The use of molecular techniques for the assessment of familial relatio
nships among social species of mammals has become relatively commonpla
ce. However, some species represent poor candidates for such studies d
ue to naturally low levels of genetic diversity, leading to unacceptab
ly large standard errors associated with estimates of relatedness. Her
e, we report on a preliminary study of genetic diversity within two po
pulations of a social species of ground squirrel, Gunnison's prairie d
og (Cynomys gunnisoni) using DNA fingerprinting. We observed low level
s of diversity in the form of large mean coefficients of genetic simil
arity among individuals occupying the same population. Overall similar
ity, determined from the combined data, yielded by three minisatellite
probes, ranged from 55 to 61%. These values place Gunnison's prairie
dog at the extreme upper end of the range of similarity values reporte
d for outbred species of mammals (ca. 0.20-0.50). As a partial means o
f explaining these results, and as a means of comparing our results to
those of similar studies using allozymes, we determined the level of
differentiation between our two study colonies in the form of an F-sta
tistic analog. A value of 0.11 (+/- 2.26 x 10(-3)) was obtained and is
similar to values reported from allozyme studies (0.07-0.12). A signi
ficance test of this value yielded a positive result (D = 5.63, d.f. =
1, P < 0.025), demonstrating that gene flow between populations is li
mited, a factor that may help to maintain low levels of diversity.