Presentation for the Dark Side of Comparative Methods symposium at Evolution 2014.

1. Modeling Character Evolution with
Phylogenetic Uncertainty
April M. Wright
Matthew C. Brandley
Kathleen Lyons
David M. Hillis

2. Is it possible to re-evolve the egg?
● Viviparity has evolved many times from
oviparity
John Gould via WikiMedia Commons David Hillis

3. Is it possible to re-evolve the egg?
● Viviparity has evolved many times from
oviparity
Does the reverse ever occur?

4. Oviparity as a Dollo Trait
Complex characters, once lost, are unlikely to re-
evolve

5. Oviparity as a Dollo Trait
● Lost once in mammals
● Never re-evolved

6. Warren et al, Nature

7. 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?

8. Oviparity
Various forms
of viviparity
&
Dulvy and Reynolds

9. 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?

10. Oviparity as a Dollo Trait
● Has been proposed as a Dollo trait
○ Previous phylogenetic analyses have placed
oviparous taxa within clades of viviparous taxa

11. 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

12. 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

13. Should reversal surprise us?
● Several types of viviparity represented in
reptiles

14. Should reversal surprise us?
● Several types of viviparity represented in
reptiles
Mark Stevens via Wikimedia Commons
Toby Hudson via Wikimedia Commons

15. Should reversal surprise us?
● Several types of viviparity represented in
reptiles
Dutta and Medhi Dr. Anne Fawcett

16. A great test dataset
● Pyron and Burbrink assembled a 8000-taxon
dataset on parity mode for extant squamates

17. 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

18. 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

19. 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

20. Oviparity
Oviparity and
viviparity
Viviparity

21. 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

22. A tour of the data set

23. A tour of the data set
Snakes
Iguanids
Anguimorphs
Lacertids
Skinks
Geckos
● ~Half of
oviparous
species
represented
● ~60% of
viviparous
● 85% percent of
overall extant
Squamates

24. How much does uncertainty in the
tree affect ancestral state
reconstruction?

25. Our approach
● Estimate ancestral states across a bootstrap
sample of trees
○ Estimate trees in Examl
○ Time-scale trees using treePL

26. 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

27. 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

28. Bootstrap sample
● Trees generally very similar in the major
groups

29. Snakes
Iguanids
Anguimorphs
Lacertids
Skinks
Geckos

30. Bootstrap sample
● Trees generally very similar in the major
groups
● Most variation among tips

31. Fitting a model
● Full BiSSe model
○ Two speciation parameters
○ Two extinction parameters
○ Two transition rates

32. Fitting a model
● Full BiSSe model
○ Two speciation parameters
○ Two extinction parameters
○ Two transition rates
One of each
parameter for
each oviparity
and viviparity

33. Fitting a model

34. Two speciation parameters
Speciation Rates
Frequency
Speciation
rate -
viviparous
taxa
Speciation
rate -
oviparous
taxa
MLE estimate
of parameter

35. Two extinction parametersFrequency
Extinction Rates
Extinction
rate -
oviparous
taxa
Extinction
rate -
viviparous
taxa

36. Two transition parametersFrequency
Transition Rates
Viviparity to
oviparity
transition
rate
Oviparity
to
viviparity
transition
rate

37. Two transition parametersFrequency
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

38. Support for viviparity as root state
7%
Support for oviparity as root state 93%

39. Strong support for oviparity as the
root state of squamates
Oviparity
Viviparity
Support Values

40. Support for oviparity as root is
strong

41. 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

42. Thank you!
● David Swofford
● Dan Warren
● Rich FitzJohn and Matt Pennell
● Alex Pyron and Frank Burbrink
WrightAprilM