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Hominin increase in cranial capacity, courtesy of Luke Jostins

A few years ago a statistical geneticist at Cambridge’s Sanger Institute, Luke Jostins, posted the chart above using data from fossils on cranial capacity of hominins (the human lineage). As you can see there was a gradual increase in cranial capacity until ~250,000 years before the present, and then a more rapid increase. I should also note that from what I know about the empirical data, mean human cranial capacity peaked around the Last Glacial Maximum. Our brains have been shrinking, even relative to our body sizes (we’re not as large as we were during the Ice Age). But that’s neither here nor there. In the comments Jostins observes:

The data above includes all known Homo skulls, but none of the results change if you exclude the 24 Neandertals. In fact, you see the same results if you exclude Sapiens but keep Neandertals; the trends are pan-Homo, and aren’t confined to a specific lineage….

In other words: the secular increase in cranial capacity for our lineage extends millions of years back into the past, and also shifts laterally to “side-branches” (with our specific terminal node, H. sapiens sapiens, as a reference). This is why I often contend as an aside that humanity was to some extent inevitable. By humanity I do not mean H. sapiens sapiens, the descendants of a subset of African hominins who flourished ~100,000 years before the present, but intelligent and cultural hominins who would inevitably construct a technological civilization. The parallel trends across the different distinct branches of the hominin family tree which Luke Jostins observed indicated to me that our lineage was not special, but simply first. That is, if African hominins were exterminated by aliens ~100,000 years before the present, at some point something akin to H. sapiens sapiens in creativity and rapidity of cultural production would eventually arise (in all likelihood later, but possibly earlier!).

This does not mean that I think humanity was inevitable upon earth. For most of the history of this planet life was unicellular. I do not find it implausible that life on earth may have reached its “sell by” date due to astronomical events before the emergence of complex organisms (in fact, from what I have heard the end of life is going to occur ~1 billion years into the future due to the persistent increase in the energy output of Sol, not ~4 billion years in the future when Sol turns into a red giant). But, once complex organisms arose it does seem that further complexity was inevitable. This was Richard Dawkins’ case in The Ancestor’s Tale based simply on the descriptive record. But did the emergence of complex organisms necessarily entail the evolution of a technological species? I don’t think so. It took 500 million years for that to occur (it does not seem that coal resources formed hundreds of millions of years ago were tapped before humans). Given enough time obviously a technological species would evolve (e.g., extend the time of evaluation to 1 trillion years), but note that the earth has only ~5 billion years. Homo arrived on the scene in the last 20% of that interval.

Here I am positing at a minimum two not excessively likely or inevitable events over a 5 billion year time span which would lead to a hyper-technological and cultural species:

- The emergence of multicellular life

- The emergence of a lineage with the propensities of Homo

One Homo evolved and expanded outside of Africa I suspect that something of the form of a technological civilization became inevitable n this planet. We see parallelism in our own short post-Pleistocene epoch. Multiple human societies shifted from hunter-gatherers to agriculturalists over the past 10,000 years. The experience of the New World civilizations in particular illustrates that human universal tendencies are real. Not only were “game changing” cultural forms such as agriculture and literacy invented independently during the Holocene, but they were not invented during earlier interglacials (at least in all likelihood).

Khufu, Necho, Augustus and Napoleon

Why not? Well, consider the cultural torpidity of Paleolithic toolkits, which might persist for hundreds of thousands of years! I suspect some of this due to biology. But even over the Holocene we do perceive that cultural change has proceeded at a more rapid clip as time has progressed (i.e., at a minimum cultural change has been accelerating, and it may be that the rate of acceleration itself is increasing!). Consider that the civilization of ancient Egypt spanned at least 2,000 years. Though there are clear differences, the continuity between Old Kingdom Egypt and the last dynasties before the Assyrian and Persian conquests is very obvious to us, and would be obvious to ancient Egyptians. In contrast, 2,000 years separates us from Augustan Rome. The continuities here are clear as well (e.g., the Roman alphabet), but the cultural change is also clear (if you wish to argue that the early modern and modern period are sui generis, the 1,500 year interval from Augustan Rome to the Neo-Classical Renaissance would still be a stark contrast when compared against an ancient Egyptian reference*, despite the latter’s aping of the forms of the former).

So far I have focused on the vertical dimension of time. But there is also the lateral dimension, of cross-fertilization across the branches of the hominin family tree. The admixture of a Neanderthal element into non-Africans has started to become widely accepted recently, thanks to the confluence of archaeology and genomics in the field of ancient DNA. Even if one rejects the viability of Neanderthal admixture, the solution to the conundrum of these results must still entail stepping away from a simple model of recent exclusive origin of humans from a small African population. There are also hints of admixture with other archaic lineages on the Pacific fringe, and within Africa.

Until recently it was common to posit that modern humans, our own lineage, had some special genius which allowed it to sweep the field and extinguish our cousins. The qualitative result of Luke Jostins’ plot was known; that other hominin lineages also exhibited encephalization. In fact, it was a curious fact that Neanderthals on average had larger cranial capacities than anatomically modern humans. But the reality remained that we replaced them, ergo, we must have a special genius. Until the lack of distinction between Neanderthals and modern humans on loci implicated in the necessary (if not sufficient) competency of language that trait was a prime candidate for what made “us” special. But now I put “us” in quotation marks. The data do point to an overwhelming descent from an African or near-African population for non-Africans over the past 100,000 years. But the “archaic admixture” is not trivial. What was they are us, and we have become what they might have been.

For over two centuries there has been a debate in the West between monogenesis and polygenesis. The former is the position that humankind derives from one single pair or population (the former a straightforward recapitulation of the standard Abrahamic model). The latter is the position that different races of humans derive from different proto-humans, or, for the Christian polygenists that only Europeans descent from Adam and Eve (the other races being “non-Adamic”). Echoes of this conflict persist down to the present era. Many of the earlier partisans of “Out of Africa” have claimed that the proponents of multiregionalism were latter-day polygenists (not without total justification in some cases).

But the conflict between monogenism and polygenism is not the appropriate frame for what is being unveiled by reality before our eyes. What we see in the creation of modern humanity is a monogenic base inflected with the flavors of polygenism. Modern humans descend, by and large, from an expansion of an African population over the past 200,000 years. But on the margins there are other strands and filaments of ancestry which tie disparate populations back to lineages which branched off far earlier from the main trunk. At a minimum hundreds of thousands, and perhaps an order of 1 million years, before our own age. Today genomics avails of us the statistical power to extract out these discordant signals from the fluid “Out of Africa” narrative, but I would not be surprised if in the near future we stumble upon more and more “long branches” of less noteworthy quantity. Admixture is likely to be an old and persistent story in the hominin lineage, with only the most recent substantial bouts of separation and hybridization being of notice and curiosity at this moment in time.

What does all this mean? And why have I juxtaposed deep time natural history across the tree of life with inferences of relatively recent paleoanthropology? Let’s start with two propositions:

- Technological civilization, an outward manifestation of radically complex sentience, is not inevitable, though it is probable given certain preconditions (I believe that the existence of Homo increased its probability to ~1.0 over a reasonable time period)

- Radically complex sentience is not the monopoly of a particular exclusive lineage which accrues its genius from a particular specific forebear

John Farrell has pointed out the possible issues that the Roman Catholic church may have with the new model of human origins. But the Catholic church is only but a reflection of more general human strain of thought. Descent-groups, whether real or fictive, loom large in the human imagination. The evolutionary rationale for this is not too hard to explain, but we co-opt the importance of kinship in many different domains. Like evolution, human cultural forms simply take what is already present, and retrofit and modify elements to taste.

So why are humans special? And why do humans have inalienable rights? Many of us may not agree with the proposition that we are the descendants of Adam and Eve, and therefore we were granted the divine grace of eternal souls. But a hint of this logic can be found in the assumptions of many thinkers who do not agree with the propositions of the Roman Catholic church. Recently I listened to Sherry Turkle arguing against a reliance on “robot companions” which are able to exhibit the verisimilitude of human emotions for those who may be lacking in companionship (e.g., the aged and infirm). Though Turkles’ arguments were not without foundation, some of her arguments were of the form that “they are not us, they are not real, we are real. And that matters.” This is certainly true now, but will it always be? Who is this “they” and this “we”? And what does “real” mean? Are emotions a mysterious human quality, which will remain outside of the grasp of those who do not descend from Adam, literal or metaphorical?

If there arises a point where non-human sentience is a reality, do they have the same rights as we? Though the difference is radical in terms of quantity to some extent I think we know the answer: they are human by the way they are, not by the way their ancestors were. The “taint” of admixture with diverse lineages across the present human tree of life has not resulted in an updating of our understanding of human rights. That is because the idea that we are all the children of Adam, or the descendants of mitochondrial Eve, is a post facto justification for our understanding of what the rights of humanity are, adn what humanity is. And what it is is a particular ecological niche, a way of being, not being who descend down in a line of biological relationship from a particular person or persons.

* The cultural fundamentals of Old Kingdom Egypt arguably persisted in a living fossil form in the temple at Philae down to the 6th century A.D.! Therefore, a 3,500 year lineage of literature continuity.

Image credits: all public domain images from Wikpedia

(Republished from Discover/GNXP by permission of author or representative)
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Interesting piece in LiveScience, What We Learned About Our Human Ancestors in 2011. The author highlights the likelihood of a lot of admixture across very diverged lineages, as well as the nascent “Out of Arabia” hypothesis. This quote from Michael Hammer gets at where we’re “going next”:

“We’ve probably just scratched the surface of what we might find,” Hammer added. “We only looked at a small number of regions of the genome. This coming year, you’ll see a lot of progress made with full genome data. This year, we should be able to confirm what we found and go way beyond that.”

I think the the lowest hanging fruit in terms of “paradigm shift” was the renewed opening to admixture with “archaic” lineages in 2010 and 2011. Before that point it was reasonable for anyone to respond to these hypotheses with a recitation of the “Out of Africa” orthodoxy. Now no longer. If admixture did no occur, then we’re talking about strange results which still need explaining with a novel model (e.g., lots of “structure” in the “Out of Africa” population due to admixture within Africa). But as the low hanging fruit is picked, researchers are now going to spread themselves out throughout the grove, hunting for numerous odds and ends. In all likelihood the picture is going to get complex, but hopefully it will be more accurate.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Human Evolution, Human origins 
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ResearchBlogging.orgThe Pith: I review a recent paper which argues for a southern African origin of modern humanity. I argue that the statistical inference shouldn’t be trusted as the final word. This paper reinforces previously known facts, but does not add much that both novel and robust.

I have now read the paper which I expressed a touch of skepticism toward yesterday. Do note, I did not dispute the validity of their results. They seem eminently plausible. I was simply skeptical that we could, with any level of robustness, claim that anatomically modern humans arose in southern vs. eastern, or western, Africa. If I had to bet, my rank order would be southern ~ eastern > western. But my confidence in my assessment is very low.

First things first. You should read the whole paper, since someone paid for it to be open access. Second, much props to whoever decided to put their original SNP data online. I’ve already pulled it down, and sent off emails to Zack, David, and Dienekes. There are some northern African populations which allow us to expand beyond the Mozabites, though unfortunately there are only 55,000 SNPs in that case (I haven’t merged the data, so I don’t know how much will remain after combining with HapMap or HGDP data set).

The abstract:

Africa is inferred to be the continent of origin for all modern human populations, but the details of human prehistory and evolution in Africa remain largely obscure owing to the complex histories of hundreds of distinct populations. We present data for more than 580,000 SNPs for several hunter-gatherer populations: the Hadza and Sandawe of Tanzania, and the ≠Khomani Bushmen of South Africa, including speakers of the nearly extinct N|u language. We find that African hunter-gatherer populations today remain highly differentiated, encompassing major components of variation that are not found in other African populations. Hunter-gatherer populations also tend to have the lowest levels of genome-wide linkage disequilibrium among 27 African populations. We analyzed geographic patterns of linkage disequilibrium and population differentiation, as measured by FST, in Africa. The observed patterns are consistent with an origin of modern humans in southern Africa rather than eastern Africa, as is generally assumed. Additionally, genetic variation in African hunter-gatherer populations has been significantly affected by interaction with farmers and herders over the past 5,000 y, through both severe population bottlenecks and sex-biased migration. However, African hunter-gatherer populations continue to maintain the highest levels of genetic diversity in the world.

Why would hunter-gatherers have so much diversity? The historical and ethnographic data here are clear: it is not that hunter-gatherers are particularly diverse, but that descendants of farming populations tend to be less diverse, and most of the world’s population are descendants of farmers. To give a classic example, ~30,000 Puritans and fellow travelers who arrived in the 1630s to New England gave rise to ~700,000 New Englanders in 1790. This is a growth by a factor of 3 to 4 per generation. And, this does not include the substantial back migration to England during the 1650s, as well as the fact that there was already spillover of New Englanders to other regions of the American colonies in the 17th and 18th centuries (e.g., eastern Long Island was dominated by New Englanders). 30,000 is not small enough to constitute a bottleneck genetically, but one can imagine much smaller founding populations rapidly compounding as agriculturalists push their way through ecologically constraining bottlenecks.

For Africa we have a good candidate for this phenomenon: the Bantu expansion. This rise of African farmers began around the region of eastern Nigeria and Cameroon ~ 3,000 years ago. It swept east, toward the lakes of eastern Africa, and down along the Atlantic coast toward modern day Angola. Between 1,000 and 2,000 years ago in its broad outlines the expansion had crested, reaching its limit in southern Africa, where the climatic regime was not favorable for their tropical agricultural toolkit (e.g., the Cape region has a Mediterranean climate). Here you still have the hunter-gatherer Bushmen, and other Khoisan groups such as the Nama, who practiced animal husbandry. By and large this expansion seems to have resulted in a great deal of biological replacement of previous peoples. South African Bantu speakers, such as Desmond Tutu, share more with Nigerians genetically than they do with the nearby Bushmen, though there has been some admixture on the frontier among Xhosa.

As I have stated, most of this paper elicits little objection from me. The major issue that I do take objection to is the inference that these results indicate the likelihood of southern, not eastern, Africa, being the origin of anatomically modern humanity. The authors do point out that many of the hallmarks of modern humanity have their earliest dates in southern, not eastern, Africa. That does add to the plausibility of their overall case, and I would be curious as to the opinion of someone more versed in the material culture and fossil remains to weigh in. But that’s where we started, not where we are, assuming that their specific contribution to the model does push it forward. So I’ll focus on the genetic data. Here’s the point which seems tendentious to me:

…Regressions of LD on distance from southwestern Africa were highly statistically significant (at 5-Kb windows, P ≈ 4.9 × 10−6) (Fig. 2C). Best-fit (Materials and Methods) locations based on LD are consistent with a common origin in southern Africa. A point of origin in southwestern Africa was approximately 300–1,000 times more likely than in eastern Africa….

If you’ve calculated regressions, you know that this can be quite the art. They are sensitive to various assumptions, as well as the data you throw into them. They’re dumb algorithms, so they’ll give you a result, even if it doesn’t always make sense. To really understand why I remain moderately skeptical of the inference in this paper, you need to look at figure 2B. I’ve reedited a bit for style. Also, some of the groups were so obscure that even I didn’t know them, so I just put in their nation.

On the y axis is linkage disequilibrium. Basically, population bottlenecks, and admixture events, along with localized selective sweeps, can elevate this statistic. The LD statistic for non-African populations is invariably higher than for African ones, and the further away, the higher the value. On the x axis is the distance from their inferred point of origin of the human expansion in south-eastern Africa. The Hadza seem to have gone through a recent bottleneck (or, are going through it now) according to other measures in the paper, so no surprise that they’re deviated above the trend line. The other hunter-gatherer groups, the Bushmen and Pygmies (Namibian and South African Bushmen, the the Biaka from western Congo and the Mbuti from the east of that nation) have low LD values, consistent with relatively stable and deep time histories for the populations, when viewed as a coherent whole (all humans have equally ancient lineages, but coherent populations can be older, or younger, depending on how you view them). My main issue is this: once you remove the non-Sub-Saharan African populations the trend line is far less stark. The Fang, who are a Bantu group near the point of origin of that language family, have nearly the same LD as some of the hunter-gatherer groups. The Mandenka, in far western Africa, have elevated LD vis-a-vis hunter-gatherers, but not nearly so much as the groups with more “northern” admixture (e.g., the Fulani).

The moral of the story here is to not just rely on the final numbers generated by statistical methods, which can be quite of a large magnitude, but look at the figures and try to make sense of them. Overall, I would say that this paper presents many interesting results, but the most robust look to be confirming what we know previously, rather than increasing the probability of a novel locus for the point of origin of modern humans (though the southern origin already gains some support from archaeology).

Citation: Brenna M. Henn, Christopher R. Gignoux, Matthew Jobin, Julie M. Granka, J. M. Macpherson, Jeffrey M. Kidd, Laura Rodríguez-Botigué, Sohini Ramachandran, Lawrence Hon, Abra Brisbin, Alice A. Lin, Peter A. Underhill, David Comas, Kenneth K. Kidd, Paul J. Norman, Peter Parham, Carlos D. Bustamante, Joanna L. Mountain, & Marcus W. Feldman (2011). Hunter-gatherer genomic diversity suggests a southern African origin for modern humans PNAS : 10.1073/pnas.1017511108

Image credit: Mark Dingemanse.

(Republished from Discover/GNXP by permission of author or representative)
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Razib Khan
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