Phylogeography of the bitter apple, Citrullus colocynthis

Citrullus colocynthis is a desert plant with a rich history as an important medicinal plant and as a source of valuable oil. Its small seeds appear in several early Egyptian, Lybian and Near Eastern sites from about 4000 BC. Sequence information deduced from several polymorphic intergenic cpDNA regions and a relatively large intron (0.6 kb) at the transit sequence of single-copy nuclear gene G3pdh showed clear geographical structure among C. colocynthis accessions. Region specific haplotypes with different nucleotide substitution rates were observed. The highest number of substitution events occurred in C. colocynthis selections from India and Pakistan, the lowest number in accessions from the Middle Eastern and West Asian region (Iran, Israel, and Afghanistan). Population level variation at the noncoding cpDNA and G3pdh intron are congruent. Indels at two cpDNA regions and unique nuclear and cpDNA substitutions indicate the direction of migration from the African continent into the Middle East and the Far East. C. colocynthis collected in Australia showed the highest sequence homology with accessions from Cyprus and Morocco. Divergent lineages are restricted to portions of the species range. Possible causes of this pattern include restricted migration and gene flow between regions, and differences in population size of divergent haplotypes based on differential patterns of environmental adaptation.