Reconciling African Elephant Phylogenies Figure 7. Quantification of the effectiveness of individual STR loci for establishing the provenance of African elephants. Each locus was tested for the ability to distinguish between forest and savanna elephants, between southern and eastern African savanna elephants, and between elephants at the two most populous locales within various regions. (Top) The Shannon Information Content (SIC) is plotted for four pairwise comparisons between locales for STR loci (note that the y-axis scale differs among comparisons). The maximum SIC does not always occur at the 0.5 admixture value since the locus may be more effective at distinguishing one population than the other. (Bottom) Most loci were better at distinguishing forest and savanna elephants than at distinguishing between two regional locales. Some STR loci, such as p18, are consistently informative for distinguishing between elephants from different locales; other loci such as p16 are consistently uninformative. This suggests that p18 should be used, and p16 replaced, when selecting a set of STR loci for use in establishing the origins of poached ivory. This quantitative approach comparing different STRs for their utility can be used to identify an improved set of STR loci that would enhance the ability to establish the origins of confiscated ivory [44]. doi:10.1371/journal.pone.0020642.g007 proportion overall, but some individual values deviated. For example, the maximum SIC for p11 in the Kruger-Namibia comparison (the gray line, second in height) occurred slightly towards the left, thus the information content is not the same. The maximum SIC does not always occur at the 0.5 admixture value since a locus may be more effective at distinguishing one popu- lation than the other. For example, if the major allele frequency is about 50% in population one, but 100% in population two, it would be more effective to use the given marker to identify individuals from population one in population two than vice versa. As has been shown in the case of human STRs [44], our results suggested that replacement of relatively uninformative loci by highly informative loci could produce a set of markers with an ability much greater than that of the current set of randomly chosen markers to establish the provenance of illegally poached ivory. For example, when we used 4 STRs with low SIC values (p11, p14, p15, p16) in a STRUCTURE analysis, they did not distinguish Kruger elephants at all from Namibian elephants, as 50% of each population fell into each of the partitions at K = 2 (using only these two populations). However, using 4 STRs with high SIC values (p12, p17, p18, p29) in a similar analysis did begin to differentiate elephants between these two locales: using only these two populations, at K = 2 the values for STRUCTURE partitions 1 and 2 were 0.36 and 0.64, respectively, for Kruger elephants; while they were 0.61 and 0.39, respectively, for Nami- bia elephants. This quantitative approach comparing different STRs for their SIC can thus identify an improved set of STR loci to utilize for the purpose of assigning the geographic provenance of elephants. Discussion Two species of elephant are present in Africa Our new data and reanalyses of previous data reconciled the mtDNA phylogeographic patterns present among African ele- phants to the two-species division that is evident from nuclear DNA and morphological analyses. Previous studies found a deep and almost complete nuclear genetic separation of African ele- phants into forest and savanna species, with a few hybrids detected primarily in the regions where tropical forest and savanna habitats PLoS ONE | www.plosone.org 10 June 2011 | Volume 6 | Issue 6 | e20642