A case study of apparent conflict between molecular phylogenies: the interrelationships of African elephants

Recent molecular phylogenies of the African elephants suggest that there is an evolutionary structure within Loxodonta africana. Some nuclear results (Roca et al., 2001) support the separation of the forest African elephant subspecies L. a. cyclotis as a species distinct from the savannah elephant L. a. africana, on the basis of the recognition of both forming highly divergent (reciprocally monophyletic) clades. Conversely, a mitochondrial survey (Eggert et al., 2002), while admitting a geographic partitioning of the genetic structure within African elephants, suggests retaining the status quo. They recognize three diagnosible entities (western, central and south-eastern Africa) with non-overlapping ranges within L. africana sensu lato. In order to address these conflicting views (historical fragmentation and speciation or isolation by distance, respectively), we have sequenced two datasets of 1961 bp (for 50 elephants) and about 3700 bp, respectively (for 20 elephants) of the mitochondrial DNA for both forms of elephants (cyclotis and africana). They span the cytochrome b gene, the control region and several RNAs. When compared with former mtDNA data, they provide the most comprehensive view of the African elephant phylogeny (78 mtDNA haplotypes, of which 44 are new) and provide the first insight into populations from the Democratic Republic of Congo. The genetic diversity of mtDNA was appraised and the stability of alternative phylogenetic trees was investigated. Our results are inconsistent with both those prior studies. They revealed two highly divergent molecular clades referred to as F and S, that do not conform to the morphological delineations of cyclotis and africana. A non-negligible proportion of specimens of L. a. africana display haplotypes prevailing in forest elephant populations (clade F). The geographic distribution of clades and areas of their co-occurrence support the hypothesis of incomplete isolation between forest and savannah African elephant populations, followed by recurrent interbreeding between the two forms. We state that the conclusions of prior studies resulted from insufficient character and/or geographic sampling. We conclude that there is no satisfying argument which can recognize two or more species of African elephants. We briefly comment on the meaning of such an attitude in a conservation viewpoint.