Dan Graur

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Molecular Phylogenetics

• Dan Graur

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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 Homepage (University of
Arizona) http//phylogeny.arizona.edu/tree/phyloge
ny.html
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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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preciptin test
George Henry Falkiner Nuttall 1862-1937 Blood
Immunity and Blood Relationship (1904)
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preciptin test
The closest relatives of humans are the apes,
followed in order of relatedness, by the Old
World monkeys, the New World monkeys, the
prosimians, and the ungulates.
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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

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Before we can answer phylogenetic questions, we
have to deal with the concept of species
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1. What is a species?2. How do species
originate?
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Species Concepts

• Species concepts are linked to views on how
  species originate.
• Early views were associated with a creationist
  view and were non-evolutionary.
• Today, some species concepts take evolution into
  account and attempt to address problems that are
  associated with biological entities that are
  evolving rather than immutable.

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Species Concepts

• There are many difficulties associated with the
  definition of species.
• Concepts that work well for some groups of
  organisms do not necessarily work for other
  organisms. Also, concepts that work well for
  extant species do not always apply to the case of
  fossil species.

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1. The Typological Species Concept

• Species are discrete, stable, and unchanging.
• The concept dates back to Aristotle (384 BCE 322
  BCE).
• Linnaeus (1707 1778), who held a creationist
  view, defined a type (typus) specimen for each
  species and provided it with a Latin binomial.
• Individuals were assigned to a species if they
  had the characteristic morphology of the type.

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1. The Typological Species Concept
Most Typological Species Are Defined on the basis
on morphology morphospecies
Other Typological Species May be Defined on the
basis on serotype (serospecies), genotype
(genospecies)
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Clusiella albiflora
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Cabramatta New South Wales, 11101959 C. E.
Chadwick on trunk of dead Acacia fulcata.
Jaczyk, F. (1966). Ein neue Laemosaccus aus
New-Südwales (Australien). Annalen des
Naturhistorischen Museums in Wien 63 213-214.
Laemosaccus chadwicki Jaczyk
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1. The Typological Species Concept

• The basic Linnaean system remains in place today
  despite its non-evolutionary stance on the origin
  of species.
• The idea of morphospecies has practical value,
  especially for paleontologists that must rely
  heavily on morphological features.

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2. The Phenetic or Numerical Taxonomy Species
Concept

• A species is defined as a set of organisms that
  resemble one another and is distinct from other
  sets (no ideal type).
• A modern outgrowth of the typological concept.
  Evolutionary change is acknowledged, but
  phenotypic similarity is used for defining
  species.
• Numerical measurements of as many characters as
  possible are used to define clusters of organisms.

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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.
• Mayrs 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 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 in practice.

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4. The Evolutionary/Phylogenetic Species
Concept (the theory)

• Promoted mainly by George Gaylord Simpson
• An evolutionary species is a lineage (an
  ancestor descendant sequence of populations),
  evolving separately from others and with its own
  unitary evolutionary role and historical
  tendencies.

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4. The Evolutionary/Phylogenetic Species
Concept (the practice)

• A species is the smallest diagnosable cluster of
  individual organisms within which there is a
  parental pattern of ancestry and descent.
• Species are not recognized strictly in terms of
  whether they can be diagnosed, i.e., whether or
  not they have unique morphological, biochemical,
  or physiological phenotypes.

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4. The good things about the Phylogenetic
Species Concept

• This species definition derives from an
  evolutionary perspective of ancestry and descent.
  
• It results in a natural hierarchical
  classification.

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Carolus Linnaeus (1707-1778)
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The Linnaean hierarchy
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4. The bad things about the Phylogenetic
Species Concept

• We may end up with too many taxa

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The Linnaean hierarchy of Panthera leo (1/2)
Euteleostomi (bony) Sarcopterygii
(lobe-finned fish tetrapods) Tetrapoda (4
legs) Amniota (amnion)
Mammalia (mammals) Theria
(internal egg) Eutheria
(placenta) Carnivora
(carnivores) Fissipedia
(terrestrial carnivores)
Felidae (cats)
Pantherinae (big cats)
Panthera (lion, jaguar, leopard, tiger)
Panthera leo (lion)
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The Linnaean hierarchy of Panthera leo (2/2)
Eukarya (nucleated cells) Opisthokonta
(fungi metazoans) Metazoa
(multicellulars) Eumetazoa
(animals) Bilateria (bilateral
symmetry) Coelomata
(mesodermal cavity)
Deuterostomia (secondary mouth)
Chordata (chordates)
Craniata (head)
Vertebrata
(vertebrae) Gnathostomata
(jaws)
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4. The bad things about the Phylogenetic
Species Concept

• The definition of species is arbitrary.

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Is there a perfect "species concept?
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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 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. 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.
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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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OK, so we do not have an answer to What is a
species?What is The Origin of Species?
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Wood frog Rana sylvatica
Northern leopard frog Rana pipiens
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What kind of data?
Molecular (DNA, RNA, proteins)
atcgatcgtgatcgatcgtagcatcgatgcatcgtacg
MWRCPYCGKRQWCMWG
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.
Gertrude Stein A rose is a rose is a rose is a
rose.
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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 flattened."
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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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Microbial morphologies are mostly very simple,
i.e., they provide only very few characters for
comparative studies.
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Small subunit ribosomal RNA
18S or 16S rRNA
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Proconsul
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.
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