Dr Laura Emery LauraEmeryebiacuk wwwebiacuk Objectives After this tutorial you should be able to Discuss the impact of a range of biological phenomena upon phylogenetic inference ID: 920046
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Slide1
Phylogenetic Interpretation
Dr Laura Emery
Laura.Emery@ebi.ac.uk
www.ebi.ac.uk
Slide2Objectives
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)
Slide3Phylogenetic interpretation
is essential throughout data analysis
Data assessment
- known biology
-
additional data (e.g. geography)
Decide upon and implement
method
Phylogenetic Result(s)
Formulate hypotheses
Answered your question?
Investigate unexpected and unresolved aspects further- consider including more data
Final phylogeny and analysis
Can you validate this?
Yes
No
No
Yes
Slide4Phylogenetic
interpretation skill setTree-thinking skills
Revise: relatedness,
trait
evolution, confidence, homology
Knowledge
of phylogenetic methods and their limitations Knowledge of biological processes affecting sequence evolutiongene duplication, recombination, horizontal gene transfer, population genetic processes, and many more!
Knowledge of the data you wish to interpretCovered in introduction to phylogenies
Slide5Recap of tree-thinking skills
Relatedness
Trait evolution
Confidence
Homology
Slide61. Relatedness
: taxa that share a more recent common ancestor are more closely related
most
recent common ancestor shared with
first
cousin
most
recent common ancestor shared with
second
cousin
Slide72. Trait
evolutionIt 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 traitsIt is often useful to construct alternative scenariosThen we have to decide upon the most plausible (character state methods e.g. MP and ML can be applied)
Slide8Example:
The Evolution of Mitochondria
o
rigin
of eukaryotes
Ginger
et al
. 2010
Slide9Example: The Evolution of Mitochondria
o
rigin
of eukaryotes
Ginger
et al
. 2010
G = gain
L = loss
Scenario
one:
Mitochondria evolved from
mitosomes
G
G
G
G
G
G
G
G
G
G
G
G
Slide10Example: The Evolution of Mitochondria
o
rigin
of eukaryotes
Ginger
et al
. 2010
G
G = gain
L = loss
Scenario
two:
Mitochondria occurred at the origin of eukaryotes
L
G
L
G
G
L
L
Slide113. Tree
Confidence Question
Does this tree support the grouping of
pelecaniforms
and
ciconiiforms
as a monophyletic group?
Slide124. Homology
is similarity due to shared ancestry
Example
: limbs and
wings
Limbs
are
homologous they share a common ancestorWings are not homologous they are an analogous as they have evolved similarity independently
Slide13Homology Q
uestion: 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 timesMoreau
et al. 2006
Slide14Homology Q
uestion: 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 timesMoreau
et al. 2006
G
L
LL
L
L
L
L
Scenario one: Trap-jaws are homologous
Slide15Homology Q
uestion: 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 timesMoreau
et al. 2006
Scenario
two:
Trap-jaws are analogous
G
G
G
G
more
parsimonious
Slide16Phylogenetic
interpretation skill setTree-thinking skills
Revise: relatedness,
trait
evolution, confidence, homology
Knowledge
of phylogenetic methods and their limitations Knowledge of biological processes affecting sequence evolutiongene duplication, recombination, horizontal gene transfer, population genetic processes, and many more!
Knowledge of the data you wish to interpretCovered in introduction to phylogenies
Slide17Processes that affect sequence evolution
Gene/genome
duplication and divergence
Recombination
Horizontal gene
transfer
CoevolutionMigrationRate and time of divergence Other
Slide181. 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
Slide19Gene
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
Slide202. Recombination
Single or small numbers of events:Within genesBetween genes
Where there is extensive recombination - a
phylogenetic approach is
inappropriate (not tree-like)
Slide21Recombination example: Dengue-2 virus
d
ata from E. Holmes, figure from A.
Rambaut
Slide22Recombination Question
Can you spot the recombinant strain?
Mauro
et al
2003
Slide233. Horizontal
Gene
Transfer (HGT/LGT)
H
orizontal 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
Slide24Phylogenetics
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
Slide25Horizontal gene transfer question
Can you spot the horizontally transferred gene?
Slide264. Coevolution
Where parasites or symbionts
co-evolve with their hosts, both
topologies are expected to be very similar.
Weiss 2009 from Reed et al 2007
Slide27Coevolution
QuestionDo these phylogenies provide evidence that the lice are inherited vertically?
Hafner
& Nadler 1988
Slide286. Migration
Patterns of migration influence phylogenetic topology,
especially in structured populations
Slide29Phylogeography
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
Slide30Migration
Question
What can you infer about patterns of migration
of the Taiwanese stag-beetle based
upon this phylogeny
?
Black
= Taiwan
Slide315.
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 evidencee.g. dates of sample isolationGenetic 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
DEA
B
Slide32Is there
a molecular clock?
Zuckerland
and Pauling (1962)
No.
substitutions in haemoglobin roughly proportional to time based upon fossil datings
Slide33Dating divergence with a molecular clock
We know time
T
since a and c diverged
We want to find out time
X since a and b divergedUse T to estimate the evolutionary rate r
r = d(a-c) / 2TUse r to estimate time X X = 1/2
(d(a-b) / r)
X
d =
genetic distance
(
branch length
)
Slide34Dating Drosophila Divergence around Hawaii
Fleischer, McIntosh &
Tarr
1998
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
Slide35Dating 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
Time
Fleischer, McIntosh &
Tarr
1998
gradient = evolutionary rate
NB
: Not all species exhibit a molecular clock!
Slide367. Other
biological processes can complicate molecular analyses
Population genetic processes
Epidemiological
processes
Gene
conversionCodon biasHypermutable sitesConcerted evolutionReassortmentMany more…
Slide37Summary: 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 evolutiongene duplication, recombination, horizontal gene transfer, population genetic processes, and many more!
Knowledge of the data you wish to interpretCovered in introduction to phylogenies
Slide38Further 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
Slide39Train 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
Slide40Acknowledgements
People
Andrew
Rambaut
(University of Edinburgh
) …and the EBI training teamPaul 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…
Slide41Thank you!
www.ebi.ac.ukTwitter: @emblebi
Facebook:
EMBLEBI
Slide42Now 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!