Pause

Things are going to be slow for a while, because I’ll be recovering from bypass surgery (happens tomorrow).

 

 

Posted in Uncategorized | 61 Comments

Something else

Razib has talked about this – here’s what I think.

The various sweeping alleles that have made Europeans and North Asians have light skin  were not favored because they helped you garner extra vitamin D, at least not mostly. This is apparent from the allelic structure.  There is a single sweeping variant for SLC24A5: if paleness was the point, many partial loss-of-function alleles would be favored, rather like what we see with G6PD deficiency (a malaria defense).  But there is only one: so loss of function is not the point (or at least not the sole point): that particular variant has some other advantage, a big one.  The fact that it’s favored up on the Ethiopian plateau is another sign that it isn’t driven by vitamin D. There is only one blue-eye mutation (OCA2), only one main blond mutation (KITLG). The SLC24A5 mutation has by far the largest effect on skin color – if it isn’t being selected for paleness,  the  sweeping alleles of other coloration genes aren’t either.  Probably not even MC1R – it has many common loss-of-function mutations, which implies that loss of function is favored – but probably not because of the paleness. Something else.

If you’re close enough to the equator, you need dark skin, and the genes in these pathways are constrained – not free to change. But if they are free to change, then a change that improves fitness through a pleiotropic effect is now free to spread, since the resulting paleness is bearable. In many cases that would require a specific change, not just loss of function  – so we see an allelic structure unlike that of G6PD.

The same is likely the case with the various sweeping skin-color alleles in East Asia (although they are less colorful).

So we need to figure out what useful thing  these mutations actually do.  Dropping the vitamin D hypothesis raises lots of questions.

Posted in Genetics, Skin color | 96 Comments

Infertilty Belt

Infertility Belt

It used to be the case (considerably less so today) that a significant fraction of women in central Africa, up to tens of percent in some areas, were infertile or subfertile, due to various STDs.  This seems to have been true for quite a while, up until the 1990s and back some indefinite amount of time, probably at least one or two centuries.  It might be older than that, but at this point nobody knows.  There was enough infertility that colonial administrators worried about keeping up the population, in the days before readily available antibiotics:  for example, the population of Gabon seems to have decreased between 1930 and 1950.

Most of this infertility was caused through  tubal scarring caused by gonorrhea and chlamydal infections.

If this pattern was around long enough, there could have been significant selection for resistance to the relevant pathogens, possibly generating high frequencies of alleles with odd or unpleasant side effects, as with  malaria and sickle-cell/thalassemia etc.  This would depend on the age of the behavior patterns that made this possible, on the antiquity of  the pathogens causing those STDs, etc.

 

 

 

 

Posted in Uncategorized | 24 Comments

TLRs, PAMPs, and Alley Oop

I hear that some Eurasians  – probably more than some – have Neanderthal or Denisovan versions of TLRs.  Not surprising: we’ve already seen this happen with other immune system genes – HLA variants , OAS1, STAT2  all have adaptive variants that originated with archaic humans.

TLRs   (Toll-Like Receptors) are just plain interesting, but I don’t think many people are familiar with them.  They’re part of the innate immune system:  they don’t learn from experience, as happens with the adaptive immune system (recombination,  clonal selection and all that): they just know.  Born that way.

They sense pathogens by detecting molecular patterns characteristic of major classes of pathogens that we just don’t have.  These are called PAMPs (pathogen-associated molecular patterns). They can detect  lipopolysaccharide (LPS), characteristic of gram-negative bacteria. and peptidoglycan, characteristic of gram-positive bacteria. Some detect viral-double-stranded RNA.

There are ten TLRs in humans.   Generally, they react with molecular patterns  that we don’t even have. TLR-1 recognizes bacterial lipoprotein and peptidoglycans (strep and staph), TLR-2  recognizes bacterial peptidoglycans( gram-positive bacteria)  and zymosan (fungi), TLR-3 double stranded RNA (viruses) ,  TLR-4 lipopolysaccharides (salmonella) , TLR-5 bacterial flagella (listeria) , TLR-6 bacterial lipoprotein, TLR-7 single-stranded RNA (viruses) , TLR-8 single-stranded RNA(viruses) , TLR-9 CpG DNA (bacteria) .  TLR-10 appears to play an inhibitory role, down-regulating TLR-2 .

Back in the days when vaccine development was cutting-edge, I think that people knew that the body automatically reacted to some pathogens, but it has taken a long time to discover the complex details, not that we’re quite done yet.

P.S. according to some, one factor inducing Pygmyization was the high pathogen load in dense tropical jungles.  I don’t know if that was the case, but if so, considering  that it looks as if African Pygmies (also Bushmen) admixed a bit  with a very divergent hominid population (more divergent than Neanderthals) , it wouldn’t be surprising if they picked up some immune system gene variants that helped deal with that jungle environment.

Posted in Uncategorized | Tagged , | 32 Comments

First* Peoples

There are two new papers out on the early colonization of the Americas, one in Science and one in Nature.  The Science paper claims that all Amerindians stem from a single Siberian population that moved into Beringia about 23,000 years ago and entered America about 15,000 years ago, splitting into northern and southern branches about 13,000 years ago. They also found a touch of Australo-Melanesian ancestry among some, not all, living Amerindians – they saw it in Aleuts and the Surui ( Amazonian Indians). They concluded that this ancestry must have arrived well after the initial colonization of the New World:    “The widely scattered and differential affinity of Native Americans to the Australo-Melanesians, ranging from a strong signal in the Surui to much weaker signal in northern Amerindians such as Ojibwa, points to this gene flow occurring after the initial peopling by Native American ancestors.” In much the same way, the fact that you see widely different amount of Bushman admixture in Bantu groups  in southern Africa ( a lot in the Xhosa, almost none in some other groups) suggests that the Bushmen arrived after the Bantu,  except that it doesn’t of course.

The Nature paper concentrates on the Australo-Melanesian story: they see it mainly in the Amazon Basin,  1-2%. The  closest extant population is the Onge, pygmies of the Andaman Islands, but you see this anomalous relatedness in the Papuans, Australian Aborigines, Mamanwa (Philippine Negritos), and at lower levels in a number of groups in South Asia. In many Amerindian groups this component is much weaker or nonexistent.

The authors of the Nature paper believe that this admixture most likely happened before the settlement of the Americas, but they aren’t sure: the linkage disequilibrium says some time between 40,000 and 4,000 years ago, probably after the Ancient North  Eurasians mixed into the Amerindians. They talk about population Y, a separate movement into the Americas by a population that had probably already acquired this Australo-Melanesian component.

The background fact is that the earliest skeletons, especially in Brazil, look like Australo-Melanesians.  Long skulls.  If population Y were almost entirely standard Amerindian, with only a smidgen of Australo-Melanesian ancestry, they would have looked like Amerindians.  On the other hand, if the original settlers of the Americas were mostly or entirely Australo-Melanesian (or more exactly something vaguely related to those existing populations) they would have those long, narrow skulls.  This is the Paleoamerican model – and if true, it means that an Onge-like population arrived first, and that the incoming Amerinds almost completely wiped out them out later,  with here and there a bit of admixture.

As I understand the law, this would mean that we have to build little casinos inside the existing casinos.  For some small establishments, this might mean designating the proceeds of a single slot machine to various Amazonian tribes, or possibly to the Onge as next of kin.

* It’s complicated.

Posted in Uncategorized | 114 Comments

Baby Steps

Very early settlers of North America had at least some ability to make water-crossings, since there is  there is evidence of early human activity on the Channel Islands off California (Santa Rosa, for example).  But by the time they crossed the continent and reached the Gulf Coast, those traditions had decayed and had to be re-invented: the islands of the Caribbean were not settled until several thousand years later.  There were various odd animals on some of those islands, for example ground sloths the size of a bear.  They did not go extinct at the same time as the large animals on the mainland: they waited for people to show up and then kicked the bucket.  Which is odd if you think that climate change or an impact caused those mainland extinctions.

CIA_map_of_the_Caribbean

When humans did arrive, they seem to have started in Trinidad (very close to the South American coast) and moved up the Lesser Antilles. This seems to have happened repeatedly with successive waves of invaders, the last being the Caribs.

This suggests that a chain of islands with fairly small separations is a good recipe for developing your maritime capabilities, and maybe that was the case for the road that started with Bali and continued on to Sahul and the Solomon islands, back in the day.

Posted in Uncategorized | 23 Comments

Brain Topography

Although Richard Nisbett has written about long-term differences in cognitive style between East and West,  he is, I think, dismissive of the possibility that biology might explain such differences, or any other mental differences – at least publicly. He had a piece in the New York Times titled “All Brains Are the Same Color”, for example.

But as it turns out,  the three-dimensional geometry of the cortical surface is highly predictive of individuals’ genetic ancestry – there are regional differences in the folding and gyrification, as well as volume and cortical area.  I already knew that the Chinese had decided to develop their own brain anatomical atlas, due to average differences between European and  Chinese brains, but this article takes it farther.

Posted in Uncategorized | 52 Comments