Phylogenetic Interpretation

1. Phylogenetic Interpretation Dr Laura Emery Laura.Emery@ebi.ac.uk www.ebi.ac.uk

2. Objectives • After this tutorial you should be able to… • Discuss the impact of a range of biological phenomena upon phylogenetic inference • Appreciate some challenges and limitations of phylogenetic approach • Interpret published phylogenies (and your own)

3. Phylogenetic interpretation is essential throughout data analysis Phylogenetic Result(s) Formulate hypotheses • Data assessment • - known biology • - additional data (e.g. geography) Decide upon and implement method Investigate unexpected and unresolved aspects further - consider including more data Answered your question? No No Yes Can you validate this? Final phylogeny and analysis Yes

4. Phylogenetic interpretation skill set • Tree-thinking skills • Revise: relatedness, trait evolution, confidence, homology • Knowledge of phylogenetic methods and their limitations • Knowledge of biological processesaffecting sequence evolution • gene duplication, recombination, horizontal gene transfer, population genetic processes, and many more! • Knowledge of the data you wish to interpret Covered in introduction to phylogenies

5. Recap of tree-thinking skills • Relatedness • Trait evolution • Confidence • Homology

6. 1. Relatedness: taxa that share a more recent common ancestor are more closely related most recent common ancestor shared with second cousin most recent common ancestor shared with first cousin

7. 2. Trait evolution • It can be useful to map traits onto phylogenies as a first step in inferringtheir evolutionary histories • Interpreting trait evolution in its phylogenetic context is rarely straightforward! • Assumptions must be made regarding the loss and gain of traits • It is often useful to construct alternative scenarios • Then we have to decide upon the most plausible (character state methods e.g. MP and ML can be applied)

8. Example: The Evolution of Mitochondria origin of eukaryotes Ginger et al. 2010

9. Example: The Evolution of Mitochondria G = gain L = loss G G G G G G G G G G G G origin of eukaryotes Ginger et al. 2010 Scenario one: Mitochondria evolved from mitosomes

10. Example: The Evolution of Mitochondria G = gain L = loss G L G L G L G L origin of eukaryotes Ginger et al. 2010 Scenario two: Mitochondria occurred at the origin of eukaryotes

11. 3. Tree Confidence Question Does this tree support the grouping of pelecaniforms and ciconiiforms as a monophyletic group?

12. 4. Homology is similarity due to shared ancestry Example: limbs and wings • Limbs are homologous they share a common ancestor • Wings are not homologous they are an analogous as they have evolved similarity independently

13. Homology Question: Trap-jaws in ants Based on this phylogeny, which scenario do you think is more likely? • trap-jaws are homologous • trap-jaws are analogous and have evolved independently four times Moreau et al. 2006

14. Homology Question: Trap-jaws in ants Based on this phylogeny, which scenario do you think is more likely? • trap-jaws are homologous • trap-jaws are analogous and have evolved independently four times L L L L G L L L Moreau et al. 2006 Scenario one: Trap-jaws are homologous

15. Homology Question: Trap-jaws in ants G Based on this phylogeny, which scenario do you think is more likely? • trap-jaws are homologous • trap-jaws are analogous and have evolved independently four times G G G more parsimonious Moreau et al. 2006 Scenario two: Trap-jaws are analogous

16. Phylogenetic interpretation skill set • Tree-thinking skills • Revise: relatedness, trait evolution, confidence, homology • Knowledge of phylogenetic methods and their limitations • Knowledge of biological processesaffecting sequence evolution • gene duplication, recombination, horizontal gene transfer, population genetic processes, and many more! • Knowledge of the data you wish to interpret Covered in introduction to phylogenies

17. Processes that affect sequence evolution • Gene/genome duplication and divergence • Recombination • Horizontal gene transfer • Coevolution • Migration • Rate and time of divergence • Other

18. 1. Gene duplication Gene duplication and subsequent divergence can result in novel gene functions (it can also result in pseudogenes) • Genes that are homologous due to gene duplication are paralogous • Genes that are homologous due to speciation are orthologous

19. Gene duplication question This is a tree of gene family that has undergone one gene duplication event in its evolutionary past. Where on the tree did this occur? Is the event well-supported? Cells Tissues & Organs 2007

20. 2. Recombination • Single or small numbers of events: • Within genes • Between genes • Where there is extensive recombination - a phylogenetic approach is inappropriate (not tree-like)

21. Recombination example: Dengue-2 virus data from E. Holmes, figure from A. Rambaut

22. Recombination Question Can you spot the recombinant strain? Mauro et al 2003

23. 3. Horizontal Gene Transfer (HGT/LGT) Horizontal gene transfer violates the assumption that sequences have evolved in a tree-like manner • Where sparse, can be detected by comparing with species phylogeny • Where extensive, phylogenetic approach is inappropriate Gogarten & Townsend 2005

24. Phylogenetics is not appropriate for highly recombinant taxa • Recombination and horizontal gene transfer produce networks • Avoid phylogenetics for: • Intraspecific sexual species (recombination at each meiosis) • Asexual species with extensive HGT (e.g. some Bacteria) • Phylogenetics assumes that patterns of relatedness among taxa follow a tree-like structure

25. Horizontal gene transfer question Can you spot the horizontally transferred gene?

26. 4. Coevolution Where parasites or symbiontsco-evolve with their hosts, both topologies are expected to be very similar. Weiss 2009 from Reed et al 2007

27. Coevolution Question Do these phylogenies provide evidence that the lice are inherited vertically? Hafner & Nadler 1988

28. 6. Migration Patterns of migration influence phylogenetic topology, especially in structured populations

29. Phylogeography example: Chimpanzees P. troglodytes and P.schweinfurthii are more dissimilar than you would expect given their proximity > Chimpanzees can't cross rivers! Gaoet al 1999

30. Migration Question What can you infer about patterns of migration of the Taiwanese stag-beetle based upon this phylogeny? Black = Taiwan

31. 5. Rate and time of divergence • Phylogenies can be used to date divergence times when some temporal information is known • e.g. carbon dating from fossil evidence • e.g. dates of sample isolation • Genetic change = Evolutionary rate x Divergence time (substitutions/site) (substitutions/site/year) (years) • If all lineages evolve at the same rate (i.e. there is a molecular clock) then branch lengths should reflect divergences times A B C E D

32. Is there a molecular clock? • Zuckerlandand Pauling (1962) • No. substitutions in haemoglobin roughly proportional to time based upon fossil datings

33. Dating divergence with a molecular clock We know time Tsince a and c diverged We want to find out time Xsince a and b diverged • Use T to estimate the evolutionary rate r r = d(a-c) / 2T • Use r to estimate time X X= 1/2 (d(a-b) / r) d = genetic distance (branch length) X

34. Dating Drosophila Divergence around Hawaii • The volcanic activity around Hawaii has produced a chain of islands; the oldest is furthest away from the mainland • Several species including Drosophila have diverged with island formation Figure Andrew Rambaut from Fleischer, McIntosh &Tarr 1998

35. Dating Drosophila Divergence in Hawaii • Island formation dates reflecting species’ divergence were plotted against genetic distance (branch length) • Genetic distance scaled linearly with divergences date, indicating the presence of a molecular clock • Genetic distance • gradient = evolutionary rate • NB: Not all species exhibit a molecular clock! • Time Fleischer, McIntosh &Tarr 1998

36. 7. Other biological processes can complicate molecular analyses • Population genetic processes • Epidemiological processes • Gene conversion • Codon bias • Hypermutablesites • Concerted evolution • Reassortment • Many more…

37. Summary: Phylogenetic interpretation skill set • Tree-thinking skills • Revise: relatedness, trait evolution, confidence, homology • Knowledge of phylogenetic methods and their limitations • Knowledge of biological processesaffecting sequence evolution • gene duplication, recombination, horizontal gene transfer, population genetic processes, and many more! • Knowledge of the data you wish to interpret Covered in introduction to phylogenies

38. Further Reading • Molecular Evolution: A Phylogenetic Approach (1998) Roderic D M Page & Edward C Holmes, Blackwell Science, Oxford. • The Phylogenetic Handbook (2003), Marco Salemi and Anne-MiekeVandammeEds, Cambridge University Press, Cambridge. • Inferring Phylogenies (2003) Joseph Felsenstein, Sinauer. • Molecular Evolution (1997) Wen-Hsiung Li , Sinauer

39. Train online • Free online courses • Learn in your own time, at your own pace • Created for life-science researchers • No previous knowledge of bioinformatics needed www.ebi.ac.uk/training/online

40. Acknowledgements People • Andrew Rambaut(University of Edinburgh) …and the EBI training team • Paul Sharp (University of Edinburgh) • Nick Goldman (EMBL-EBI) • Benjamin Redelings (Duke University) • Brian Moore (University of California, Davis) • Olivier Gascuel (University of Montpelier) • Aiden Budd (EMBL-EBI) FundingEMBL member states and…

41. Thank you! www.ebi.ac.uk Twitter: @emblebi Facebook: EMBLEBI

42. Now it's your turn… • Open your tutorial manual and begin Tree-thinking quiz 2 (appendix 2) • The manual is available to download from: http://www.ebi.ac.uk/training/course/scuola-di-bioinformatica-2013 • When you are finished you can mark your own. • Remember to ask for help at any stage!