Pan-Homo split: 11-17 million years ago

Chimpanzee mutation rate is largely determined by fathers' age and, overall, implies a Pan-Homo divergence rate of ~13 million years (95% CI: 11-17 Ma), about double than usually assumed by conservative scholastic inertia.

Oliver Venn et al., Strong male bias drives germline mutation in chimpanzees. Science 2014. Pay per view → LINK [doi:10.1126/science.344.6189.1272]

cc Matthew Hoelscher

The focus of this study are the important differences between patrilineal and matrilineal mutation rate depending on the father's age among chimpanzees, notably more biased than among humans. However the resulting estimate for Pan-Homo divergence is not less important because it radically challenges the usual assumptions of 5-7 Ma, repeated once and again in molecular clock estimates, which are based on studies that are already quite obsolete.

In the studied captive population of Western chimpanzees 30 out of 35 mutations happened in the paternal lineage, and these increase with the father's age. No effect could be attributed to maternal age or familiar peculiarities.

Interestingly most of these patrilineal mutations happen near the telomeres, an effect not seen in female line mutations.

Owing to this gender bias, the mutation rate of the X chromosome among chimpanzees is 74% that of autosomal DNA (in humans: 85%). 

The gender bias in mutation rate and its differential with humans is attributed to differences in mating systems among great apes, with chimpanzees having the greatest competition among males, what is reflected in testicle size. They predict that gorillas (who experience less competition between males) will show less patrilineal mutation rate bias than humans and chimpanzees.

This is probably the more synthetic paragraph from the study:

Under a model in which the mutation rate increases linearly with parental age, the rate of neutral substitution is the ratio of the average number of mutations inherited per generation to the average parental age. We predict the neutral substitution rate to be ~0.46 × 10⁻⁹ per base pair (bp) per year in chimpanzees, compared to estimates in humans of ~0.51 × 10⁻⁹ bp⁻¹ year⁻¹ (9). These results are consistent with near-identical levels of lineage-specific sequence divergence (12) but surprising given the differences in paternal age effect. In the intersection of the autosomal genome accessible in this study and regions where human and chimpanzee genomes can be aligned with high confidence, the rate is slightly lower (0.45 × 10⁻⁹ bp⁻¹ year⁻¹) and the level of divergence is 1.2% (13), implying an average time to the most common ancestor of 13 million years, assuming uniformity of the mutation rate over this time (95% ETPI 11 to 17 million years; table S11).

13 million years of the hominid line

This is not at all the first study to highlight the extreme dubiousness of the usual scholastic assumptions regarding the Pan-Homo divergence, which taint so many genetic studies, turning their chronological estimates totally worthless.

In 2010, Wilkinson et al. estimated a Pan-Homo divergence rate of 8-10 Ma. In 2012 Langergraber et al. recalibrated previous studies getting a Pan-Homo divergence bracket of 6.78-13.45 Ma (fig.2), while the divergence from Gorilla would be significantly older: 8.31-20.0.

Fig. 1 from Langergraber 2012. Legend: Diagram illustrating the branching pattern and timing of the splits between humans, chimpanzees, bonobos, western gorillas, and eastern gorillas. The paler shading indicates the range of split times inferred in this study. Cartoon skulls indicate approximate age of the indicated fossil remains, but do not imply that these fossils were necessarily on those ancestral lineages or that entire crania actually exist for these forms.

A key fossil affecting this controversy is Sahelanthropus tchadiensis (Toumaï), which has been recently confirmed to be in the human line on several hardly questionable traits and is dated to c. 7 Ma.

A related debate is whether primates in general are much older than usually claimed and lived already in the Jurassic, something suggested by the already mentioned Wilkinson study and also by Heads 2010. Here a major issue is that mainline conservative estimates would have the ancestors of New World monkeys swimming (island hoping) to South America, something that those monkeys (and most other primates) simply will not do. The radiation of primates to South America and possibly also Madagascar is much better explained if these animals could just tree-hop, rather than island-hop to their destinations. However this would demand a radical revision of the usual age estimate for vertebrate radiation, what so far lacks fossil support (but lack of evidence is not evidence of lack, you know: fossil ages can only be taken as terminus ante quem dates and not absolute direct references).

But this is a side question, what really matters to us is that our ancestors split from the chimpanzee line c. 13 Ma (according to this study) and not after 8 Ma in any case (weighting all the evidence). This not just renders most "molecular clock" estimates useless and effectively false (wrong, erroneous, inadequate, misleading, junk, pseudoscientific...) but also help us to rethink our ancestral history in the African savannas since long before we became humans (Homo sp.)

Looking for some ecological context clues, I found this 1996 study by Jean Maley, which shows that Africa was largely humid in the early Miocene (smectite: evidence of water) but that it became increasingly arid towards the middle Miocene (kaolinite: evidence of sand). Up to this key ecological change of the Middle Miocene, the rainforest extended all the way to Egypt and East Africa. This kind of ecology allows for the common ancestor of African great apes to have arrived and first diverged in a jungle-dominated ecology and, later, for the speciation event leading to humans (bipedalism) to have happened as this once widespread jungle became scarcer, yielding to deserts and savanna.

Sahelanthropus (from fossilized.org)

It just makes all sense that the evolution of bipedalism was coincident with the vanishing of that originally widespread jungle environment whose dating is of approx. 13 Ma ago. However it must be said that the consolidation of the Sahara only happened much later, c. 7 Ma ago, already approaching the Pliocene.

Regardless of the exact split-time, a big question I have on hominid evolution is how on Earth did our small-brained and small-toothed precursors like Toumaï survive in the open savannas and grasslands without fire nor weapons. Even if they resorted to trees (isolated or in patches) for refuge, there were already felines of the saber-toothed family roaming in Africa and these big cats were no doubt be able  to climb on trees and in some cases they have been shown to predate on australopithecines. How could our precursors in the hominin line be able to face this menace without the advantage of speed (as ruminants have) or good defenses? Were their strong forelimbs, together with team action enough to confront the threat of predators? Did they use primitive weapons such as branches and stone throwing?

Claim of 13 Ma Pan-Homo split

[Update (Jun 29): new entry on this issue available].

[Update: the origin of this news is Venn 2014 but I could not find the mention of the 13 Ma split initially, as it was not something they underlined at all. I will write something as soon as possible. Thanks to all the people who helped my confused mind].

Live Science reports this week that the divergence of the human and chimpanzee lines may be as old as 13 million years. This is the oldest range of what Langergraber 2012 suggested (8-13 Ma in Fig.1, although in text they wrote "6.8-11.6 Ma") and older than the Wilkinson 2010 estimates (8-10 Ma), and would totally break all the usual "molecular clocks" so extremely abused in human genetics because it is double of the usual scholastic mindless parroting (5-7 Ma, which are necessarily too recent because they do not allow for Sahelanthropus' evolution and not even for bonobo evolution under the protection of the mighty Congo river).

Sadly the article includes no reference to the source, not even the name of the scientists involved, and I could not find it any reference online. For a moment I thought it could be another new study on gender bias in chimpanzee mutation rate (Venn et al. 2014 (ppv)) but after getting a copy it does not seem to have any direct relation.

So I would appreciate if someone can give me a lead on where this claim may come from.

Astrocytes: a key "wiring" element behind human intelligence

Recent experiments with mice have shown that those with transplanted human glial cells known as astrocytes perform much better in learning and memory tests afterwards.

Xiaoning Han et al., Forebrain Engraftment by Human Glial Progenitor Cells Enhances Synaptic Plasticity and Learning in Adult Mice. Stem Cell 2013. Pay per view → LINK [doi:10.1016/j.stem.2012.12.015]

See the news article at Science Daily for details. 

One wonders if they gave mice some sort of humanity and the many ethical questions behind this experiment, of course. But what got me wondering after that is do chimpanzees have the same kind of astrocytes as we do?

And the answer seems to be yes but no.

Nancy A. Oberheim et al., Uniquely Hominid Features of Adult Human Astrocytes. The Journal of Neuroscience 2009. Freely accessible → LINK [doi:10.1523/​JNEUROSCI.4707-08.2009]

Chimpanzees and humans share a type of astrocytes not found in our monkey or rodent relatives but the density and complexity of these particular glial cells in humans is much greater than in chimpanzees.

Fig 2 (legend)

One of the most striking features distinguishing humans and chimpanzee from other lower primate and rodent astrocytes was the presence of a previously undescribed pool of morphologically distinct GFAP⁺ cells residing in layers 5–6, characterized by long fibers with prominent varicosities (Fig. 2A). (...) In our analysis of primate tissue, we were able to locate a small number of varicose projection astrocytes within layers 5 or 6 of the chimpanzee cortex (Fig. 2A, inset). These cells differed from those seen in human in that they were smaller and less complex, with fewer main GFAP⁺ processes.

This is not the only difference, another subgroup, the interlaminar astrocytes also shows differences:

In addition to being more numerous than their chimpanzee counterparts, the morphology of interlaminar astrocytes is subtly different in humans. Human interlaminar astrocytes have small spheroid cell bodies and several short processes that contribute to the pial glial limitains, creating a thick network of GFAP fibers not seen in the primate.

A third category, the protoplasmatic astrocytes, is also different:

... the average diameter of protoplasmic cortical astrocytes in the chimpanzee brain was 81.7 ± 1.9 μm (n = 36), which is significantly smaller than human astrocytes, but significantly larger than protoplasmic astrocytes in mouse brain...

So what about cetaceans, which include some of the non-human animals most famed for their intellectual capabilities? The brain structure seems different, so maybe not as easy to compare as with our closest relatives, also cetaceans do not seem so well researched. But we know (source) that at least that the proportion of glial cells in bottlenose dolphin forebrains is almost double than that of humans:

Glial cells outnumber neurons by at least 6 to 1 but the ratio differs in different parts of the nervous system. The ratio can be 100 glials to 1 neuron along nerves in the white matter tracts in the brain; in the frontal cortex the ratio is 4 to 1. Interestingly, whales and dolphins have 7 glials for every neuron in their gigantic forebrains. (Fields, R. Douglas, PhD. The Other Brain. P P 24. NY:Simon & Schuster, 2009.)

Chromosome scale evolution among Hominidae (great apes, humans)

I won't surely be able to make justice here to this most interesting but highly technical paper but mention must be done of it in any case:

Marta Farré et al., Recombination Rates and Genomic Shuffling in Human and Chimpanzee—A New Twist in the Chromosomal Speciation Theory. Molecular Biology and Evolution, 2012. Open access → LINK [doi: 10.1093/molbev/mss272]

Abstract

A long-standing question in evolutionary biology concerns the effect of recombination in shaping the genomic architecture of organisms and, in particular, how this impacts the speciation process. Despite efforts employed in the last decade, the role of chromosomal reorganizations in the human–chimpanzee speciation process remains unresolved. Through whole-genome comparisons, we have analyzed the genome-wide impact of genomic shuffling in the distribution of human recombination rates during the human–chimpanzee speciation process. We have constructed a highly refined map of the reorganizations and evolutionary breakpoint regions in the human and chimpanzee genomes based on orthologous genes and genome sequence alignments. The analysis of the most recent human and chimpanzee recombination maps inferred from genome-wide single-nucleotide polymorphism data revealed that the standardized recombination rate was significantly lower in rearranged than in collinear chromosomes. In fact, rearranged chromosomes presented significantly lower recombination rates than chromosomes that have been maintained since the ancestor of great apes, and this was related with the lineage in which they become fixed. Importantly, inverted regions had lower recombination rates than collinear and noninverted regions, independently of the effect of centromeres. Our observations have implications for the chromosomal speciation theory, providing new evidences for the contribution of inversions in suppressing recombination in mammals. 

Maybe most interesting, at least for the casual reader, is this graph:

Fig. 1.

Evolutionary history of human chromosomes superimposed on the phylogeny of great apes. Black lines within the phylogenetic tree represent the ancestral state of the chromosomes, whereas red and orange lines represent the rearranged forms. Orangutan maintains the ancestral form for orthologous chromosomes 3 and 11, whereas human, chimpanzee, and gorilla forms are derived. Orthologous chromosomes 1, 2, and 18 have been rearranged in the lineage leading to humans, whereas orthologous chromosomes 4, 9, 15, 16, and 17 are rearranged in the lineage leading to chimpanzee. Ancestral chromosome 5 has been maintained in orangutan and human but has suffered two independent inversions in chimpanzee and gorilla, respectively. Chromosome 7 has suffered one inversion, which has been fixed in gorilla, and another inversion has been fixed in the lineage leading to human and chimpanzee. Chromosome 10 underwent one inversion that was fixed in human and chimpanzee, and a new inversion fixed in gorilla. Finally, chromosome 12 has maintained the ancestral form in humans and orangutans but has undergone an inversion that has been fixed in chimpanzee and gorilla, therefore, the polymorphic state has persisted across multiple speciation nodes (gorilla–human–chimpanzee and human–chimp).

→ large original version

No changes at this scale happened in the other eight autosomes (6, 8, 13, 14, 19, 20, 21, and 22) in any of the four genera. 

Warning must be done about the timeline, which should be twice as old at least for the Pan-Homo split.

It is interesting to notice that Pan (chimpanzee) and Gorilla share a derived form of the chromosome 12, indicating that the Homininae split was not too clean, possibly with gorilla introgression into chimpanzees. 

It is also interesting to realize that orangutans (Pongo) are extremely conservative in the genome (all 22 chromosomes, what means that surely the common ancestor of all Hominidae was more similar to modern orangutans than to any other branch. 

Finally I find notable that our chimpanzee cousins are actually more evolved than us, literally, a blunt numerical truth that is strongly counterintuitive for our anthropocentric vision of biology and evolution. While us humans have conserved 15 ancestral chromosomes (almost as many as gorillas: 16), chimpanzees only conserved 11, evolving one step (red lines) 9 chromosomes (humans 6, gorillas 5) and two steps (orange lines) two chromosomes (humans and gorillas just one).



PS- On the other hand, our Homo branch has a peculiar chromosomal rearrangement that puts up quite apart from the rest of Hominidae: two ancestral chromosomes got fused into a single one (chromosome 2) in our line. This may well have been decisive in our reproductive divergence from Pan and even maybe Gorilla, crafting a very impassable biological barrier. (Not in the paper, just my afterthought).

Incidentally, a 2006 study (Wainwright 2006) claimed to have found some strong correlation between cognitive abilities (not just IQ but also other more creative aspects of the mind) and areas of chromosome 2. With the usual caution I guess it is worth mentioning here.

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.

Latest genetic news (links)

Anthropological and genetic news have been piling up in this strike journey. I'm not sure if I will be able to address all as they may deserve so I'm listing them here in very quick review.

My apologies because I meant that the "links" format would be over but if people overseas (and in some cases also in Europe) insist on working in the general strike journey and publishing things all around, all I can do is this (or risking not even doing anything at all).

Chimpanzee enterotype variation is just like ours. 

Even if our genomes have diverged the microscopic environments we host in our guts are almost exactly the same, with three different types depending exclusively on diet.

Andrew H. Moeller et al., Chimpanzees and humans harbour compositionally similar gut enterotypes. Nature Communications, 2012. Pay per view ··> LINK [doi:10.1038/ncomms2159]

Abstract

Microbes inhabiting the human gastrointestinal tract tend to adopt one of three characteristic community structures, called ‘enterotypes’, each of which is overrepresented by a distinct set of bacterial genera. Here we report that the gut microbiotae of chimpanzees also assort into enterotypes and that these chimpanzee enterotypes are compositionally analogous to those of humans. Through the analysis of longitudinal samples, we show that the microbial signatures of the enterotypes are stable over time, but that individual hosts switch between enterotypes over periods longer than a year. These results support the hypothesis that enterotypic variation was present in populations of great apes before the divergence of humans and chimpanzees.

A more detailed review can be found at John Hawks' Weblog.

Fig. 1 (a) Left chimpanzee enterotypes, right human ones

High altitude adaptions in Ethiopia

Research on Ethiopian genetic nuances with a Basque name as lead researcher:

Gorka Alkorta Aranburu et al., The genetic architecture of adaptations (sic) to high altitude in Ethiopia. Pre-pub at arXiv, 2012. Freely accessible ··> LINK [ref. code: arXiv:1211.3053 [q-bio.PE]]

Abstract

Although hypoxia is a major stress on physiological processes, several human populations have survived for millennia at high altitudes, suggesting that they have adapted to hypoxic conditions. This hypothesis was recently corroborated by studies of Tibetan highlanders, which showed that polymorphisms in candidate genes show signatures of natural selection as well as well-replicated association signals for variation in hemoglobin levels. We extended genomic analysis to two Ethiopian ethnic groups: Amhara and Oromo. For each ethnic group, we sampled low and high altitude residents, thus allowing genetic and phenotypic comparisons across altitudes and across ethnic groups. Genome-wide SNP genotype data were collected in these samples by using Illumina arrays. We find that variants associated with hemoglobin variation among Tibetans or other variants at the same loci do not influence the trait in Ethiopians. However, in the Amhara, SNP rs10803083 is associated with hemoglobin levels at genome-wide levels of significance. No significant genotype association was observed for oxygen saturation levels in either ethnic group. Approaches based on allele frequency divergence did not detect outliers in candidate hypoxia genes, but the most differentiated variants between high- and lowlanders have a clear role in pathogen defense. Interestingly, a significant excess of allele frequency divergence was consistently detected for genes involved in cell cycle control, DNA damage and repair, thus pointing to new pathways for high altitude adaptations. Finally, a comparison of CpG methylation levels between high- and lowlanders found several significant signals at individual genes in the Oromo. 

H/t: Haldane's Sieve. 

An extensive review can be found at Ethio Helix (where else?)

Pig and boar genomes and evolutionary history

Martien A.M. Groenen et al., Analyses of pig genomes provide insight into porcine demography and evolution. Nature 2012. Open access ··> LINK [doi:10.1038/nature11622]

Abstract

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ~1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

Fig. 3 - reconstructed/estimated demographic history of boars

Less obvious strategies in long term evolutionary co-adaption

Interesting read on how competition can cause the formation of deep evolutionary valleys or gorges from which it is most difficult to exit and are therefore evolutionarily stable.

Eric Chastain et al., Defensive complexity and the phylogenetic conservation of immune control. Pre-pub at arXiv, 2012. Freely accessible ··> LINK [ref code: arXiv:1211.2878 [q-bio.PE]]

Abstract

One strategy for winning a coevolutionary struggle is to evolve rapidly. Most of the literature on host-pathogen coevolution focuses on this phenomenon, and looks for consequent evidence of coevolutionary arms races. An alternative strategy, less often considered in the literature, is to deter rapid evolutionary change by the opponent. To study how this can be done, we construct an evolutionary game between a controller that must process information, and an adversary that can tamper with this information processing. In this game, a species can foil its antagonist by processing information in a way that is hard for the antagonist to manipulate. We show that the structure of the information processing system induces a fitness landscape on which the adversary population evolves. Complex processing logic can carve long, deep fitness valleys that slow adaptive evolution in the adversary population. We suggest that this type of defensive complexity on the part of the vertebrate adaptive immune system may be an important element of coevolutionary dynamics between pathogens and their vertebrate hosts. Furthermore, we cite evidence that the immune control logic is phylogenetically conserved in mammalian lineages. Thus our model of defensive complexity suggests a new hypothesis for the lower rates of evolution for immune control logic compared to other immune structures. 

H/t: Haldane's Sieve.

Genetics and psychology in relation to heroin use and abuse

Ting Li et al., Pathways to Age of Onset of Heroin Use: A Structural Model Approach Exploring the Relationship of the COMT Gene, Impulsivity and Childhood Trauma. PLoS ONE, 2012. Open access ··> LINK [doi:10.1371/journal.pone.0048735] 

Abstract

Background

The interaction of the association of dopamine genes, impulsivity and childhood trauma with substance abuse remains unclear.

Objectives

To clarify the impacts and the interactions of the Catechol -O-methyltransferase (COMT) gene, impulsivity and childhood trauma on the age of onset of heroin use among heroin dependent patients in China.

Methods

202 male and 248 female inpatients who meet DSM-IV criteria of heroin dependence were enrolled. Impulsivity and childhood trauma were measured using BIS-11 (Barratt Impulsiveness Scale-11) and ETISR-SF (Early Trauma Inventory Self Report-Short Form). The single nucleotide polymorphism (SNP) rs737866 on the COMT gene-which has previously been associated with heroin abuse, was genotyped using a DNA sequence detection system. Structural equations model was used to assess the interaction paths between these factors and the age of onset of heroin use.

Principal Findings

Chi-square test indicated the individuals with TT allele have earlier age of onset of heroin use than those with CT or CC allele. In the correlation analysis, the severity of childhood trauma was positively correlated to impulsive score, but both of them were negatively related to the age of onset of heroin use. In structure equation model, both the COMT gene and childhood trauma had impacts on the age of onset of heroin use directly or via impulsive personality.

Conclusions

Our findings indicated that the COMT gene, impulsive personality traits and childhood trauma experience were interacted to impact the age of onset of heroin use, which play a critical role in the development of heroin dependence. The impact of environmental factor was greater than the COMT gene in the development of heroin dependence.

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.

Some chimp-human differences are epigenetic

Nothing related to brain function this time but rather to attributes that our jungle cousins seem to be at advantage compared to us. Notably chimpanzees almost never have cancer or some other diseases, like mental disorders, which we suffer a lot. This new research suggests it may be because of low methylation levels in humans (i.e. epigenetics, hinting at environmental causes rather than pure inheritance).

Jia Zeng et al., Divergent Whole-Genome Methylation Maps of Human and Chimpanzee Brains Reveal Epigenetic Basis of Human Regulatory Evolution. AJHG 2012. Pay per view (free after 6 months embargo) ··> LINK [doi:10.1016/j.ajhg.2012.07.024]

Abstract

DNA methylation is a pervasive epigenetic DNA modification that strongly affects chromatin regulation and gene expression. To date, it remains largely unknown how patterns of DNA methylation differ between closely related species and whether such differences contribute to species-specific phenotypes. To investigate these questions, we generated nucleotide-resolution whole-genome methylation maps of the prefrontal cortex of multiple humans and chimpanzees. Levels and patterns of DNA methylation vary across individuals within species according to the age and the sex of the individuals. We also found extensive species-level divergence in patterns of DNA methylation and that hundreds of genes exhibit significantly lower levels of promoter methylation in the human brain than in the chimpanzee brain. Furthermore, we investigated the functional consequences of methylation differences in humans and chimpanzees by integrating data on gene expression generated with next-generation sequencing methods, and we found a strong relationship between differential methylation and gene expression. Finally, we found that differentially methylated genes are strikingly enriched with loci associated with neurological disorders, psychological disorders, and cancers. Our results demonstrate that differential DNA methylation might be an important molecular mechanism driving gene-expression divergence between human and chimpanzee brains and might potentially contribute to the evolution of disease vulnerabilities. Thus, comparative studies of humans and chimpanzees stand to identify key epigenomic modifications underlying the evolution of human-specific traits.

See also the article at Science Daily.

Increased complexity in certain regions sets apart human and chimp brains

Frontal lobe (CC-BY-SA-2.1-jp)

This paper looks like a very important research piece for the understanding of the human mind, of what makes our brains specifically human and ultimately of what makes ourselves what we are.

Genevieve Konopka et al., Human-Specific Transcriptional Networks in the Brain. Neuron 2012. (Freely accessible apparently) ··> LINK [doi:10.1016/j.neuron.2012.05.034]

Summary

Understanding human-specific patterns of brain gene expression and regulation can provide key insights into human brain evolution and speciation. Here, we use next-generation sequencing, and Illumina and Affymetrix microarray platforms, to compare the transcriptome of human, chimpanzee, and macaque telencephalon. Our analysis reveals a predominance of genes differentially expressed within human frontal lobe and a striking increase in transcriptional complexity specific to the human lineage in the frontal lobe. In contrast, caudate nucleus gene expression is highly conserved. We also identify gene coexpression signatures related to either neuronal processes or neuropsychiatric diseases, including a human-specific module with CLOCK as its hub gene and another module enriched for neuronal morphological processes and genes coexpressed with FOXP2, a gene important for language evolution. These data demonstrate that transcriptional networks have undergone evolutionary remodeling even within a given brain region, providing a window through which to view the foundation of uniquely human cognitive capacities.

Hippocampus (CC-BY-SA-2.1-jp)

For what I could understand, mostly from the press release, the authors unveiled increased complexity of the gene expression modulating three regions of our brains: the frontal cortex, the hippocampus and the striatum.

It is not a mere matter of size but specially one of much increased complexity in the wiring of these three regions what seems to make our brains unique. 

The research also reinforces the apparent importance of the much debated genes CLOCK (affecting circadian rhythms, mood, pregnancy and metabolism), FOXP1 and FOXP2 (related specially with speech), whose connectivity is much increased in humans in comparison with our ape cousins.

Tandem repeat accumulation drives evolution in great apes

Tandem repeats (also known as mini-/microsatellites) used to be considered 'neutral' junk genome, yet they are proving themselves quite more than just that.

M. Farré et al. Assessing the Role of Tandem Repeats in Shaping the Genomic Architecture of Great Apes. PLoS ONE 2011. Open access.

Among other things, this paper is a great manual to better understanding the differences between great apes (including humans) chromosome by chromosome:

Chromosome 1.

Human chromosome 1 is considered to be the derived form, showing a pericentric inversion when compared to chimpanzee and orangutan chromosome 1. The human tandem repeat landscape also differs from the other two great apes (HSA vs PTR: p-value = 0.006; HSA vs PPY: p-value = 0.000).

Chromosome 2.

It is well known that human chromosome 2 derives from the ancestral form by a fusion of two hominoid homolog chromosomes [1]. The ancestral 2a form corresponds to HSA2pq and also has suffered a pericentric inversion in the human form, whereas the ancestral 2b form has not suffered further reorganizations. The tandem repeat contour is different between human and the other great apes regarding chromosome 2a form (HSA vs PTR: p-value = 0.000; HSA vs PPY: p-value = 0.000) but is maintained in the homologous chromosome 2b form (HSA vs PTR: p-value = 0.738; HSA vs PPY: p-value = 0.192).

Chromosome 3.

Human and chimpanzee chromosomes are the derived forms, with an inverted region compared to orangutan chromosome. The tandem repeats distribution confirms this pattern (HSA vs PTR: p-value = 0.062; HSA vs PPY: p-value = 0.009).

Chromosome 4.

All the great apes have a derivative chromosome 4 that evolved differently since their common ancestor. We found a different tandem repeats distribution between human and chimpanzee forms but the same distribution between human and orangutan forms (HSA vs PTR: p-value = 0.022; HSA vs PPY: p-value = 0.272).

Chromosome 5.

Human chromosome is considered the ancestral form, whereas the chimpanzee and the orangutan have derived forms due to pericentric inversions. The tandem repeats landscape is consistent with this pattern (HSA vs PTR: p-value = 0.031; HSA vs PPY: p-value = 0.001).

Chromosome 6.

The three species shared the same chromosome form, which is considered to be ancestral. We found the same tandem repeat profile between human and chimpanzee (HSA vs PTR: p-value = 0.069) but it differs between human and orangutan (HSA vs PPY: p-value = 0.003).

Chromosome 7.

The orangutan chromosome represents the ancestral form, while human and chimpanzee share a pericentric inversion. We found the same tandem repeats pattern in human and chimpanzee (HSA vs PTR: p-value = 0.203) but this was different in orangutan (HSA vs PPY: p-value = 0.050) (Fig. 4a).

Chromosome 8.

The three hominoid species share the same form but we detected an insertion of ~3Mb in the orangutan chromosome 8 (Table 2). This difference is reflected in the tandem repeats landscape, being equal between human and chimpanzee (p-value = 0.128) but different in orangutan (p-value = 0.009) (Fig. 4b).

Chromosome 9.

All three species have different chromosomal forms, being the orangutan chromosome the ancestral one. Tandem repeats distribution is consistent with these differences (HSA vs PTR: p-value = 0.002; HSA vs PPY: p-value = 0.000).

Chromosome 10.

Orangutan chromosome 10 is considered to be the ancestral form, which differs from human and chimpanzee forms by a paracentric inversion. We found that human and orangutan have a different tandem repeat pattern (p-value = 0.001) as well as human and chimpanzee (p-value = 0.010), although the same pattern between these two species was expected.

Chromosome 11.

The ancestral chromosome form is conserved in orangutan, which differs from the human chromosome by a pericentric inversion and from chimpanzee by a pericentric inversion and an insertion of ~400 Kb (Table 2). These differences are also reflected in the tandem repeat distribution (HSA vs PTR: p-value = 0.016; HSA vs PPY: p-value = 0.000).

Chromosome 12.

Human and orangutan share the same form, which is considered the ancestral. Chimpanzee differs from them by a pericentric inversion. In this case, the tandem repeats landscape is different between human and chimpanzee (p-value = 0.050) and between human and orangutan (p-value = 0.004).

Chromosome 13.

Human and chimpanzee share the same form and have the same tandem repeats pattern (p-value = 0.072), while orangutan have a ~100Kb insertion (Table 2) and shows a different tandem repeats pattern (p-value = 0.003).

Chromosome 14.

All great apes share the same chromosome form and also the same tandem repeats landscape (HSA vs PTR: p-value = 0.051; HSA vs PPY: p-value = 0.051).

Chromosome 15.

All great apes have different chromosome forms and different tandem repeats profile (HSA vs PTR: p-value = 0.004; HSA vs PPY: p-value = 0.001).

Chromosome 16.

All great apes have different chromosome forms and different tandem repeats profile (HSA vs PTR: p-value = 0.001; HSA vs PPY: p-value = 0.000).

Chromosome 17.

Human and orangutan share the same ancestral form, while chimpanzee suffered a pericentric inversion. This pattern is in agreement with the tandem repeats distribution (HSA vs PTR: p-value = 0.030; HSA vs PPY: p-value = 0.106).

Chromosome 18.

Chimpanzee and orangutan share a chromosome form ancestral to great apes, which differs from the human by a pericentric inversion. This is not observed in the tandem repeats profile, given that all the species share the same distribution (HSA vs PTR: p-value = 0.095; HSA vs PPY: p-value = 0.206).

Chromosome 19, 20, 21 and 22.

All great apes share the same chromosome form and also the same tandem repeats landscape [HSA19 (PTR: p-value = 0.127; PPY: p-value = 0.161) HSA20 (PTR: p-value = 0.138; PPY: p-value = 0.051) HSA21 (PTR: p-value = 0.106; PPY: p-value = 0.111) HSA22 (PTR: p-value = 0.082; PPY: p-value = 0.051)].

Chromosome X.

Human and chimpanzee share the same ancestral form while orangutan has a ~2Mb insertion (Table 2). Tandem repeat pattern is in agreement with human-orangutan evolution (p-value = 0.021) but not with human-chimpanzee history (p-value = 0.000).

But while this is most interesting, it is not the only or main finding of this paper: the authors find that tandem repeats accumulate in the evolutionary breakpoint regions (EBRs) at higher rate than expected under neutrality conditions. Instead the homologous synteny blocks (HSB), highly conserved areas, display lower rate of tandem repeats than expected. 

Although no specific repeat motif was exclusively present in EBRs or HSBs, 17 different microsatellites motifs were significantly accumulated in EBRs. Notably, out of these overrepresented tandem repeats, the AAAT was the most frequently detected. It has been described that this motif could form single-stranded coils [24], favoring chromatin instability and increasing the likelihood to break.

Lots of news

Stories of interest are accumulating at my "to do" folder these days. While I may later on deal with some of them in detail, here there is a synthesis:


Prehistory & archaeology:

Unusual hanging decorative/utilitarian retouching stone (left) found at Irikaitz (Zestoa, Gipuzkoa, Basque Country). The item has been dated to c. 25,000 years ago, what may well make it Aurignacian (Gravettian is of very late arrival to the area).

Hanging objects of stone are rare and most belong to later periods (cf. Praileaitz of Magdalenian era).

··> Pileta de Prehistoria[es], video at EiTB[es].

Neanderfollia[cat] mentions that life expectancy seems to have increased dramatically in the Upper Paleolithic. ··> Daily Mail, also discussed at GNXP.

Bronze Age pottery at Hala Sultan Tekke (Larnaca, Cyprus),  indicates mayor contacts with Mycenaean Greece, including import of pottery. Also goddess figurine found, which may be local. ··> Cyprus Mail.

Claims of grave goods indicating when old men became powerful in Traisen Valley (Austria). The study compared burials of the 2200-1800 BCE period (Late Chalcolithic) with the 1900-1600 BCE one (Early Bronze Age). Both elderly women and men gained burial goods  in the later period but men elder were buried with copper axes (quite useless but surely a prestige item), which appears more valuable than the regular axes of young and adult men. ··> Live Science.



Genetics:

A new paper on autsomal variation of Basques in comparison with other populations (by Kristin L. Young, freely accessible at PubMed) is something I want to dedicate some more time when I have it. By the moment:

Fig.2 - Multidimensional Scaling plot of genetic distance (click to expand) - Basques: black dots

Neanderfollia[cat] also mentions a research on several full human genomes that estimates that Humankind may have shrank suddenly c. 100,000 years ago, at the same time that the various populations scattered through the world. They also claim that genetic exchange however continued (with Bushmen too) until c. 20 Ka ago. It raises my eyebrows so high that they have melted with my other hair but must mention anyhow. ··> Daily Mail.


Dienekes mentions a couple of somewhat interesting open access papers:

• A study on genotypes  and surnames in the UK (which I have not read yet)
• A study on Przewalski horse genetics that finds that they are not ancestors of domestic horse but a parallel branch

Bigger heads (and eye sockets) meant  to process dimmer light, not to increase intelligence, research claims. ··> SD.

Jaw bones shaped mostly by diet, not genes. Narrow jaws indicate soft cooked diet, broad ones a harder type of food. Researched on two isolated Native American populations but IMO lacks controls and it could be argued that the differential evolution is genetically programmed in each population regardless of diet. ··> SD.

IQ-specific genes too diluted to be found ··> Medical Press.

Math ability is inborn (but don't count on the genes to be found anytime soon) ··> SD.

Endurance gene found. A gene exists that makes us non-Olympic or marathon-level quality meat. ··> SD.

Chimpanzees are spontaneously generous and don't like demanding friends ··> SD.

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.

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:

James K. Rilling et al., Differences between chimpanzees and bonobos in neural systems supporting social cognition. Social Cognitive and Affective Neuroscience, 2011. Pay per view.

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.