Reconciling African Elephant Phylogenies Figure 6. West African elephants–a distinct third species? This map, depicting the mis-assignment of elephants to the wrong locales by an STR-based assignment method, does not lend support to the hypothesis that West African elephants are a distinct species. Assignment data is from Wasser et al. [26], but plotted geographically with forest elephant locales in green and savanna locales in orange. Arrowheads indicate the direction of misassignment (e.g., elephants in GR were assigned wrongly to TI); lines without arrowheads indicate that misassignments occurred in both directions. Each misassignment would be an indication of genetic similarity between elephants at the two locales. Among the hundreds of elephants assigned using STRs [26], there is no overlap in cross-assignments between forest and savanna elephant groups, even in cases where some forest and savanna elephant locales were geographically much closer between than within species (e.g. BE is closer to DS than to most other savanna locales); nor did misassignment ever occur between Asian and African elephants. By contrast, a very high degree of cross-assignment is evident between locales in West Africa and those in Central Africa, an indication of substantial genetic similarity between elephants in the two forest blocks, which fails to provide support for the hypothesis that a distinct elephant species inhabits West Africa [14,15]. Locales are as in Figure 1, with additional locales: BI-Bia, BM-Banyang Mbo, DJ-Dja, MG-Mago, MI-Mikumi, MO-Mole, RU-Ruaha, TI-Tai, TZ-Tsavo [26]. doi:10.1371/journal.pone.0020642.g006 misassignment between Congolian and Guinean block forest ele- phants (Figure 6) suggested that nuclear genetic similarity exists between forest elephants in the two forest blocks. The genetic similarity implied by the misassignment of elephants between the two forest blocks fails to provide support for the hypothesis that the elephants of West Africa comprise a distinct species [14]. Quantifying STR loci for their utility in assigning geographic provenance Besides taxonomy and population structure, the other major area in which genetics can contribute to African elephant con- servation is in the geographic assignment of ivory samples [20,21,22,23,24,26]. Current geographic assignment methods for elephants and ivory that use STRs may sometimes be imprecise or inaccurate (Figure 6) [7,24,25,26]. The mis-assignments depicted in Figure 6, for example, show that room exists for improvement of genetic markers to establish the provenance of elephants (and their ivory). Furthermore, the considerable variation in allelic size range for different STR loci used in the current study (Table S2) suggested that some STR loci would prove more effective than others for genetically assigning an elephant to its geographic origin. While previous studies have shown that STR genotypes can be used to assign ivory to its geographic region of origin [7,24,25,26], they have not attempted to rate the effectiveness of individual STR loci in assignment studies. We therefore adopted methods used in admixture mapping of human disease genes, for which genetic markers have been identified that have a high ability to distinguish among human lineages of different geographic origin [41,42,43,44], to determine the utility of each elephant STR locus for geographic assignment. In order to quantify the ability of different genetic markers to assign the provenance of elephants, the Shannon Information Content (SIC) [45] of each microsatellite locus was estimated. The SIC is often preferred over other measures of informativeness because many other measures do not consider the influence of centrality, whereby alleles that are absent (or nearly so) in one population will be more informative than those common in both populations [41,42]. The SIC quantifies the informativeness of the marker or set of markers in determining the ancestral state (or source of origin) of the loci [41,42]. In the case of a biallelic locus such as a microsatellite in an elephant sample of unknown provenance, it is necessary to know the frequency of the alleles in the parental populations from Africa, information that was provided by our current STR data. The ability of each of our STR loci to differentiate among elephants from different locales is shown in Figure 7. Each locus was tested for the ability to distinguish between forest and savanna elephants, between southern and eastern African savanna ele- phants, and between elephants at the two most sampled locales within various regions. Highly informative loci for a given pair of populations had the highest values of SIC, for example, p04 in the Kruger-Namibia comparison (Figure 7, top). For almost all markers (except p04), the highest information content was present in the savanna-forest comparison, with the next most informa- tive comparisons coming in a distant second (Figure 7, bottom). Most maximum SIC values coincided with the 50% admixture PLoS ONE | www.plosone.org 9 June 2011 | Volume 6 | Issue 6 | e20642