elephants between West and Central African locales (Figure 6). This suggested that genetic similarities were present between West African and Central African forest elephants, and fails to lend support to the hypothesis that West African elephants comprise a distinct species. Eggert et al. (2002) [15] also had hypothesized that in West Africa the elephants ‘‘do not divide into separate forest and savanna forms’’, while Johnson et al. (2007) [16] state that in West Africa ‘‘savannah elephants are indistinguishable at both the mitochondrial and morphological level from their forest counter- parts.’’ These hypotheses are difficult to reconcile with the conclusion drawn by Groves (2000) based on morphometric mea- surements on elephant skulls from across Africa, that some West African elephants were ‘‘firmly confirmed as L. cyclotis’’ in discri- minant analyses [64]. Photographic evidence has also suggested that both forest and savanna elephants can be distinguished in West Africa [64,65]. Among the highly disrupted habitats of West Africa [17,66,67] forest elephants currently range into some regions outside the tropical forest [64,65]. However, historical surveys have concluded that most elephants in West Africa were eradicated by the first decades of the twentieth century, due to the ivory trade [66,67,68]. The impact was greater on savanna than on forest populations [66,67]; thus one cannot readily assume that current geographic distributions of the elephant species in West Africa reflect their historic patterns. Eggert et al. (2002) [15] had inferred nuclear relationships among their elephants using four STR loci, with the highest bootstrap values on nuclear phylograms supporting a clade that grouped the West African elephants of Mali with those of nearby savanna populations in Waza and Be´noue´ in Cameroon. It may not be possible to draw strong inferences from just four STR loci (especially as the placement of some populations such as Addo had likely been affected by inbreeding). Nonetheless, three of four STR loci genotyped by Eggert et al. (2002) [15] show similar allele sizes between Mali and either Waza or Be´noue´ (or both). The fourth locus was not similar in allele sizes between Mali and the Came- roon locales; however for locus LA5, the frequency of allele 191 was 1.00 in Mali and 0.46 in Waza, but 0.00 in all other savanna or forest locales sampled by Eggert et al. (2002) [15]; for locus LA6, the three highest frequencies for allele 172 were found in Mali (1.00), Waza (0.50), and Be´noue´ (0.27); and for locus LafMS02, the three highest frequencies for allele 150 were also in Mali (1.00), Waza (0.50), and Be´noue´ (0.27). Since Waza and Be´noue´ elephants have been shown by all nuclear DNA analyses including the current ones to partition as savanna elephants (Figures 1, 2, 5, 6), this suggests that the West African elephants in Mali may be genetically similar to other savanna elephants, a suggestion sup- ported by the presence of S clade mtDNA in Mali (Figure 4, arrow). Thus, in the published STR dataset [15] it is difficult to find strong evidence for the hypothesis that Mali elephants may belong to a different species than Cameroon savanna elephants. ‘‘Mitochondrial essentialism’’ and the conservation of Africa’s elephants Given that mtDNA haplotypes among elephants are an unreliable indicator of overall genetic similarity (Figure 5) [4], it is unfortunate that mtDNA alone continues to be used as a guide to elephant genealogical affinities. This ‘‘mitochondrial essential- ism,’’ the continuing use of mtDNA to partition populations and species, among elephants where morphological and nuclear markers have established that mtDNA patterns may be inaccurate or misleading, might lead to adverse results for elephant con- servation, as the following examples illustrate: If mtDNA data were used as the sole basis for elephant taxonomy and population Reconciling African Elephant Phylogenies structure, elephants in the Guinean forest block could be recom- mended for translocation to the deserts of Mali, on the grounds that their mtDNA similarity implies that they must be genetically similar. Likewise, relying on mtDNA to infer population structure would mean that savanna elephants from Tanzania could be moved west into the Congolian tropical forest, since forest and savanna elephants in these regions share similar F clade mtDNAs. Either of these translocations would be inappropriate, since even while carrying mtDNA from the same haplogroup, individuals in forest and savanna locations are very different in nuclear genotypes (Figure 5), belong to different species [4], and are thus unlikely to thrive when moved to the wrong habitats. Although the examples are extreme, it may be equally troublesome that mtDNA-based misinterpretations of African elephant taxonomy constitute an unacknowledged potential hindrance to their proper conservation by convincing conservation groups to ‘‘continue to treat African elephants as a single species’’ [17]. Improving the utility of nuclear genetic markers for fighting the ivory trade Along with the destruction of habitats, one of the major threats to elephant populations is illegal hunting for the ivory trade. DNA has been successfully extracted from ivory [22,23], while previous studies have shown that STR genotypes can be used to assign ivory to its geographic region of origin [20,21,24,26]. However, previous studies have not attempted to rate each STR locus for its utility in assignment. In an attempt to further improve STR-based assignment methods, our STR loci were subjected to a novel analysis to assess their Shannon Information Content (SIC) using pairwise population comparisons to quantify their ability to distinguish elephants living in one geographic region or location from those living in a second region or location, which would gauge their utility for ivory forensics. For each comparison, some loci had a much higher SIC than others (Figure 7), suggesting that some STR loci would be much better than others for establishing the provenance of ivory. Our method permits the quantification of previously developed and current STR loci, and should permit the assessment of novel markers before they are brought into widespread use. Those loci that demonstrate an enhanced ability to distinguish among geographic locales can be chosen for inclusion in STR panels for ivory forensics. Our analysis makes it possible to develop a panel of STR markers, each component of which has a much a higher SIC than the current (randomly chosen) markers, and thus more effective for inferring the pro- venance of illegally poached ivory. Increased accuracy of assign- ment would enhance the ability of conservation, anti-corruption and law-enforcement efforts to identify elephant populations being targeted by poachers. Thus enhanced STR panels have the potential of aiding the conservation of Africa’s two species of elephant. Materials and Methods Samples The study was conducted in compliance with the University of Illinois Institutional Animal Care and Use Committed (IACUC) approved protocol number 09036. Samples were obtained in full compliance with required CITES (Convention on Interna- tional Trade in Endangered Species of Wild Fauna and Flora) and other permits. As previously described, samples were collected from wild African elephants (Loxodonta) primarily by biopsy darting [11,27,69] of individuals from distinct herds. Blood samples were collected from Asian elephants and from Coco, a male forest elephant (Loxodonta cyclotis) from Sierra Leone, which had been PLoS ONE | www.plosone.org 13 June 2011 | Volume 6 | Issue 6 | e20642