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How to Build A TreeEdie Espejo
4 March 2016, ENT198
How to Build A TreeEdie Espejo
@ The Moore Lab
Better
Presentation Overview• Keywords
• A Closer Look at Nodes
• Motivation
• Central Question
• Methods
• Expectations
3
Keywords to Begin With
4
Phylogenetics Chronogram Speciation Event
The study of the evolutionary relationships of organisms (while a phylogeny is an estimate of evolutionary relationships)
5
Phylogenetics
A time tree; the branch lengths of these trees are proportional to time
6
Chronogram
When one species becomes two; nodes represent speciation events in phylogenies
7
Speciation Event
When one species becomes two; nodes represent speciation events in phylogenies
8
Speciation Event
A will represent a node in the following slides.
Nodes Closer to PresentThis implies that speciation happens at a constant exponential rate
D. simulans
D. sechellia
D. melanogaster
D. yakuba
D. ananassae
Obscura group
Present
Origin of Group Present Day
Nodes Closer to PresentThis implies that speciation happens at a constant exponential rate
ln(N
umbe
r of S
peci
es)
Nodes Closer to RootThis implies an early burst of speciation
D. persimilis
D. pseudoobscuraD. ananassae
Melanogaster Subgroup
Root
Origin of Group Present Day
Nodes Closer to RootThis implies an early burst of speciation
ln(N
umbe
r of S
peci
es)
If the nodes are closer to the root in time trees, then there must have been an early burst of speciation.
13
If the nodes are closer to the root in time trees, then there must have been an early burst of speciation.
False
14
" . . . the use of very poor partitioning schemes can occasionally lead to strongly supported but
incorrect inferences from phylogenetic analyses."
15
The Effects of Partitioning on Phylogenetic Inference
David Kainer, Robert Lanfear, from "Conclusion":
In other words:
Partitioning phylogenies incorrectly can lead to biased trees
16
The Effects of Partitioning on Phylogenetic Inference
David Kainer, Robert Lanfear, from "Conclusion":
PartitioningPartitioning is the process of directing different portions of an alignment to different substitution
models
PartitioningPartitioning is the process of directing different portions of an alignment to different substitution
models
A substitution model is a mathematical description the process of evolution of DNA
An Alignment of Sequence Data
Partitioning It One Way
Gene 1 Gene 2
The Same Alignment
Partitioning It Another Way
Partition 1 Partition 2 Partition 3
Partition 1 Partition 2 Partition 3
So which partitioning scheme will yield the better tree?
An important result:
Overly simplistic substitution models lead to trees that imply an early burst of speciation
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Underparameterized Model of Sequence Evolution Leads to Bias in the Estimation of Diversification Rates from Molecular Phylogenies
Liam Revell, Luke Harmon, Richard Glor
What is the effect of partitioning schemes on divergence time estimates?
Question
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By Gene BIC AIC Everything ApartAll together
Partitioning Schemes
LEAST VARIATION
Partitioning schemes account for the evolutionary process across a sequence
data alignment
MOST VARIATION
By Gene BIC AIC Everything ApartAll together
Partitioning Schemes
Bayesian Information
Criterion
Akaike Information
Criterion
Get sequence data Align the sequence data
By Gene BIC AIC
Create chronograms
Everything ApartAll together
Create chronograms
31
Use Marginal Likelihood to rank the fit of partitioning schemes to the sequence data from best to worst
Draw Conclusions
Based on previous studies:Suboptimal partitioning will lead to
biased time trees
Expectations
32
Based on previous studies:If we partition too little, we will infer trees that support an early burst of speciation
Expectations
33
The notion of an early burst of speciation may not be properly supported.
Expectations
34
The Moore Lab and RSPIB
Acknowledgements
35