1. Phylogenetic Interpretation
Dr Laura Emery

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)
We don't have enough time to go into any of these methods in great depth, and if you want to fully understand how they work, then you will need to go away and do some extra reading. But the point of this tutorial is to make you aware of some of the most commonly available methods, their assumptions and limitations. And also to direct you to information that you can read up on if you want further help

3. Phylogenetic interpretation is essential throughout data analysis
Data assessment
- known biology
- additional data (e.g. geography)
Formulate hypotheses
Decide upon and implement
method
Phylogenetic Result(s)
Investigate unexpected and unresolved aspects further
- consider including more data
Answered your question? No No
We often get asked: how should I interpret my own data?
Data analysis is more complex then many lab biologists expect
Every stage in this process requires the ability to interpret phylogenies
Caveat: Finished versus unfinished analyses and their interpretation
Most of the examples we will look at today have been fully analysed
When you come to analyse your own data, initially things will not look so straightforward since data analysis is an iterative process. Nevertheless the concept you will learn in this lecture still apply. The chances are that you will be able to reach fewer conclusions when you first come to analyse your own data. Please be patient and persistents
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 processes affecting 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
1. We will be introducing a few more tree thinking skills but we dealt with these in the first session with this morning
2. It is important to know that phylogenetic methods to the extent that you know what assumptions they are making and their limitations, and you know how to interpret relevant statistical information
3. Knowledge of biology-that's it will cover in this session. Will do this by examining case studies based upon real data, so you can see what kind of trees and patterns of evolution produced from these processes
4. Knowledge of the data you are attempting to interpret

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
You are more closely related to your first cousin than you are to your second cousin because the most recent common ancestor that you share with your first cousin i.e. your grandmother was born more recently than the most recent common ancestor that you share with your second cousin (i.e. your great-grandmother)

7. 2. Trait evolution
It can be useful to map traits onto phylogenies as a first step in inferring their 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
Convergent evolution (analogy rather than homology). Trap-jaws are believed to have evolved independently at least 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
Convergent evolution (analogy rather than homology). Trap-jaws are believed to have evolved independently at least four times G L L L
Moreau et al. 2006
Scenario one: Trap-jaws are homologous

15. 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 G G
Trap-jaws or an evolutionary adaptation that allow ants to shut their jaws at 145mph to attack prey and escape predation, as it propels them into the air!
Convergent evolution (analogy rather than homology). Trap-jaws are believed to have evolved independently at least four times 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 processes affecting 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
1. We will be introducing a few more tree thinking skills but we dealt with these in the first session with this morning
2. It is important to know that phylogenetic methods to the extent that you know what assumptions they are making and their limitations, and you know how to interpret relevant statistical information
3. Knowledge of biology-that's it will cover in this session. Will do this by examining case studies based upon real data, so you can see what kind of trees and patterns of evolution produced from these processes
4. Knowledge of the data you are attempting to interpret

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?
SPARC and SPARCL1
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)
Cut and pasting of gene/genome segments

21. Recombination example: Dengue-2 virus
Strain highlighted in red box is a recombinant
Others highlighted are two strains from the same mosquito
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
Phylogenetics assumes that patterns of relatedness among taxa follow a tree- like structure
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)

25. Horizontal gene transfer question
Can you spot the horizontally transferred gene?
Bombyx is a silk moth

26. 4. Coevolution
Where parasites or symbionts co-evolve with their hosts, both topologies are expected to be very similar.
The parasites are inherited vertically
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!
Gao et al 1999

30. Migration Question
What can you infer about patterns of migration of the Taiwanese stag- beetle based upon this phylogeny? Black = Taiwan
Assuming even sampling, it looks as the beetle originated in China and has radiated outwards

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 C D E A B

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

33. Dating divergence with a molecular clockX
d = genetic distance (branch length)
We know time T since a and c diverged
We want to find out time X since 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)

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
Hypermutable sites
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 processes affecting 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
1. We will be introducing a few more tree thinking skills but we dealt with these in the first session with this morning
2. It is important to know that phylogenetic methods to the extent that you know what assumptions they are making and their limitations, and you know how to interpret relevant statistical information
3. Knowledge of biology-that's it will cover in this session. Will do this by examining case studies based upon real data, so you can see what kind of trees and patterns of evolution produced from these processes
4. Knowledge of the data you are attempting to interpret

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-Mieke Vandamme Eds, Cambridge University Press, Cambridge.
Inferring Phylogenies (2003) Joseph Felsenstein, Sinauer.
Molecular Evolution (1997) Wen-Hsiung Li , Sinauer

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

40. Acknowledgements People Funding EMBL member states and…
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)
Funding EMBL member states and…

41. Thank you!
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:
2013
When you are finished you can mark your own.
Remember to ask for help at any stage!