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1 Introduction
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An overview of molecular evolution, or what is
molecular evolution?
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Molecular Evolution theory and examples
Theory e.g., the equilibrium between mutations,
selection, and drift Examples e.g., chimpanzees
and humans share a common ancestor that lived
approximately 4 million years ago Exercises
e.g., compute the score of a given maximum
parsimony tree
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Molecular Evolution deals with two subjects

• The evolution of molecular entities, e.g., genes,
  proteins, introns, inteins, chromosomal
  arrangements
• 2. The evolution of organisms and biological
  complexes, e.g., species, higher taxa,
  coevolutionary systems, ecological niches, and
  migratory patterns, by using molecular data.

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Molecular Evolution deals only with events
occurring after the emergence of biological
systems that possess replicable genetic material.
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Molecular Evolution the foundations

• Systematics (Linnaeus).
• Evolutionary Mechanisms (Darwin, Lamarck)
• Genetics (Mendel)
• Populations Genetics (Malthus)
• Nucleic Acid Research (Miescher)

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1 Introduction
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Classification
Systematics is the science of naming and
classifying organisms in regard to their natural
relationships.
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Macrolepiota procera tasty
Lepiota cristata highly poisonous
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Classification
Systematics is the science of naming and
classifying organisms in regard to their natural
relationships.
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4,400 species of animals and 7,700 species of
plants
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Linnaeus's scientific thought

• God has created the world, it is possible to
  understand God's wisdom by studying His creation.
  
• As he wrote in the preface to a late edition of
  Systema Naturae Creationis telluris est gloria
  Dei ex opere Naturae per Hominem solum -- The
  Earth's creation is the glory of God, as seen
  from the works of Nature by Man alone.

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Animal and plant classifications
The modern system of classifying all living
plants and animals, and fossils, is called the
binomial system, and was founded by Carl Linnaeus
(1707-1778). A genus and species is identified
for each organism, Homo sapiens being one such
example. Similar species may be grouped in a
single genus (pl. genera).
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Modern classification
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Principle of subordinationof characters
Antoine Laurent de Jussieu developed a natural
system as early as 1774, incorporating a natural
classification system along with Linnaeus
binomial nomenclature
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Fabaceae plant family
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Darwinian revolution(Origin of species 1859)

• If organisms have similar organs it is because
  they have a common ancestor.
• Finding similar organs is finding evolutionary
  relationships.
• Classification became evolutionary
  classification.

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From classification to tree of life
Dasypus novemcinctus
Elephas maximus
Homo sapiens
Mus musculus
Ursus arctos
Canis familiaris
Hyaena hyaena
Felis catus
Panthera leo
Pantera pardus
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Phylogenetic tree
Dasypus novemcinctus
Elephas maximus
Homo sapiens
Mus musculus
Ursus arctos
Canis familiaris
Hyaena hyaena
Felis catus
Panthera leo
Pantera pardus
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Phylogenetic tree
Dasypus novemcinctus
Elephas maximus
Homo sapiens
Mus musculus
Ursus arctos
Canis familiaris
Hyaena hyaena
Felis catus
Panthera leo
Pantera pardus
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How are done classification

• Organisms are classified based on the presence of
  shared characters that present morphological
  innovations.
• Such characters are called synapomorphies

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Example of synapomorphies
Mammal characteristics Hairs. Milk.
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Example of synapomorphies
Bird characteristic Feathers
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Example of synapomorphies
Fabaceae plant family Characteristic Flower
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Father of modern taxonomy
Emil Hans Willi Hennig (1913 1976) German
biologist who is considered the founder of
phylogenetic systematics, also known as
cladistics. As a taxonomist, he specialised in
dipterans (ordinary flies and mosquitoes).
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Inferences of putative ancestor
Putative ancestor of placental mammal
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In some cases it is difficult to find
synapomorphies
anthrax bacteria (Bacillus anthracis)
Escherichia coli
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Animal with unknown relationships
Myxozoa (fish parasites)
Placozoa (simplest known animal)
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Intermediate conclusion

• Classical classifications are based on
  morphological characters
• However, morphological characters are not enough
  to solve all the morphological classification

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Molecular Evolution deals with two subjects

• The evolution of organisms and biological
  complexes by using molecular data.
• (e.g., species, higher taxa, coevolutionary
  systems, and migratory patterns)
• The evolution of molecular entities
• (e.g., genes, proteins, chromosomal arrangements)

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How molecular characters are obtained
DNA extraction
Species
Tissue sample
Sequencing the gene
Amplification of a chosen gene
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How evolutionary relationships are inferred
Species
Sequence
Inferred evolutionary relationships
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Example of surprising findings

• Classical taxonomy five kingdom

(bacteria)
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Example of surprising findings

• Bacteria are form of two different groups the
  Archea and the Eubacteria

Woese C, Fox G (1977). Proc Natl Acad Sci USA 74
(11) 508890
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Intermediate conclusion

• Molecular characters have changed our vision of
  evolutionary relationships.

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Example of surprising findings

• Moles and hedgehog

Springer MS, Burk A, Kavanagh JR, et al. PNAS 94
(25) 13754-13759 (1997)
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Old hypothesis
Mole
Hedgehog
Horse
Elephant
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Molecular results
Horse
Mole
Hedgehog
Elephant
African Mole
African Hedgehog
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African continent 65 Mya