Friday, January 10, 2014

Did a key mutation dramatically expand where humans could live?

The figure above from the PLOS One article shows the proportion of people able to obtain the key biochemical from plants in yellow and the proportion of the Eurasian variant that lacks that gene in blue.
A new study suggests that humans were able to spread out and take over the world because of a new DNA change (or mutation) that popped up in their DNA 85,000 or so years ago. . . . it let them get away with just eating plants for good brain development. . . .
Human brains are sort of like modern electronics – they need rare materials to have them work as well as they should. While an iPhone needs various rare Earth minerals, human brains need lots of something called long chain polyunsaturated fatty acids or LC-PUFAs. Humans are terrible at making these fatty acids on their own and so have to get them from their diet (sort of like vitamin C).  Unfortunately for our ancestors, humans aren’t very good at turning a plant’s fatty acids into the ones they need.  And even though we are good at getting them from animals, we didn’t start hunting in a big way until around 50,000 years ago. Human ancestors probably got these fatty acids from fish and other aquatic animals.  In fact, scientists have long hypothesized that our ancestors’ need for aquatic animals was a big reason humans were such stick-in-the-muds for almost 100,000 years.  Their inability to get the brain food they needed from plants kept them trapped by the water’s edge, unable to spread across the globe. And yet, humans did start to spread in earnest across Africa around 60-80,000 years ago. This is thousands of years before there is any evidence that they did a lot of hunting of land animals. Clearly something changed sometime just before these humans started moving away from the shore.

A group of researchers thinks that the answer might lie in a mutation that allowed ancient humans to better use plant fatty acids to make the LC-PUFAs they needed for their brains.  Now humans could eat plants to get enough nutrients and so could migrate and conquer the world. The evidence to support this idea is the fact that Africans have a certain DNA difference that Asians and Europeans do not.  This difference strengthens an enzyme (FADS1) that converts plant fatty acids into the ones humans need for their brains.  In other words, Africans have a mutation that allows them to get at least some of their brain fatty acids from plants. When the researchers looked at the DNA surrounding this enzyme in Africans, they saw fewer DNA differences than expected.  This is a telltale sign that once the mutation appeared, it quickly spread through the population (a “selective sweep” in genetics lingo).  So once a few people were able to use plants effectively, they were off and running and quickly populated the world. A close look at the DNA also allowed these scientists to estimate that the mutation first appeared around 85,000 years ago (which fits the story nicely). . . . The actual number from the paper is 85,000 +/- 84,000 years ago.

The researchers also think that this DNA difference doesn’t come without a cost.  They conclude this from the fact that the mutation is no longer than common in Asians and Europeans.  The idea is that once humans could hunt for land animals, they no longer needed to rely on plants and so the mutation was lost. Of course another possibility is that the humans that headed for Europe and Asia just happened not to have this DNA difference any more.

From here which cites Mathias, et al., Adaptive Evolution of the FADS Gene Cluster within Africa (PLOS One September 19, 2012) (open access).

The Controversial Evolutionary Breakthrough Theories

The hypothesis that a small number of key evolutionary mutation with behavioral impact provided a breakthrough that gave modern humans a distinct evolutionary fitness advantage culminating the dominance of modern humans in the Holocene era, and perhaps not actually occurring until a punctuated evolutionary advance at the dawn of the Upper Paleolithic era is a controversial one.  Critics look at the evidence on brain size and see instead a steady and gradual convergent evolution over the course of hominin evolution in all hominin species.

The term "anatomically modern humans" in human evolution and anthropology reflects the notion that "behaviorally modern humans" may have been the product of an Upper Paleolithic or similar behavioral evolutionary package of genetic mutations that took place tens of thousands of years after modern humans had bodies substantially similar to our own.

Indeed, critics question the assumption that gracile modern humans were really smarter in any meaningful way than Neanderthals.  Judged by standard proxies for intelligence like brain size relative to body size, they may actually have been slightly smarter than modern humans.  And, increasing evidence of modest levels of admixture on many occasions between different varieties of archaic homins and between archaic hominins and modern humans also casts doubt on the notion that "anatomically modern humans" are even truly a biological species, as opposed to a mere subspecies of a diverse single modern hominin species that may extend as far back as, perhaps, Homo Erectus. Compare the anatomical and behavioral diversity of domestic dogs, which are undoubtedly a single species.

Problems With The Narrative

1.  Was large scale terrestrial hunting really that rare until 50,000 years ago?

There are many problems with the narrative quoted above. The notion that modern humans were reliant upon fish as their primary source of meat until 50,000 years ago is certainly news to me.  The paper cites for this proposition: Flinn MV, Geary DC, Ward CV, "Ecological dominance, social competition, and coalitionary arms races: Why humans evolved extraordinary intelligence" (2005). Evolut Human Behav 26: 10–46. This source does assert that hunting of large game increased around this time, but offers no factual support or citations to other sources for this key assertion.  

From context, this vague assertion whose dating isn't very precisely pinned down seems to be a backhanded reference to the earliest evidence of megafauna extinctions, but those can also be explained by theories such as the co-evolution of African megafauna with modern humans that left them less vulnerable to the appearance of modern humans, and to the theory that modern humans were more ecologically dominant in arid plains than they were in jungles preventing mass megafauna extinctions before modern humans arrived in these niche ecological zones.

A recent study from Morocco showing that Mesolithic hunter-gatherer populations there that relied heavily on acorns and shellfish for their diet had high rates of tooth decay atypical of hunter-gather populations elsewhere also suggest that heavy reliance on cereals for food was atypical of pre-Neolithic forager populations.  This disfavors the notion that large scale terrestrial hunting was a late arrival in the modern human hunter-gatherer diet.

Flinn, et al., also argues in their 2005 paper in support of the "evolutionary breakthrough" hypothesis that there are no other extant hominin species, but increasingly, it looks as if as recently as 25,000-28,000 years ago there may have been as many as three to five other extant hominin species (the last of the Neanderthals, up to two archaic hominin species in Africa that admixed with modern humans as recently as 10,000 years ago, and at least one or two species from a greater Denisovan/H. Florensis hominin clade which may have persisted a long time on Flores at least and perhaps in relict populations elsewhere as well).  This conclusion tends to disfavor their overall conceptual scheme.

2.  Why is the adaptation least fixed where it would seem to be most needed?

Access to fish as an important limitation on Out of Africa expansion seems an odd for a wave of migration that was predominantly coastal until well into the Upper Paleolithic, particular when the people who would seem to have the greatest need for the mutation in Eurasia don't have it in great numbers.

What do we know about early modern human hunter-gatherer subsistence?

There is certainly archaeological evidence from 70,000 years ago and before of modern human fishing activity from middens and from evidence of harpoon fishing in Africa.

There is also evidence that modern human Cro-Magnons in Europe tended to have more diverse diets favoring smaller game than the diets of contemporaneous Neanderthals who focused more on bringing down big game like mammoths.

There were what appear to be human driven (or at least correlated) mega-fauna extinctions close in time to the appearance of significant and expanding populations of modern humans in Europe, Siberia, Japan, Australia, Oceania, and the Americas (although this evidence is much less pronounced for more tropical areas in Africa, India and Southeast Asia) which demonstrate that these populations clearly did engage in significant terrestrial hunting.  

Supportable Aspects Of The Narrative

There is good evidence in uniparental genetics for a modern human dispersal within African at a date which is 60,000-80,000 years ago as measured by mutation rate dating in Y-DNA and mtDNA which is also close in time to the estimate time of an Out of Africa dispersal measured by the same kind of mutation rate dating.

Indeed, there is a fair argument that the Out of Africa expansion and the expansion of modern humans within Africa were really pretty much the same phenomena operating in different geographic directions.

The possibility that modern human meat consumption was largely confined to fish for the first half of its evolutionary history or so, also restores some viability to the observations associated with the largely discredited "aquatic ape" hypothesis for explaining anatomical differences between modern humans and our closest primate ancestors.

There Clearly Is a Fitness Based Selection Story To Be Told Related To This Gene

Mathias, et al. (2012) do make an unimpeachable case that the gene that allows chemicals critical to brain development to be obtained from plant as well as animal sources which has reached fixation in African modern humans is indeed the subject of a fitness driven selective sweep sometime at or after the time that modern humans arose and before the Out of Africa event.  And, they also are very convincing in their argument regarding the purpose that these gene serves in brain function and nutritional processing.

There are relatively few such clear examples of a distinct fitness based selection of a particular gene in modern humans, so this story has to be a significant one.  Any gene that was the subject of a fitness based selection that was fitness enhancing enough to reach fixation at some point very likely does tell the tale of an important evolutionary pressure that modern humans faced in their prehistory, although determining the exact nature of that evolutionary pressure is more challenging.  

Large numbers of people lived or died based upon whether or not they had this gene sometime in modern human prehistory in Africa.  Likewise, it is clear that something abated that selective pressure sometime after modern humans left Africa.  But, it is hard to say more than that from the scant archaeological evidence regarding the lives of anatomically modern humans in Africa during the 75,000 to 100,000 or more years prior to their expansion out of Africa.

Issues Related To Dating The African Plant Nutrition Processing Mutation and Its Eurasian Variant

The quoted mutation rate date from the Mathias paper in 2012 which is better expressed as 1,000-169,000 years before present is pretty much meaningless for a species whose oldest skeletal remains have been dated to around 195,000 years ago.  

Even a 195,000 years ago figure for its appearance would be less than 1.5 standard deviations from the mean, something with a p-value of 0.10 or more.  For example, it would not be at all implausible given the date generated from genetic date for this gene to associate the appearance of this gene not with the expansion of modern humans within Africa midway through their evolutionary history, and instead with the package of genetic mutations that make modern humans as a species distinct from earlier archaic hominins.  

But, the fact that it is present in Africans and progressively more rare in Europeans means that it probably arose before modern humans left Africa (around 85,000 years ago based upon autosomal mutation rate dating, but more likely around 120,000 years ago based upon archaeological evidence), and not later, even though the genetic evidence would allow for a more recent date.

In order words, the narrative behind the events that caused this gene to reach fixation in African modern humans is clearly a story that is part of our shared pre-Out of African African heritage.

Similarly, the subsequent mutation displacing it in many Eurasians (which has reached fixation only in the Americas and there probably only due to founder effects) may have arisen before West Eurasian-East Eurasian divide around the same time as Neanderthal admixture, as the advent of the mtDNA M and N clades, and as the divide between the B and CT Y-DNA clades.  The latest mutation rate data put these events at about 85,000 years before present, a date whose absolute calendar year accuracy is dubious but whose systemic error is shared pretty much proportionately by other mutation rate dates, particularly autosomal ones for Y-DNA.

This secondary mutation is clearly part of the early Out of Africa story.

Meta Point and Other Commentary

I covered this story when I first came across it and must have overlooked it at the time that it came out for some reason (I had a lot going on at the time).

Maju covered the story when it broke and shared many of the same skepticisms that I do.  Dienekes also had skeptical commentary when it came out.

Part of his confusion, however, follows from a misunderstanding of a key point when he states: "The same logic that applies in Africa should apply in Eurasia-plus but the fact is that Eurasians retain the ancestral allele and related genetic bloc without obvious damage to the brains." In fact, neither the African nor the Eurasian allelles are ancestral. The Eurasian allelle is a mutation that arises after the African one, which in turn replaced an ancestral allelle that no one carries any longer (a point that presumably could be confirmed now from primate or Neanderthal or Denisovan DNA).

The story I quote above also does a decent job of explaining the purpose of this gene which was a point that Maju had found confusing about the paper and its suggested narrative.

What Other Narratives Could Make Sense?

It is notable that the Eurasian version of the gene has not reached fixation anywhere except the Americas.

Could another narrative make sense of the facts?

Suppose that in Africa, modern humans experienced periodic episodes when hunting did not generate enough meat to make up a meaningful portion of the band's diet for some reason and the band instead relied on gathering plants as in the case of the acorn eaters of Mesolithic Morocco.  During these periods people who lacked the gene allowing them to obtain the right biochemicals from plants would suffer impaired brain development and soon enough selection would remove people without this gene from the population causing the gene to reach fixation in Africa.

This ability to live on plants when their ancestors were obligate meat eaters may even be an important reason why modern humans rather than other archaic hominins ultimately become the dominant hominin species in Africa.

But, then suppose that the Eurasian version of these gene appears in someone just before or just after the Out of Africa migration to Arabia.  Indeed, let us suppose that this gene appears in descendants of a tribal leader who is observant enough to notice that his descendants thrive when they grow up eating enough meat, but fair poorly when they grow up eating predominantly vegetables.

Then, this tribe is hit with an extended patch of bad hunting and has to make a choice: stay in the same general vicinity and subsist predominantly on vegetables or take a big risk by making a major migration into unknown territory in the hope of finding game to kill to get meat so his descendants can grow up healthy.

Facing this choice, the tribal leader takes the risky course unlike all of his ancestors, so that he can save his descendants.  He also has the good fortune to do so at a time when the gamble pays off and there is meat to be found in the great unknown territory that no modern human has hunted in before at the time.  Voila, some portion of the founding population of Eurasia has this mutation and develops norms that encourage further exploration when hunting is weak locally, and hence they conquer the world.

1 comment:

Anonymous said...

Very stimulating discussion of this genetic information, thanks a lot.
Perhaps fossil anatomical & other data can help us further here.
Apparently Pleistocene Homo populations trekked along coasts & later inland along rivers: intercontinental diaspora of erectus-like people, island colonisations, typically found amid edible & sometimes marine shellfish, drastic brain expansion (DHA), pachy-osteo-sclerosis (POS: thick & dense = heavy bones, cranially & postcranially), flattened & long skulls (platycephaly), dorso-ventrally flattened femora (platymeria), very broad body (large thorax & iliac flaring): all this independently contradicts running hypotheses, and suggests a littoral lifestyle including shallow diving, feeding on shallow aquatic & presumably also waterside animals & plants: shellfish, perhaps seaweeds, bird & turtle eggs, coconuts, stranded whales etc.
Later Pleistocene archaic Homo (e.g. heidelbergensis, neanderthal) got less heavy bones: they seasonally followed the rivers inland (cf salmon trek?), butchered carcasses in mud or reeds, sometimes ate cattails & waterlilies (traces on neanderthal tools or dental calculus), etc.
But only H.sapiens (Omo & Herto after c 200 ka in E.Africa) loss of POS & of platymeria, higher & shorter skull vaults (& perhaps some brain reduction), strong basi-cranial flexion (more downward eye direction), stretched & very long legs (femora & esp.tibiae), which suggests they abandoned shallow diving, but often waded bipedally for shallow water & waterside animals & plants (presumably mostly in fresh waters according to our kidney features, e.g. rice). Perhaps this transition was facilitated by the development of distance weapons, e.g. spears to catch fish etc.?
In a sense, we are still (fresh)waterside animals. That land animals are very dangerous still today (bears=Beowulf, lions=Gilgamesh, wolves etc.) suggests that leaving the waterside was very recent.
According to your discussion, Africans (inland expansion?) & non-Africans (out of Africa) after c 80 ka seem to have followed somewhat different pathways.
-econiche Homo
-Laden Verhaegen
-Rhys Evans Vaneechoutte