Bonobos fall partly within Chimpanzee genetic variability

That is what a new paper has found after studying extensively Pan sp. genetic diversity:

A. Fischer, Bonobos Fall within the Genomic Variation of Chimpanzees. PLoS ONE, 2011. Open access. 

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.

This is very easy to appreciate in fig. 2, showing 50% majority consensus tree for mtDNA (mt) and each of the fifteen nuclear regions (a to o):

Red: bonobos - Other colors: several chimpanzee populations

We can see that Bonobos are monophyletic for all categories but that chimpanzees retain much more of the shared ancestral diversity for many of them. 

We see:

• strict bonobo/chimp dichotomy in mtDNA and nuclear regions b, d, e and i only
• bonobos as one of several branches of the the greater Pan family in nuclear regions c, f, h, k and o
• bonobos as derived within an otherwise chimpanzee branch in regions a, g, j, l, m and n. 

This unequal relation between the two Pan species may serve as reference when considering other speciation processes, including those leading to ourselves. 

Update (Jul 1): a somewhat related paper (which I am not going to comment) was just published:

G. schubert et al., Male-Mediated Gene Flow in Patrilocal Primates. PLoS ONE 2011. Open Access.