There’s an excellent paper up at Cell right now, Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant. It synthesizes genomics, computational modeling, as well as the effective execution of mouse models to explore non-pathological phenotypic variation in humans. It was likely due the last element that this paper, which pushes the boundary on human evolutionary genomics, found its way to Cell (and the “impact factor” of course).
The focus here is on EDAR, a locus you may have heard of before. By fiddling with the EDAR locus researchers had earlier created “Asian mice.” More specifically, mice which exhibit a set of phenotypes which are known to distinguish East Asians from other populations, specifically around hair form and skin gland development. More generally EDAR is implicated in development of ectodermal tissues. That’s a very broad purview, so it isn’t surprising that modifying this locus results in a host of phenotypic changes. The figure above illustrates the modern distribution of the mutation which is found in East Asians in HGDP populations.
One thing to note is that the derived East Asian form of EDAR is found in Amerindian populations which certainly diverged from East Asians > 10,000 years before the present (more likely 15-20,000 years before the present). The two populations in West Eurasia where you find the derived East Asian EDAR variant are Hazaras and Uyghurs, both likely the products of recent admixture between East and West Eurasian populations. In Melanesia the EDAR frequency is correlated with Austronesian admixture. Not on the map, but also known, is that the Munda (Austro-Asiatic) tribal populations of South Asia also have low, but non-trivial, frequencies of East Asian EDAR. In this they are exceptional among South Asian groups without recent East Asian admixture. This lends credence to the idea that the Munda are descendants in part of Austro-Asiatic peoples intrusive from Southeast Asia, where most Austro-Asiatic languages are present.
Who to trust? That is the question when you don’t know very much (all of us). Trust is precious, and to some extent sacred. That’s why I can flip out when I realize after the fact that someone more informed than me in field X sampled biased their argument in a way they knew was shady to support a proposition they were forwarding. What’s the point of that? Who cares if you win at a particular bull-session? You’re burning through cultural capital. And not that most of my interlocutors care, but I’m likely to never trust them again on anything.
In any case, this came to mind when I ran across a James Fallows’ post at The Atlantic. Here’s a screenshot of the appropriate section, with my underlines:
Well, not really…but in some ways close enough judged against the initial reference point of where I started on certain questions. Dienekes contends:
This will help us understand both: the ancestors of non-Africans did not come forth fully formed, like Athena from Zeus’s head, having spent millennia of perfecting their craft and honing their minds by perforating shells and scratching lines in some South African cave. Instead, they may been plain old-style hunter-gatherers who stumbled into Asia by doing what they always did: following the food. At the same time, the UP/LSA revolution may not have been effected by a new and improved type of human bursting into the scene and replacing Neandertals and assorted dummies, but rather as a cultural revolution that spread across a species that already had the genetic potential for it, and was already firmly established in both Africa and Asia.
The former position, that the Out-of-Africa population were genetically endowed supermen who blitzkrieged other humans ~50,000 years ago was probably the most common position ~10 years ago. It’s outlined by Richard Klein in The Dawn of Human Culture. A contrasting argument was put forth at about the same time by Stephen Oppenheimer in The Real Eve. With 10 years of hindsight much of Oppenheimer’s model leaves much to be desired, but the one aspect which I laughed at at the time, but now give much more credit to, is the proposition that the Out-of-Africa migration was an expression of a cultural revolution in a proximate sense, rather than a biological revolution.
The always informative Ann Gibbons has a piece in Slate, The Neanderthal in My Family Tree. There is almost nothing new for regular readers of this weblog, but it’s rather awesome that Slate is now publishing stuff like this. Many people are simply unaware of the new paleogenomics. Case in point, a good friend who has a doctorate in chemical physics, and was totally unaware a year after the seminal Science paper on Neandertal admixture of the likelihood of Neandertal admixture!
Nevertheless, I think it is important for me to be repetitive and highlight a disagreement I have with the Gibbons’ piece. She says:
New Scientist has a piece up, Europeans did not inherit pale skins from Neanderthals, based on a paper I blogged last month. One thing that I hadn’t though about in detail…how did anatomically modern humans of various shades perceive Neandertals of various shades? For example, it seems highly likely that there were swarthy Neandertals and pale Neandertals. Similarly, there were swarthy modern humans, and soon enough pale ones. Skin color is a very salient trait. Very different populations phylogenetically, Sub-Saharan Africans, Melanesians, and South Asians, have been defined as “black.” Did modern humans perceive Middle Eastern Neandertals, who may have been relatively dark, as much closer to humanlike status because of their similar complexion to anatomically modern Middle Eastern humans? Did they perceive European Neandertals, who may on average have been much lighter, as fundamentally different?
When doing physical reconstructions it seems to me that the gross morphology of Neandertals has been more emphasized. Their brow ridges, large prominent noses, and stocky body plans. But in this manner perhaps they’re like our imaginings of ancient Greek temples as alabaster white. In reality the temples of antiquity and many public buildings were festooned with color. Similarly, Neandertals came in all shades.
John Hawks prompts to reemphasize an aspect of my thinking which has undergone a revolution over the past 10 years. I pointed to it in my post on the Khoe-San. In short, the common anatomically modern human ancestors of Khoe-San and non-Khoe-San may not have been people. Rather, people may have evolved over the past 100-200,000 years ago. Of course the term “people” is not quite as scientific as you might like. In philosophy and law you have debates about “personhood”. Granting the utility of these debates I am basically saying that the common ancestor of Khoe-San and non-Khoe-San may not have been persons, as well understand them. Though, as a person myself, I do think they were persons. At this point I am willing to push the class “person” rather far back in time.
As I suggested earlier there is an implicit assumption that personhood is a shared derived trait of our species. Or at least it is a consensus today that all extant members of H. sapiens are persons. Since Khoe-San are persons, the common ancestor of Khoe-San and non-Khoe-San must also be persons if personhood is a shared derived trait. But, we also know that there are many aspects of realized personhood on a sociological or cultural scale which seem to diminish the further back in time you go. For example, the Oldowan lithic technology persisted for ~1 million years. A common modern conception of persons is that persons in the aggregate are simply never so static. Persons have culture, and culture is protean. Therefore, one might infer from the nature of Oldowan technological torpor that the producers of that technology were not persons.
Over at Haldane’s Sieve there are more than preprints posted, there are commentaries from the authors as well. For example, for The genetic prehistory of southern Africa, the first author, Dr. Joseph K. Pickrell, has a extended comment up.
But occasionally you get contributions & perspectives from non-authors which are very interesting. And it is to one of these I want to draw your attention, Thoughts on: The date of interbreeding between Neandertals and modern humans. It’s a comment on The date of interbreeding between Neandertals and modern humans. In the post Dr. Graham Coop contends:
At this point you are likely saying: well we know that Neandertals existed as a [somewhat] separate population/species who are these population X you keep talking about and where are their remains? Population X could easily be a subset of what we call Neandertals, in which case you’ve been reading this all for no reason [if you only want to know if we interbred with Neandertals]. However, my view is that in the next decade of ancient human population history things are going to get really interesting. We have already seen this from the Denisovian papers [1,2], and the work of ancient admixture in Africa (e.g. Hammer et al. 2011, Lachance et al. 2012). We will likely discover a bunch of cryptic somewhat distinct ancient populations, that we’ve previously [rightly] grouped into a relatively small number of labels based on their morphology and timing in the fossil record. We are not going to have names for many of these groups, but with large amounts of genomic data [ancient and modern] we are going to find all sorts of population structure. The question then becomes not an issue of naming these populations, but understanding the divergence and population genetic relationship among them.
This is a bold contention, and I suspect some physical anthropologists will take issue with it. But it’s a testable prediction. We’ll know if it’s panned out in 2020. I may still be blogging between now and then, and so I will now self-importantly label this “Coop’s Conjecture.” Is there anyone who wants to wager some money on Coop’s Conjecture? Any side of the bet you think is a sure thing?
Dienekes Pontikos has a long post up on how reticulation within phylogenetic trees may distort our perception of human natural history when we force the data into a more conventional tree (i.e., bifurcation after bifurcation). The concrete reason for this rethinking is the high probability of “archaic admixture” into the dominant genetic signal of anatomically modern African humanity, both within Africa and outside of it.
Dienekes proposes that when ancient DNA from early modern Eurasians is analyzed then a large portion of the portrait will be unmasked. For example, if high levels of admixture were present very early on then you would see very divergent regional populations because of persistence and continuity of local hominin population substructure. The pre-African Eurasians from each given region would have contributed substantially to the genetic makeup of the first modern humans who flourished in Europe and East Asia. On the other hand, if admixture was minimal, then the early Europeans and Asians would be far less distinct than their modern descents.
A new paper in Molecular Biology and Evolution, The timing of pigmentation lightening in Europeans, is rather interesting. It’s important because skin pigmentation has been one of the major successes of the first age of human genomics. In 2002 we really didn’t know the nature of normal human variation in skin color in terms of specific genes (basically, we knew about MC1R). This is what Armand Leroi observed in Mutants in 2005, wondering about our ignorance of such a salient trait. Within a few years though Leroi’s contention was out of date (in fact, while Mutants was going to press it became out of date) . Today we do know the genetic architecture of pigmentation. This is why GEDmatch can predict that my daughter’s eyes will be light brown from just her SNPs (they are currently hazel). This genomic yield was facilitated by the fact that pigmentation seems to be a trait where most human variation is controlled by half a dozen genes. In contrast, height or I.Q. are controlled by innumerable genes.
There have been several recent studies reemphasizing diet over exercise (timely because Americans are kind of fat, on average). A new piece in The New York Times looking at the Hadza of Tanzania, who are hunter-gatherers, seems to reiterate this point, Debunking the Hunter-Gatherer Workout:
We found that despite all this physical activity, the number of calories that the Hadza burned per day was indistinguishable from that of typical adults in Europe and the United States. We ran a number of statistical tests, accounting for body mass, lean body mass, age, sex and fat mass, and still found no difference in daily energy expenditure between the Hadza and their Western counterparts.
How can the Hadza be more active than we are without burning more calories? It’s not that their bodies are more efficient, allowing them to do more with less: separate measurements showed that the Hadza burn just as many calories while walking or resting as Westerners do.
We think that the Hadzas’ bodies have adjusted to the higher activity levels required for hunting and gathering by spending less energy elsewhere. Even for very active people, physical activity accounts for only a small portion of daily energy expenditure; most energy is spent behind the scenes on the myriad unseen tasks that keep our cells humming and our support systems working. If the Hadza’s bodies somehow manage to spend less energy in those areas, they could easily accommodate the elevated energy demands of hunting and gathering. And indeed, studies reporting differences in metabolic-hormone profiles between traditional and Western populations support this idea (though more work is needed).
As noted in the paper the researchers used urine samples to ascertain caloric expenditure. I’ve seen this in surveys of overweight people. One result was that many overweight people inadvertently under report their consumption (e.g., not writing down snacks that they ate) by as much as 1/3, so this is an essential check on self-reports. A reader brings up this relevant point:
Matt Ridley has a column up, Did Your Ancestor Date a Neanderthal? In it he juxtaposes the two recent papers which got some attention on the relationship of modern humans to Neandertals. To be frank I think it took too much of the “two sides/opposing views/views differ” tack. From what I can gather the scientific consensus is moving further toward admixture, rather than ancient structure. Additionally, as John Hawks states flat out the PNAS paper which casts doubt on the strength of the admixture hypothesis is not the strongest of contributions to the field(in line with David Reich and Nick Patterson’s assessments, and others who shall remain nameless).
But it’s hard to keep track of all the threads, isn’t it? One of the most tragic aspects of the death of classic “Out of Africa” is that we lost an exceedingly simple narrative which had the positives of clarity and precision. The basic outlines were reducible to one sentence: all humans today descend from a small group of modern humans alive ~100,000 years ago. At this time we do not have such an elegant replacement framework. In fact, we may never have such an elegant model which also has the merit of being true. Instead of a fully fleshed out model we have a set of disparate facts, which we can assert with various weights of strength.
Yesterday I pointed out that David Reich had a moderately dismissive attitude toward the new paper in PNAS, Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Here’s what Reich said:
…But Reich believes that the discussion would have been different if it had happened in the open. The PNAS paper questioning the Neanderthal admixture addresses issues swirling around two years ago, but not Reich and Slatkin’s latest work. “It’s been an issue for several years. They were right to work on this,” says Reich. But now, “it’s kind of an obsolete paper,” he says.
Here’s what Nick Patterson, Reich’s colleague told me via email:
Ancient structure in Africa was considered when we wrote the Green et al. paper, and we were aware that this could explain D-statistics. But the hypothesis is no longer viable as the major explanation of Neandertal genetics in Eurasia. This was discussed in the recent paper of Yang et al. (MBE, 2012). (Not referenced by the PNAS paper).
A very simple argument, that convinces me, is that the allelic frequency spectrum of Neandertal alleles in Eurasia falls off very quickly. A bottleneck flattens out the spectrum, and it turns out that the Neandertal gene flow has to be placed after the out of Africa bottleneck or the spectrum is much too flat.
The paper on the arXiv from the Reich lab (Sankararaman et al.) is trying to do something much more subtle than this and date the flow. I personally am no longer interested in explaining the introgression as ancient structure. That ship has sailed.
Of course the question of what was the genetic structure of Ancient Africa is quite open, and remains very interesting.
If Nick’s explanation is a bit cryptic for you (he was a cryptographer!), figure 2 from the Yang et al. paper lays it out quite clearly:
Dienekes reflects on the seemingly simultaneous appearance of behavioral modernityin South Africa and Europe and Australia, pending the acceptance of the most recent finds. This part is very important in my opinion:
The San people still live in several countries of southern Africa, and until the latter part of the 20th century were still mainly hunter-gatherers. But Dr. Stringer cautioned not to think of them as “living fossils,” unchanged by time. “Their genes, cultures and behaviors have undoubtedly continued to evolve in the intervening millennia,” he said.
I see no reason to think that these were the ancestors of the San. Over 45,000 years I think the most likely option is that genetic and cultural continuity will not be maintained, and these are probably a sister group to the modern peoples of Southern Africa. In any case, to address Dienekes’ confusion, I think this is one case where his non-American background shows. We know exactly what happened so long ago to kick-start modern humanity. The answer has been with us for over 40 years.
If you are interested in genomics and human evolution, a new review paper in PLoS Genetics is a must read, Genomic Data Reveal a Complex Making of Humans. A must read not because you need to agree with the thrust of the authors’ arguments, but because it provides a thorough bibliography for the last 2 to 3 years. Here is the abstract:
In the last few years, two paradigms underlying human evolution have crumbled. Modern humans have not totally replaced previous hominins without any admixture, and the expected signatures of adaptations to new environments are surprisingly lacking at the genomic level. Here we review current evidence about archaic admixture and lack of strong selective sweeps in humans. We underline the need to properly model differential admixture in various populations to correctly reconstruct past demography. We also stress the importance of taking into account the spatial dimension of human evolution, which proceeded by a series of range expansions that could have promoted both the introgression of archaic genes and background selection.
The main problem I have at this point is the general mode of range expansions, whereby population A expands as a demographic wave across a substrate of population B. These sorts of models seem to assume a sort of continuous dynamic process. In contrast, I am beginning to suspect that much of the human demographic past was characterized by discrete events. The closer to the present the more I’m convinced of this, though honestly I am now pushing back my own timing for the origins of many of the human distinctive traits, such as culture, well before behaviorally modern humans.
Forgot to highlight one of the coolest abstracts from SMBE 2012, A genomewide map of Neandertal ancestry in modern humans:
2. The map allows us to identify Neandertal alleles that have been the target of selection since introgression. We identified over 100 regions in which the frequency of Neandertal ancestry is extremely unlikely under a model of neutral evolution. The highest frequency region on chromosome 4 has a frequency of Neandertal ancestry of about 85% in Europe and overlaps CLOCK, a key gene in Circadian function in mammals. The high frequency, Neandertal-derived variant is specific to Europeans; it is not very common in East Asians. This gene has been found in other selection scans in Eurasian populations, but has never before been linked to Neandertal gene flow
The title is tongue in cheek. But I have been noting with interest Dienekes’ trial runs with TreeMix. With it he has discovered a very peculiar admixture event, at least as determined by the software. The results are below, with my clarifying labels:
Basically the software seems to be implying that there has been gene flow into the Yoruba of West Africa from from populations related to the Basque & Sardinians. The most plausible explanation for this would be that this migration event was ancient, so that later admixtures of European populations are not reflected. Whether you believe that the Basque/Sardinians are Neolithic or pre-Neolithic (i.e., that they derive from Holocene settlers, or derive from Paleolithic European substrate), it is probably true that they have a relatively long period of residence in Western Europe.
The excellent site io9 has a piece up today which is a fascinating indicator of the nature of popular science publications as a lagging indicator. It is a re-post of a piece published last April, How Mitochondrial Eve connected all humanity and rewrote human evolution. In it you have an encapsulation of a particular period in our understanding of human natural history through evolutionary genetics. Notice for example the focus on maternally transmitted lineages, mtDNA and Y chromosomes. And the citations on genealogy date to the middle aughts. The science is mostly correct as far as it goes in the details (or at least it is defensible, last I checked there was still debate as to the validity of the molecular clocks used for Y chromosomal lineages), but it misses the big picture of how we’ve reframed our understanding of the human past over the last few years. The distance between 2011 and 2009 is far greater in this sense than between 2009 and 1999 (or even 2009 and 1989!). The io9 piece is a reflection of the era before the paradigmatic rupture.
Dienekes and Maju have both commented on a new paper which looked at the likelihood of lactase persistence in Neolithic remains from Spain, but I thought I would comment on it as well. The paper is: Low prevalence of lactase persistence in Neolithic South-West Europe. The location is on the fringes of the modern Basque country, while the time frame is ~3000 BC. Table 3 shows the major result:
Lactase persistence is a dominant trait. That means any individual with at least one copy of the T allele is persistent. As Maju noted a peculiarity here is that the genotypes are not in Hardy-Weinberg Equilibrium. Specifically, there are an excess of homozygotes. Using the SJAPL location as a potentially random mating scenario you should expect ~7 T/C genotypes, not 2. Interestingly the persistent individual in the Longar location also a homozygote.
I missed this piece in Edge from Chris Stringer in November, Rethinking “Out of Africa”. He sums up his current thinking at the end:
We’ve got the lineage of the hobbit, ‘Homo floresiensis’ (in quotation marks because its human status in not yet clear), perhaps diverging more than two million years ago, evolving in isolation in southeast Asia, and apparently going extinct about 17,000 years ago.
We’ve got Homo erectus, most likely originating in Africa, giving rise to lineages which continue in the Far East in China and Java, but which eventually go extinct. In Europe, it perhaps gave rise to the species Homo antecessor, “Pioneer Man,” known from the site of Atapuerca in Spain. Again, going extinct.
In the western part of the Old World, we get the development of a new species, Homo heidelbergensis, present in Europe, Asia and Africa. We knew heidelbergensis had gone two ways, to modern humans and the Neanderthals. But we now know because of the Denisovans that actually heidelbergensis went three ways—in fact the Denisovans seem to represent an off-shoot of the Neanderthal lineage.
North of the Mediterranean, heidelbergensis gave rise to the Neanderthals, over in the Far East, it gave rise to the Denisovans. In Africa heidelbergensis evolved into modern humans, who eventually spread from Africa about 60,000 years ago, but as I mentioned, there’s evidence thatheidelbergensis populations carried on in Africa for a period of time. But we now know that the Neanderthals and the Denisovans did not go genetically extinct. They went physically extinct, but their genes were input into modern humans, perhaps in western Asia in the case of the Neanderthals. And then a smaller group of modern humans picked up DNA from the Denisovans in south east Asia.
We end up with quite a complex story, with even some of this ancient DNA coming back into modern humans within Africa. So our evolutionary story is mostly, but not absolutely, a Recent African Origin.
Now, I know that Milford Wolpoff has still not totally buried the hatchet with Stringer, but their views are actually converging a great deal. What does that tell us? Well, paleoanthropology most definitely is a science, reality and results are dictating to the intellectual antagonists.
(Via Ruchira Paul)
I wonder if in future years we’re going to look at “species debates” in the context of human evolution like we look at counting angels on the head of a pin. Over at BBC News Clive Finlayson has a rambling opinion piece up, Has ‘one species’ idea been put to bed? Finlayson, the author of The Humans Who Went Extinct: Why Neanderthals Died Out and We Survived, doesn’t seem to have a tightly focused point and the end of it all (I think warranted, considering how unsettled this area is). But he does conclude:
And a major conference is planned for September next year when experts from all over the world will meet in Gibraltar to revise our ideas about “the human niche”. After decades of bad press we are finally getting round to humanizing the enigmatic Neanderthals.