Molecular Phylogenetics

1. Molecular Phylogenetics Dan Graur

2. Objectives of molecular phylogenetics • Reconstruct the correct evolutionary relationships among biological entities • Estimate the time of divergence between biological entities • Chronicle the sequence of events along evolutionary lineages

3. Evolutionary relationships are illustrated by means of a phylogenetic tree or a dendogram.

4. Ernst Heinrich Haeckel 1834-1919

5. July 2007 July 1837

6. November 1859

7. The routes of inheritance represent the passage of genes from parents to offspring, and the branching pattern depicts a gene tree.

8. Different genes, however, may have different evolutionary histories, i.e., different routes of inheritance.

9. The routes of inheritance are confined by reproductive barriers, i.e., gene flow occurs only within a species. A species tree is a representation of splitting of species lineages.

10. Terminology

11. A phylogenetic tree or dendrogram is a graph composed of nodes and branches, in which only one branch connects any two adjacent nodes.

12. Internal External or Peripheral Branch

14. Assumptions: Bifurcation = Real speciation event Multifurcation = Lack of resolution

15. Binary tree

16. Rooted and unrooted trees

17. How many unrooted topologies are here? a b d d 1 2 b a e e c c a c e e 3 4 a b d d b c

18. In an unrooted tree with four external nodes, the internal branch is referred to as the central branch.

19. Bacterium 1 Cladogramsshow branching order - branch lengths are meaningless Bacterium 2 Bacterium 3 Eukaryote 1 Eukaryote 2 Eukaryote 3 Eukaryote 4 Phylogramsshow branch order and branch lengths Bacterium 1 Bacterium 2 Bacterium 3 Eukaryote 1 Eukaryote 2 Eukaryote 3 Eukaryote 4 Cladograms & Phylograms(collectively Dendograms)

20. Unscaled phylogram Scaled phylogram

23. The Newick format In computer programs, trees are represented in a linear form by a string of nested parentheses, enclosing taxon names (and possibly also branch lengths and bootstrap values), and separated by commas. This type of representation is called the Newick format. The originator of this format in mathematics was Arthur Cayley.

24. The Newick format The Newick format for phylogenetic trees was adopted on June 26, 1986 at an informal meeting at Newick's Lobster House in Dover, New Hampshire. The Newick format currently serves as the de facto standard for representing phylogenetic tree and is employed by almost all phylogenetic software tools. Unfortunately, it has never been described in a formal publication; the first time it is mentioned in a publication is in 1992.

25. The Newick format In the Newick format, the pattern of the parentheses indicates the topology of the tree by having each pair of parentheses enclose all members of a monophyletic group. A phylogenetic tree in the Newick format always ends in a semicolon (;). ;

26. The Newick format One can use the Newick format to write down rooted trees, unrooted trees, multifurcations, branch lengths, and bootstrap values.

27. 3 OTUs 1 unrooted tree = 3 rooted trees

28. 4 OTUs 3 unrooted trees = 15 rooted trees

29. The number of possible bifurcating rooted trees (NR) for n 2OTUs The number of possible bifurcating unrooted trees (NU) for n 3OTUs

30. ¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾ Number of OTUs Number of possible rooted tree ¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾ 2 1 3 3 4 15 5 105 6 954 7 10,395 8 135,135 9 2,027,025 10 34,459,425 15 213,458,046,676,875 20 8,200,794,532,637,891,559,375 ¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾

31. Evolution is an historical process. Only one historical narrative is true. From 8,200,794,532,637,891,559,375 possibilities, 1 possibility is true and 8,200,794,532,637,891,559,374 are false. Truth is one, falsehoods are many.

32. How do we know which of the 8,200,794,532,637,891,559,375 trees is true?

33. We don’t, we infer by using decision criteria.

34. True and inferred trees The sequence of speciation events that has led to the formation of a group of OTUs is historically unique. A tree representing the true evolutionary history is called the true tree. A tree that is obtained by using a certain set of data and a certain method of tree reconstruction is called an inferred tree. An inferred tree may or may NOT be the true tree.

35. ancestor descendant 1 descendant 2 Cladogenesis = the splitting of an evolutionary lineage into two genetically independent lineages.

36. ancestor descendant 1 descendant 2 Anagenesis = changes occurring along an evolutionary lineage.

37. In molecular phylogenetics, we assume that species are only created by cladogenesis.

38. A gene tree may differ from a species tree

39. Gene trees and species trees A a Species tree Gene tree B b D c It is often assumed that gene trees always equal species trees. This may be not be true.

40. Orthologs and paralogs paralogous b* C* A* orthologous orthologous c C* B A* a b* A mixture of orthologs and paralogs is sampled Duplication yields 2 copies (paralogs) on the same genome Ancestral gene

42. Taxon (singular); Taxa (plural) A taxon is a species or a group of species that has been given a name, e.g., Homo sapiens (modern humans), or Lepidoptera (butterflies), or herbs. There are codes of biological nomenclature which seek to ensure that every taxon has a single and stable name, and that every name is used for only one taxon.

43. Clades* • Strictly: A clade is a group of all the taxa that have been derived from a common ancestor plus the common ancestor itself. • In molecular phylogenetics: A clade is a group of taxa under study that share a common ancestor, which is not shared by any other species outside the group. *also: monophyletic groups, natural clades

44. Paraphyletic Taxa • A taxon whose common ancestor is shared by any other taxon is called a paraphyletic taxon or an invalid taxon. Reptiles are paraphyletic. 44

45. A named taxon that lacks phylogenetic validity, but is nonetheless used, is called a convenience taxon. Fish (Pisces) “a convenience fish”

46. Sister Taxa • If a clade is composed of two taxa, these are referred to as sister taxa. Birds and crocodiles are sister taxa.

47. = clades Phenotypic distance

48. Which of the following groups are not monophyletic? E. coli mouse baboon rat human chimp a. human, chimpanzee, baboon b. mouse, chimpanzee, baboon c. rat, mouse d. human, chimpanzee, baboon, rat, mouse e. E. coli, human, chimpanzee, baboon, rat, mouse

49. Which of the following groups are not monophyletic? E. coli mouse baboon rat human chimp a. human, chimpanzee, baboon b. mouse, chimpanzee, baboon c. rat, mouse d. human, chimpanzee, baboon, rat, mouse e. E. coli, human, chimpanzee, baboon, rat, mouse