the fate of y chromosomes heath blackmon

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