The genetic variability of honeybee populations Apis mellifera ligustica, i
n continental Italy, and of A. m. sicula, in Sicily, was investigated using
nuclear (microsatellite) and mitochondrial markers. Six populations (236 i
ndividual bees) and 17 populations (664 colonies) were, respectively, analy
sed using eight microsatellite loci and DraI restriction fragment length po
lymorphism (RFLP) of the cytochrome oxidase I (COI)-cytochrome oxidase II (
COII) region. Microsatellite loci globally confirmed the southeastern Europ
ean heritage of both subspecies (evolutionary branch C). However, A. m. lig
ustica mitochondrial DNA (mtDNA) appeared to be a composite of the two Euro
pean (M and C) lineages over most of the Italian peninsula, and only mitoty
pes from the African (A) lineage were found in A. m. sicula samples. This R
emonstrates a hybrid origin for both subspecies. For A. m. ligustica, the m
ost widely exported subspecies, this hybrid origin has long been obscured b
y the fact that in the main area of queen production (from which most of th
e previous ligustica bee samples originated) the M mitochondrial lineage is
absent, whereas it is present almost everywhere else in Italy. This presen
ts a new view of the evolutionary history of European honeybees. For instan
ce, the Iberian peninsula was considered as the unique refuge for the M bra
nch during the quaternary ice periods. Our results show that the Apennine p
eninsula played a similar role. The differential distribution of nuclear an
d mitochondrial markers observed in Italy seems to be a general feature of
introgressed honeybee populations. Presumably, it stems from the social nat
ure of the species in which both genome compartments are differentially aff
ected by the two (individual and colonial) reproduction levels.