Lecture 22 : Introduction to Phylogenetics

1. Lecture 22 : Introduction to Phylogenetics April 4, 2014

2. Last Time • Infinite alleles and stepwise mutation models • Introduction to neutral theory • Molecular clock

3. Today • Introduction to phylogenetics • Phylogeography • Limitations of phylogenetic analysis • Coalescence introduction • Influence of demography on coalescence time

4. Phylogenetics • Study of the evolutionary relationships among individuals, groups, or species • Relationships often represented as dichotomous branching tree • Extremely common approach for detecting and displaying relationships among genotypes • Important in evolution, systematics, and ecology (phylogeography)

5. O G P C Q H A R S I D J T U K E V L W B X M Y F Z N Ç Evolution Slide adapted from Marta Riutart

6. O P Q R S T U V W X Y Z Ç What is a phylogeny? • Homology: similarity that is the result of inheritance from a common ancestor Slide adapted from Marta Riutart

7. Group, cluster, clade Leaves, Operational Taxonomic Units (OTUs) terminal branches node interior branches Phylogenetic Tree Terms A B C D E F G H I J ROOT Slide adapted from Marta Riutart

8. Bacteria 1 Bacteria 2 Bacteria 3 Eukaryote 1 Eukaryote 2 Eukaryote 3 Eukaryote 4 Bacteria 1 Bacteria 2 Bacteria 3 Eukaryote 1 Eukaryote 2 Eukaryote 3 Eukaryote 4 Tree Topology (Bacteria1,(Bacteria2,Bacteria3),(Eukaryote1,((Eukaryote2,Eukaryote3),Eukaryote4))) Slide adapted from Marta Riutart

9. Are these trees different? How about these? http://helix.biology.mcmaster.ca

10. eukaryote eukaryote eukaryote eukaryote Rooted versus Unrooted Trees archaea archaea Unrooted tree archaea Rooted by outgroup bacteria outgroup archaea Monophyletic group archaea archaea eukaryote Monophyletic group eukaryote root eukaryote eukaryote Slide adapted from Marta Riutart

11. Rooting with D as outgroup A B D A C B C G E F D G F E Slide adapted from Marta Riutart

12. A B D A C G B E C F G D E A F B C D Now with C as outgroup G F E

13. Baum et al. Which of these four trees is different?

14. UPGMA Method • Use all pairwise comparisons to make dendrogram • UPGMA:Unweighted Pairwise Groups Method using Arithmetic Means • Hierarchically link most closely related individuals Read the Lab 11 Introduction!

15. Phenetics (distance) vs Cladistics (character state based) Lowe, Harris, and Ashton 2004

16. Parsimony Methods • Based on underlying genealogical relationships among alleles • Occam’s Razor: simplest scenario is the most likely • Useful for depicting evolutionary relationships among taxa or populations • Choose tree that requires smallest number of steps (mutations) to produce observed relationships

17. Lowe, Harris, and Ashton 2004 Choosing Phylogenetic Trees • MANY possible trees can be built for a given set of taxa • Very computationally intensive to choose among these

18. Choosing Phylogenetic Trees 9 8 9 10 9 11 9 8 7 11 9 5 Felsenstein 2004 • Many algorithms exist for searching tree space • Local optima are problem: need to traverse valleys to get to other peaks • Heuristic search: cut trees up systematically and reassemble • Branch and bound: search for optimal path through tree space

19. Choosing Phylogenetic Trees E A F Felsenstein 2004 D C B 60 60 60 Lowe, Harris, and Ashton 2004 • If multiple trees equally likely, select majority rule or consensus • Strict consensus is most conservative approach • Bootstrap data matrix (sample with replacement) to determine robustness of nodes

20. Phylogeography • The study of evolutionary relationships among individuals based on phylogenetic analysis of DNA sequences in geographic context • Can be used to infer evolutionary history of populations • Migrations • Population subdivisions • Bottlenecks/Founder Effects • Can provide insights on current relationships among populations • Connectedness of populations • Effects of landscape features on gene flow

21. Phylogeography • Topology of tree provides clues about evolutionary and ecological history of a set of populations • Dispersal creates poor correspondence between geography and tree topology • Vicariance (division of populations preventing gene flow among subpopulations) results in neat mapping of geography onto haplotypes

22. Avise 2004 Example: Pocket gophers (Geomys pinetis) • Fossorial rodent that inhabits 3-state area in the U.S. • RFLP for mtDNA of 87 individuals revealed 23 haplotypes • Parsimony network reveals geographic relationships among haplotypes • Haplotypes generally confined to single populations • Major east-west split in distribution revealed

23. Problems with using Phylogenetics for Inferring Evolution • It is a black box: starting from end point, reconstructing past based on assumed evolutionary model • Homologs versus paralogs • Hybridization • Differential evolutionary rates • Assumes coalescence

24. Gene Orthology • Phylogenetics requires unambiguous identification of orthologous genes • Paralogous genes are duplicated copies that do not share a common evolutionary history • Difficult to determine orthology relationships paralogs Lowe, Harris, Ashton 2004 paralogs paralogs orthologs