Sequence variation at a major histocompatibility complex (MHC) gene, a
ssumed to be involved in parasite and pathogen resistance, was examine
d in the endangered Gila topminnow (Poeciliopis o. occidentalis), from
the four watersheds where they remain in the United States. This is t
he first estimate of variation in MHC genes in natural populations of
an endangered species. The population that has experienced the most bo
ttlenecks historically was monomorphic for MHC variation. Another popu
lation, which earlier had been found to be the only population polymor
phic for allozymes, had five MHC alleles, four different from those fo
und in the other populations. Overall, nine different alleles were fou
nd. The four populations were highly divergent at MHC with four of the
six population pairs not sharing any alleles. However, the magnitude
of differentiation between populations on the amino-acid level varied
fivefold for the populations that shared no alleles. Using single-stra
nded conformational polymorphism (SSCP), these alleles segregated cons
istently with Mendelian expectations in families. Because of the high
genetic differentiation between these populations for a potentially ad
aptive gene, we recommend that the four watersheds be examined further
for separate conservation and management.