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Category Archives: bonobo

Hominid speciation: sudden or gradual?

It depends apparently: bonobos may have diverged quite suddenly while in other cases, including the Pan-Homo split, the process of speciation appears to have been more gradual.

Thomas Mailund et al., A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species. PLoS ONE 2012. Open access LINK [doi:10.1371/journal.pgen.1003125]

Abstract

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.

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Variation in human (modern and archaic) and chimpanzee lipoprotein APOE

This new study has some interest in understanding some details, of metabolic relevance, of the genetics of humans and our closest relatives:
Annick McIntosh et al., The Apolipoprotein E (APOE) Gene Appears Functionally Monomorphic in Chimpanzees (Pan troglodytes). PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0047760]

Abstract

Background

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.

Conclusions

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.

The relevant details are all in table 1:

Table 1. Variation at key APOE functional sites in Homo and Pan.
There is uncertainty about the correctness of the only known Neanderthal triplet.
Even if E4 seems to be the ancestral type, E3 is the most common allele in our species, ranging from 50% in most populations to as much as 90% among some tribes.
 

Bonobo genome sequenced

Ulundi (source)
The last great ape* to be sequenced has been the bonobo, it complements the Homo sapiens, Neanderthal, Denisovan (probably a hybrid), chimpanzee, gorilla and orangutan genomes:
The reference genome was sequenced from a female bonobo captive at Leizpig Zoo, known as Ulundi.
The genome will, hopefully, help understand better the genetic basis of our being as humans and, maybe also get some inferences on our prehistory. 

Stubbornly under-estimating divergence times by almost 100%

In this sense I want to emphasize that the paper insists in producing Pan-Homo and internal Pan divergence times that are irrationally low. The cause of this systematic error that persists through some literature seems to be rooted on the Homo-Pongo divergence estimate, which I do not know the details about but seems from context to be an extreme under-estimate. 
The matter was already debated in 2008 by Jenniffer L. Caswell, who explained that the Bonobo-Chimpanzee split cannot be more recent than 1.5 to 2.0 million years because it was then when the Congo River was formed separating the two populations radically (allopatric speciation). This is quite apparent in the distribution of bonobos and chimpanzees:
fig. 1a
So unless the geology is wrong, bonobos and chimpanzees diverged 1.5 to 2 million years ago, and not a mere million years ago, as this paper claims.
This has important implications for the Homo-Pan divergence age, as I have discussed again and again. Assuming that the 4.5:1 ration estimated in this paper is correct, then the actual Homo-Pan divergence age ranges between 6.8 to 9.0 million years ago (and not a mere 4.5 Ma), with a median of 7.9 Ma, quite similar to the 8 Ma estimate I have been defending since the Caswell paper was published in 2008.

See also

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* 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.

 

Bonobos fall partly within Chimpanzee genetic variability

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

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.

 
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Posted by on June 30, 2011 in bonobo, chimpanzee, Genetics

 

Bonobo and chimpanzee brains differ in wiring

Bonobo relaxing
They have similar sized brains, they look alike enough for bonobos to have been called once “pygmy chimpanzees”, and in fact they belong to the same genus (Pan) having diverged some 1.3 to 2 million years ago (or 1.7-2.6 Ma following the logical thread of a newer paper). Their differences are therefore perfectly comparable to those among Homo species (all but H. sapiens extinct by now).
For this reason and because they are very close relatives of us (we diverged some 8-10 Ma ago), the two Pan sp. species are a major reference for anthropology, not the least because they display so different psychologies and sociologies in spite of being so closely related: while chimpanzees are male-centric, hierarchical, violent and retain female sexual (and not just reproductive) cycles, bonobos are female-centric, cooperative, peaceful and joyful and have sex all the time. Bonobos are also empathic like us, while the empathy of chimpanzees is, if it exists at all, quite shallow.
Now a new paper, using non-invasive brain scan techniques, has managed to discern the differences in what we can well call central wiring in the brains of chimpanzees and bonobos:
The paper is discussed at Science Daily

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.