Evolution of a HOXB6 intergenic region within the great apes and humans

Data accumulated over the past decade from several loci suggest that nonhuman primates have a greater amount of intraspecific genetic variation relative to humans. In phylogenetic reconstructions among primates that are based on genetic data, therefore, it becomes essential to adequately sample the population(s) being analyzed. Inadequate sampling may not only underestimate variation within any given population, but such an underestimate may confound any phylogenetic or population-specific conclusions implied by the data. Here we present inter- and intraspecific data on the molecular evolution of an approximately 1·0 kb intergenic HOXB6 sequence among humans, common chimpanzees, pygmy chimpanzees, gorillas and orang-utans. To date, this study represents the most comprehensive investigation of a noncoding nuclear locus among the great apes and humans that examines the nature and amount of intraspecific variation in DNA sequences. Not only do these HOXB6 data continue to support earlier findings that Homo sapiens sapiens has less genetic variation than any great ape species (Ruano et al., 1992; Deinard and Kidd, 1995), but they strongly suggest that a high level of genetic polymorphism existed within the common ancestor of the African ape clade (Homo-Pan-Gorilla). Despite detecting two nucleotide substitutions linking Pan and Homo, we caution against concluding that the HOXB6 data definitively support a Homo-Pan clade to the exclusion of Gorilla. Rather, we believe that taking into consideration the level of genetic polymorphism that is likely to have existed within the common ancestor, the most prudent conclusion that can be made from all available data, including morphological, karyotypic and genetic data, may be that speciation among Homo-Pan-Gorilla is best represented by a 'trichotomy'.