1. Brief Introduction to the Theory of Evolution and Phylogenetic Reconstruction
Anders Gorm Pedersen
Molecular Evolution Group
Center for Biological Sequence Analysis

2. Classification: Linnaeus
Carl Linnaeus

3. Classification: Linnaeus
Hierarchical system
Kingdom (Rige)
Phylum (Række)
Class (Klasse)
Order (Orden)
Family (Familie)
Genus (Slægt)
Species (Art)

4. Classification depicted as a tree

5. Classification depicted as a tree
Species
Genus
Family
Order
Class

6. Theory of evolution
Charles Darwin

7. Phylogenetic basis of systematics
Linnaeus:
Ordering principle is God.
Darwin:
Ordering principle is shared descent from common ancestors.
Today, systematics is explicitly based on phylogeny.

8. Darwin’s four postulates
More young are produced each generation than can survive to reproduce.
Individuals in a population vary in their characteristics.
Some differences among individuals are based on genetic differences.
Individuals with favorable characteristics have higher rates of survival and reproduction.
Evolution by means of natural selection
Presence of ”design-like” features in organisms:
quite often features are there “for a reason”

9. Theory of evolution as the basis of biological understanding
”Nothing in biology makes sense, except in the light of evolution.
Without that light it becomes a pile of sundry facts - some of them interesting or curious but making no meaningful picture as a whole”
T. Dobzhansky

10. Trees: terminology

11. Trees: terminology

12. Trees: representations
Three different representations of the same tree

13. Trees: rooted vs. unrooted
A rooted tree has a single node (the root) that represents a point in time that is earlier than any other node in the tree.
A rooted tree has directionality (nodes can be ordered in terms of “earlier” or “later”).
In the rooted tree, distance between two nodes is represented along the time-axis only (the second axis just helps spread out the leafs)
Early
Late

14. Trees: rooted vs. unrooted
A rooted tree has a single node (the root) that represents a point in time that is earlier than any other node in the tree.
A rooted tree has directionality (nodes can be ordered in terms of “earlier” or “later”).
In the rooted tree, distance between two nodes is represented along the time-axis only (the second axis just helps spread out the leafs)
Early
Late

15. Trees: rooted vs. unrooted
A rooted tree has a single node (the root) that represents a point in time that is earlier than any other node in the tree.
A rooted tree has directionality (nodes can be ordered in terms of “earlier” or “later”).
In the rooted tree, distance between two nodes is represented along the time-axis only (the second axis just helps spread out the leafs)
Early
Late

16. Trees: rooted vs. unrooted
In unrooted trees there is no directionality: we do not know if a node is earlier or later than another node
Distance along branches directly represents node distance

17. Trees: rooted vs. unrooted
In unrooted trees there is no directionality: we do not know if a node is earlier or later than another node
Distance along branches directly represents node distance

18. Reconstructing a tree using non-contemporaneous data

19. Reconstructing a tree using present-day data

20. Data: molecular phylogeny
DNA sequences
genomic DNA
mitochondrial DNA
chloroplast DNA
Protein sequences
Restriction site polymorphisms
DNA/DNA hybridization
Immunological cross-reaction

21. Morphology vs. molecular data
African white-backed vulture
(old world vulture)
Andean condor
(new world vulture)
New and old world vultures seem to be closely related based on morphology.
Molecular data indicates that old world vultures are related to birds of prey (falcons, hawks, etc.) while new world vultures are more closely related to storks
Similar features presumably the result of convergent evolution

22. Molecular data: single-celled organisms
Molecular data useful for analyzing single-celled organisms (which have only few prominent morphological features).