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This study was a preliminary analysis of the genetic structure of the ectomycorrhizal species Russula discopus, tL pseudocarmecina and R. ochraceorivulosa with disjunct distributions in continental Africa and Madagascar. Phylogenetic analyses of the nuclear ITS1/5.8S/ITS2 region and the mitochondrial atp6 gene were performed with specimens from both locations for each species along with a suitable outgroup for each of the three taxa. Additional analyses of the ITS1/5.8S/ITS2 region using the African and Malagasy specimens and additional taxa in the genus Russula also were performed. R. pseudocarmecina and R. discopus both exhibited genetic structure as shown by a relatively high percentage difference in ITS and atp6 sequences, high bootstrap support for African or Malagasy groups and the presence of indels in the ITS sequence that are unique to either Africa or Madagascar. African and Malagasy groups of each species were more closely related to each other than to other taxa in Russula. Genetic structure also existed in populations of R. ochraceorivulosa, but bootstrap support was weaker than in the other two species. In addition, there was less sequence divergence in R. ochraceorivulosa and this species was the only one for which the same atp6 haplotype was found in both Africa and Madagascar. Reciprocal monophyly for all three species was consistent with the hypothesis that the same vicariance event may be responsible for the genetic structure observed here, although shorter branch lengths, lower bootstrap support and the presence of the same atp6 haplotype in Africa and Madagascar for R. ochraceorivulosa suggested slower evolutionary rates or geographical isolation after the other two taxa. In addition to the geological events that separated Africa and Madagascar, environmental changes during the Miocene or later might have had an effect on the distribution of these species. [ABSTRACT FROM AUTHOR]