TABLE 1

Marker type, spacing, allele number, heterozygosity, and mutation rate

NameTypeaCentimorgans to next locusbNo. of allelesHeterozygosityVAS-estimated μ (×104)c
HLA-BSerotype0.04260.911
HLA-CSouthern probe0.13830.584
Y104Southern probe0.0320.441
HLA-ESouthern probe0.055230.461
Y129Southern probe0.01220.410
Y158Southern probe0.0330.608
HLA-ASerotype0.01150.829
D6S265SSR0.04670.7811.019
HLA-GSouthern probe0.023220.507
HLA-FSouthern probe0.420.302
D6S306SSR0.0970.6761.081
D6S464SSR0.01110.6614.019
D6S105SSR0.1290.8221.731
D6S1260SSR0.0390.6711.439
D6S1558SSR0.1380.5101.057
D6S2231SSR0.06132120.8494.799
D6S2238SSR0.0074190.8122.719
HFESNP haplotypes0.0129
D6S2239SSR0.174430.6560.379
D6S2241SSR0.1540.5000.144
D6S1621SSR0.470.7101.339
GATASSR0.780.7610.806
D6S1545SSR160.7100.894
D6S1691SSR160.88911.800
  • a Reference for markers are given in Ajioka et al. (1997). All SSRs are dinucleotide repeats except for GATA, which is a tetranucleotide repeat.

  • b Genetic distances were calculated primarily from physical distances used in Ajioka et al. (1997); genome sequence information was used to recalculate physical distance for markers closest to HFE. On the basis of experimentally measured recombination in the region (Ajioka et al. 1997; Malfroy et al. 1997), the conversion 1cM = 5 Mb was used centromeric to HFE while the conversion 1 cM = 1 Mb was used telomeric. Estimates of recombination throughout the HLA region (i.e., farther centromeric to HLA-A) are not likely as low as 1/5 cM/Mb (Carrington 1999). Underestimates in these rates affect only the age estimates of alleles with the most haplotype sharing, producing slightly overestimated ages (making our comparisons conservative).

  • c Mutation rates were estimated on the basis of the variance in allele size (VAS) of SSRs under a one-step mutation model (Valdes et al. 1993). A constant effective population size of 104 was assumed.