Bonobos fall within the genomic variation of chimpanzees

Abstract

To gain insight into the patterns of genetic variation and evolutionary relationships within and between bonobos and chimpanzees, we sequenced 150,000 base pairs of nuclear DNA divided among 15 autosomal regions as well as the complete mitochondrial genomes from 20 bonobos and 58 chimpanzees. Except for western chimpanzees, we found poor genetic separation of chimpanzees based on sample locality. In contrast, bonobos consistently cluster together but fall as a group within the variation of chimpanzees for many of the regions. Thus, while chimpanzees retain genomic variation that predates bonobo-chimpanzee speciation, extensive lineage sorting has occurred within bonobos such that much of their genome traces its ancestry back to a single common ancestor that postdates their origin as a group separate from chimpanzees.

Figure 1. Map of population ranges.

Figure 2. 50% majority consensus tree for mtDNA (mt) and each of the fifteen nuclear regions (a to o).

Colors: red for bonobos, green, grey, blue, and yellow for western, central, eastern and vellerosus chimpanzees, respectively.

Figure 3. Plot of inferred ancestry for each individual assuming four populations, as assessed by the program Structure.

The inference was done blind to actual population labels. Individuals: 1 to 20 are bonobos, 21 to 40 central chimpanzees (with individuals 24, 27 and 40 being the ones confiscated in DRC), 31 to 60 eastern chimpanzees, 61 to 64 Nigerian-Cameroonian, 65 to 78 western chimpanzees. Colors: green for bonobos; orange, blue and red for western, central, and eastern chimpanzees, respectively.

Figure 4. Principle Component Analysis (PCA) including all individuals.

PC1 separates bonobos from chimpanzees, PC2 western chimpanzees from other chimpanzees, PC3 and PC4 are gradients of genetic variation. Colors: green for bonobos; orange, blue, red and black for western, central, eastern and Nigerian-Cameroonian chimpanzees, respectively. The significance of PC3 does not depend on the inclusion of the three chimpanzees confiscated in Democratic Republic of Congo (results not shown).