Phylogeny and Genetics

The earliest primates likely evolved from an insectivorous mammal during the late Cretaceous or Paleocene (Fleagle, 1987). Through the process of natural selection and evolutionary processes such as genetic drift, this common ancestor would give rise to a diverse phylogeny that's phylogenetic tree would grow to include both chimpanzees, bonobos, and humans. Comparative studies have shown that among existing mammals, primates, tree shrews, flying lemurs and bats are all closely related, to the extent that they are more closely related to each other than any other group of mammals (Fleagle, 1987). Once classified as a form of primitive primate (Clark, 1926), these tree shrews would go on to show brain and reproductive features that were found to be non-homologous structures to primates, prompting a reclassification as non-primates (Fleagle, 1987). Later anatomical assays would go on to identify more robust homologous features that would link the phylogenetic relationship between tree shrews and primates. The current understanding of mammal phylogeny supports tree shrews as a sister taxon of Primates (Lin et al., 2014). Thus, a common progenitor is shared between the rodent-like tree shrew, early anthropoids, and anatomically modern bonobos, chimpanzees, and humans.

Diverging from chimpanzees approximately one m.y.a., bonobos share a complicated evolutionary history concerning their divergence from chimpanzees (De Manuel et al., 2016). The most widely accepted hypothesis for this divergence is that of geographic separation of the common progenitor of chimpanzees and bonobos, resulting in allotropic speciation (Takemoto,Kawamoto, & Furuich, 2015). With bonobos inhabiting the southern-most side of the Congo River, the most cited hypothesis for this vicariance is the formation of the Congo River, an event that would have resulted in speciation if aided by genetic drift and probable bottlenecking (Takemoto,Kawamoto, & Furuich, 2015). Though widely accepted, this hypothesis is being challenged by current geographical data, creating a need to reevaluate the mechanism of speciation concerning chimpanzees and bonobos (Takemoto,Kawamoto, & Furuich, 2015). Recently, a new hypothesis is being examined. This hypothesis addresses the probability of migration from one side of the river to the other. This dispersal event may have been achievable at specific locations during periods of reduced river discharge, allowing early bonobos to easily cross, forming an independent clade from chimpanzees (Takemoto,Kawamoto, & Furuich, 2015).

As one might conclude at first glance, P. paniscus appears closely related to the common chimpanzee (P. troglodytes). This assumption is correct, as bonobos share more genetic similarities with common chimpanzees than any other primate (McHenry, 1984). Bonobos are similar in adult bodyweight to a subspecies of chimpanzees (Pan troglodytes schweinfurthii), with the most noticeable differences being that bonobos have darker faces, more gracile craniums, slimmer limbs, and longer hands and feet (Fleagle, 1987). Much of what is known about chimpanzee anatomy can be extrapolated to descriptions of bonobo anatomy, with the most apparent caveats being related to size. Chimps and bonobos are morphologically similar, though adult bonobos are more morphologically similar to immature chimpanzees (Fleagle, 1987). This being addressed, adult chimpanzees tend to have a morphology that corresponds to juvenile gorillas (Fleagle, 1987). Thus, both bonobos and chimpanzees share a common ancestor with anatomically modern humans (H. sapiens), and though there are various subspecies of chimpanzee, P. paniscus has no know subspecies, though are distinguishable from chimpanzee morphology (Fischer et al., 2011). Anatomically, though bonobos and chimps differ little on a genetic level (Fischer et al., 2011), some physical characteristics are shared more frequently between anatomically modern humans than in chimpanzees (Diogo, 2017). However, it should be noted that these similarities are minor. On a genetic level, recent investigations into the similarities and dissimilarities between the genomes of bonobo, humans, and chimpanzees have concluded that more than 3% of the human genome has more in common with bonobos and chimpanzee than chimpanzee and humans (Prufer et al., 2012). When taking into account that over 98% of the genetic information possessed by humans is shared with the chimpanzee (Gibbons, 1998) and that there are anatomical similarities between humans and bonobos, one is left to speculate whether or not bonobos are slightly closer in similarity to humans than chimpanzees.

In the genetic investigation of diverging populations, an important question is what role gene-flow plays in the process of divergence and how genetic drift influences this evolutionary process. Based on 75 complete genomes of bonobos and chimpanzees, researchers were able to identify substantial amounts of genetic material shared between central and eastern subspecies of chimpanzees and bonobos (De Manuel et al., 2016). Evidence from this investigation leads researchers to infer that genetic admixtures of alleles were introduced between the two species at two different points in history, the first event occurring 500,000 years ago and the second occurring approximately 200,000 years ago (De Manuel et al., 2016). This study shows that our closest relatives were subject to genetic admixture via successful interbreeding millennia after the initial branch-point split.