1. Male-driven evolution
Xuhua Xia

2. Number of replications in the production of sperm and egg in human
Females take ~25 cell replications to produce eggs.
Males: 1 replication of stem cells every 16 days: Add 365/16  22.8 replications per year.
Age
Male
M/F 15 36
1.4 18
104
4.2 21
173
6.9 24
241
9.7 27
310
12.4 30
378
15.1 33
447
17.9
515
20.6 39
584
23.3 42
652
26.1 45
720
28.8 48
789
31.6 51
857
34.3 54
926
37.0 57
994
39.8 60
1063
42.5 63
1131
45.2 66
1199
48.0 69
1268
50.7
 “Thus the mutation rate in the X-chromosome of females is probably less than one-tenth of that in males, …… The primordial oocytes are mostly if not all formed at birth, whereas spermatogonia go on dividing throughout the sexual life of a male. So if mutation is due to faulty copying of genes at a nuclear division, we might expect it to be commoner in males than females.”
J. B. S. Haldane The mutation rate of the gene for haemophilia and its segregation ratios in males and females. Annals of Eugenics 13:
Annals of Eugenics changed its name to the current Annals of Human Genetics in 1954.
"One-tenth" is approximate. If all children are fathered by 15-year-olds, then the ratio would be close to 1:1; if all fathers are 30 years old, then ratio would be closer to 1:10. To get a proper ratio, one needs to have the number of children sired by father of different ages. What is the ratio of sperm mutation rate versus egg mutation rate (or male mutation rate versus female mutation rate)?
Some places have younger fathers than other places. Does this affect propensity of genetic diseases? Could be a good research questions.

3. Y-linked sequences (Y) are only carried by males.
Autosomal sequences (A) are carried one half of the time by females and one half of the time by males.
X-linked sequences (X) are carried two-thirds of the time by females and one third of the time by males.
Y-linked sequences (Y) are only carried by males.
Qualitative prediction: RY > RA > RX
Quantitative prediction:
µm: mutation rate in male
µf: mutation rate in female
How to estimate
We can't directly measure µm and µf, can we express  in something measurable?
We can measure mutation rates on autosomes (µA) and X chromosome (µX).
Solve the equations for µm and µf, we have
Gene KS
PLP
0.166
HPRT
0.309
PGK1
0.329
OTC
0.509
NGFb
0.431
b-actin
0.339
Hox-1
0.469
SST
0.479
GCR
0.5
PKC-II
0.53
c-myc
0.54
ALDOA
0.55
DHFR
0.56
Renin
0.57
c-ras
0.58
a-actin
0.59
PAH
0.6
c-myb
0.61
Amy-2
0.63
TGFb
0.65
X-linked
Why did Miyata et al. (1987) take KS for µ?
Autosome
given µf  0
a = M_m/M_f
M_Y=M_m
M_A = (M_m+M_f)/2
M_X = 2*M_f/3 + M_m/3
A/Y = M_A/M_Y = (M_m+M_f)/(2*M_m) = ½ + M_f/(2M_m) = ½ + 1/(2a) = (a + 1)/(2a)
The statement that X chromosome is carried 2/3 of the time in female and 1/3 in male may not be obvious to some students. A randomly sampled X chromosome in the current generation has 2/3 of chance being found in female and 1/3 of chance being found in male
Digitized from Fig. 3 of Miyata et al. (1987)
So can't get a meaningful estimate of µf (it would be negative), but µA > µX is statistically significant by t-test (p = )
Miyata T et al. (1987). Male-driven molecular evolution: a model and nucleotide sequence analysis. Cold Spring Harbor Symp Quant Biol 52:

4. Instead of solving for µm and µf to get , Miyata et al
Instead of solving for µm and µf to get , Miyata et al. derived ratios of mutation rates for  estimation:
Minimum µX/µA is 2/3  Estimated µX/µA = 0.6 based on comparison between mouse and human, and are interpreted as consistent with a very large 
  ∞
a = M_m/M_f
M_Y=M_m
M_A = (M_m+M_f)/2
M_X = 2*M_f/3 + M_m/3
A/Y = M_A/M_Y = (M_m+M_f)/(2*M_m) = ½ + M_f/(2M_m) = ½ + 1/(2a) = (a + 1)/(2a)
The statement that X chromosome is carried 2/3 of the time in female and 1/3 in male may not be obvious to some students. A randomly sampled X chromosome in the current generation has 2/3 of chance being found in female and 1/3 of chance being found in male
However
So can't estimate ; can say that  is very large
Miyata T et al. (1987). Male-driven molecular evolution: a model and nucleotide sequence analysis. Cold Spring Harbor Symp. Quant. Biol. 52:

5. Fig. 3. in Miyata et al
PLP 0.166
HPRT 0.309
PGK
OTC 0.509
NGF 0.431
-actin 0.339
Hox
SST 0.479
GCR 0.5
PKC-II 0.53
c-myc 0.54
ALDOA 0.55
DHFR 0.56
Renin 0.57
c-ras 0.58
-actin 0.59
PAH 0.6
c-myb 0.61
Amy
TGF 0.65

6. Problem 1: Apples and Oranges
The genes on the X chromosomes are not homologous to those on the autosomes. Genes on the X chromosomes may happen to be functionally more important and strongly conserved than those on the autosomes.
Two Solution:
Use synonymous substitutions for comparison (done by Miyata et al. 1987)
Find homologous genes on X and Y to make comparisons.
Xuhua Xia

7. Shared homologous genes
All known studied mammals have two homologous zinc-finger protein-coding genes, one X-linked (Zfx) and one Y-linked (Zfy). They contain introns which are largely free from functional constraints.
For all pairwise comparisons done among human, orangutan, baboon, and squirrel monkey, Shimmin et al. (1993) found that the Y sequences were more divergent, i.e., have evolved faster, than their X-linked homologues.
Max µY/ µX = 3
Shimmin, L. C., Chang, B.H.-J., Hewett-Emmett, D. & Li, W.-H. Potentialproblemsin estimating the male-to-female mutation rate ratio from DNA sequence data. J. Mol. Evol. 37, 160–166 (1993)

8. Problem 2: selection
Alternative selection hypothesis: males have only one copy of X and genes on X are therefore more exposed to purifying selection, leading to greater conservation and lower evolutionary rate. (Does using silent substitution remove this problem?) Solution: Use the ZW system (ZW: female; ZZ: male)
Predictions
From the alternative hypothesis: genes on Z should be more conserved and evolve more slowly than autosomal genes because Z (just like X in mammals) is more exposed to selection than autosomal genes.
From the male-driven hypothesis: genes on Z should evolve faster than autosomal genes because it spend more times in males.
Miyata et al. presented this conceptual framework but did not have data on birds to test the predictions.
10 years later, the predictions were tested by Ellegren and Fridolfsson (1997. Nature Genetics 17: ) , and the male-drive hypothesis is supported (α: ).
Using silent substitution does not remove this problem. Imagine a sequence has accumulated 2 silent mutations. A deleterious mutation arrives and kills the individual carrying the sequence. This removes the two silent mutations from the population.
The textbook (Grour and Li 2000) does not specify the ZW sex-determination system correctly.

9. Controversy on α Low α (<2):
Bohossian, H. B., Skaletsky, H. & Page, D. C. Unexpectedly similar rates of nucleotide substitution found in male and female hominids. Nature 406, 622–625 (2000).
International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2000).
High α related to male/female ratio of generations in gametogenesis:
Kateryna D. Makova & Wen-Hsiung Li. Strong male-driven evolution of DNA sequences in humans and apes Nature 416: (2002)
Why so different estimates of α?

10. Complications
X is randomly inactivated with many epigenetic modifications that could increase or decrease its overall mutation rate. Solution: avoid using X and compare Y and autosomes
Ancient polymorphism (next two slides)
Xuhua Xia

11. Ancient polymorphism and small α
X chromosome and autosomes are expected to have more polymorphism than Y chromosome:
Greater effective population size
Recombination
X and autosomes are more likely to have ancient polymorphism to bias estimate of α
Speciation
X and autosome Y

12. After many papers in Nature, Science and PNAS, the field is effectively deserted and see no sign of revival in the near future.

13. Ancient polymorphism b1 b10 b3 b4 b5 b6 b7 b8 b9 b11 Mouse Rat Gibbon
Orangutan
Human
Chimp
Gorilla b2 a1
Mouse
Rat
Gibbon
Orangutan
Human
Chimp
Gorilla a9 a2 a8
a10 a3
b12
b12 a4 a5 a6
a11 a7 X Y
Global α:
α values close to the tip are smaller than those close to the root: consistent with ancient polymorphism
Lineage-specific α: bi/ai