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Background  The Nigeria-Cameroon chimpanzee ( Pan troglodytes ellioti)  is found in the Gulf of Guinea biodiversity hotspot located in western equatorial Africa. This subspecies is threatened by habitat fragmentation due to logging and agricultural development, hunting for the bushmeat trade, and possibly climate change. Although  P. t. ellioti  appears to be geographically separated from the neighboring central chimpanzee ( P. t. troglodytes ) by the Sanaga River, recent population genetics studies of chimpanzees from across this region suggest that additional factors may also be important in their separation. The main aims of this study were: 1) to model the distribution of suitable habitat for  P. t. ellioti  across Cameroon and Nigeria, and  P. t. troglodytes  in southern Cameroon, 2) to determine which environmental factors best predict their optimal habitats, and 3) to compare modeled niches and test for their levels of divergence from one another. A final aim of this study was to examine the ways that climate change might impact suitable chimpanzee habitat across the region under various scenarios.    Results  Ecological niche models (ENMs) were created using the software package Maxent for the three populations of chimpanzees that have been inferred to exist in Cameroon and eastern Nigeria: ( i )  P. t. troglodytes  in southern Cameroon, ( ii )  P. t. ellioti  in northwestern Cameroon, and ( iii )  P. t. ellioti  in central Cameroon. ENMs for each population were compared using the niche comparison test in ENMtools, which revealed complete niche divergence with very little geographic overlap of suitable habitat between populations.    Conclusions  These findings suggest that a positive relationship may exist between environmental variation and the partitioning of genetic variation found in chimpanzees across this region. ENMs for each population were also projected under three different climate change scenarios for years 2020, 2050, and 2080. Suitable habitat of  P. t. ellioti  in northwest Cameroon / eastern Nigeria is expected to remain largely unchanged through 2080 in all considered scenarios. In contrast,  P. t. ellioti  in central Cameroon, which represents half of the population of this subspecies, is expected to experience drastic reductions in its ecotone habitat over the coming century.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-014-0275-z) contains supplementary material, which is available to authorized users.

Chimpanzee population structure in Cameroon and Nigeria is associated with habitat variation that may be lost under climate change