Reconciling African Elephant Phylogenies Figure 2. Species subdivisions and population substructure among African elephants. (A) Distinctiveness of forest and savanna elephant species and the pattern of hybridization between forest and savanna elephants was demonstrated using the program STRUCTURE, which applies a model-based clustering algorithm to identify subgroups that have distinctive allele frequencies [30]. The two partitions correspond to African forest elephant ancestry (green) and African savanna elephant ancestry (orange), and each is confined almost exclusively ($99.4%) to locales in, respectively, tropical forest and non-tropical forest habitats (Figure 1). Garamba (GR) is the only population that spans an intermediate habitat zone containing both forest and savanna vegetation, and both types of elephants [3,28]. (B) A factorial correspondence analysis (FCA) implemented using the software GENETIX [35] reveals the distinctiveness of forest and savanna elephants, with a very limited degree of hybridization. A total of 555 African elephant individuals (75 forest, 19 Garamba, and 461 savanna elephants) were used in the analysis. The two major axes determined by the FCA were used; plotted on the x- and y-axes, respectively accounting for 6.68% and 2.26% of the total variability. Savanna elephants formed a group distinct from the group formed by forest plus Garamba elephants. With only one exception (GR0020), hybrid elephants do not occupy the middle space between forest and savanna elephants; rather, they tend to show only a low level of admixture [4]. (C) Neighbor-joining phylogram depicting the genetic relationships among elephants by locale, based on the STR data using the chord distance. Elephants from savanna (orange) and forest (green) locales form distinct groups. Locale abbreviations are as in Figure 1. doi:10.1371/journal.pone.0020642.g002 PLoS ONE | www.plosone.org 4 June 2011 | Volume 6 | Issue 6 | e20642