The fate of Y chromosomes Heath Blackmon

1. The fate of Y chromosomes • Heath Blackmon

2. Sexually Antagonistic Allele Inversion Dominant Male Determining Allele Inversion Autosomes X Y X Y X Y X Y

3. Intermittent Recombination Gene Gains Muller’s Ratchet Background Selection Gene Duplication Genetic Hitchhiking Intrachromosomal Gene Conversion Hill-Robertson Effect

4. Recent Work • Largely comparative genomics using groups of sequenced Y chromosomes or autosomes that have become sex determining in some lineages. • My Approach • Sacrifice the genomic detail but expand the number of species. Use a comparative phylogenetic approach with karyotypes.

5. Coleoptera

6. Coleoptera karyotype database • 1978 Compilation ~2,000 records • New data from ~200 publications 6+ languages • 4,726 records • 1,302 genera • 56 families • 2-34 Autosomes • 30 Sex Chromosome Systems • B Chromosomes • Haplodiploidy and Parthenogenesis

7. 4,118 Taxa with Sex Chromosome Data

8. 4,118 Taxa with Sex Chromosome Data

9. Sequence Alignment Downloaded 2763 seq 7 genes 1136 taxa (2 mit. 5 nuc.) Final data set 1040 taxa Adephaga Polyphaga

10. Polyphaga 744species Adephaga 296 species

11. Distribution of Sex Chromosome Systems among Suborders of Coleoptera

12. Coding Methods 2 State 3 State

13. Two State Character Coding • Model 2.1 Model 2.2 Three State Character Coding Model 3.1 Model 3.3 Model 3.6

14. Bayes Factors: Model Selection Log Bayes Factor = log pr(D|ѲAlt) – log pr(D| ѲNull) Support for the more complex model 0-2 Barely worth mentioning 2-6 Substantial 6-10 Strong > 10 Decisive

15. Model 2.1 and 2.2 in Adephaga 2 State Coding Harmonic Mean of the Likelihood 1-Rate 2-Rates Bayes Factor 1.9

16. Model 2.1 and 2.2 in Polyphaga 2 State Coding Harmonic Mean of the Likelihood 2-Rates 1-Rate Bayes Factor 11.8

17. Model 3.1, 3.3, and 3.6 in Polyphaga 3 State Coding Harmonic Mean of the Likelihood Bayes Factor 17.54 6-Rates 1-Rate 3-Rates

18. Model Choice

19. Model Adequacy: Posterior Predictive SimulationsCould our model and phylogeny have given rise to the observed data? 1 2 3 4 5 6 θ1 θ2 θ3 θ4 θ5 θ6

20. Interpretation of PPS results Good Model Poor Model Observed Data Observed Data

24. Posterior predictive distribution of sex chromosome systems states in Polyphaga ● Realized Data 1500 Simulated Data Sets ● X0 Root (120) ● XY Root (840) ● Xy+ Root (540) 100% Xy+ 100% XO 100% XY

25. ■Polyphaga ■Adephaga

26. Polyphaga Adephaga X Y X Y X

27. Polyphaga Adephaga X Y 5.3% 0.3% X Y X

29. How can we explain this result? • Existing “genic” models of Y chromosome decay predict that the completely non-recombining Y should be lost more frequently. • Adephaga: Antagonistic selection • Selection to reduce recombination • Selection for faithful segregation • Polyphaga: Antagonism is resolved • The rate of Y chromosome loss is driven simply by the benefit of keeping the Y.

30. Sexual selection, which implies the possession of considerable perceptive powers and of strong passions, seems to have been more effective with the Lamelicorns than any other family of the Coleoptera… -Darwin 1871 The Descent of Man. Vol. 1 pg. 377

31. Emlen et al. 2006

32. http://www.zin.ru

33. Acknowledgements • Jeffery Demuth • Esther Betran • Paul Chippendale • Trey Fondon • Matthew Fujita • Jeremy Brown • Matt Mosley • David Sanchez • Matt Steffenson • Jacobo Velasco • Eric Watson