meet [4,6,7]. This genetic separation into forest and savanna elephant species has now been demonstrated using slower-evolving nuclear autosomal sequences, faster-evolving autosomal STRs, sequences of multiple X-linked loci, and Y-chromosome sequenc- es, and was recently supported following comparison of hundreds of nuclear sequences across proboscideans [4,5,6,7]. The lack of gene flow between forest and savanna populations, despite the existence of a hybrid zone, has especially supported their status as species under the biological species concept [46,47,48] (as previously discussed [1]): among 1764 savanna elephant X-chro- mosome sequences previously examined, 1762 (99.9%) had been found to be haplotypes not present among forest elephants, while not a single savanna elephant nuclear haplotype has ever been reported in a tropical forest elephant population [4]. Likewise, among Y-chromosome sequences examined in 205 male ele- phants, there had been only one hybrid exception to the otherwise complete separation into distinctive forest and savanna elephant clades [4]. The Bayesian STRUCTURE analysis conducted for the current study used a novel set of STR loci to support and extend these conclusions. Few forest–savanna elephant hybrids were identified by STRUCTURE, and for each species the proportion of admixture from the other species was inferred to be under one percent. Previous studies have convincingly reported data sup- porting the ‘‘polyphyly of the forest and savannah [mtDNA] haplotypes’’ [12] and ‘‘multiple refugial mitochondrial lineages’’ [16], and these observations are also in accordance with mtDNA patterns found among the elephants used for the current study [4]. However, based on these mtDNA patterns, it had been further hypothesized that ‘‘interbreeding has had a major impact on the reciprocal integrity of extant forest and savannah elephants’’ [12], and that ‘‘recurrent hybridization among them render[s] a simple forest/savannah elephant split inapplicable to modern African elephant populations’’ [16]. Yet these hypotheses regarding the overall genomic affinities of African elephants were not supported by the results of nuclear genotyping (Figures 1, 2, 5). The current genetic assignment and factorial correspondence analyses demon- strate nuclear genetic partitioning between forest and savanna elephants (Figures 1, 2), with nuclear admixture between species at under one percent, even in the face of widespread forest clade mtDNA introgression in the same savanna elephants (Figure 5) [4]. Should incongruent mtDNA patterns in African elephants have been anticipated? Our results also strongly support the observation that mtDNA patterns in elephants are incongruent with their overall population structure [1,4,13]. Before discussing the observed genetic patterns in detail, it is worth considering whether the phylogeographic patterns of mitochondrial genetic markers should have been expected to be incongruent with those of nuclear markers, given the social structure of elephants. Elephant females reaching maturity remain with their natal core social group or ‘‘herd’’ [49,50]. Since females are not typically exchanged between herds [49,50], mitochondrial gene flow between herds will be essentially nonexistent, and only changes in the geographic ranges of the core social groups would alter the phylogeography of mtDNA hap- lotypes. Since the mitochondrial genome is only transmitted maternally, there is an important consequence of the matrilineal and matrilocal structure of core social groups among elephants: the mitochondrial genome is necessarily coupled to the geographic range of the core social group. By contrast, males leave the natal herd and mediate gene flow between herds and across the African landscape [1,49,50,51]. This is consistent with the observation that Reconciling African Elephant Phylogenies sex differences in dispersal tend to be high among long-lived, highly social, polygynous mammals [52,53]. Since males can transmit every locus except mtDNA, the mitochondrial genome is subject to an extremely circumscribed evolutionary trajectory very different from that affecting every other genetic locus [1,54]. For example, were two herds of dif- ferent mtDNA and nuclear genotypes to continuously inhabit adjacent ranges for hundreds of generations, the two locales would become indistinguishable in terms of nuclear markers (even at the fastest-evolving nuclear markers) due to male-mediated gene flow. Yet since females are not typically exchanged between two herds, in principle there might be no mitochondrial gene flow between the locales, and even between adjacent herds the mtDNA genetic differences would persist and might even increase due to novel mutations within each lineage. The combination of matrilocal social structure and intense male reproductive competition greatly increases the effective population size and coalescent of the mtDNA genome relative to nuclear loci [54,55]. Thus mtDNA could provide a signal of ancient population partitioning that would not be at all reflective of the overall current population structure [55]. By contrast, not a single nuclear locus is ‘‘bound to the herd’’ like mtDNA. Males in one generation can transmit nuclear alleles from their natal herd to other herds. This occurs regardless of whether or not males traverse long distances. Males of one gene- ration may transmit nuclear alleles to a nearby herd; their male offspring can then transmit them to even more distant herds, and thus nuclear alleles have the potential to traverse the African landscape. One notable point in this regard is that females do transmit their nuclear genetic endowment to male offspring, thus all of their nuclear alleles (autosomal or X-linked) thereby become easily transmitted across the landscape. Among genetic markers, only the mtDNA molecule is subject to the severe demographic constraint of being bound to the herd. All other elephant genetic markers are geographically unbound and subject to widespread and (compared to mtDNA) relatively rapid transmission across the geographic landscape [54]. Since the mtDNA would be expected to have a phylogeographic pattern that is unique and different from that of any other genetic loci, use of this marker in elephants should have been expected to lead to quite faulty inferences regarding their overall population structure or systematics [55]. Similar incongruence between mtDNA and nuclear phylogeo- graphic patterns has been reported among a number of other mammalian taxa and, in cases where two species hybridize, genetic markers transmitted by the more highly dispersing sex were found to better delimit species [56]. Reconciling the phylogeography of mtDNA and nuclear DNA in African elephants We have quantified the relationship between the proportion of elephants in a population that carry S clade savanna mtDNA and the proportion of the population assigned to forest- or savanna- elephant nuclear genetic partitions (Figure 5). Surprisingly, the presence of S clade mtDNA among even a few elephants, even at low frequencies, or even in a nearby location (Figures 4 and 5), was sufficient to confer overwhelmingly savanna elephant nuclear genotypes to the elephants (Figure 5). By establishing the identity or similarity of mtDNA designations that differed across studies (Figure 3 and Figure S2), we could also analyze the geographic distribution of F clade and S clade mtDNA for hundreds of previously sequenced haplotypes in 81 locations across the ranges of forest and savanna elephants. This revealed that S clade mtDNA was only carried by elephants across the traditionally accepted range of the savanna elephant. S clade mtDNA was PLoS ONE | www.plosone.org 11 June 2011 | Volume 6 | Issue 6 | e20642