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Background    Rhipicephalus sanguineus  belongs to a complex of hard tick species with high veterinary-medical significance. Recently, new phylogenetic units have been discovered within  R. sanguineus , which therefore needs taxonomic revision. The present study was initiated to provide new information on the phylogeography of relevant haplotypes from less studied regions of Europe and Africa. With this aim, molecular-phylogenetic analyses of two mitochondrial markers were performed on 50 ticks collected in Hungary, the Balkans, countries along the Mediterranean Sea, Kenya and Ivory Coast.    Results  In the “temperate lineage” of  R. sanguineus , based on cytochrome  c  oxidase subunit 1 ( cox 1) and 16S rRNA genes,  Rhipicephalus  sp. I was only found in the eastern part of the Mediterranean Basin (with relatively homogenous haplotypes), whereas  Rhipicephalus  sp. II occurred in the middle-to-western part of this region (with phylogenetically dichotomous haplotypes). Ticks identified as  R. leporis  (based on morphology and  cox 1 gene) were found in Kenya and Ivory Coast. These clustered phylogenetically within  R. sanguineus  ( s.l .) (“tropical lineage”).    Conclusions  In the Mediterranean Basin two mitochondrial lineages of  R. sanguineus , i.e.  Rhipicephalus  sp. I and  Rhipicephalus  sp. II exist, which show different geographical distribution. Therefore, data from this study confirm limited gene flow between  Rhipicephalus  sp. I and  Rhipicephalus  sp. II, but more evidence (analyses of nuclear markers, extensive morphological and biological comparison etc.) are necessary to infer if they belong to different species or not. The phylogenetic relationships of eastern and western African ticks, which align with  R. leporis , need to be studied further within  R. sanguineus  ( s.l .) (“tropical lineage”).

East and west separation of Rhipicephalus sanguineus mitochondrial lineages in the Mediterranean Basin