the fate of y chromosomes heath blackmon
DESCRIPTION
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 PresentationTRANSCRIPT
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The fate of Y chromosomesHeath Blackmon
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X Y
Sexually Antagonistic Allele
Dominant Male Determining Allele
Inversion
X Y
Inversion
X Y X YAutosomes
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Muller’s Ratchet
BackgroundSelection
GeneticHitchhiking
Hill-RobertsonEffect
Gene Gains
IntrachromosomalGene Conversion
IntermittentRecombination
Gene Duplication
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• 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.
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Coleoptera
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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
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4,118 Taxa with Sex Chromosome Data
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4,118 Taxa with Sex Chromosome Data
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Sequence AlignmentDownloaded 2763 seq 7 genes 1136 taxa (2 mit. 5 nuc.)
Final data set 1040 taxa
Adephaga
Polyphaga
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Polyphaga 744species
Adephaga 296 species
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Distribution of Sex Chromosome Systems among Suborders of Coleoptera
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2 State
Coding Methods
3 State
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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 -
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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
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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
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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
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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
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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
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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
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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
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● 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
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XO XY Xy+XO - .018 .016XY .011 - .062Xy+ .004 .018 -
XO XYXO - .053XY .053 -
■ Polyphaga
■ Adephaga
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X
X YX Y
Polyphaga Adephaga
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X
X YX Y
0.3% 5.3%
Polyphaga Adephaga
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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.
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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
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Emlen et al. 2006
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http://www.zin.ru
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Acknowledgements• Jeffery Demuth• Esther Betran• Paul Chippendale• Trey Fondon• Matthew Fujita
• Jeremy Brown
• Matt Mosley• David Sanchez• Matt Steffenson• Jacobo Velasco• Eric Watson