We present a hidden Markov model (HMM) for inferring gradual isolation
between two populations during speciation, modelled as a time interval
with restricted gene flow. The HMM describes the history of adjacent
nucleotides in two genomic sequences, such that the nucleotides can be
separated by recombination, can migrate between populations, or can
coalesce at variable time points, all dependent on the parameters of the
model, which are the effective population sizes, splitting times,
recombination rate, and migration rate. We show by extensive simulations
that the HMM can accurately infer all parameters except the
recombination rate, which is biased downwards. Inference is robust to
variation in the mutation rate and the recombination rate over the
sequence and also robust to unknown phase of genomes unless they are
very closely related. We provide a test for whether divergence is
gradual or instantaneous, and we apply the model to three key divergence
processes in great apes: (a) the bonobo and common chimpanzee, (b) the
eastern and western gorilla, and (c) the Sumatran and Bornean
orang-utan. We find that the bonobo and chimpanzee appear to have
undergone a clear split, whereas the divergence processes of the gorilla
and orang-utan species occurred over several hundred thousands years
with gene flow stopping quite recently. We also apply the model to the Homo/Pan speciation event and find that the most likely scenario involves an extended period of gene flow during speciation.
Category Archives: bonobo
The human apolipoprotein E (APOE) gene is polymorphic, with three primary alleles (E2, E3, E4) that differ at two key non-synonymous sites. These alleles are functionally different in how they bind to lipoproteins, and this genetic variation is associated with phenotypic variation for several medical traits, including cholesterol levels, cardiovascular health, Alzheimer’s disease risk, and longevity. The relative frequencies of these alleles vary across human populations, and the evolution and maintenance of this diversity is much debated. Previous studies comparing human and chimpanzee APOE sequences found that the chimpanzee sequence is most similar to the human E4 allele, although the resulting chimpanzee protein might function like the protein coded for by the human E3 allele. However, these studies have used sequence data from a single chimpanzee and do not consider whether chimpanzees, like humans, show intra-specific and subspecific variation at this locus.
Methodology and Principal Findings
To examine potential intraspecific variation, we sequenced the APOE gene of 32 chimpanzees. This sample included 20 captive individuals representing the western subspecies (P. troglodytes verus) and 12 wild individuals representing the eastern subspecies (P. t. schweinfurthii). Variation in our resulting sequences was limited to one non-coding, intronic SNP, which showed fixed differences between the two subspecies. We also compared APOE sequences for all available ape genera and fossil hominins. The bonobo APOE protein is identical to that of the chimpanzee, and the Denisovan APOE exhibits all four human-specific, non-synonymous changes and appears functionally similar to the human E4 allele.
We found no coding variation within and between chimpanzee populations, suggesting that the maintenance of functionally diverse APOE polymorphisms is a unique feature of human evolution.
|Table 1. Variation at key APOE functional sites in Homo and Pan.|
Stubbornly under-estimating divergence times by almost 100%
- Category: bonobo at my old blog Leherensuge
- Category: bonobo at this blog
- Category: human evolution
- Molecular clock obscuring the real origin of primates
- Chimps and humans diverged 8 million years ago
* Note: I know someone will say that Homo sp. are not “apes” but I say Homo are a subset of the great apes clade (Hominidae) phylogenetically and therefore great apes ourselves – something to be irrationally proud of, of course.
AbstractTo 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.
|Red: bonobos – Other colors: several chimpanzee populations|
- 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.
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.
|A look at chimpanzee (L) and bonobo (R) central network (from the press release)|
Interestingly (from the SD article):
The results showed that bonobos have more developed circuitry for key nodes within the limbic system, the so-called emotional part of the brain, including the amygdala, the hypothalamus and the anterior insula. The anterior insula and the amygdala are both implicated in human empathy.“We also found that the pathway connecting the amygdala and the prefrontal cortex is larger in bonobos than chimpanzees,” Rilling says. “When our amygdala senses that our actions are causing someone else distress, we may use that pathway to adjust our behavior in a prosocial direction.”Chimpanzees have better developed visual system pathways, according to the analysis. Previous research has suggested that those pathways are important for tool use, a skill which chimpanzees appear better at than bonobos.