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

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Keywords to Begin With

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Phylogenetics Chronogram Speciation Event

The study of the evolutionary relationships of organisms (while a phylogeny is an estimate of evolutionary relationships)

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Phylogenetics

A time tree; the branch lengths of these trees are proportional to time

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Chronogram

When one species becomes two; nodes represent speciation events in phylogenies

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Speciation Event

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.

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.

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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":

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":

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

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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

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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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