single species of elephant’’ [12]. Eggert et al. (2002) [14,15] have hypothesized that the elephants ‘‘of west Africa belong to a newly recognized and yet to be formally named species’’ [14]. Johnson et al. (2007) have stated that ‘‘the classification of species into savannah and forest may not reflect their evolutionary history but simply the habitat in which they currently exist’’; and that Africa’s elephants fall into three or four ‘‘groups’’ with ‘‘implications for taxonomy’’ [16]. By contrast, analyzing both mtDNA and nuclear genetic patterns within the same individuals and populations, Roca et al. (2005) [4] discovered that the non-monophyletic mtDNA pattern was strongly incongruent with patterns present among nuclear markers (characterized as ‘‘cyto[or mito]-nuclear genomic dissociation’’), and therefore did not detract from the two-species model for living Loxodonta taxa [1]. These sometimes strikingly opposed interpretations of molecular data are influenced by the types of genetic markers used [1]. Thus, despite exceptionally intensive genetic analysis, opposing taxo- nomic designations of African elephants persist to date, and the African Elephant Specialist Group and Species Survival Commis- sion of the International Union for the Conservation of Nature (IUCN) have cited the multiplicity of taxonomic interpretations of genetic data as justification for its decision to ‘‘continue to treat African elephants as a single species’’ [17]. A 2011 published survey of conservation priorities among afrotherian mammals con- cluded that resolution of the relationships and diversity among African elephants constitutes an ‘‘urgent priority’’ given ‘‘the important conservation implications of elephant taxonomy’’ [18]. In this study, we sought to resolve these apparent conflicts by further examining nuclear and mtDNA patterns among savanna elephants using a novel set of short tandem repeat (STR) loci in African forest and savanna elephants that had previously been typed for mtDNA. Employing a Bayesian clustering approach, we sought to better quantify the degree and geographic extent of hybridization based on these STR loci. We examined the rela- tionships between mtDNA and nuclear patterns in these elephants and determined what these patterns imply about evolutionary relationships of almost a thousand African elephants from 81 geo- graphic locales for which mtDNA sequence had been previously generated. We determined whether geographically mapping the mtDNA and nuclear genetic partitions among the elephants of Africa might provide additional insights into resolving the differing assertions regarding their taxonomic status. We found that our novel approach to mtDNA analysis could reconcile the apparent conflict previously reported between mitochondrial and nuclear phylogenies in African elephants [12]. Based on this systematic clarification, we further sought to improve upon the other major area in which genetics can contri- bute to African elephant conservation: the forensic analysis of ivory samples. Although the Convention on International Trade in Endangered Species (CITES) banned the ivory trade in 1989, large numbers of elephants continue to be poached for their tusks, and the illegal trade in ivory is a major threat to their conservation [19]. Since ivory is often confiscated in markets far from the locations where elephants are poached, DNA markers have been used to identify the source population of confiscated ivory [20,21]. Wasser and colleagues have successfully extracted DNA from small amounts of elephant ivory [22,23], and applied spatial smoothing methods to allele frequencies of STRs in order to assign ivory to its source. Using this approach, they have genotyped tusks of smuggled ivory and assigned them as originating within a par- ticular range country [24]. The success of these methods is encouraging, though further enhancement of the accuracy and precision of assignment would be desirable [25,26]. We therefore also sought to improve DNA-based methods for tracking ivory by Reconciling African Elephant Phylogenies developing a means of quantifying the effectiveness of each of our STR loci for assigning elephants to their place of origin, and to identify those STR loci most and least effective at geographic assignment. Results Samples of African elephants collected primarily by dart biopsy, as previously described [11,27], were grouped by geographic location of collection (Figure 1). Samples were grouped into 17 savanna locales and 5 forest locales, all except for the elephants of Garamba, which are from a region historically of mixed forest and savanna habitats [28] where both types of elephants have been reported based on morphology [3,10], and where hybrids have been detected based on morphology [10] or nuclear genotypes [4,6,7]. Samples recently collected included forest elephants from the Bili Forest in the Democratic Republic of Congo, a location previously not included in elephant genetic studies; and a forest elephant sample from the Paris Zoo (France) of Sierra Leone origin (Figure 1) [29]. We also report from previously sampled locations [7] the STR genotypes of a much larger number of individuals. A total of 555 African elephant individuals (75 forest, 19 Garamba and 461 savanna elephants) were successfully geno- typed, along with 9 Asian elephants (Elephas maximus), using fifteen microsatellite loci, including newly developed loci (Tables S1, S2), with a minimum of 11 loci used for each of the analyses. Summary statistics for the loci are shown in Table S2. Genetic separation between forest and savanna African elephants Bayesian clustering analysis was performed on the microsatellite data using the program STRUCTURE [30], with strong evidence for K = 2 clusters among African elephants (Table S3) [31]. With K = 2, the clusters showed a geographic split that corresponded closely to the split between forest and savanna elephants (Figures 1, 2), in agreement with previous studies of morphology and nuclear genetic markers [1,2,3,4,6,7,13,32,33]. Every elephant from a tropical forest locale was identified as completely or primarily of forest elephant ancestry (Cluster 1 in green), while not a single elephant assigned primarily or completely to cluster 1 was from a location outside of tropical forest or mixed habitat (Figure 2). Likewise, every individual from a locale outside the tropical forest range was identified as primarily or completely savanna- elephant like (Cluster 2 in orange) in genotype, while elephants assigned predominantly or completely to Cluster 2 were all from locales outside the tropical forest range (Figure 2). There were no exceptions. The overall contributions of Clusters 1 and 2 (forest elephant and savanna elephant genotypes, respectively) to the elephant population at each locale are shown in Figure 1. Across all ele- phants at tropical forest locales, the estimated percentage assign- ment to the forest elephant cluster averaged 99.5%. Among all savanna elephants, assignment to the savanna elephant cluster averaged 99.4%. In some cases, a low level of ancestry was assigned to the cluster of the other species. Some of these represent the few individuals that previous nuclear sequences have shown to be hybrids [4,6,7]. For others, the small proportion partitioned to the other species may reflect lower limits of resolution for the software STRUCTURE. One of our locales, Garamba, is in a region of the Democratic Republic of Congo that historically included both forest and savanna habitats [28,34]. Previous genetic studies also established the presence of hybrid nuclear genotypes in our Garamba samples [4,6,7]. This finding is supported by the current analysis, which PLoS ONE | www.plosone.org 2 June 2011 | Volume 6 | Issue 6 | e20642