Supplementary Table 9. Methods used to estimate the male-specific ages of each of the MSY sequences and genes, shown in Figure 8.
Sequence or gene	Genes and/or pseudogenes	Ks	Sources of age estimation	Male-specific age (millions of years)
X-transposed	TGIF2LY, PCDH11Y	0.011	Schwartz A, et al.  Hum. Mol. Genet. 7, 1 (1998); Bohossian HB, Skaletsky H & Page DC.  Nature 406, 622 (2000)	4
Chr 1 transposition	PPP1R12BP	0.034	†	7
Chr 15 transposition	CSPG4LY, GOLGA2LY	0.042	†	9
Chr 21 transposition	TPTEP	0.047	†	10
Chr 13 transposition	SLC25A15P, ADPRTL1P	0.070	†	14
Chr 3 transposition	DAZ, KIAA0084P	0.147§	Comparative mapping; Seboun E, et al. Genomics 41, 227 (1997)	30
Group 4$	AMELY, OA1P*, PRKY, ADLICANP*, ARSFP, ARSEP, ARSDP, GYG2P, KALP, VCY, NLGN4Y*, STSP	0.081	40 million years ago from Lahn BT & Page DC.  Science 278, 675 (1997)	40
Chr 19 transposition	ZNF381P	0.37	†	75
Group 3	ZFY, TBL1Y*, APXLP*, USP9Y, DBY, CASKP, UTY, TMSB4Y, OFD1P2*, CYorf15A*, CYorf15B*, EIF1AY, BCoRP*	0.28	Lahn BT & Page DC.  Science 278, 675 (1997)	100
Group 2	SMCY	0.47	Lahn BT & Page DC.  Science 278, 675 (1997)	150
TSPY	TSPY	0.71	Vogel T, et al. Cytogenet Cell Genet 81, 265 (1998)	150
CDY	CDY	0.75	†	150
Group 1	SRY, RPS4Y, RBMY	0.98	Lahn BT & Page DC.  Science 278, 675 (1997)	280
† Based on a Ks molecular clock calibrated by the chromosome 3 transposition.  See the row for the Chr 3 transposition.
§ Based on the weighted average of Ks between DAZ and DAZL and between KIAA0084P and KIAA0084.
$ Approximately 3 Mb of MSY genomic sequence was assigned to Group 4 based on sequence divergence from homologous X-chromosomal sequence.
* Genes newly assigned to their group based on Ks estimates.