CS 177 Phylogenetics I

1. CS 177 Phylogenetics I Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Model of sequence evolution Phylogenetic trees and networks Cladistic and phenetic methods Computer software and demos Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy

2. (very) basic advanced Phylogenetic Inference I Recommended readings A science primer: Phylogenetics http://www.ncbi.nlm.nih.gov/About/primer/phylo.html Brown, S.M. (2000) Bioinformatics, Eaton Publishing, pp. 145-160 Brown, S.M.: Molecular Phylogenetics www.med.nyu.edu/rcr/rcr/course/PPT/phylogen.ppt Hillis, D.M.; Moritz, G. & Mable, B.K. (1996) Molecular Systematics, 2. Edition, Sinauer Associates, 655 pp. Mount, D.W. (2001) Bioinformatics,Cold Spring Harbor Lab Press, pp.237-280 Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy

3. CS 177 Phylogenetic Inference I Evolution The theory of evolution is the foundation upon which all of modern biology is built From anatomy to behavior to genomics, the scientific method requires an appreciation of changes in organisms over time It is impossible to evaluate relationships among gene sequences without taking into consideration the way these sequences have been modified over time Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy Ernst Haeckel (1834-1919)

4. CS 177 Phylogenetic Inference I Relationships Similarity searches and multiple alignments of sequences naturally lead to the question “How are these sequences related?” and more generally: “How are the organisms from which these sequences come related?” Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy

5. Classifying Organisms Nomenclature is the science of naming organisms Evolution has created an enormous diversity, so how do we deal with it? Names allow us to talk about groups of organisms. - Scientific names were originally descriptive phrases; not practical - Binomial nomenclature > Developed by Linnaeus, a Swedish naturalist > Names are in Latin, formerly the language of science > binomials - names consisting of two parts > The generic name is a noun. > The epithet is a descriptive adjective. - Thus a species' name is two words e.g. Homo sapiens Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy Carolus Linnaeus (1707-1778)

6. Classifying Organisms Taxonomyis the science of the classification of organisms Taxonomy deals with the naming and ordering of taxa. The Linnaean hierarchy: 1. Kingdom 2. Division 3. Class 4. Order 5. Family 6. Genus 7. Species Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy Evolutionary distance

7. Classifying Organisms Systematics is the science of the relationships of organisms Systematics is the science of how organisms are related and the evidence for those relationships Systematics is divided primarily into phylogenetics and taxonomy Speciation -- the origin of new species from previously existing ones - anagenesis - one species changes into another over time - cladogenesis - one species splits to make two Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy Reconstruct evolutionary history Phylogeny

8. Phylogenetics Phylogenetics is the science of the pattern of evolution. A. Evolutionary biology is the study of the processes that generate diversity, while phylogenetics is the study of the pattern of diversity produced by those processes. B. The central problem of phylogenetics: 1. How do we determine the relationships between species? 2. Use evidence from shared characteristics, not differences 3. Use homologies, not analogies 4. Use derived condition, not ancestral a. synapomorphy - shared derived characteristic b. plesiomorphy - ancestral characteristic C. Cladistics is phylogenetics based on synapomorphies. 1. Cladistic classification creates and names taxa based only on synapomorphies. 2. This is the principle of monophyly 3. monophyletic, paraphyletic, polyphyletic 4. Cladistics is now the preferred approach to phylogeny Review of protein structures Need for analyses of protein structures Sources of protein structure information Computational Modeling The phylogeny and classification of life as proposed by Haeckel (1866)

9. Phylogenetics Evolutionary theory states that groups of similar organisms are descendedfrom a common ancestor. Phylogenetic systematics is a method of taxonomic classification basedon their evolutionary history. It was developed by Hennig, a German entomologist, in 1950. Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy Willi Hennig (1913-1976)

10. Phylogenetics Phylogenetics is the science of the pattern of evolution Evolutionary biology versus phylogenetics - Evolutionary biology is the study of the processes that generate diversity - Phylogenetics is the study of the pattern of diversity produced by those processes Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy

11. Phylogenetics Who uses phylogenetics? Some examples: Evolutionary biologists (e.g. reconstructing tree of life) Systematists (e.g. classification of groups) Anthropologists (e.g. origin of human populations) Forensics (e.g. transmission of HIV virus to a rape victim) Parasitologists (e.g. phylogeny of parasites, co-evolution) Epidemiologists (e.g. reconstruction of disease transmission) Genomics/Proteomics (e.g. homology comparison of new proteins) Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy

12. Phylogenetic trees The central problem of phylogenetics: how do we determine the relationships between taxa? Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy in phylogenetic studies, the most convenient way of presenting evolutionary relationships among a group of organisms is the phylogenetic tree

13. Phylogenetic trees Node: a branchpoint in a tree (a presumed ancestral OTU) Branch: defines the relationship between the taxa in terms of descent and ancestry Topology: the branching patterns of the tree Branch length (scaled trees only): represents the number of changes that have occurred in the branch Root: the common ancestor of all taxa Clade: a group of two or more taxa or DNA sequences that includes both their common ancestor and all their descendents Operational Taxonomic Unit (OTU): taxonomic level of sampling selected by the user to be used in a study, such as individuals, populations, species, genera, or bacterial strains Branch Node Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy Clade Root

14. Phylogenetic trees There are many ways of drawing a tree Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy

15. Phylogenetic trees There are many ways of drawing a tree E D C B A = = Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy

16. Phylogenetic trees There are many ways of drawing a tree = = Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy no meaning

17. = / Phylogenetic trees There are many ways of drawing a tree Bifurcation Trifurcation Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy Bifurcation versus Multifurcation (e.g. Trifurcation) Multifurcation (also called polytomy): a node in a tree that connects more than three branches. A multifurcation may represent a lack of resolution because of too few data available for inferring the phylogeny (in which case it is said to be a soft multifurcation) or it may represent the hypothesized simultaneous splitting of several lineages (in which case it is said to be a hard multifurcation).

18. Phylogenetic trees Trees can be scaled or unscaled (with or without branch lengths) Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy

19. Unrooted tree Rooted tree D B A C C A Root Root B D D B A C C A Root Root B D Phylogenetic trees Trees can be unrooted or rooted Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy

20. Phylogenetic trees Trees can be unrooted or rooted Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy These trees showfive different evolutionary relationships among the taxa!

21. Phylogenetic trees Possible evolutionary trees Taxa (n): 4 2 3 Taxa (n) Unrooted/rooted 2 1/1 3 1/3 4 3/15 Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy

22. Phylogenetic trees Possible evolutionary trees Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy

23. Use information from ancestors Phylogenetic trees How to root? In most cases not available Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy

24. Use statistical tools will root trees automatically (e.g. mid-point rooting) Phylogenetic trees How to root? Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy This must involve assumptions … BEWARE!

25. - the outgroup should be a taxon known to be less closely related to the rest ofthe taxa (ingroups) - it should ideally be as closely related as possible to the rest of the taxa while still satisfying the above condition Phylogenetic trees How to root? Using “outgroups” Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy

26. Phylogenetic trees Exercise: rooted/unrooted; scaled/unscaled A B C Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Homology and homoplasy F D E

27. Phylogenetics • What are useful characters? • Use homologies, not analogies! • Homology: common ancestry of two or more character states • Analogy: similarity of character states not due to shared ancestry • - Homoplasy: a collection of phenomena that leads to similarities in character states for reasons other than inheritance from a common ancestor (e.g. convergence, parallelism, reversal) • Homoplasy is huge problemin morphology data sets! • But in molecular data sets, too! Taxonomy and phylogenetics Phylogenetic trees Homology and homoplasy Cladistic versus phenetic analyses Cactaceae and Euphorbiaceae

28. Phylogenetics Molecular data and homoplasy gene sequences represent character data characters are positions in the sequence (not all workers agree; some say one gene is one character) character states are the nucleotides in the sequence (or amino acids in the case of proteins) Taxonomy and phylogenetics Phylogenetic trees Homology and homoplasy Cladistic versus phenetic analyses Problems: the probability that two nucleotides are the same just by chance mutation is 25% what to do with insertions or deletions (which may themselves be characters) homoplasy in sequences may cause alignment errors

29. Phylogenetics Molecular data and homoplasy: Orthologs vs. Paralogs When comparing gene sequences, it is important to distinguish between identical vs. merely similar genes in different organisms Orthologs are homologous genes in different species with analogous functions Paralogs are similar genes that are the result of a gene duplication A phylogeny that includes both orthologs and paralogs is likely to be incorrect Sometimes phylogenetic analysis is the best way to determine if a new gene is an ortholog or paralog to other known genes Taxonomy and phylogenetics Phylogenetic trees Homology and homoplasy Cladistic versus phenetic analyses

30. Phylogenetics What are useful characters? • Use derived condition, not ancestral • Synapomorphy (shared derived character): homologous traits share the same character state because it originated in their immediate common ancestor • Plesiomorphy (shared ancestral character”): homologous traits share the same character state because they are inherited from a common distant ancestor Taxonomy and phylogenetics Phylogenetic trees Homology and homoplasy Cladistic versus phenetic analyses

31. Phenetics versus cladistics Within the field of taxonomy there are two different methods and philosophies of building phylogenetic trees: cladistic and phenetic • Phenetic methods construct trees (phenograms) by considering the current states of characters without regard to the evolutionary history that brought the species to their current phenotypes;phenograms are based on overall similarity • Cladistic methods construct trees (cladograms) rely on assumptions about ancestral relationships as well as on current data;cladograms are based on character evolution (e.g. shared derived characters) Cladistics is becoming the method of choice; it is considered to be more powerfuland to provide more realistic estimates, however, it is slower than phenetic algorithms

32. Phenetics vs. cladistics An example

33. 4 3 5 overall similarity Phenetics vs. cladistics Phenetic (overall similarity) A B C

34. 2 1 shared derived characters 1 Phenetics vs. cladistics Cladistics (character evolution; e.g. shared derived characters) A B C

35. Model of sequence evolution The problem - A basic process in the evolution of a sequence is change in that sequence over time - Now we are interested in a mathematical model to describe that - It is essential to have such a model to understand the mechanisms of change and is required to estimate both the rate of evolution and the evolutionary history of sequences

36. Pyrimidine (C4N2H4) Purine (C5N4H4) base + sugar + phosphate Thymine Adenine Cytosine Guanine Model of sequence evolution Nucleotide

37. Models of sequence evolution Examples Jukes-Cantor model (1969) All substitutions have an equal probability and base frequencies are equal

38. Models of sequence evolution Examples Felsenstein (1981) All substitutions have an equal probability, but there are unequal base frequencies

39. Models of sequence evolution Examples Kimura 2 parameter model (K2P) (1980) Transitions and transversions have different probabilities

40. Models of sequence evolution Examples Hasegawa, Kishino & Yano (HKY) (1985) Transitions and transversions have different probabilities,base frequencies are unequal

41. Models of sequence evolution Examples General time reversible model (GTR) Different probabilities for each substitution,base frequencies are unequal

42. Models of sequence evolution a G A Jukes-Cantor b b b b C T a K2P Felsenstein HKY GTR

43. More models of sequence evolution … • Currently, there are more than 60 models described • plus gamma distribution and invariable sites • accuracy of models rapidly decreases for highly divergent sequences • problem: more complicated models tend to be less accurate (and slower) • How to pick an appropriate model? • use a maximum likelihood ratio test • - implemented in Modeltest 3.06 (Posada & Crandall, 1998)

44. B Equal base frequencies Null model = JC -lnL0 = 3369.2803 Alternative model = F81 -lnL1 = 3342.5513 2(lnL1-lnL0) = 53.4580 df = 3 P-value = <0.000001 C Model selected: TVM+G -lnL = 2911.3660 More models of sequence evolution … Example for Modeltest file JC = 3158.0095 F81 = 3121.2188 K80 = 2994.6611 HKY = 2924.4182 TrNef = 2994.5491 TrN = 2923.6340 K81 = 2987.6548 K81uf = 2923.5620 TIMef = 2987.6196 TIM = 2922.9878 TVMef = 2983.3450 TVM = 2922.1970 SYM = 2983.3069 GTR = 2921.1187 A

45.  helix  sheet Did the Florida dentist infect his patients with HIV? Taxonomy and phylogenetics Phylogenetic trees Homology and homoplasy Cladistic versus phenetic analyses From Ou et al. (1992) and Page & Holmes (1998)