Partitioning Presentation
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Transcript of Partitioning Presentation
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How to Build A TreeEdie Espejo
4 March 2016, ENT198
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How to Build A TreeEdie Espejo
@ The Moore Lab
Better
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Presentation Overview• Keywords
• A Closer Look at Nodes
• Motivation
• Central Question
• Methods
• Expectations
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Keywords to Begin With
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Phylogenetics Chronogram Speciation Event
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The study of the evolutionary relationships of organisms (while a phylogeny is an estimate of evolutionary relationships)
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Phylogenetics
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A time tree; the branch lengths of these trees are proportional to time
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Chronogram
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When one species becomes two; nodes represent speciation events in phylogenies
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Speciation Event
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When one species becomes two; nodes represent speciation events in phylogenies
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Speciation Event
A will represent a node in the following slides.
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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
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Nodes Closer to PresentThis implies that speciation happens at a constant exponential rate
ln(N
umbe
r of S
peci
es)
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Nodes Closer to RootThis implies an early burst of speciation
D. persimilis
D. pseudoobscuraD. ananassae
Melanogaster Subgroup
Root
Origin of Group Present Day
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Nodes Closer to RootThis implies an early burst of speciation
ln(N
umbe
r of S
peci
es)
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If the nodes are closer to the root in time trees, then there must have been an early burst of speciation.
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If the nodes are closer to the root in time trees, then there must have been an early burst of speciation.
False
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" . . . the use of very poor partitioning schemes can occasionally lead to strongly supported but
incorrect inferences from phylogenetic analyses."
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The Effects of Partitioning on Phylogenetic Inference
David Kainer, Robert Lanfear, from "Conclusion":
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In other words:
Partitioning phylogenies incorrectly can lead to biased trees
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The Effects of Partitioning on Phylogenetic Inference
David Kainer, Robert Lanfear, from "Conclusion":
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PartitioningPartitioning is the process of directing different portions of an alignment to different substitution
models
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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
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An Alignment of Sequence Data
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Partitioning It One Way
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Gene 1 Gene 2
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The Same Alignment
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Partitioning It Another Way
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Partition 1 Partition 2 Partition 3
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Partition 1 Partition 2 Partition 3
So which partitioning scheme will yield the better tree?
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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
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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
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By Gene BIC AIC Everything ApartAll together
Partitioning Schemes
Bayesian Information
Criterion
Akaike Information
Criterion
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Get sequence data Align the sequence data
By Gene BIC AIC
Create chronograms
Everything ApartAll together
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Create chronograms
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Use Marginal Likelihood to rank the fit of partitioning schemes to the sequence data from best to worst
Draw Conclusions
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Based on previous studies:Suboptimal partitioning will lead to
biased time trees
Expectations
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Based on previous studies:If we partition too little, we will infer trees that support an early burst of speciation
Expectations
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The notion of an early burst of speciation may not be properly supported.
Expectations
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The Moore Lab and RSPIB
Acknowledgements
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