Category Archives: immunity

Echoes from the Past (Oct 14) – the genetic isolation of humankind

I’m planning an entry on Paleolithic and Neolithic navigation but meanwhile, here it goes some stuff (mariner or not) that I find interesting.
Homo genus became genetically isolate thanks to natural spermicide
H. erectus (female) reconstruction
A critical change in a immune system molecule, from Neu5Gc to Neu5Ac, made our ancestors effectively isolated from our cousins from the Pan genus and probably also from the then common australopithecines. 
This change would simply kill any non-human sperm in the uterus or, would it manage to succeed, the resultant fetus. This incompatibility with other hominins may have been critical in the process of speciation of the first Homo species such as Homo erectus, Homo habilis or maybe A. sediba. 
··> Science Daily, Darius Ghaderi et al. at PNAS (PPV for six months or freely accessible in some world regions).

Human thumb (Neanderthal or H. heidelbergensis) found in Sardinia
The finding of a thumb bone in Sardinia, dated to 250-300,000 years ago, may help break the fantasy of ancient humans not being able to navigate. This finding adds to those of Crete (c. 190 Ka ago and the famous Flores hominin), all of which must have crossed vast spans of sea in order to get to their destinations, implying at least some level of navigation. 
In the discussion at NeanderFollia, David indicated further evidence of archaic navigation I was unaware of: H. erectus must have reached Flores c. 900,000 years ago, in what is probably the most ancient navigation feat we can confirm ··> John Hawks, Environmental Grafitti, Adam Brumm et al. at Nature (PPV).
Also there is at least some uncertainty of H. ergaster or some other human species maybe crossing to Europe via the Strait of Gibraltar at similar dates as in Flores or maybe even earlier, but, because of the various possible routes involved this is less conclusive. Instead, Flores, Sardinia and Crete have not been connected to the mainland at any time in the biological history of the genus Homo.
Art workshop found in South Africa
A number of shells with indications of having held ochre have been found in the important site of Blombos Cave, South Africa. The shells had holes which suggest that they were used as containers. Other tools, such as hammers and knives, to work the clay, have also been found.

Babies know justice instictively
While actual perception and interest on fairness varies, a good deal of human babies (15 months old) clearly show interest in fair sharing and will actively share. Other babies have less interest in fairness however but they will share anyhow, even if in a less generous manner. 
Malaria research casts doubt on mitochondrial DNA ‘molecular clock’

It seems that the molecular clock is not on streak. Recently it was radically challenged for Y-DNA and it seems obvious that it will not survive in general, at least without radical revisions. A crucial assumption for the molecular clock hypothesis is that the clock ticks regularly or almost so. 
Well, it does not seem to be the case of mtDNA either: certainly not for the primate parasite Plasmodium sp

The use of fossils from the host as absolute calibration and the assumption of a strict clock likely underestimate time when performing molecular dating analyses on malarial parasites. Indeed, by exploring different calibration points, we found that the time for the radiation of primate parasites may have taken place in the Eocene, a time consistent with the radiation of African anthropoids. The radiation of the four human parasite lineages was part of such events. 

Celtic astronomical kurgan found in Germany
Dated to the 7th century BCE, the plan of a burial mound (or kurgan) of the Hallstatt period in the early Celtic area of Southern Germany has been reported. Allegedly the disposition of the wooden posts around the mound inform about the astronomy of the Moon, primarily, and the Sun and they may even describe constellations.

Altamira at risk on short-sighted tourism greed

Millán Mozota denounces at his blog, echoing other researchers, the short-sighted attitude of the Cantabrian authorities who have decided to open the Altamira cave to the public again in spite of the dramatic risk for the art in it.

In the last decade, considerable attention has been paid to the deterioration of the caves that house the world’s most prominent Paleolithic rock art. This is exemplified by the caves of Lascaux (Dordogne, France) (1) and Altamira (Cantabria, Spain), both declared World Heritage Sites. The Altamira Cave has been closed to visitors since 2002. Since 2010, reopening the Altamira Cave has been under consideration. We argue that research indicates the need to preserve the cave by keeping it closed in the near future.

The public can enjoy a replica of part of the cave at the nearby museum.
Iberian Neolithic idols
While in Spanish language, I can’t but call your attention to this fifth article of Neolítico de la Península Ibérica on the diverse array of idols known from the Neolithic and Chalcolithic of Iberia. Even if you can’t read any Spanish, you will no doubt gather some information and visual recreation from simply watching the many images and maps included in this blogpost. For example:

Orange ovals: “eyed” idols (oculados), brown ovals: “plate” idols (ídolos placa)

··> Neolítico de la Península Ibérica[es].

Last minute news:  some iris pattern genetics unveiled ··> The Spitoon.


Strong introgression of non-Sapiens antigens in ‘Eurasian’ modern humans (but not in Africa)

HLA-A11: the legacy of H. erectus in ourselves
Please read the updates below because some of the claims may not be sustainable (however others are plausible).

Prof. Peter Parham (Stanford University, USA) has found that some of the most common immunologic alleles among non-African modern humans have been adopted from other species of Homo living in Eurasia upon the migration out of Africa. 

This would be a typical case of introgression, a process in which, by means of lesser admixture highly adaptive alleles from another population are adopted. The logic here is that Neanderthals and other Eurasian hominins would be much better adapted to Eurasian-specific diseases, while our species would initially be  adapted to African-specific diseases instead. 
According to New Scientist:
One allele, HLA-C*0702, is common in modern Europeans and Asians but never seen in Africans; Parham found it in the Neanderthal genome, suggesting it made its way into H. sapiens of non-African descent through interbreeding. HLA-A*11 had a similar story: it is mostly found in Asians and never in Africans, and Parham found it in the Denisovan genome, again suggesting its source was interbreeding outside of Africa.


Half of European HLA-A alleles come from other hominins, says Parham, and that figure rises to 72 per cent for people in China, and over 90 per cent for those in Papua New Guinea.

The dominance of Denisovan alleles in Eastern Eurasia is coincident with my theory of these Denisovan specimens being hybrids of H. erectus and Neanderthals and acting actually as a proxy for H. erectus, with whom some of our ancestors would have hybridized in SE Asia, where this hominin is known to have existed until very late dates compatible with our arrival to the region.
Besides HLA, only Melanesians show some clear (albeit very minor) Denisovan admixture, but in the realm of antigens, the legacy of H. erectus has been clearly stronger. 


News found thanks to Neanderfollia[cat].

See also in this blog:

Update: John Hawks, who has also been studying HLA, has objections to the conclusion that these alleles come from Denisovans or Neanderthals. For what I could gather he has two objections:
  • Age estimates, which are high risk slippery terrain.
  • Insufficient resolution of the genetics of the archaic hominin genomes. 

Important Update (Jun 18): the “Neanderthal” allele probably Sapiens, the “Denisovan” one may stand:

Hawks (same post, updated or did I miss it in first read?) directs us to a database of allele frequencies through the World, which would seem a most useful reference site. There we get clear evidence that the “Neanderthal” allele HLA*C:0702 probably migrated with our ancestors from Africa and needs no introgression explanation at all. The allele is frequent enough in many African populations peaking among the Baka Pygmies with 15%.

More complicated is the case of the allegedly Denisovan (Erectus) alleles HLA*A11. A look at the database is very clear: no native African population (south of the Sahara) has it at all except the creole ones of Cape Verde and Sao Tome (where it has without doubt recent European origin) and, crucially, a sample from Kampala, Uganda, where it reaches 4.3%.

This sample one is the only one that could suggest an African origin for this set of haplotypes. It could be argued however that as some genetic back-flow from Asia exists in the area, this case is explained by genetic back-flow. However the apportion is rather high, almost as high as Moroccan Berbers, Italians or Macedonians. Even the largest possible Asian source (Omanis: 11.4%) does not seem to be large enough to justify this island of HLA*A11 in Kampala.

Additionally the Nilotic Nandi of nearby Kenya are reported to have 0% of the controversial alleles. It is really hard to explain how this island of HLA*A11 arose in Kampala. But on the other hand, the fact that it is such an isolated finding is equally suspicious: if the allele (essentially HLA*A11:01) was so old in Africa, we should expect it to be found at least a very low frequencies in other populations.

Fine that malaria or other tropical diseases may have played a contrary selective role, as Hawks argues, but still the allele could, should, have survived in populations not affected by this disease. Also Uganda is not less Malaria-prone than Kenya (or most other nearby countries). So this explanation is not satisfactory.

A very localized founder effect of Asian origin (or a reporting error maybe) would seem to be at the origin of this anomaly. Also no African presence of variants 02, 03 or 04 has ever been reported.

Of course, we must always await for further data and research, but on the grounds of what we have now, I would say that:

  • Claim 1: HLA*C0702 is a Neanderthal introgressed allele. Busted!
  • Claim 2: HLA*A11 (several alleles) is a Denisovan (Erectus probably) introgressed allele. Plausible (but watch that Kampala island in Africa). 

Update (Aug 26):

The reference paper is:

Laurent Abi-Rached et al., The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans. Science, 2011. Pay per view

The supplementary material however is freely available


Do health and reproductive drive cancel each other?

This seems to be the case in a population of feral sheep from a remote Scottish island. Individuals with better immunity, and therefore longer-lived, do not manage to reproduce as successfully as their less healthy peers. However, in the long run they compensate that by participating in more reproductive seasons over their lives.

The two tendencies in dynamic equilibrium run along families.

Full story at Science Daily.

Ref. Andrea L. Graham et al. Fitness Correlates of Heritable Variation in Antibody Responsiveness in a Wild Mammal. Science, 2010. Pay per view.


Posted by on October 29, 2010 in biology, dynamic equilibrium, immunity, Scotland, sheep