Reconciling African Elephant Phylogenies Figure 1. Location map and nuclear genetic clustering of sampled elephant populations in Africa. The map portrays the extent of tropical forest (dark green), and the forest-savanna transition zone (light green) [28]. Bar plots for each locale represent the average contribution to the genotypes of elephants made by forest (green) or savanna (orange) elephants, as partitioned using the program STRUCTURE (K = 2) using data from 11 microsatellite loci (see Figure 2). STRUCTURE cluster 1 (green) comprised 99.5% of forest populations and 0.6% of savanna populations. Cluster 2 (orange) comprised 0.5% of forest populations and 99.4% of savanna populations. Sampling locations in forest habitats were: DS-Dzanga Sangha, Central African Republic; OD-Odzala, Congo (Brazzaville); BF-Bili Forest, Congo (Kinshasa); LO-Lope, Gabon; and SL-Sierra Leone (one zoo individual). Savanna locations: CH-Chobe, MA-Mashatu, SA-Savuti in Botswana; BE-Benoue, WA-Waza in Cameroon; AB-Aberdares, AM-Amboseli, KE- Central Kenya/Laikipia, MK-Mount Kenya in Kenya; NA-Northern Namibia/Etosha; KR-Kruger in South Africa; NG-Ngorongoro, SE-Serengeti, TA- Tarangire in Tanzania; HW-Hwange, SW-Sengwa, ZZ-Zambezi in Zimbabwe. GR-Garamba is located in the Guinea-Congolian/Sudanian transition zone of vegetation in D.R. Congo that historically included a mixture of forest and secondary grasslands [28] suitable for both African elephant groups [3]. doi:10.1371/journal.pone.0020642.g001 indicated that Garamba has the greatest degree of nuclear gene- tic admixture detected between forest and savanna elephants (Figure 1), although with a much larger proportion of ancestry par- titioned to the forest cluster (90.8%; Figure 1). Individual hybrids previously identified using nuclear gene sequences (notably in Be´noue´ and Garamba) [4,6] are also apparent in the STRUC- TURE analysis (Figure 2). No genetic hybrid has ever been previously detected among elephants in locations deep in the tropical forest [4,6,7], although among the savanna elephants two individuals in Cameroon had been identified as hybrids [4]. Overall, the elephants in Cameroon did demonstrate a slightly lower overall assignment to the savanna cluster than other savanna locales, with 95.6% assignment to the savanna cluster for Be´noue´ elephants, and 99.7% assignment for Waza; although even in Cameroon savannas, the forest elephant genetic contribution was quite limited (Figures 1 and 2). Contrary to the hypothesis that forest-savanna elephant hybrids are both common and widespread [12,16] these findings support the view that hybrids are rare and limited in geographic distribution (Figures 1, 2) [1], as the overall proportion of genotypes inferred to derive from admixture with the other species was less than one percent for both forest and savanna elephants. A factorial correspondence analysis (FCA) implemented using the software GENETIX [35] also demonstrated distinctiveness between forest and savanna elephants (Figure 2). The low degree of hybridization, even among the few populations that contain hybrids, was also evident in this analysis. Figure 2 shows the rep- resentation of the two major axes determined by the FCA in a combined analysis of all African elephants. The 461 savanna elephants formed a distinct group from 75 forest elephants. The apparent genetic diversity of the forest/Garamba elephants is noteworthy (and likely accounts for much of the variability in the FCA), especially given that many more savanna elephants from a wider geographic range were used for the analysis, and given that ascertainment bias would tend to increase the relative diversity of the savanna elephants in which most of the STR markers were selected for their polymorphism (Table S1). The lack of true genetic intermediates was striking in the FCA. With only one exception (GR0020), hybrid elephants did not occupy the middle space between forest and savanna species; rather, they tended to show only a low level of admixture, even in the hybrid zone of Garamba (Figure 2). Thus hybridization of forest and savanna elephants has not led to a ‘‘hybrid swarm’’ condition in which some populations are comprised primarily of genetic hybrids between the two species. Genetic relationships among different locales were also inferred from the STR data using the chord distance. The elephants from savanna and forest locales formed two distinctive phylogenetic clusters (Figure 2). Likewise, our STRUCTURE results were not different after (1) the number of individual savanna elephants was PLoS ONE | www.plosone.org 3 June 2011 | Volume 6 | Issue 6 | e20642