The coffee berry borer beetle Hypothenemus hampei (Ferrari) (Curculion
idae: Scolytinae) is the major insect pest of coffee and has spread to
most of the coffee-growing countries of the world. This beetle also d
isplays an unusual rife cycle, with regular sibling mating. This regul
ar inbreeding and the population bottlenecks occurring on colonization
of new regions should lead to low levels of genetic diversity. We wer
e therefore interested in determining the level of nucleotide variatio
n in nuclear and mitochondrial genomes of this beetle worldwide. Here
we show that two nuclear loci (Resistance to dieldrin and ITS2) are co
mpletely invariant, whereas some variability is maintained at a mitoch
ondrial locus (COI), probably corresponding to a higher mutation rate
in the mitochondrial genome. Phylogenetic analysis of the mitochondria
l data shows only two clades of beetle haplotypes outside of Kenya, th
e proposed origin of the species. These data confirm that inbreeding g
reatly reduces nucleotide variation and suggest the recent global spre
ad of only two inbreeding lines of this bark beetle.