Paul R. Sesink Clee

Species evolve from populations with ancestor-descendant relationships in a bifurcating process shaped by geography, gene flow, genetic drift, and natural selection leading to local adaptation to prevailing environmental and ecological conditions. Building on this foundational understanding, we explored local adaptation in chimpanzees ( Pan troglodytes ) at a key geographical intersection in Cameroon where the two main chimpanzee phylogenetic lineages converge. The Nigeria-Cameroon chimpanzee ( P. t. ellioti ) and central chimpanzee ( P. t. troglodytes ) last shared a common ancestor about 500 thousand years ago, with occasional gene flow between them. The evolutionary processes driving their prolonged separation are not fully understood, but neutral evolutionary mechanisms alone cannot account for the observed divergence pattern. Cameroon is often referred to as ‘Africa in miniature’ because the Gulf of Guinea Forest, Congo Basin Forest, and savanna converge there, forming an ecotone. Thus, this contact zone between subspecies in Cameroon provides a unique natural laboratory that enabled us to investigate how environmental variation and natural selection shape divergence in chimpanzees. We developed a genome-wide panel of single-nucleotide polymorphisms (SNPs) in 112 wild chimpanzees sampled in multiple habitats across this contact zone. We augmented SNP discovery by sequencing eight new chimpanzee genomes from Cameroon and analyzing them with previously published chimpanzee genomes. We found that P. t. ellioti and P. t. troglodytes diverged from one another around 478,000 years ago and occasionally exchange migrants. We identified 1,690 unique SNPs across 905 genes associated with 31 environmental variables that describe the habitat. These genes are involved in essential biological processes, including immune response, neurological development, behavior, and dietary adaptations. This study highlights the importance of understanding the geographical context of natural selection, paving the way for future studies to interpret evidence for genetic variation with phenotypic traits and deepening our understanding of how populations diverge in response to environmental pressures. Author Summary: We investigated how local adaptation contributes to shaping the diversification of chimpanzee subspecies at the geographical convergence point for the two major branches of the chimpanzee phylogenetic tree. We analyzed genome-wide SNP genotypes of 112 chimpanzees sampled from natural communities located in this understudied area. We used tiered methods that identified 905 genes subject to selection, each associated with one or more of 31 environmental predictors describing the habitat. We found strong signals of selection in immune response genes that separate P. t. troglodytes from P. t. ellioti , highlighting the important role of different pathogen histories in their evolution. We also found evidence of selection in genes associated with neurological development, behavior, and diet, that separate both the subspecies and populations of P. t. ellioti that occupy different niches. These findings suggest that ecological and cultural factors may also contribute to shaping the diversification of chimpanzees across the contact zone.

Biomod2EZ is a suite of R scripts to use in conjunction with the Biomod2 R package by Thuiller et al. (2016) that is used to create ensemble ecological niche models using up to 11 different modeling techniques. Biomod2EZ adds to the functionality of Biomod2 (Thuiller et al. 2016) by incorporating a report generation feature, detailed script annotation, and sample dataset/tutorial to ease the transition from ecological niche modeling using a Graphical User Interface to the coding environment of the R framework (R Development Core Team, 2016).

Chimpanzees (Pan troglodytes) can be divided into four subspecies. Substantial phylogenetic evidence suggests that these subspecies can be grouped into two distinct lineages: a western African group that includes P. t. verus and P. t. ellioti and a central/eastern African group that includes P. t. troglodytes and P. t. schweinfurthii. The geographic division of these two lineages occurs in Cameroon, where the rages of P. t. ellioti and P. t. troglodytes appear to converge at the Sanaga River. Remarkably, few population genetic studies have included wild chimpanzees from this region. We analyzed microsatellite genotypes of 187 wild, unrelated chimpanzees, and mitochondrial control region sequencing data from 604 chimpanzees. We found that chimpanzees in Cameroon and eastern Nigeria comprise at least two, and likely three populations. Both the mtDNA and microsatellite data suggest that there is a primary separation of P. t. troglodytes in southern Cameroon from P. t. ellioti north and west of the Sanaga River. These two populations split ~200-250 thousand years ago (kya), but have exchanged one migrant per generation since separating. In addition, P. t. ellioti consists of two populations that split from one another ~4 kya. One population is located in the rainforests of western Cameroon and eastern Nigeria, whereas the second population appears to be confined to a savannah-woodland mosaic in central Cameroon. Our findings suggest that there are as many as three genetically distinct populations of chimpanzees in Cameroon and eastern Nigeria. P. t. troglodytes in southern Cameroon comprises one population that is separated from two populations of P. t. ellioti in western and central Cameroon, respectively. P. t. ellioti and P. t. troglodytes appear to be characterized by a pattern of isolation-with-migration, and thus, we propose that neutral processes alone can not explain the differentiation of P. t. ellioti and P. t. troglodytes.

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. 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. 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.

The mechanisms that underlie the diversification of tropical animals remain poorly understood, but new approaches that combine geo-spatial modeling with spatially explicit genetic data are providing fresh insights on this topic. Data about the diversification of tropical mammals remain particularly sparse, and vanishingly few opportunities exist to study endangered large mammals that increasingly exist only in isolated pockets. The chimpanzees of Cameroon represent a unique opportunity to examine the mechanisms that promote genetic differentiation in tropical mammals because the region is home to two chimpanzee subspecies: Pan troglodytes ellioti and P. t. trogolodytes. Their ranges converge in central Cameroon, which is a geographically, climatically and environmentally complex region that presents an unparalleled opportunity to examine the roles of rivers and/or environmental variation in influencing the evolution of chimpanzee populations. We analyzed microsatellite genotypes and mtDNA HVRI sequencing data from wild chimpanzees sampled at a fine geographic scale across Cameroon and eastern Nigeria using a spatially explicit approach based upon Generalized Dissimilarity Modeling. Both the Sanaga River and environmental variation were found to contribute to driving separation of the subspecies. The importance of environmental variation differed among subspecies. Gene-environment associations were weak in P. t. troglodytes, whereas environmental variation was found to play a much larger role in shaping patterns of genetic differentiation in P. t. ellioti. We found that both the Sanaga River and environmental variation likely play a role in shaping patterns of chimpanzee genetic diversity. Future studies using single nucleotide polymorphism (SNP) data are necessary to further understand how rivers and environmental variation contribute to shaping patterns of genetic variation in chimpanzees.