Molecular
Phylogenetics
Dan Graur
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Objectives of phylogenetics
• Reconstruct the correct genealogical ties
among biological entities
• Estimate the time of divergence between
biological entities
• Chronicle the sequence of events along
evolutionary lineages
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Molecular phylogenetics
Molecular phylogenetics = The study of
evolutionary relationships among biological
entities (individuals, populations, species, or
higher taxa), by using a combination of
molecular data (such as DNA and protein
sequences, presence or absence of
transposable elements, and gene-order data)
and statistical techniques.
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Some history…
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Charles Darwin to Thomas Huxley
(1857)
“The time will come I
believe, though I
shall not live to see
it, when we shall
have fairly true
genealogical
[phylogenetic] trees
of each great
kingdom of nature.”
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The Tree of Life Web Project
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tolweb.org
The first study to employ molecular data in phylogenetics
preciptin test
George Henry Falkiner Nuttall
1862-1937
Blood Immunity and Blood Relationship (1904)
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preciptin test
“If we accept the degree of blood reaction as an
index of the degree of blood-relationship within the
Anthropoidea, then we find that the Old World apes
are more closely allied to man than are the New
World apes, and this is exactly in accordance with
the opinion expressed by Darwin.”
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Nomenclature, Systematics,
Phylogenetics, Taxonomy, &
Classification
• Nomenclature = the naming of organisms
• Classification = the assignment of taxa to
groups of organisms
• Taxonomy = Nomenclature + Classification
• Phylogenetics = Evolutionary patterns &
relationships among organisms
• Systematics = Taxonomy + Phylogenetics 9
What is a “species”?
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“Species” Concepts
• There are many difficulties associated with the
definition of “species.”
• Definitions that work well for some groups of
organisms do not necessarily work for other
organisms (extant versus fossil species).
• Some species concepts take evolution into
account and attempt to address problems that
are associated with a species being an evolving
rather than an immutable biological entity.
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1. The Typological “Species”
Concept
• Species are discrete, stable, and unchanging.
• The concept dates back to Aristotle, adopted by
Linnaeus.
• The description of the species is based on a holotype. A
holotype is a single specimen of the organism on which
the formal description of the species is based.
Additional specimens used in the description are
referred to as paratypes.
• Individuals are assigned to a species if they have the
characteristic morphology of the holotype.
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Collection site: Cabramatta, New South Wales, Australia, on
trunk of dead Acacia fulcata.
Date: 11/10/1959
Collector: C. E. Chadwick
Jaczyk F. 1966. Ein neue Laemosaccus aus New-Südwales
(Australien). Annalen des Naturhistorischen Museums in Wien1363:
213-214. Laemosaccus chadwicki Jaczyk
2. The Phenetic or Numerical
Taxonomy “Species” Concept
• A species is defined as a set of organisms that
resemble one another and are distinct from other
sets (there is no ideal holotype, but only a statistical
agglomerate).
• A modern outgrowth of the typological concept.
• Numerical measurements of as many characters as
possible are used to define clusters of organisms (ad
hoc species).
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4 legs
black
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3. The Biological “Species”
Concept
• The biological species concept was proposed by
Theodosius Dobzhansky in the 1930s. It has been
elaborated on and reworked by Verne Grant, Julian
Huxley and Ernst Mayr.
Mayr’s definition: “Species are groups of
interbreeding natural populations that are
reproductively isolated from other such
groups.”
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3. The good things about the
Biological “Species” Concept
• Species are cohesive gene pools that are held
together by gene flow. Organisms in a species
are defined by the exchange of genes, or at least
by the potential to exchange genes. Gene flow is
the “glue” that holds a species together.
• Biological species are reproductively isolated
from each other. Reproductive isolation severes
the ties that bind populations together and
allows populations to diverge from each other.
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4. The bad things about the
Biological “Species” Concept
• The concept applies only to sexually
reproducing species and has no application to
asexual organisms.
• The concept cannot be applied to fossils or
museum specimens.
• Overlapping ranges and partial interbreeding
render the biological species concept difficult
to apply.
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4. The Evolutionary/Phylogenetic
“Species” Concept (the theory)
• Promoted mainly by George Gaylord
Simpson
• An evolutionary species is a lineage (ancestordescendant populations), evolving separately
from other lineages.
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The good things about the
Phylogenetic “Species” Concept
• This species definition derives from an
evolutionary perspective of ancestry and
descent.
The bad things about the
Phylogenetic “Species” Concept
• It is inapplicable to species that do not abide
by the tree metaphor (e.g., bacteria, wheat).
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5. The Intuitive “Species” Concept
Bored with her husband and her polo-playing
lover, will the middle-aged heroine go away
with the young man who gave her a lift when
her car broke down?
Can the state of Ohio, consistent
with the First Amendment, ban
the showing of the film The
Lovers (Les Amants) which has
been deemed obscene?
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5. The Intuitive “Species” Concept
“Hard-core pornography — I shall not today attempt to define the
kinds of material I understand to be embraced within that
shorthand description, and perhaps I could never succeed in
intelligibly doing so. But I know it when I see it.”
Justice Potter Stewart (1964) in Jacobellis vs. Ohio
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5. The Intuitive “Species” Concept
“Nor shall I here discuss the various definitions
which have been given of the term species. No
one definition has as yet satisfied all naturalists;
yet every naturalist knows vaguely what he
means when he speaks of a species.”
Charles Darwin. 1859. The Origin of Species.
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5. The Intuitive “Species” Concept
“I look at the term species as one arbitrarily
given, for the sake of convenience, to a group of
organisms resembling each other.”
Charles Darwin. 1859. The Origin of Species by
Means of Natural Selection.
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How do species originate?
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Wood frog
Rana sylvatica
Northern leopard frog
Rana pipiens
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Reproductive isolation by negative
epistasis
Dobzhansky-Muller-[Bateson] model for the origin
of reproductive isolation
Reproductive isolation by negative
epistasis
The loci Lethal hybrid rescue (Lhr) and Hybrid male
rescue (Hmr) in Drosophila simulans and Drosophila
melanogaster interact with each other in a manner
predicted by the Dobzhansky-Muller.
Brideau NJ, Flores HA, Wang J, Maheshwari S, Wang X, Barbash
DA. 2006. Two Dobzhansky-Muller genes interact to cause hybrid
lethality in Drosophila. Science 314:1292-1295.
What kind of data?
Molecular (DNA, RNA, proteins)
Morphological (soft tissue, hard tissue,
extant, extinct)
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Advantages of Molecular Data:
1. Molecular entities are strictly heritable.
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Advantages of Molecular Data:
2. The description of molecular characters
is unambiguous.
A TTAC is a TTAC is a TTAC is
a TTAC.”
Sorry, Gertrud
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Advantages of Molecular Data:
2. The description of molecular characters
is unambiguous.
The third amino acid in the preproinsulin of the
rabbit (Oryctolagus cuniculus) is always serine, and
the homologous position in the preproinsulin of the
golden hamster (Mesocricetus auratus) is always
leucine.
Morphological descriptions frequently contain such
ambiguous modifiers as "thin," "reduced," "slightly
elongated," "partially enclosed," and "somewhat
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flattened."
Advantages of Molecular Data:
3. There is some regularity to the
evolution of molecular traits.
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Advantages of Molecular Data:
4. Molecular data are amenable to
quantitative treatment.
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Advantages of Molecular Data:
5. Homology assessment is easier than
with morphological traits.
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Advantages of Molecular Data:
6. Molecular data are robust to evolutionary
distance.
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Advantages of Molecular Data:
7. Molecular data are abundant.
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Example: Microbial morphologies are very
simple, i.e., they provide only very few
characters for comparative studies. In
contrast, molecular variation is abundant.
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Proconsul
Black: Parts found in situ by Tom Withworth in 1951.
Blue: Parts found in museum drawers by Alan Walker &
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Martin Pickford during the restoration in 1985.