A year ago there was hope that a finished
sequence of the human genome would soon be
publicly available and would give a more reliable
locus order than an unconstrained radiation
hybrid or genetic map. Alas, there are now
different draft orders for each region, none of
which may be correct because of gaps, uncertain
polarity of contigs, and errors in assembly.
Shortly before these drafts became available, we
analysed allelic association (also called linkage
disequilibrium, LD) in the FRAX region in a
large sample of haplotypes (Ennis et al. 2000).
We demonstrate here that this material
discriminates among alternative draft orders. To
express support for discrimination between two
values of χ2 = −2 ln L we use the Akaike criterion
AIC = df[χ2/min χ2 −1]. Excluding premutations and full mutations at FMR1, all maps have 715 degrees of freedom (df) among 717 pairs
of alleles after accepting L = 0 and estimating M,
∈ in the Malecot equation E(ρ) = Me −∈d, where
ρ is the association between a pair of alleles at
distance d. An AIC in excess of 2 provides
evidence against a map with the larger χ2 .