1. Plant diversification with respect to different sexual systems1
Plant diversification with respect to different sexual systems
Niv Sabath
November 2014
N. Sabath, T. Ashman, E. Goldberg, R. Ming, S.P. Otto, J. Vamosi, M. Einhorn, L. Glick, and I. Mayrose. In prep.

2. Sexual reproduction Old – at least a billion years
Primary method of reproduction in plants and animals
Advantages:
Increased genetic variation -> adaptation
DNA repair
Reduce accumulation of deleterious mutations
Affects speciation – cost of rarity

3. Sexual systems Dioecy Hermaphrodite
male and female organs in same individual
separate male and female

4. Sexual systems Dioecy Hermaphrodite Animals 95% Plants 6%
male and female organs in same individual
separate male and female

5. Sexual systems Dioecy Hermaphrodite Animals 95% Plants 6% Speciation
male and female organs in same individual
separate male and female
Speciation
Extinction
Transition

6. Association between sexual systems and diversification?
Dioecy
Hermaphrodite
Animals
95%
Plants 6%
male and female organs in same individual
separate male and female
Speciation
Extinction
Transition
Association between sexual systems and diversification?
Diversification = Speciation - Extinction

7. Sexual systems in flowering plants
Dioecy
Hermaphrodite

8. Sexual systems in flowering plants
Dioecy
Hermaphrodite
Disruption of self-incompatibility
Dioecy
– common in trees and in the tropics:
- prevent inbreeding depression when SI is broken
When there is an advantage to producing large seeds – enabled by separation of male and female functions.
Where individuals of a species may occur at low density with large distances between them
favored where non-specific pollinators, of the kind that tend to be associated with dioecy, tend to be found.
Miller, J. S., & Venable, D. L. (2000). Polyploidy and the evolution of gender dimorphism in plants. Science

9. Sexual systems in flowering plants
Dioecy
Hermaphrodite

10. Sexual systems in flowering plants
Strict Dioecy
Dioecy
Hermaphrodite

11. Sexual systems in flowering plants
Broad Dioecy
Dioecy
Hermaphrodite

12. Methods Data collection (sequences, sexual systems, plant attributes)
Phylogenetic reconstruction (MAFT, MrBayes)
Diversification analysis – BiSSE
Association with plant attributes (growth form, life cycle, …)

13. Diversification analysis – BiSSE Binary State Speciation and Extinction (Maddison et al. 2007)
Likelihood function 1
speciation0
extinction0
speciation1
extinction1
q10
q01
calculate the probability that a group of extant species would have evolved as observed, given a particular model of the character's effect.
describe the chance that a lineage beginning at time t with state 0 or 1 would evolve into a clade like that observed to have descended from node N, closer to the present 

14. Use MCMC for Bayesian analysis
Diversification analysis – BiSSE Binary State Speciation and Extinction (Maddison et al. 2007)
Use MCMC for Bayesian analysis
calculate the probability that a group of extant species would have evolved as observed, given a particular model of the character's effect.
Use MCMC for Bayesian analysis and obtain the posterior distribution of these parameters

15. PP(r0>r1) = %of MCMC steps in which r0 > r1
Diversification analysis – BiSSE Binary State Speciation and Extinction (Maddison et al. 2007)
Asses significance
To test whether extinction and speciation rates differ among sexual systems, we calculated the percentage of BiSSE MCMC steps in which a given rate (e.g., λ , μ, or r) was higher for non-dioecious lineages than for dioecious lineages (i.e., the posterior probability, PP, of a higher rate in N than in D lineages) for each genus. For example, PP(λN > λD) is the percentage of post burn-in steps in which λN > λD. To assess significance over the whole dataset, we used a one-sample t-test with a mean equal to 50%, testing the null hypothesis that diversification rates in the D state should be higher than those in the N state half of the time, treating the PP value of from each genus as a single data point. 
 Wilcoxon.
PP(r0>r1) = %of MCMC steps in which r0 > r1

16. PP(r0>r1) = %of MCMC steps in which r0 > r1
Diversification analysis – BiSSE Binary State Speciation and Extinction (Maddison et al. 2007)
Asses significance
To test whether extinction and speciation rates differ among sexual systems, we calculated the percentage of BiSSE MCMC steps in which a given rate (e.g., λ , μ, or r) was higher for non-dioecious lineages than for dioecious lineages (i.e., the posterior probability, PP, of a higher rate in N than in D lineages) for each genus. For example, PP(λN > λD) is the percentage of post burn-in steps in which λN > λD. To assess significance over the whole dataset, we used a one-sample t-test with a mean equal to 50%, testing the null hypothesis that diversification rates in the D state should be higher than those in the N state half of the time, treating the PP value of from each genus as a single data point. 
 Wilcoxon.
PP(r0>r1) = %of MCMC steps in which r0 > r1
For one dataset: > PP(r0>r1) > 97.5
For multiple datasets: median(PP(r0>r1)) <> 50

17. Data
57 genera species 38% with state assignment 20% dioecy, 80% others

18. Filter out genera with less than 10 species and 2 in each state
Data
57 genera species 38% with state assignment 20% dioecy, 80% others
Filter out genera with less than 10 species and 2 in each state
38 genera

19. Filter out genera with less than 10 species and 2 in each state
Data
57 genera species 38% with state assignment 20% dioecy, 80% others
Filter out genera with less than 10 species and 2 in each state
38 genera
Filter out genera with PP differ by >20% between runs with different priors
28 genera

20. Results
Bimodal distribution: dioecy is associated with high diversification in some genera and low in others
Diversification

21. Results Diversification is driven by speciation, not extinction

22. Results
No association with plant attributes

23. self-compatibility (SC) vs. self-incompatibility (SI)?

24. self-compatibility (SC) vs. self-incompatibility (SI)?
Bimodal distribution of self-incompatibility (Raduski et al. Evolution, 2011)

25. self-compatibility (SC) vs. self-incompatibility (SI)?
Goldberg et al. (Science 2010) showed that hermaphrodite SC species diversify slower than SI species

26. Weak points Strong effect of sample size – a more conservative filter?
Diversification

27. Weak points
Effect of trait distribution