Reconciling African Elephant Phylogenies et al. (2002) [37]. The ‘‘clade F’’ identified by Debruyne (2005) [12] proved synonymous with the other clade designations shown in green; the ‘‘clade S’’ identified by Debruyne (2005) [12] proved synonymous with the other clade designations shown in orange [4,12,13,16]. Supplementary Figure S2 details the overlapping informative sequences that established the relationships shown across the datasets. doi:10.1371/journal.pone.0020642.g003 made the suggestion that forest and savanna elephants have a geographically expansive hybrid zone with large numbers of hybrids present across Africa [12,16], based on the often unstated assumption that the proportions of forest-savanna nuclear markers in a population likely reflect the proportion of F and S clade mtDNA markers. In Figure 5, the dashed line shows this ‘‘presumed’’ relationship if the proportions of S and F clade mtDNAs are assumed to serve as accurate estimators of the overall contribution of savanna and forest lineages to the nuclear genetic makeup of the elephants. If this were the case, many savanna populations should have a high proportion of forest elephant admixture. Instead, the actual data showed that no relationship existed for savanna elephants between the proportion of F to S clade mtDNA and the degree of hybridization present in the locales. Thus the suggestion that African regions that include both F clade and S clade elephants represent geographically extensive hybrid zones in which both forest and savanna elephants are present and the populations are a mixture of the two [12,16] is contradicted by the current data for Cameroon, Southern and Eastern Africa (Figure 5). Since the lack of association between mtDNA and nuclear patterns holds true for these three regions, one may also question the validity of taxonomic and population genetic inferences drawn from analogous mtDNA patterns in West Africa. Nuclear genetic similarity between Central and West African elephants The Guinean forest block in West Africa is currently not contiguous with the Congolian forest block in Central Africa [28,40]. One genetic study that conducted extensive sampling of elephants in West Africa hypothesized that West African elephants may comprise a third species of elephant, separate from forest and savanna elephants in the rest of Africa [14,15]. The single elephant in our sample from a West African locale in the Guinean forest block, for which the mtDNA haplotype [29] further established its West African origin [15], clustered with the Central African Figure 4. The distribution of ‘‘S’’ clade mtDNA across the African continent corresponds to the distribution of savanna elephants. The map shows the distribution of S clade mtDNA across Africa, using results reported by all previous continent-wide studies of elephant mtDNA in Africa [4,12,13,15,16,36,37], with results shown by location. A plus sign (orange) on the map indicates that S clade mtDNA was present at the location (whether or not F clade mtDNA was also detected). A triangle indicates that S clade was not detected in the sample. S clade mtDNA was completely absent across the entire range of forest elephants at 30 tropical forest locales (dark green) across West and Central Africa. By contrast, at some savanna locales where S clade was not detected in some samples, such as Botswana, the apparent absence of S clade was likely due to an insufficient numbers of elephants being sampled, since other nearby samples did detect S clade. The presence or absence of S clade mtDNA was found to be highly significantly associated with type of habitat (tropical forest vs. other or mixed habitats; Fisher’s exact test, two-tailed p,1024). The distribution of S clade closely corresponds to the geographic distribution of savanna elephant habitat, morphology and nuclear genotypes [2,3,4,6,7]. The arrow indicates that the mtDNA S clade haplogroup was also present in West African savanna elephant populations. Further information on sample types and locations is supplied in Supplementary Figure S3. doi:10.1371/journal.pone.0020642.g004 PLoS ONE | www.plosone.org 7 June 2011 | Volume 6 | Issue 6 | e20642