of Character States Character
states may be ranked by relative antiquity
into (1) primitive or ancestral
(plesiomorphy) (2) derived or novel (apomorphy)
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Taxonomic Distribution of Character States A
primitive state that is shared by several taxa is
a symplesiomorphy. A derived state that is
shared by several taxa is a synapomorphy. A
derived character state unique to a particular
taxon is an autapomorphy. A character state
that is shared by several taxa due to
convergence, parallelism and reversals, rather
than due to common descent, is a homoplasy.
sympathy synapse syllable system
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homoplasy
apomorphy (autapomorphy)
synapomorphy
symplesiomorphy
D
C
C
B
A
A
B
A
C
A
A
A
plesiomorphy
A
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Distance Data
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Most molecular data yield character states that
are subsequently converted into distances.
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Some molecular data can only be expressed as
distances.
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