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The fate of Y chromosomes Heath Blackmon. Sexually Antagonistic Allele. Inversion. Dominant M ale Determining A llele. Inversion. Autosomes. X Y. X Y. X Y. X Y. Intermittent Recombination. Gene Gains. Muller’s Ratchet. Background Selection. - PowerPoint PPT Presentation
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The fate of Y chromosomesHeath Blackmon
X Y
Sexually Antagonistic Allele
Dominant Male Determining Allele
Inversion
X Y
Inversion
X Y X YAutosomes
Muller’s Ratchet
BackgroundSelection
GeneticHitchhiking
Hill-RobertsonEffect
Gene Gains
IntrachromosomalGene Conversion
IntermittentRecombination
Gene Duplication
• 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.
Coleoptera
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
4,118 Taxa with Sex Chromosome Data
4,118 Taxa with Sex Chromosome Data
Sequence AlignmentDownloaded 2763 seq 7 genes 1136 taxa (2 mit. 5 nuc.)
Final data set 1040 taxa
Adephaga
Polyphaga
Polyphaga 744species
Adephaga 296 species
Distribution of Sex Chromosome Systems among Suborders of Coleoptera
2 State
Coding Methods
3 State
Two State Character Coding
Model 2.1
Model 2.2
Three State Character Coding
Model 3.1
Model 3.3
Model 3.6
XY Xy+ XOXY - a aXy+ a - aXO a a -
XY Xy+ XOXY - a bXy+ a - cXO b c -
XY Xy+ XOXY - a bXy+ c - dXO e f -
XY XOXY - aXO a -
XY XOXY - aXO b -
Bayes Factors: Model Selection
Log Bayes Factor = log pr(D|ѲAlt) – log pr(D| ѲNull)
Support for the more complex model0-2 Barely worth mentioning2-6 Substantial6-10 Strong> 10 Decisive
XO XY
XO - a
XY b -
XO XY
XO - a
XY a -
Harmonic Mean of the Likelihood
1-Rate 2-Rates
1-Rate 2-Rates
-108-107-106-105-104-103-102-101-100
-99-98
-103.5-102.6
Bayes Factor 1.9
Model 2.1 and 2.2 in Adephaga2 State Coding
1-Rate 2-Rates
-132-131-130-129-128-127-126-125-124-123-122
-131.2
-125.3
XO XY
XO - a
XY a -
XO XY
XO - a
XY b -
Harmonic Mean of the Likelihood1-Rate 2-Rates
Bayes Factor 11.8
Model 2.1 and 2.2 in Polyphaga2 State Coding
Harmonic Mean of the Likelihood
Series1
-420
-410
-400
-390
-380
-370
-360
-408.72
-388.18
-379.41
Bayes Factor 17.54
1-Rate
XO XY XY+
XO - a a
XY a - a
XY+ a a -
3-Rate
XO XY XY+
XO - a b
XY a - c
XY+ b c -
6 Rate
XO XY XY+
XO - a b
XY d - c
XY+ e f -
1-Rate 6-Rates3-Rates
Model 3.1, 3.3, and 3.6 in Polyphaga3 State Coding
Model Choice
Estimated Marginal Likelihood ValuesModel 2.1 2.2 3.1 3.3 3.6
Polyphaga -131.2 -125.3 -408.72 -388.18 -379.41
Adephaga -103.5 -102.6 2 and 3 state coding models are equivalent in Adephaga
Model Adequacy: Posterior Predictive Simulations
Could our model and phylogeny have given rise to the observed data?
θ1
1
θ2
2
θ3
3
θ4
4
θ5
5
θ6
6
Interpretation of PPS results
0 35 70105
140175
210245
2800
40
80
120
160
200
Taxa in State A
Freq
uenc
y
Observed Data
0 30 60 90120
150180
210240
2700
40
80
120
160
200
Taxa in State A
Freq
uenc
y
Observed Data
Good Model Poor Model
● Realized Data1500 Simulated Data Sets ● X0 Root (120) ● XY Root (840) ● Xy+ Root (540)
100% Xy+
100% XO 100% XY
Posterior predictive distribution of sex chromosome systems states in Polyphaga
XO XY Xy+XO - .018 .016XY .011 - .062Xy+ .004 .018 -
XO XYXO - .053XY .053 -
■ Polyphaga
■ Adephaga
X
X YX Y
Polyphaga Adephaga
X
X YX Y
0.3% 5.3%
Polyphaga Adephaga
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.
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
Emlen et al. 2006
http://www.zin.ru
Acknowledgements• Jeffery Demuth• Esther Betran• Paul Chippendale• Trey Fondon• Matthew Fujita
• Jeremy Brown
• Matt Mosley• David Sanchez• Matt Steffenson• Jacobo Velasco• Eric Watson