What is molecular evolution?

1. What is molecular evolution?

2. 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

3. Jacques Lucien Monod 1910-1976

4. “Molecular Evolution” deals with two subjects: The evolution of molecular entities, e.g., genes, genomes, proteins, introns, chromosomal arrangements… 2. The evolution of organisms and biological complexes, e.g., species, higher taxa, coevolutionary systems, ecological niches, migratory patterns… by using molecular data.

5. Components of Molecular Evolution (I) Descriptive Aspects of Molecular Evolution: “Intronless prokaryotes have evolved from introned ancestors, i.e., bacteria and archaea lost their introns.” “Chimpanzees and humans are descended from a common ancestor that lived 4-6 million years ago.” “RNA genomes evolve faster than DNA genomes.”

6. Components of Molecular Evolution (II)

7. Components of Molecular Evolution (III) Methodological Aspects of Molecular Evolution “Maximum parsimony search times can be shortened considerably through branch-and-bound algorithm.” “Ultrametric phylogenetic trees are always reconstructed exactly with UPGMA.”

9. Classification: Linnaeus Carl Linnaeus 1707-1778

10. Classification: Linnaeus • Hierarchical system • Kingdom • Phylum • Class • Order • Family • Genus • Species

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

12. Species • A fundamental category of taxonomic classification, ranking below a genus or subgenus and consisting of related organisms capable of interbreeding. • An organism belonging to such a category, represented in binomial nomenclature by an uncapitalized Latin adjective or noun following a capitalized genus name, as in Ananas comosus, the pineapple, and Equus caballus, the horse.

13. Genus • pl Genera • A taxonomic category ranking below a family and above a species and generally consisting of a group of species exhibiting similar characteristics. • In taxonomic nomenclature the genus name is used, either alone or followed by a Latin adjective or epithet, to form the name of a species.

14. Family • pl families • A taxonomic category of related organisms ranking below an order and above a genus. • A family usually consists of several genera. • For example, lions, tigers, cheetahs, and house cats belong to the same biological family. • Human beings belong to the biological family of hominids.

15. Classification depicted as a tree

16. Order • The classification lower than a class and higher than a family. • Dogs and cats belong to the order of carnivores; human beings, monkeys, and apes belong to the order of primates. • Flies and mosquitoes belong to the same order; so do birch trees and oak trees.

17. Class • class Cyanobacteria, Cyanophyceae, class Cyanophyceae — photosynthetic bacteria found in fresh and salt water; once thought to be algae: blue-green algae • Amphibia, class Amphibia — frogs; toads; newts; salamanders; caecilians • Reptilia, class Reptilia — class of cold-blooded air-breathing vertebrates with completely ossified skeleton and a body usually covered with scales or horny plates; once the dominant land animals • Anapsida, subclass Anapsida — oldest known reptiles: turtles; extinct Permian forms

18. Theory of evolution Charles Darwin 1809-1882

19. 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.

20. Darwin’s four postulates • Each generation more offspring is born than the environment can support - a fraction of offspring dies without leaving any offspring of its own. • 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”

21. Molecular Evolution is an Interdisciplinary Endeavor.

22. Course of Tal Pupko • Stories, stories…

23. Story 3

24. Thomas Malthus (1766-1834) Malthus observed that in nature plants and animals produce far more offsprings than can survive, and that Man too is capable of overproducing if left unchecked. Malthus was a political economist who was concerned about, what he saw as, the decline of living conditions in 19th century England.

25. Thomas Malthus (1766-1834) • He blamed this decline on three elements: • The overproduction of young. • The inability of resources to keep up with the rising human population. • The irresponsibility of the lower classes. To combat this, Malthus suggested that the family size of the lower class ought to be regulated such that poor families do not produce more children than they can support…

26. Thomas Malthus (1766-1834) Darwin and Wallace read Malthus, and extended his logic further than Malthus himself could ever take. They realized that producing more offsprings than can survive establishes a competitive environment among siblings, and that the variation among siblings would produce some individuals with a slightly greater chance of survival.

27. “A simple model of population growth” Assumptions: Time is measured in generations, i.e., the model is discrete. Generations are nonoverlapping. Let w be the average progeny per individual. Let N(t) denote the number of individuals in time t. Then N(t)= wN(t-1). Thus N(t) = N(0)wt.

28. “A simple model of population growth” The concept of “average fitness”: Let n1,n2,…,nk be the number of k types in a population at time t-1, and the fitnesses of these types be w1,…,wk. Assume N(t) = n1+n2+…nk. What is the ratio between N(t+1) and N(t)? The average fitness will be:

29. “A simple model of population growth” • Assume that the average fitness from generation to generation is not constant. Let w(1) be the average fitness in generation 1, w(2) in generation 2, etc’... Now: • G(w) is the geometric mean of the w’s.

30. “A less simple model of population growth” • In this model N(t) is large, and in a time interval Δt, a fraction bΔt of the population produce an offspring, and a fraction dΔt die. Thus, • Where m is (b-d). As Δt->0, this becomes • Comparing the 2 models we obtain:

31. “A less simple model of population growth” • Thus, m=ln(w), and a w of 2 (population doubles each year), is the same as m=ln(2)=0.693. • m is called the Malthusian parameter.

32. Story 4

33. Friedrich Miescher (1844-1895) isolates DNA for the first time. • Miescher, a Swiss scientist, wanted to study the chemistry of cells.

34. Miescher chose to study white blood cells, which are abundant in pus, and were abundantly available to him in bandages from a hospital near his university. ( Pus = “MUGLA” )

35. Miescher isolated a material rich in phosphorus from the cells and called it nuclein.

36. He found nuclein in other types of cells as well, including salmon sperm.

37. In the early 1900s, other scientists began to describe the chemical properties of DNA in much more detail.

38. The lab, a part of the University of Tübingen in southern Germany. The lab is located in the vaults of an old castle. Friedrich Miescher (1844-1895).

39. Origin(s) of Life

40. Story 5

41. Beginning

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