1 Dan Graur Molecular Molecular Phylogenetics Phylogenetics
Transcript
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1 Dan Graur Molecular Phylogenetics
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2 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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3 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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4 ? Some history
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5 Charles Darwin to Thomas Huxley (1857) 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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6 The Tree of Life Web Project tolweb.org
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7 George Henry Falkiner Nuttall 1862-1937 Blood Immunity and
Blood Relationship (1904) preciptin test The first study to employ
molecular data in phylogenetics
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8 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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9 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
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10 What is aspecies? What is a species?
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11 There are many difficulties associated with the definition
of species.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).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.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.
Species Concepts
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12 1. The Typological Species Concept Species are discrete,
stable, and unchanging.Species are discrete, stable, and
unchanging. The concept dates back to Aristotle, adopted by
Linnaeus.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.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.Individuals are
assigned to a species if they have the characteristic morphology of
the holotype.
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13 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-Sdwales
(Australien). Annalen des Naturhistorischen Museums in Wien 63:
213-214. Laemosaccus chadwicki Jaczyk
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14 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 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.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).Numerical measurements of as many
characters as possible are used to define clusters of organisms (ad
hoc species).
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15 4 legs black
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16 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.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. Mayrs
definition: Species are groups of interbreeding natural populations
that are reproductively isolated from other such groups. Mayrs
definition: Species are groups of interbreeding natural populations
that are reproductively isolated from other such groups.
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17 3. The good things about the Biological Species Concept
Species are cohesive gene poolsSpecies 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 isolatedBiological 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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18 The concept applies only to sexually reproducing species and
has no application to asexual organisms.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.The concept cannot be applied to fossils or museum
specimens. Overlapping ranges and partial interbreeding render the
biological species concept difficult to apply.Overlapping ranges
and partial interbreeding render the biological species concept
difficult to apply. 4. The bad things about the Biological Species
Concept
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19 4. The Evolutionary/Phylogenetic Species Concept (the
theory) Promoted mainly by George Gaylord SimpsonPromoted mainly by
George Gaylord Simpson An evolutionary species is a lineage
(ancestor- descendant populations), evolving separately from other
lineages.An evolutionary species is a lineage (ancestor- descendant
populations), evolving separately from other lineages.
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20 The good things about the Phylogenetic Species Concept This
species definition derives from an evolutionary perspective of
ancestry and descent.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).It is inapplicable to species that do not abide by the tree
metaphor (e.g., bacteria, wheat).
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22 5. The Intuitive Species Concept 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? 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?
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23 5. The Intuitive Species Concept pornography 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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24 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. 5. The Intuitive Species Concept
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25 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. 5. The Intuitive Species Concept
Dobzhansky-Muller-[Bateson] model for the origin of
reproductive isolation Reproductive isolation by negative
epistasis
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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.
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33 Molecular (DNA, RNA, proteins) What kind of data?
Morphological (soft tissue, hard tissue, extant, extinct)
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34 Advantages of Molecular Data: 1. Molecular entities are
strictly heritable.
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35 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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36 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 flattened."
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37 Advantages of Molecular Data: 3. There is some regularity to
the evolution of molecular traits.
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38 Advantages of Molecular Data: 4. Molecular data are amenable
to quantitative treatment.
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39 Advantages of Molecular Data: 5. Homology assessment is
easier than with morphological traits.
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40 Advantages of Molecular Data: 6. Molecular data are robust
to evolutionary distance.
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41 Advantages of Molecular Data: 7. Molecular data are
abundant.
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42 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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44 Black: Parts found in situ by Tom Withworth in 1951. Blue:
Parts found in museum drawers by Alan Walker & Martin Pickford
during the restoration in 1985. Proconsul