Saturday, 11 February 2012

Were they right after all?


Modern humans entered the Americas from northern Eurasia. As they entered tropical environments farther south, they had to evolve new genetic adaptations from scratch. They no longer had the ones their remote forbearers had back in Africa. (Source)

OK, so modern humans have archaic admixture, and the degree of admixture seems to be highest among sub-Saharan Africans and Melanesians. But what does this factoid mean? Does it mean anything at all?

One school of thought says it means nothing at all. Ernst Mayr held this view:


The claim has been made that species owe much of their genetic variability to introgressive hybridization. However, all the evidence contradicts this conclusion so far as animals is concerned. Not only are F1 hybrids between good species very rare, but where they occur the hybrids (even when not sterile) are demonstrably of inferior viability. The few genes that occasionally introgress into the parental species are not co-adapted […] and are selected against. Introgressive hybridization seems to be a negligible source of genetic variation in animals. (Mayr, 1970, p. 80)


“Co-adaptation” means that genes are selected for their ability to work with other genes. “On one genetic background a given gene may add to the fitness of the genotype; on another genetic background the same gene may create an unbalance and produce a severely deleterious effect” (Mayr, 1970, p. 169).

Yet some genes seem to be of the “stand alone” sort. We see this when genetically modified organisms are created, such as by transferring an antibiotic-producing gene from a microbe to a cultivated plant.

Mayr also overlooked the possibility that introgressing genes might benefit a species that is expanding into new territory and gradually displacing the native species. Such genes can circumvent the need to evolve genetic adaptations that already exist in the native population. This argument was used by Greg Cochran, John Hawkes, and Henry Harpending a few years back, when they thought that the most recent microcephalin variant had introgressed from the Neanderthals. Another case of Neanderthal introgression seemed to be the diversification of European hair colors, via the MC1R gene:

A few years ago, I was thinking about Out-of-Africa, and it occurred to me that we probably picked up a lot of favorable alleles from Neanderthals […] Looking at the new article in PNAS, I'd say that Bruce Lahn and company have probably found one.[…]

Now if the Neanderthals were really effectively isolated before we expanded into their territory, they'd have a lot of significantly different alleles. Some would have involved various kinds of regional adaptations, which might be a good thing to have in Eurasia. (MC1R?) But it's entirely possible that some alleles solved adaptive problems that had existed in Africa as well - but solved them better.

Brains had expanded over the last half-million years in both Africans and Neanderthals, but it seems likely that those changes in size and structure were driven by different mutations, just as light skin in Europe and East Asia was. The Neanderthals had slightly bigger brains than Africans: obviously those brains were useful for _something_.

[…] So when you think about the cultural explosion that occurred shortly after we overwhelmed the Neanderthals (cave paintings, sculptures, new tools and weapons, all that jazz) - well, you have to wonder if assimilating a passel of adaptive alleles in a few thousand years, way more than the typical number that would arise and become established over such a short time span, didn't give us a hell of a boost. There are signs of behavioral modernity a bit earlier in Africa - but those ostrich eggshells are dull as hell compared to Gravettian cave paintings. Expansion out of Africa must itself be a sign of new capabilities (I'd bet on sophisticated language) but you only see full-fledged behavioral modernity in the European Upper Paleolithic...
(Cochran, 2006)

Since then, the Neanderthal genome has been fully reconstructed. The most recent microcephalin variant isn’t on it. Nor are the European MC1R alleles. It seems that the best laid theories of mice and men gang aft agley.

No one likes to be proved wrong. Especially in public. For some time yet, certain people will be busy flogging the dead horse of Neanderthal introgression. Will they find anything? Undoubtedly. Anything to do with intelligence or artistic creativity? Probably not.

In all fairness, we’re not giving the theory of adaptive introgression a decent chance by looking only at Neanderthal admixture in modern Europeans. That degree of admixture is only 1 to 4% (perhaps less if we adjust for archaic admixture in modern Africans). We might have more luck looking at sub-Saharan Africans, who have as much as 15% archaic admixture.

In sub-Saharan Africa, the main genetic change since the advent of modern humans has been the replacement of hunter-gatherers by farming peoples. This process began perhaps 6,000 to 7,000 years ago near the Niger’s headwaters. A small core population of hoe farmers progressively expanded westward and southward, eventually occupying almost the whole of sub-Saharan Africa, except for a few marginal environments in central and southern Africa inhabited by Pygmy and Khoisan hunter-gatherers (Murdock, 1959, pp. 44, 64-68).

This new means of subsistence set off a cascade of social and, ultimately, biological changes. Year-round farming enabled women to provide for themselves and their children with little male assistance. Because more men could afford a second wife, the polygyny rate soared from around 5% of all sexual unions to 20-40%. Men now had to compete more fiercely against each other for access to women, the result being selection for greater stature, muscle mass, and bone strength. Many of these changes were and still are testosterone-mediated, i.e., through higher testosterone levels in young adult males or through testosterone receptors that bind the target molecule more effectively. Other changes may have been initially testosterone-mediated and then gradually hardwired (Frost, 2001; Frost, 2008).

A similar process has affected Amerindian farming peoples in the tropical New World, but not to the same degree. Among the Yanomamö, an agricultural people of Amazonia, 10 to 20% of all men have more than one wife at any time (Hames, 1995). They are thus more polygynous than non-tropical Amerindians but not as polygynous as tropical Africans. Their bodies likewise don’t show the same degree of robustness. Despite living in the tropics for millennia, they still look remarkably Arctic-adapted. As Holliday (1997, pp. 425-426) notes:

Despite having as much as 18,000 years of selection in environments as diverse as those found in the Old World, body mass and proportion clines in the Americas are less steep than those in the Old World. […] In fact, as Hulse (1960) pointed out, Amerindians, even in the tropics, tend to possess some “arctic” adaptations.

In Mesoamerica, farming began about 6,000 to 7,000 years ago—the same time depth as in West Africa (although there is evidence of proto-agriculture going back to 12,000 years ago in West Africa). The difference between the two culture areas seems to have been more in the speed of co-evolution with this new means of subsistence, and especially with its social consequences. Briefly put, natural selection has had less raw material to work with among tropical Amerindians than among sub-Saharan Africans. Because modern humans entered the Americas from northern Eurasia, their genetic variability had been whittled down to the bare minimum for Arctic survival. They have thus evolved more slowly away from anatomical traits and behavioral predispositions that were originally meant for Arctic environments.

This is in contrast to the relatively rapid change in morphology that we see in sub-Saharan Africa—from a small, gracile, and almost childlike appearance, as typified by Pygmies and Khoisans, to a much larger and more robust body form. Just as radical has been the shift from a low rate of polygyny to a very high one.

Did evolution get a helping hand in sub-Saharan Africa? Was this change in physique facilitated by introgression of archaic genes? Perhaps Greg Cochran and John Hawkes were right after all. They just had the wrong example.

A final point

This leads to another point. It’s inexact to say that genetic introgression speeds up evolution. Rather, it speeds up evolution along a certain trajectory … to the detriment of other possible trajectories.

Take the example of tropical Amerindians. With the advent of year-round farming, they started down the same path that sub-Saharan Africans were taking on the other side of the Atlantic, i.e., more reproductive autonomy for women, lower cost of polygyny for men, higher incidence of polygyny, more male-male competition for access to women, etc.

But their progress down that path was slower. They had less of the relevant genetic variability for natural selection to act on. Meanwhile, another path opened up. This was the one leading to the formation of more complex societies, such as the Mayans, the Toltecs, and the Aztecs in Mesoamerica, and the Incas in South America. They were able to take that path because of their relatively low level of male-male rivalry. There was consequently less need for pacification—a key precondition for development of complex social relations (i.e., State formation, specialization of labor, creation of roads and other public infrastructures, etc.).

This was not the case in sub-Saharan Africa. The high rate of polygyny, and hence male-male competition, became a serious impediment to the creation—and survival—of complex societies.

References

Cochran, G. (2006). Neanderthal introgression & microcephalin, Gene Expression, November 8
http://www.gnxp.com/blog/2006/11/neanderthal-introgression.php

Frost, P. (2008). Sexual selection and human geographic variation, Special Issue: Proceedings of the 2nd Annual Meeting of the NorthEastern Evolutionary Psychology Society. Journal of Social, Evolutionary, and Cultural Psychology, 2(4),169-191. http://137.140.1.71/jsec/articles/volume2/issue4/NEEPSfrost.pdf

Frost, P. (2001). Polygyny and sex ratios, Encyclopedia of Birth Control, V.L. Bullough (ed.), Santa Barbara (Cal.): ABC-CLIO, pp. 218-223.

Hames, R. (1995). Yanomamö, Varying Adaptations of Foraging Horticulturalists, Just in Time Anthropology series, Prentice Hall and Simon & Schuster, supplemental readings for Ember and Ember's Anthropology, 8th edition.

Holliday, T.W. (1997). Body proportions in Late Pleistocene Europe and modern human origins, Journal of Human Evolution, 32, 423-447.

Murdock, G.P. (1959). Africa. Its Peoples and Their Culture History. New York: McGraw-Hill.

18 comments:

Ben10 said...

You've heard about the 42 000 years old paintings in spanish caves, atributed to neanderthal.


I lost the link unfortunatly, but in the comments, somebody asked a question that always bothered me too, why didn't neandertahl or modern sapiens never painted each other?

Sean said...

According to the 'introgression in Europe for modern brainpower' hypothesis, the Mayans should not have been the first to symbolize the concept of nothing (or zero). But they were.

The archaics' testosteronization may have aided African agriculturists. Digit ratios predict polygyny in early apes, Ardipithecus, Neanderthals and early modern humans

Sean said...

John Hawks: Which population in the 1000 Genomes Project samples has the most Neandertal similarity?

Are we ever going to see Australian aborigines included in these comparisons.

Anonymous said...

The PC Police will brand you a heretic.

Anonymous said...

Peter,

What's your view on the Solutrean hypothesis?

The first inhabitants of the Americas may have been whites called Solutreans. The Indians may have been latecomers who invaded and genocided the whites who were original and native to the Americas before the Indians.

There’s a new book that argues strongly in favor of it:

http://smithsonianscience.org/2012/01/new-book-across-atlantic-ice-the-origin-of-americas-clovis-culture/

Anonymous said...

Peter,

I was wondering if we could see a few words from you about the differences in Neanderthal admixture fractions between populations - http://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/1000-genomes-introgression-among-populations-2012.html.

Particularly the finding where "Yoruba have substantially more Neandertal similarity than Luhya. This may seem counter-intuitive, because the geographic location of Luhya in East Africa might seem better placed for Neandertal similarity to appear, whether through ancient population structure and ILS or through recent gene flow or backmigration into Africa of Neandertal descendants.

Instead, it looks like the Yoruba are the recipients of Neandertal genes, whether by means of ancient population structure or introgression and recent trans-Saharan gene flow. "


Is there any explanation in your model, or do we even need one? Or any way this information (presumably unknown at the time of writing that hypothesis) supports or removes support from that hypothesis?

Thanks.

Matt said...

Peter, this is a very original adapation of the archaic introgression concept.

But I have the following criticisms/questions:

Peter: This is in contrast to the relatively rapid change in morphology that we see in sub-Saharan Africa—from a small, gracile, and almost childlike appearance, as typified by Pygmies and Khoisans, to a much larger and more robust body form. Just as radical has been the shift from a low rate of polygyny to a very high one.

Are you sure about this? Upper Paleolithic European people are very large and robust aren't they and the internal dynamics in the European region favour reductions in body size with agriculture. There weren't any small and dainty Paleolithic or even Mesolithic European men and women. I think agriculture and size reduction in stature and robusticity are correlated in a way that generally find stature and robusticity decreases with agriculture.

http://www.ncbi.nlm.nih.gov/pubmed/21507735

"The impact of agriculture, accompanied by increasing population density and a rise in infectious disease, was observed to decrease stature in populations from across the entire globe and regardless of the temporal period during which agriculture was adopted, including Europe, Africa, the Middle East, Asia, South America, and North America."

Fair enough to propose "Well, there's path dependence and sometimes small-framed populations get larger and sometimes small-framed populations get larger, depending on what genes they have, and that more diverse sets of genes may enable you to go to a ".

But I'm not sure how well we can know that pygmy or khoi-san or hadza (the hadza are pretty small) types are ancestral (let alone the exclusive ancestors) to current West African populations - don't we have basically no fossil record there? pygmy or khoi-san or hadza may just specialised modern hunter gatherers don't really represent the ancestors of West African farmers. and the record above it seems like generally agriculturalists are smaller.

Plus, aren't African archaics generally pretty small? There's a tendency to stature increase in the human family, with H. Sap being the tallest and largest (of course, being less robust corrected for stature) and having the longest legs (and shortest arms and torso) relative to body size. It doesn't seem promising a priori to look to them for mutations and evolutionary changes towards large stature there - particularly given that Africans don't seem like a group who have a different leg:arm ratio.

I know there was an estimate that Nariokotome Boy was very tall (http://en.wikipedia.org/wiki/Turkana_Boy) but he seems to have been estimated down to 1.63 m due to differences in growth rates - not to mention being a sample size of 1.

Sean:The archaics' testosteronization may have aided African agriculturists.

http://library.thinkquest.org/26070/gather/entries/27.html

Human males and females produce more testosterone than chimpanzee males and females, respectively (Winter et al., 1980). Chimpanzee and human females produce similar levels of estradiol (Winter et al., 1980) and progesterone (Hobson et al., 1976). I suggest early differences in testosterone levels started species divergence and promoted hominid evolution.

Not too sure this is accurate, but the only comparison of between hominid testosterone I am aware of.

Chimpanzees seem pretty polygynous, although perhaps that inaccurately characterizes their mating system.

Perhaps archaic homo had higher circulating t or more responsive receptors than us, while we have more than chimps though?

gcochran said...

You really need to keep up with the literature.

Sean said...

How to Think Like a Neandertal. It is a very silly book, published this year.

Peter Frost said...

Ben,

Modern humans might have painted pictures of Neanderthals. We may not be recognizing these pictures for what they really are.

Sean,

The degree of Neanderthal introgression is about the same for Europeans and Amerindians. It seems to have happened at a very early point in time, perhaps within a zone of hybridization that covered parts of the Middle East and even northeast Africa.

Anon,

I believe that the earliest humans in the Americas were physically and culturally similar to the Solutreans of Western Europe. But this simply reflects the fact that prior to 20,000 BP a single breeding population extended from southwestern France to Beringia. It was only after the glacial maximum that west and east Eurasians became different from each other.

Anon,

Yes, I read that post by John Hawkes. It looks like measurement of Neanderthal admixture is also picking up Afro-archaic admixture. This is consistent with my argument that Afro-archaic admixture is higher in western and southern Africans than in eastern Africans (because modern humans spread out from an epicenter somewhere in eastern Africa).

On the other hand, if the Afro-archaics were simply a southern variety of Neanderthal, we might all be a lot more Neanderthal than I previously thought.

Matt,

Non-tropical farming is qualitatively different from tropical farming. Tropical farming is largely women's work. The men play a secondary role and spend much of their energy fighting over women. War itself is seen as a means of gaining sexual access to women. It is this male-male rivalry that drives natural selection for increased male size and robustness.

You don't get this evolutionary sequence with non-tropical farming. Women cannot farm on their own. They need assistance from men for food procurement, especially in winter. It's a very different set-up.

The Afro-archaics seem to have been fairly large, i.e., Boskop man. In any case, I'm not sure this point is relevant to the issue of archaic introgression. Modern humans might have got genes that better mobilize testosterone, for instance. Genes for increased stature were probably not a serious evolutionary constraint. You can go from pygmy to Dinka in a few thousand years if the selection pressure is strong enough.

Greg,

Feel free to enlighten me.

Anonymous said...

But this simply reflects the fact that prior to 20,000 BP a single breeding population extended from southwestern France to Beringia.

How is that possible?

SW France and Beringia are basically at the furthest, opposite ends of Eurasia.

It seems more plausible that people from SW France sailed along the north Atlantic to the Americas.

Ben10 said...

"Modern humans might have painted pictures of Neanderthals. We may not be recognizing these pictures for what they really are"

Well, maybe but they were pretty good at painting, better than at sculpting. Here is a link that shows many venuses along with a long alphabetical list of caves and painting sites on the left. If you go to "Chauvet" the oldest ~40 000 years old cave in France, you won't see any obvious neanderthal figures.

http://www.donsmaps.com/venus.html

Peter Frost said...

Anon,

From southwestern France to Manchuria, there is an unbroken corridor of lowlying grassland. Even within historic times, people freely moved back and forth within this zone, e.g., Huns, Turco-Tartars, Mongols.

It was the glacial maximum, with the creation of ice caps along the Urals and glacial lakes along the Ob River that restricted east-west gene flow through this corridor. After the ice age, this decrease in gene flow was further reduced by a trend toward farming and sedentarization in both Europe and East Asia.


Ben,

I'm going from memory here, but I remember seeing French cave paintings that seemed to depict creatures with human faces and furry bodies. The interpretation was that these were imaginary creatures.

Sean said...

I kind of get the impression it's the highly derived West European Neanderthals, the ones with the seriously large (and peculiarly shaped) brains, that Gregory Cochran thinks provided the useful introgression, not the 'generalized' Neanderthals found elsewhere. If the western European Neanderthals were so different( see HERE) maybe only a minimal number of matings with modern humans occurred, but with western European Neanderthals of special traits. That could have been enough for the brain capacity boost. Anyway Amerindians wouldn't have the western European Neanderthal alleles. So they should have been very far behind.

Anonymous said...

From southwestern France to Manchuria, there is an unbroken corridor of lowlying grassland. Even within historic times, people freely moved back and forth within this zone, e.g., Huns, Turco-Tartars, Mongols.

This was before horses and the wheel, though.

It's hard to believe there would be a single breeding population between SW France and Beringia maintained by people traveling by foot.

Are you suggesting that people regularly walked back and forth between SW France and Beringia?

Anonymous said...

Peter Frost wrote: "..sub-Saharan Africans, who have as much as 15% archaic admixture...."


What fill up the remaining 85%?

How much (in %) of sub-Saharan Africans genes do they share with chimpanzees?

Ben10 said...

'La grotte du sorcier' depicts 2 humanoids
http://www.donsmaps.com/sorcier.html
The 'head with a bestial face' could be an animal or a human elongated face. Altamira has the 'Bird man', Lascaux its own sorcerer etc. All this suggests the Chamans were often wearing dead animal heads or skulls for their ceremonies.

For the Neanderthals, at la Chapelle aux Saints
http://www.donsmaps.com/chapelleauxsaints.html
There is an excellent reconstitution of a Neanderthal with his face projected forward and almost no neck, The reconstitution from marcellin Boule keeps an African allure, to me. These guys didn't even get any tooth decay! From this site, here is their bill of health:
" No vitamin deficiency
No nutritional deficiency
Absence of tooth decay
No unknown diseases
Little trauma
No traces of surgery or skull surgery
No osteoporosis or other age related diseases because they most often die before these signs appear.. "

What did they died of then?

Peter Frost said...

Sean,

Well, yes, but the level of Neanderthal admixture is only slightly higher in Europeans than in Asians. That seems to suggest that most of the introgression happened when modern humans began to spread into the Middle East.

Anon,

There was no barrier to gene flow from southwestern France to Manchuria. The absence of barriers, together with the lack of large sedentary populations, would have maintained a single breeding population.

Anon,

The remaining 85% came from modern humans.

We don't really know the answer to your second question for any human population. You may have heard the figure of 98% genetic similarity between chimps and humans, but that refers only to gene sequences (or amino acid sequences). In theory, every single human gene could be 2% different from its chimp counterpart. And a 2% difference can greatly affect the way a gene functions.

Ben,

Yes, shamanism is the usual explanation.

Neanderthals had a diet that was low in sugar. They also died fairly young. Their bodies may even have been programmed to die at a younger age.

What did they die of? Accidents of various sorts, probably. The same is true for modern hunter-gatherers. A few are lucky to live to old age, but most don't.