Date post: | 23-Aug-2014 |
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Modeling Character Evolution with Phylogenetic Uncertainty
April M. WrightMatthew C. Brandley
Kathleen LyonsDavid M. Hillis
Is it possible to re-evolve the egg?
● Viviparity has evolved many times from oviparity
John Gould via WikiMedia Commons David Hillis
Is it possible to re-evolve the egg?
● Viviparity has evolved many times from oviparity
Does the reverse ever occur?
Oviparity as a Dollo Trait
Complex characters, once lost, are unlikely to re-evolve
Oviparity as a Dollo Trait
● Lost once in mammals● Never re-evolved
Warren et al, Nature
Oviparity as a Dollo Trait
● Lost once in mammals○ Never re-evolved
● Transition to viviparity observed almost 30 times in fish○ Evidence of re-evolution of oviparity?
Oviparity
Various forms of viviparity&
Dulvy and Reynolds
Oviparity as a Dollo Trait
● Lost once in mammals○ Never re-evolved
● Transition to viviparity observed almost 30 times in fish○ Evidence of re-evolution of oviparity?
● Transition to viviparity observed over 100 times in squamates○ Has oviparity re-evolved?
Oviparity as a Dollo Trait
● Has been proposed as a Dollo trait○ Previous phylogenetic analyses have placed
oviparous taxa within clades of viviparous taxa
Oviparity as a Dollo Trait● Has been proposed as a Dollo trait
○ Previous phylogenetic analyses have placed oviparous taxa within clades of viviparous taxa
○ Suggests possibility of reversals
Kris Kendall San Diego Zoo
Oviparity as a Dollo Trait
● Previous phylogenetic analyses have placed oviparous taxa within clades of viviparous taxa
● Comparative work by Fenwick et al. and Lynch and Wagner have supported reversibility in this trait
Should reversal surprise us?
● Several types of viviparity represented in reptiles
Should reversal surprise us?● Several types of viviparity represented in
reptiles
Mark Stevens via Wikimedia CommonsToby Hudson via Wikimedia Commons
Should reversal surprise us?● Several types of viviparity represented in
reptiles
Dutta and Medhi Dr. Anne Fawcett
A great test dataset
● Pyron and Burbrink assembled a 8000-taxon dataset on parity mode for extant squamates
A great test dataset
● Pyron and Burbrink assembled a 8000-taxon dataset on parity mode for extant squamates
● Coupled with a 4200-taxon tree○ 3950 taxa overlap
A great test dataset
● Their analysis:○ Fit a probabilistic model of character change to
these data○ Estimated ancestral states○ Concluded that the root state of the squamate tree
was viviparous, with strong statistical support
An ‘open’ question
● A maximum likelihood tree is a point estimate
● The root state of squamates had previously been thought to be oviparous, based on tetrapod phylogeny
Oviparity
Oviparity and viviparity
Viviparity
An ‘open’ question
● A maximum likelihood tree is a point estimate
● The root state of squamates had previously been thought to be oviparous, based on tetrapod phylogeny
● And a lovely, open dataset
A tour of the data set
A tour of the data set
Snakes
Iguanids
Anguimorphs
LacertidsSkinks
Geckos
● ~Half of oviparous species represented
● ~60% of viviparous
● 85% percent of overall extant Squamates
How much does uncertainty in the tree affect ancestral state
reconstruction?
Our approach
● Estimate ancestral states across a bootstrap sample of trees○ Estimate trees in Examl○ Time-scale trees using treePL
Our approach
● Estimate ancestral states across a bootstrap sample of trees○ Estimate trees in Examl○ Time-scale trees using treePL
● Fit a probabilistic model of character evolution to each tree in sample
Our approach
● Estimate ancestral states across a bootstrap sample of trees○ Estimate trees in Examl○ Time-scale trees using treePL
● Fit a probabilistic model of character evolution to each tree in sample
● Visualize the uncertainty in model parameters and ancestral states
Bootstrap sample
● Trees generally very similar in the major groups
Snakes
Iguanids
Anguimorphs
LacertidsSkinks
Geckos
Bootstrap sample
● Trees generally very similar in the major groups
● Most variation among tips
Fitting a model● Full BiSSe model
○ Two speciation parameters
○ Two extinction parameters
○ Two transition rates
Fitting a model● Full BiSSe model
○ Two speciation parameters
○ Two extinction parameters
○ Two transition rates
One of each parameter for each oviparity and viviparity
Fitting a model
Two speciation parameters
Speciation Rates
Freq
uenc
y
Speciation rate - viviparous taxa
Speciation rate - oviparous taxa
MLE estimate of parameter
Two extinction parametersFr
eque
ncy
Extinction Rates
Extinction rate - oviparous taxa
Extinction rate - viviparous taxa
Two transition parametersFr
eque
ncy
Transition Rates
Viviparity to oviparity transition rate
Oviparity to viviparity transition rate
Two transition parametersFr
eque
ncy
Transition Rates
Viviparity to oviparity transition rate
Oviparity to viviparity transition rate
1-2 reversals to oviparity
7-13 transitions to viviparity
23 transitions to viviparity
Support for viviparity as root state 7%
Support for oviparity as root state 93%
Strong support for oviparity as the root state of squamates
Oviparity
Viviparity
Support Values
Support for oviparity as root is strong
Conclusions
● Strongest support for ancestral oviparity● Viviparity associated with higher speciation● Much higher transition rate from oviparity to
viviparity than the reverse○ But, one or two reversals to oviparity are supported
with this method● Looking at a point estimate of topology can
be misleading
Thank you!● David Swofford● Dan Warren● Rich FitzJohn and Matt Pennell● Alex Pyron and Frank Burbrink
WrightAprilM