Friday, August 31, 2012

Religion And Food Production

Consider the following conjecture.

For any given technological tool kit and ecological niche there are favored approaches to producing food and more generally overall basic form of economic organization.  Some of the medium grained possibilities (between coarse grained and fine grained) might be terrestrial hunting and gathering, fishing, herding, hoe based farming, plough based farming, irrigation based farming, raiding, mechanized farming and industrial production, post-industrial economic organization.

For any of these modes of food production (although types of basic economic organization might be a more accurate terminology), there is a particular set of values, cultural norms, modes of collective organization, scale of collective organization and type of political culture that is favored.  The values and social organization that works for a herder is to a great extent determined by this mode of food production and is something along the lines of a "culture of honor."  Plough based farming may favor patriachal societies, while hoe based farming may not have that bias.  Irrigation based farming may favor authoritarian political structures, while terrestrial hunter and gatherer societies may have a natural bias towards a more democratic political bent.

A religion's metaphysical structures and concepts don't matter much.  Mostly, in practice, religion serves as an embodiment and means of transmitting a set of values and collective organization techniques and structures associated with a particular method of food production.  Iron age Judaism and current era 7th century Islam both coded similar herder values and modes of collective organization, even though the former has only angels, while the later has both angels and jinn, as subordinate metaphysical actors.

Different forms of the same religion can occupy different places in this typology of religions.  Iron Age Judaism as it was practiced then may embody a set of values and collective organization associated with a different mode of food production than Rabbinic Judaism.  Southern Baptist Christianity as practiced may embody a different mode of food production than Episcopalianism.  In terms of their cultural message two religions with the same name, overlapping ceremonial components, and the same holy scriptures may be entirely different in practice.

The cultural message and collective organization approaches that a religion as practiced codes is much more important than the labels and window dressing of metaphysics that officially embody a religion's core metaphysical doctrines which can be deceiving and create a false sense of unity where none exists in the important essentials.  Interpretive doctrines have a great capacity to overcome otherwise obvious direct pronouncements of an ancient religious text.  Contrawise, it is possible to have a coherent culture associated with a particular mode of food production, in some modes of food production anyway, without some of the metaphysical elements we have come to think of as definitional components of a religion.  For example, concepts like karma and tao can be perfectly servicable alternatives to a metaphysical structure in which the way the metaphysical power acts with moral purpose in the world is through anthropomorphic beings conceptualized as "gods" rather than as pervasive cosmic forces or principles.  There may be some metaphysical structures, however, that are an easier fit to particular methods of food production and collective organization than others.  The natural tendency is to have a metaphysical world whose organization mirrors the way people understand their own world to really work.  Structures like the feudal language of the Christian New Testament, or the Olympian Council of Greek mythology mirror the political structures of their days.  Animist metaphysical structures may come naturally to people in hunter-gatherer societies who live at the whim of the countless plants and animals around them rather than the judgments of select groups of human leaders.

Connecting this economically determinist chain of reasoning together, the content of real world religions suddenly becomes far less random.  Rather than being arbitrary, a religion as practiced by a particular group of people at a particular time starts to look like something largely determined by the technologies and ecological circumstances that are formative for its adherents, which in turn drive their mode of food production in their formative period, which in turn drives the values and collective organizational forms that work best, which in turn drives much of the substantive content of the religion of those adherents as they practice it.  When a society has more than one mode of food production operating as parallel subcultures of the society at the same time, each subculture or caste of each society that practice a particular mode of food production may have its own way of practicing its religion, even if some or all of them on the surface claim to be practicing the same religion, or at least, the "true" version of the same religion.  Complex societies with multiple subcultures and centeralized government may need either a doctrine that calls for the toleration of multiple religious views as the First Amendment to the United States Constitution does, or a religion succeptible to have subcultures within it that publicly claim to be the same creed, in order to function.

When a society undergoes a transformation in its food production mode, sooner or later, its religion as practiced will catch up, although there may be some lag time from a most recent formative period to the present particular when a society or subculture is evolving to a new food production mode rapidly.  It may take a number of generations, for example, for a religion which was a herder religion in its most recent formative period to adapt to the economic realities of the present through intepretive, organizational and ritual adjustments.  For example, many religions practiced in the United States are in the process of adapting to new conceptions about gender and sexual orientation which are driven by a shift towards a postindustrial mode of economic organization which are driven by  new technological developments within the options made available by our evolving ecological constraints like those associated with the tail end of a century old petroleum based economy.

While not entirely inevitable, and while the specific formalisms and symbols that a religion expresses itself may be driven by historical baggage and may be path dependent, the substantive aspects of a religion that influence how people act in real life a strongly biased by economic realities that are in turn strongly biased by technological realities.  People who have values and inclinations about how to organize people in the society that work for its current stage of development and mode of food production will prospect and religions that reflect these views will prosper with them or be intepreted to become congruent with them, while people who have values and inclinations about how to organize people that are a poor fit for the current mode of food production will not prosper and religions that reflect their values will stagnate or die.

Denisovan Dilution Revisited: People Of The Dog?

In my post yesterday, I dismissed the possibility that the presence of Denisovan DNA in populations to the east of Wallace line and its absence to the west of the Wallace line was not easily explained by dilution of the Denisovan admixed population because East Indonesia has a substantial Paleolithic substrate and because the level of dilution required (on the order of a factor of sixty for South China relative to Papuans) would be so great. Have I dismissed this possibility too easily?

The evidence can be marshalled to give some support to a dilution narrative.

A Dilution By Paleolithic Y-DNA Haplogroup O Men Scenario

There is a stark difference in Y-DNA haplogroup frequencies on either side of the Wallace line. To the east are high frequencies of populations typical of Sahul populations (i.e. Australia and Papua New Guinea), with a modest amount of Austronesian (i.e. Neolithic seafarer) contribution that there is very strong evidence to suggest dates to the last five thousand years or so. On the other sided of the line, for example, on the island of Bali, the percentage of Y-DNA that is something other than Y-DNA haplogroup O is quite small, about 4%, with some of the Y-DNA haplogroup O attributable to Austronesian sources and some attributable to some other migration into Western Indonesia. While the ratio isn't quite sixty to one the cline is certainly steep and could explain much of the variance in Denisovan admixture.

One plausible time for the non-Austronesian lineages of Y-DNA haplogroup O to arrive in Western Indonesia would have been when Sundaland was attached to mainland Asia. The region where non-Austronesian lineages of Y-DNA haplogroup O are common correspond to the territory of Sundaland which was a continuous land mass attached by land to mainland Asia during the Last Glacial Maximum around 20,000 years ago. Even for people with some seafaring abilities more primative than that of the Austronesians, mass migration across land is easier than mass migration across water and the distribution of these lineages closely matches a terrestrial passage at that point in time.

This isn't the whole story, however. We know from a wealth of historical examples that when farmers and herders encroach onto the territory of a hunting and gathering population, that the former's advantages in terms of numbers and technology almost always overwhelms the hunters and gatherers resulting in major demographic shifts towards to food producing migrants. But, it is not at all obvious, in general, that one hunter-gatherer population ought to be able to overwhelm another hunter-gatherer population without a good reason. And the farming and herding were not developed until long after the last glacial maximum that lowered sea levels of join Sundaland to mainland Asia (nor, for that matter, was pottery).

One can easily imagine good reasons in a first contract between modern human hunter-gatherers and Denisovan hunter-gatherers. But, how can we explain how first wave migrants kindred to the Sahul population wave, could be totally dominated by the people who were bears of non-Austronesian lineages of Y-DNA haplogroup O?

After all, the kin of the Sahul population were notable for their superior maritime accomplishments relative to all hominins who came before them and to all who came afterwards until the Austronesians. The people of Sahul were able in a historical eye blink to bring about the extinction of megafauna every bit as frightening and huge as the monsters in fairy tales, without even having metal weapons or armor. Arguably the people of Sahul were exceptionally advanced and hence an unlikely candidate to fall en masse to the migration of another Paleolithic hunter-gatherer population into their territory. They managed to island hop across Western Indonesia when it was not connected by land into a single Sundaland penninsula, to cross the Wallace line, and to cross the sea from Wallacia to reach Sahul. In contrast, the non-Austronesian lineages of Y-DNA haplogroup O apparently needed a land bridge and never managed to cross the Wallace line in large numbers and didn't cause the extinction of ferocious giant predators.

I put aside, for the moment, the argument that these were non-Austronesian Neolithic migrants at the time that they came to Western Indonesia, because it stretched estimates of the age of these lineages more than one would like, is not associated with any known Neolithic population, and may not be necessary for the reasons set forth below.

The Dog Domestication Advantage.

So, what could the Paleolithic Y-DNA haplogroup O people have had twenty thousand years ago that gave them a decisive advantage over the awesome hunters of the first wave migrants who were kin to the Sahul people in Western Indonesia that left the first wavers totally marginalized even before the Austronesians arrived?

The most plausible explanation I can muster is a simple one. The Paleolithic Y-DNA haplogroup O people had domesticated dogs; the people who were vastly diluted by them did not.

The Sahul people did not have dogs until an archaeologically well documented moment when a handful of dingos migrated to Australia around 8,000 years ago from a stock found in Southeast Asian wild dogs. The arrival of the dingo in Australia caused a continent wide secondary mass extinction that eliminated many species that had survived the megafauna extinction that accompanied the appearance of modern humans in Australia. This mass extinction is a testiment to the impact that domesticated dogs could have on hunting and gathering economics.

Sahul populations certainly didn't have dogs twenty-thousand years ago, long before the dingo was introduced. So it stands to reason that their kin in Island Southeast Asia didn't either.

The domestication of dogs took place long before any of the other plant or animal domestications associated with the any of the several independent Neolithic revolutions. But, dog domestication had to have happened by the time that the founding population of the Americas arrived in Beringia right around the time of the Last Glacial Maximum and the existence of the Sundaland penninsula as a terrestrially connected land mass connected to the Southeast Asian mainland. In other words, dog domestication probably happened before peoples with men predominantly from Y-DNA haplogroup O swept across Western Indonesia.

While different studies reach different conclusions, some of the efforts to identify the principle ancestral source of the overwhelming majority of modern domestic dogs suggest a Southeast Asian progenitor, near the likely geographic point of origin of the non-Austronesian lineages of Y-DNA haplogroup O.

Dogs can explain how a Paleolithic hunter-gatherer population with dogs could totally marginalize a Paleolithic hunter-gatherer population without them. Since the advantage provided by dogs to hunter-gatherer populations are largely limited to terrestrial hunting and gatherering, the domestication of dogs could also shift the relative desirability of a terrestrial hunting and gathering strategy relative to a maritime fishing strategy, causing the maritime capabilities of populations that domesticated dogs to wither from disuse, particularly in areas where fishing had previously been only marginally superior to terrestrial hunting and gathering as a food collection method.

Y-DNA haplogroup O must have arisen sometime after first contact with the Denisovans. Its phylogeny makes clear that it isn't as old as the Sahul Y-DNA lineages. If Y-DNA haplogroup O arose in an area that was temporarily purged or nearly purged of Denisovan populations by the direct effects of the Toba eruption when humans first settled there (i.e. leaving Denisovans in numbers not significant enough to have a meaningful interaction or impact on the modern humans migrating into the area anywhere but Java island and points to it east in Island Southeast Asia and in East Asia), then the ancestors of the modern humans who settled in mainland Southeast Asia, Borneo and Sumatra without going further, would not have been Denisovan admixed except from slight percentages due to back migrations from the kin of Sahul-like populations. And, one of these mainland Southeast Asian populations probably gave rise ot the Y-DNA haplogroup O lineages.

The high level of homogeneity of the Y-DNA haplogroups of East Asia similarly argue the point that extreme levels of dilution of prior Sahul-like waves of migrants though multiple waves of Paleolithic and Neolithic migration of populations who can trace their origins to Denisovan-free Southeast Asia, making any Denisovan ancestry that remains almost imperceptable, isn't all that implausibe in East Asia.

Other Possible Demographic Impacts Of Y-DNA O Expansion

Of course, the dog domestication advantage I suggest as a possible source for the expansion of men with Y-DNA haplogroup O could also have directly devistated any relict Denisovan populations, in addition to diluting the contributions of first wave modern humans admixed with Denisovans in the modern human gene pool in Asia.

An expansion of a population predominantly made up of Y-DNA haplogroup O men that really did have such a great advantage over other Paleolithic peoples could also have dramatically marginalized populations where Y-DNA haplogroup D was predominant except in places like the Andaman Islands, Japan, and LGM refugia in Tibet, that this population, which had inferior martime capabilities, could not reach.

Limits On Y-DNA O Expansion

The same jungles and mountains that provided an effective barrier to modern human migration into Denisovan territory in Asia prior to the Toba eruption, however, may also once it had grown back tens of thousands of years later, have also mutated the capacity of Y-DNA haplogroup O men to back migrate en mass and dilute into irrelevance the populations of South Asia until they received the further boost of Asian Neolithic technologies like rice cultivation that brought Austroasiatic peoples into Northeast India.

The Limits Of Early Sahul Wave Maritime Capabilities

It is also worth keeping in mind that proto-Sahulean maritime capabilities should not be unduly exaggerated. Yet, they managed to island hop across the small straights of Western Indonesia, across the Wallace line, and then from Wallacia to Papua New Guinea and Australia, respectively. Yes, there is some evidence of very early deep sea fishing in Melanesia at around that point in time. But, the developments we don't see also speaks volumes.

The proto-Sahuleans did not settle the remainder of Oceania. They also did not settle Japan or the Andaman Islands. The Azores Islands in Europe were not settled by modern humans until the Bronze Age, long after the Upper Paleolithic revolution in which the proto-Sahuleans seems to have participated. There is considerable genetic evidence that Papuans and Aboriginal Australians did not experience much population exchange at all starting shortly after their founding populations were established. It took twelve thousand years or so from the domestication of the dog to the introduction of the dingo to Australia and the introduction of the dingo to Australia shows strong genetic traces of being a single event. There is also no sign of meaningful modern human population exchange between Sahul (or its successors) until sometime after the introduction of the dingo (and perhaps no more recently than the expansion of the Austronesians).

This evidence suggests that the possibility that apart from just a handful of isolated instances of one way voyages beyond the line of sight involving only a very small Sahul founding population, perhaps numbering something on the order of a hundred people (Australian aboriginal tradition speaks of seven canoes at a time when there were no domesticated animals, even dogs), that their navigational capacabilities may have been limited to navigation within a line of sight to the mainland. It appears from the evidence that there was virtually no intentional maritime trade between Sahul and the rest of Southeast Asia from this twelve thousand year time period, and probably from as far back as 40,000 years ago until sometime quite a bit later than 8,000 years ago, perhaps as late as the point at which contact with the Austronesians began. Even if the original founding populations of Sahul and Wallacia were competent deep sea mariners, the Sahuleans themselves appear to have promptly lost this technology. When the sea ultimately separated Tasmania and the rest of Australia there was no maritime travel between the two across the relatively shallow straight. The much later development of martime capabilities in the waters between the Island of Formosa and mainland China that ultimately culminated in the Austronesian's extraordinary maritime capabilities seems to have been an independent development not traceable to the Sahulean martime tradition.

Thursday, August 30, 2012

High Resolution Denisovan Genetics

Several commentators have reviewed the last high resolution sequencing of the Denisovian genome, but John Hawks does has done a lot of research on the ancient Neanderthal genome has some of the most insightful comments.

There is Denisovan admixture in Sahul populations but not other Asians

First, he notes that the detailed findings confirm prior results on Densisovan admixture:

The mixture with a whole-genome sample from Papua New Guinea is estimated at 6% Denisovan ancestry. Confirming the later paper by Reich and colleagues, the new analysis finds no significant evidence of Denisovan ancestry in a mainland south Chinese (Han Dai) individual, and can exclude it down to a very small fraction:

However, in contrast to a recent study proposing more allele sharing between Denisova and populations from southern China, such as the Dai, than with populations from northern China, such as the Han, we find less Denisovan allele sharing with the Dai than with the Han (although non-significantly so, Z = –0.9). Further analysis shows that if Denisovans contributed any DNA to the Dai, it represents less than 0.1% of their genomes today.
That is a mystery to be explained. How did Asians end up lacking any evidence of Denisovan ancestry, when the peoples of Sahul (Australia and New Guinea) have six percent? . . . The early modern humans who were the ancestors of present Sahulian peoples surely came from Asia, and they surely mixed with Denisovans there somewhere, right? But today there's no sign that present Asian peoples descended from those early Asian peoples.

A Narrative The Could Explain The Geography Of Denisovan Admixture

My most recent analysis of this mystery was in a post from a week and a half ago. First, I argue that Denisovans are either Homo Erectus or an admixed derivative of them, and that Homo Flores, in turn, is a Homo Erectus subspecies that has experienced island dwarfism. I'll restate and expand upon one plausible narrative below.


To be clear, I'm not claiming that the evidence proves that this narrative is true. Instead, I want to suggest that this is a narrative that would consistently explain everything we know so far without making any assumptions more outlandish than necessary to fit the facts. It don't claim that there aren't only plausible narratives that could also be true, only that I can't come up with any more plausible narratives and neither has anyone else. This is a hypothesis, not a proof. I have also taken the indulgence of relying on memory rather than looking up the published articles that back some of my assertions on Southeast Asian population genetics that I read a couple of years ago or so, and hence not linking to them, in order to save time in the process of drafting an already long post.

An Admixture In Flores Only Scenario

In my previous post, I concluded my analysis with the following summary:

[I]t isn't inconceivable to me that almost all "Denisovian" admixture in modern humans is actually traceable to a dozen or two instance of admixture with members of the species Homo Flores on the island of Flores, and that a strong flight instinct of Homo Erectus population members who did not experience dwarfism and had someplace to which they could flee, together with a modern human perception of those who did not experience dwarfism as more primate than fellow hominin, could have meant that there was no meaningful amount of archaic hominin admixture anywhere else in Southeast Asia or East Asia (with a possible exception probably involving even fewer instances of admixture relative to the founding population in the Philippines).

Why Not A Dilution Hypothesis?

One of the key reasons to favor a Flores admixture location over a mainland Asian one, in the 20/20 hindsight of the known facts that I didn't mention in my previous post is that too much of the population genetic makeup of island Southest Asia is too old to be explained by a land bridge crossing along the then geographically united Sunda penninsula during the Last Glacial Maximum. Likewise it is not a good fit to a predominant population source during the Austronesian expansion that is the source for the languages of the region just a few thousand years ago.

Genetically, some island Southeast Asia looks a bit like some of the populations of the far Northeastern corner of Europe. They show some of the highest levels of pre-Neolithic ancestry on their respective continents, only island Southeast Asia didn't have to be entirely repopulated after the Last Glacial Maximum from scratch, so its Paleolithic ancestry component is much older. (See also this paper on indigenous Malaysian genetics, this paper on Eastern Indonesian genetics, this paper, Island Southeast Asian genetics, here, this paper on Indonesian Y-DNA, Indonesian autosomal genetics, here, here, here, here, here, here, here, here, here, and here.)

This, together with the very low percentages of Denisovan admixture in island Southeast Asians relative to the Sahul populations, makes the most sensible scenario to explain the low levels of Neanderthal admixture seen in Europeans, i.e. archaic ancestry dilution by post-admixture waves of migrants look much less convicincing in Asia than it does in Europe.

The numbers for a dilution hypothesis work in Europe and are supported by the recent evidence of the Otzi genome. But, to explain the results via dilution, you need the Sunda and South Chinese populations to have experienced sixty times as much dilution as the Sahul populations, yet to retain in island Southeast Asia a very large percentage of early Paleolithic population genetics that is quite distinct from that of East Asia. After controlling for inferred levels of Austronesian gene flow, there is still a huge disparity in Denisovan admixture and even less of an explanation for how one Paleolithic modern human population could have so totally replaced a prior one. The genes of island Southeast Asian populations don't show that there was near total population replacement when these islands were joined to the mainland as part of the Sunda penninsula around 20,000 years ago. In short, the numbers just don't work to explain the geography of a Denisovan admixture with dilution from subsequent migration waves alone.

Suggestive Evidence To Favor Denisovans Flight And/Or Slaughter

The new high resolution study's conclusion that the Denisovans may have had a quite low effective population size is congruent, however, with a "flee don't f--k" scenario outside Flores, all of the way to Siberia. I've hypothesized for some time, based on the inferior tool kit found in Asia prior to the arrival of modern humans, that the population density of archaic Asians may have been quite a bit lower than the population density of Neanderthals or modern humans hunter-gatherers in comparably favorable environments. This inference is also suggested on the ground that Homo Erectus was also probably less intelligent than either Neanderthals or modern humans were given their brain case sizes relative to body size.

A greatly outnumbered, technologically inferior, less intelligent population of Asian Denisovans (i.e. late Asian Homo Erectus) would probably be more inclined to flee in the face of newcomers when they were so clearly outmatched, rather than trying to stand their ground and co-exist as the Neanderthals, who were probably a more equal match for modern human newcomers, apparently did. Since the Denisovan's had a smaller population, they might have a greater capacity to flee as well, at least on the mainland, where they weren't cornered.

Of course, seeing some of their peers who didn't flee get slaughtered by incoming modern human tribes could easily have helped motivate the Denisovan decision to flee rather than fight or co-exist with modern humans. We can probably never know if how violent the first contact events were for sure. Given the record of megafauna extinctions likely caused by modern humans, the income modern human tribes would probably have been capable of carrying out a Denisovan genocide leaving only a tiny diasporan population in places like Siberia and Flores, whether or not they actually did so.

How Did Denisovans Hold On So Long Before Collapsing?

My best guess is that the main reason that intellectually and technologically outmatched Denisovans were able to hold out for so long despite potential competition from rival archaic and modern hominin populations is that the jungles of Southeast Asia and the mountains of Zomia were an effective barrier to the migration of populations of archaic hominins large enough to be threatening to small tribes of Denisovan hunter-gatherers.

The Toba Eruption Opens The Gates To Southeast Asia

This may have changed when ash fall from the Toba explosion ca. 75,000 temporarily killed of the jungle. The eruption would also have reduced the population size of the Denisovans in the area between South Asia and Southeast Asia who used to live there. Even if the Toba explosion by itself wasn't sufficient to wipe out a Denisovan population, if it had had the luxury of recooperating without competition from other slightly more fit hominins, it may have so depleted Denisovan populations in this region that they promptly went extinct in this range under the additional indignity of an inmigrating population of modern humans who outnumbered them and were even slightly better hunters in the suddenly unfamiliar volcano ash ravaged landscape than they were, particularly in light of how static their lithic culture was, which suggests that they may have not been very innovative or adaptable.

The ash fall area from the Toba eruption is much more consistent with an event that opens the door for migration from South Asia to Southeast Asia than it is with an event that drives the large Out of Africa migration in a single wave all the way to Asia (see also here). This region would have been much harder hit by the Toba eruption than the more distant territory in South Asia where we know that modern humans encountered Toba ash fall. So any barrier effect that the presence of existing Denisovan tribes presence may have posed would have also been eliminated at least temporarily.

Toba ash would have fallen upon and reduced the habitability of all of what is now Burma, Thailand, Malaysia, Cambodia, Laos and Vietnam, the island of Hainan in South China, much of the island of Borneo, all of the island of Sumatra in Indonesia, the island of Palawan in the Phillipines, and just a little bit of western Java. But, most of the island of Java, the Philippines (except the island of Palawan), and everything east of the Wallace line, would have had no direct effects from the Toba eruption.

The parts of island Southeast Asia and the Phillipines other than the island of Java and a few islands in the Phillipines that weren't mostly within the ashfall area of the Toba eruption is a good match for the areas where there appear to be traces of Denisovan admixture, while none of the areas within the ash fall region of the Toba eruption show any trace of Denisovan admixture.

Denisovan Cave itself, in Siberia, would have been connected to the part of East Asia where Toba's ash did not reach, and would have been within the northern reach of the archaeologically estimated range of Homo Erectus. So, modern humans populating the vacuum left by the Toba eruption may have encounted very few Denisovan's relative to their own numbers if this is when they made their entry into the Asian continent (a date consistent with reasonably calculated mutation rate ages in Asia) until they had made their way all the way from India to South China.

Furthermore, it appears that the Northern part of the Denisovan range in Siberia and maybe even Northern China, may have been entirely depopulated during the last glacial maximum, and much of the intermediate territory consists of highlands in Zomia, Tibet, and Mongolia (see the paleoclimate map here) where I am not aware of any evidence of Homo erectus archaeology. If the Denisovans like the Neanderthals didn't have the ability to make weather proof shelters of their own and craft warm clothing, these places may have been inaccessible to them. The only lowlands between the Denisovan Cave (which can be reached via mountain valley passes for the most part that are warmer than the Central Siberian steppe to the north, or through the Central Siberian Plateau during the summer), and the eastern fringe of the Toba ash fall area in mainland Asia, are in Eastern China, Korea and Manchuria. The modern human edge over the Denisovans in these areas which were not as tropical, may have been greater than it was in Southeast Asia and South China.

The archaeological evidence shows that modern humans had already left Africa at least 25,000 to 30,000 years before this eruption. And, we know that there were modern humans in South Asia who survived the Toba eruption who could have taken advantage of the new migration options the temporary destruction of Southeast Asian jungles by ash fall could have opened up. We also know from African population genetics, that a large tropical jungle such as the Congo could be just as formidable a barrier to the migration of sustainable paleolithic hunter-gatherers as an ocean or a high mountain range.

When the Toba eruption opened, it the gates of the region to modern human populations already resident in South Asia, and they surged into Southeast Asia. The Denisovans retreated before there was any meaningful opportunity for admixture all the way to Siberia. Island Southeast Asians had less of an opportunity to flee, but these quite small populations of non-dwarf late Homo Erectus may have seemed too threatening to the early modern human populations to be tolerated and may have instead have been simply wiped out (or at least were not integrated socially enough to give rise to admixture).

Denisovan Matings May Have Been Less Fruitful Than Neanderthal Matings Due To Greater Genetic Distance

Given that Denisovans were more genetically distant from modern humans than Neanderthals (probably more like 1,800,000 years of separation instead of 500,000 years of separation), it may also have been the case that the yield of fertile offspring from mating between Denisovans and modern humans may have been lower, and hence a longer period of co-existence may have been necessary for a comparable level of introgression into the modern human population to accumulate.

Prolonged Co-Existence On Flores Would Have Allowed Plenty Of Time For Introgression Even With Very Few Fertile Hybrids

But, this could have happened during the archaeologically long period of co-existence (tens of thousands of years) between modern humans and Homo Flores on the island of Flores which is geographically cheek by jowl. In this context, introgression could accumulate over a considerable amount of time (perhaps 25,000-30,000 years) even if the interspecies couplings weren't very fertile on average. If the modern human effective population size was small, it wouldn't take many successful interspecies hybrid children per generation on average in the 1,000 generations of co-existence between a hypothesized Toba explosion driven entry of modern humans in the region and the colonization of Sahul by modern humans.

Alternatively, perhaps an initial modern human population in Flores had an effective population size of only a dozen or two individuals (or less), which is quite possible if the gene pool of the Sahul migrants was subsequently expanded by a small number of Upper Paleolithic people as I suggest below, given current levels of genetic diversity of these populations. This would make sense in a scenario in which the original modern humans in Sahul were shipwrecked there and didn't have the maritime skills to intentionally navigate across the Wallace line or to Sahul until Upper Paleolithic people arrived. If this was true, and admixture took place only in the initial moment of the most dire population bottle neck, one could obtain all of the observed level of Denisovan admixture in the Sahul populations from just one or two pregnancies in the first generation. It should probably be possible to estimate the effective population size of the Denisovan population that contributed to the Sahul gene pool with enough high resolution genomes from that population to describe the diversity in the parts of their genome not found in other modern humans, and an analysis that showed that this effective population was just one or two individuals wouldn't surprise me, although it certainly isn't compelled by what we know so far.

In a slight variation of the shipwreck scenario that has the virtue of relying less on random chance, perhaps there was just one instance of Denisovan admixture (either just one fertile hybrid child, or one Denisovan-modern human mated couple with multiple children) on the island of Java. Perhaps due to hunting and gathering competition from modern humans, and perhaps due to warfare with modern humans as well in which the Denisovan's were outnumbered and outfought (and at hunter-gatherer population densities, the populations of both groups on the island of Javan would have been quite small - there were perhaps 45,000 Neanderthals by a census measure in all of Europe and Java was much smaller than Europe), the Densivoan of Java were pushed over into extinction soon thereafter. Perhaps the family of the hybrid child was persecuted by the other modern humans on the island. Perhaps the hybrid child and a small group of supporters made up of extended family and close friends were willing, in order to flee this persecution in a way that would leave it forever behind them attempt a risky one way trip across the straight and hence across Wallace line with inferior early Paleolithic rafts. In this scenario, the migrants would have had no interest in even trying to return to Java and hence no incentive to refine their successful boat design. This scenario would also produce the admixture ratios we see today in the Sahul population.

Expansion Into Sahul May Have Required An Upper Paleolithic Boost

The expansion from Flores or some other island on the east side of the Wallace line to the Sahul may have been faciliated by advantages associated with the arrival of a second wave of modern humans, who were integrated with first wave modern humans before expanding further to the Sahul. This second wave may have been expanding themselves due to the advantages, whatever they were, that drove the larger Upper Paloelithic revolution.

For example, in a scenario that also keeps the initial population size of modern humans in Flores low enough to make it sensible for them to treat Homo Flores on a more equal footing that their kin in Southeast Asia had previously, perhaps the first wave modern human residents of Flores arrived only by maritime misadventure and didn't have the boating technology to return back across the Wallace line to their fellow modern humans. This group of shipwrecked men and women wouldn't have been nearly as impressive and intimidating to the indigeneous archaic hominins as the intentionally migrating populations who crossed the less daunting waters on the other side of the Wallace line, and as dwarves, wouldn't have been seemed like as much of a threat to the shipwrecked men and women.

These first wave modern humans may not have had the capacity to intentionally navigate across the Wallace line or beyond to Sahul in large enough numbers to establish a sustainable population. This capacity may have arrived only much later when a small population of much more competent mariners at the most distant fringe of Upper Paleolithic revolution population expansion, informed by the technological advances of the Upper Paleolithic revolution, arrived and were integrated into the existing population in Flores. By the time the wave of newcomers appeared on the scene, the first wave modern human population may have already received considerable Homo Flores introgression into the small modern human population of Flores over a thousand generations of co-existence on that island that was carried on by the migrants to the Sahul.

This two wave migration theory would explain another of the long standing mysteries of Paleolithic migration in Asia. There is pretty good archaeological evidence pointing to the time that Sahul was first colonized by modern humans about 45,000 years ago. The genetic evidence indicates that the founding population of Sahul was quite small but was phylogenetically quite diverse and also that the Papuan and Australian proto-populations underwent a schism almost immediately upon arrival, with both branches having almost all parts of this phylogenetic diversity. Yet, there were modern humans in South Asia at the time of the Toba eruption and there were modern humans in mainland Southeast Asia at least 63,000 years ago.

Why did it take so much longer for them to reach the Sahul than the rest of Asia?

Modern humans made it from Beringia to the far reaches of South America in just a few thousand years and the distance from mainland Southeast Asia to Papua New Guinea and Australia is much shorter. A scenario with a first wave of modern humans who managed to cross the Wallace line only by accident and a second wave of Upper Paleolithic modern humans who could do it on purpose a thousand generations later, would explain this gap. One of the things that may have made the Upper Paleolithic era revolutionary may have been a revolution in boating technology.

The measured levels Neanderthal admixture in Asians relative to Europeans contradicts prior research.

Second, Hawks notes that their finding on the relative levels of Neanderthal admixture differ from prior research:

To me at the moment, this is the most interesting paragraph of the new paper:
Interestingly, we find that Denisovans share more alleles with the three populations from eastern Asia and South America (Dai, Han, and Karitiana) than with the two European populations (French and Sardinian) (Z = 5.3). However, this does not appear to be due to Denisovan gene flow into the ancestors of present-day Asians, since the excess archaic material is more closely related to Neandertals than to Denisovans. We estimate that the proportion of Neandertal ancestry in Europe is 24% lower than in eastern Asia and South America (95% C.I. 12–36%). One possible explanation is that there were at least two independent Neandertal gene flow events into modern humans. An alternative explanation is a single Neandertal gene flow event followed by dilution of the Neandertal proportion in the ancestors of Europeans due to later migration out of Africa. However, this would require about 24% of the present-day European gene pool to be derived from African migrations subsequent to the Neandertal admixture.

This is a very interesting result, partially because it is the opposite of what we are finding. As I explained earlier this year, we are finding Europeans to share more Neandertal alleles than Asians do. The difference in our results has been much smaller than 24%; really only an increase of less than 0.5% on the whole genome, or maybe 10% relative to the overall amount in Europe (which is on the order of 3%).

Hawks considers some possible sources of the discrepency. Given the flat contradiction between the studies using methods whose differences are subtle, it is hard to know the cause of the discrepency. On balance, my intuition is to give greater credit to the findings of Hawks group, because his group studied much larger sample sizes and their is some meaningful variation in Neanderthal admixture levels in Eurasians in the 1000 Genomes sample. The large discrepency may simply be a matter of random chance whose statistical significance (Z=5.3) is overestimated because the data are more structured than the statistical assumptions from the new study, using samples from just three European and two Asian populations assumes.

The question of whether there was one round of Neanderthal admixture, or two or more with some regional differentiation that just happened to produce roughly similar levels of Neanderthal admixture since the processes were similar and played out in similar ways, is beyond the scope of this post and complicated by the discrepencies in the reported empirical results.

Denisovan Effective Population Size Was Small And Fell When Modern Humans Appeared

Third, he notes that there are indications in the genomic evidence of population decline in Denisovans and Neanderthals to a low effective population size coinciding temporally more or less with the arrival of modern humans:

It has become possible to make some good estimates of demographic history using only a single diploid genome, using a technique developed by Li and Durbin. Meyer and colleagues applied this technique to the Denisova genome, finding that its genetic history contrasts with that of living human populations:

To estimate how Denisovan and modern human population sizes have changed over time we applied a Markovian coalescent model to all genomes analyzed. This shows that present-day human genomes share similar population size changes, in particular a more than two-fold increase in size before 125,000–250,000 years ago (depending on the mutation rates assumed). Denisovans, in contrast, show a drastic decline in size at the time when the modern human population began to expand.

There is not yet enough data from Neandertal genomes to apply the same method, but to the extent that we understand their diversity, they show a similar picture. These archaic humans in Eurasia had much, much smaller effective population sizes than the ancient population of Africa.

Of course, we know for a fact that the Denisovan are no more, that they co-existed at least briefly with modern humans, and that modern human population size has grown over time. Any model that indicated something different when applied to the data would have to have been wrong, and the confidence intervals for the dates provided by the model are wide enough to fit all of the plausible scenarios. There is also considerable mischief that goes into interpreting what effective population size means in the context of a very late relict population of a species on the verge of extinction that Hawks explores a little.

But, as I've noted above, there are plausible reasons to think that Asian Homo Erectus might have had a fairly small effective population size that fell when modern humans arrived and that the Denisovan reflects Asian Homo Erectus ancestry.

Wednesday, August 29, 2012

Could Higgs Boson Bump Be A Mix Of Mesons?

John Moffat, a physicist at the Perimeter Institute also known for one of the lesser known relativistic modified gravity proposals, explores the possibility that the Higgs boson resonance could be a linear combination of two heavy quark mesons aka quarkonium (top-antitop and bottom-antibotton) using a mixing angle from existing physics, which would be pseudoscalar (i.e. a composite particle with an overall spin of zero, rather than a fundamental particle with spin zero).

He also describes the experimental tests necessary to distinguish the two possibilities which would in may respect have very similar properties. The easiest way to distinguish the two is via the spin-parity of the particle which could be determined through analysis of the angular distribution of the particle's decay products.

His proposal culminates about five years of papers he has written on Higgsless versions of the Standard Model.  While he is a frequent advocate for unconventional theoretical explanations of the evidence in fundamental physics, he is no crackpot, he is asking the right kinds of questions, and his proposals of experimentally testable alternatives to the Standard Model that don't involve SUSY is a valuable one that deserves more attention in contexts like analysis of LHC results.

Tuesday, August 28, 2012

Stray Thoughts

* Razib's pinboard at Gene Expression notes the Wikipedia article on the Vedda language. Until it became extinct or moribund in the 1990s it was the language of a hunter-gatherer group of Sri Lanka. It was one of the last South Asian languages that was originally neither part of the Dravidian nor the Indo-Aryan nor the Austro-Asiatic nor the Tibeto-Burman language families of South Asia, although continued exposure to the local Dravidian language over 2,500 to 3,000 years resulted in substantial borrowing of words between the two, with some Vedda words borrowed from early Dravidian dialects that are no longer used in modern Dravidian languages.

The Vedda language is a vivid reminder of that fact that 6,000 years ago, almost nobody in India spoke either the Dravidian languages, which started to rapidly expand with the South Indian Neolithic around then, or the Indo-Aryan languages, which probably appeared in South Asia around 4,000 years ago. Austro-Asiatic languages (i.e. the Munda languages of South Asia) are probably roughly contemporaneous in their arrival from Southeast Asia with these two language families and probably arrived around the same time as rice cultivation began in India. The Tibeto-Burman languages are the most recent arrivals in South Asia and form the most genetically distinct populations of India. Most of the preceding South Asian languages went extinct in prehistory before they were attested. But, it is a mistake to think of the Dravidian languages as the language family of the indigeneous hunter-gatherers of India since times immemorial. If Proto-Dravidian was indigeneous to India at all, it was probably spoken only by one small tribe that happened to be the first to master farming in the region.

* Similar points about the pre-Indo-European linguistic landscape can be made about Europe at a fairly similar time depth (at least relative to the appearance of the Neolithic revolution there).

* I have never really taken seriously the possibility that there could have been Bronze Age maritime trade with West Africa, even though there was martime trade with East Africa at least as far back as the early Iron Age and quite possibly much earlier. But, a new post at Maju's blog notes increasing evidence of Bronze Age maritime colonization of the Azore Islands in the Atlantic Ocean. West Africa would have been no harder to reach. So, the possibility of Bronze Age maritime trade with West Africa while still somewhat doubtful, is no longer something that seems highly unlikely.

* The use of the wheel for practical transportation purposes is about 5,500 years old and probably originated in the Pontic-Caspian Steppe. The existence of a common source word for this in Proto-Indo-European lingustic reconstructions argues for the youth of this language family and its origins on the Steppe, as do borrowings of even very archaic forms of Indo-European words into Uralic languages.

* It is not at all obvious that the root of the Anatolian Indo-European languages (most famously Hittite), is in fact in Anatolia. The earliest attestations and archaeological indications of the earliest cores of the Hittite people and the Indo-Aryans is about 4,000 years ago and both populations introduce metal working techniques that were invented only a little earlier in the Caucasus mountains. Other kinds of historical and archaeological evidence point to both as being intrusive, and the arrival of Indo-European Greek speakers in the Aegean region is a historically attested event and happened within the last 4,500 years.

* Early Iron Age Judaism, as described in the Torah, looked a lot more like modern fundamentalist Islam in practice than it does like the Rabbinic Judaism of the last two thousand years. The last two thousand years also marks a time, when, despite significant modern endogamy preferences among Jews, the genetic evidence indicates that the people of the Jewish diaspora admixed heavily with non-Jewish peoples. By ancestry, Ashkenazi and Sephardi Jews are much less Semitic than, for example, modern Saudi Arabians.

Friday, August 24, 2012

Irrigation Incompatible With Democracy

An in depth analysis shows that irrigated farming, measured not by actual irrigation, but by potential crop yields from irrigation, is a causal factor in authoritarian government structures.

Presumably, the theory is that the coordination of effort required to establish and manage irrigated agriculture requires centralized authority and that the easiest way to achieve such centralization is with an authoritarian government whose legitimacy flows from the value added by the irrigated farming system relative to the status quo. Rainfall based agriculture apparently does not empirically show such strong tendencies towards authoritarian government.

Tuesday, August 21, 2012


Zomia shown in an intermediate scope definition that includes Tibet and Northern India as well as the core Southeast Asian highland area. "The exact boundaries of Zomia differ among scholars: all would include the highlands of north Indochina (north Vietnam and all Laos), Thailand, the Shan Hills of northern Burma, and the mountains of Southwest China, others extend the region as far West as Tibet, north India, Pakistan, and Afghanistan." (Text and illustration credit to Wikipedia.)

My attention is directed towards Zomia today, of course, because the oldest skull in Asia (outside the Near East) that definitively identified as modern human and also definitively dated (63,000 years old) was recently found in the northern mountains of Laos (a country that is entirely within Zomia).

Zomia, rather than being the land of Zombies, is the geographic region that includes the highland that are between separate India and China, and are bounded on the South by coastal Southeast Asia:

Zomia is a geographical term coined in 2002 by historian Willem van Schendel of the University of Amsterdam to refer to the huge massif of mainland Southeast Asia that has historically been beyond the control of governments based in the population centers of the lowlands. . . . The name is from Zomi, a term for highlander common to several related Tibeto-Burman languages spoken in the India-Bangladesh-Burma border area.

These areas share a common elevated, rugged terrain, and have been the home of ethnic minorities that have preserved their local cultures by residing far from state control and influence. Other scholars have used the term to discuss the similar ways that Southeast Asian governments have handled minority groups.

The region covers more than 2.5 million square kilometers known as the “Southeast Asian Massif” and comprises nearly one hundred million marginal peoples. This large area is inside the fringe of nine states and at the middle of none, stretching across the standard regional designations (South Asia, East Asia, and Southeast Asia) . . . . It . . . [is] an original entity of study . . . a different way in which to study regions.

[According to Professor James C. Scott,] the tribes in Zomia are conscious refugees from modernity itself, choosing to live in more primitive, locally-based economies. . . .

[Hill tribes] seen from the valley kingdoms as “our living ancestors,” “what we were like before we discovered wet-rice cultivation, Buddhism, and civilization” [are on the contrary] best understood as runaway, fugitive, maroon communities who have, over the course of two millennia, been fleeing the oppressions of state-making projects in the valleys — slavery, conscription, taxes, corvée labor, epidemics, and warfare.

Scott goes on to add that Zomia is the biggest remaining area of Earth whose inhabitants have not been completely absorbed by nation-states, although that time is coming to an end. Though Zomia is exceptionally diverse linguistically, the languages spoken in the hills are distinct from those spoken in the plains. Kinship structures, at least formally, also distinguish the hills from the lowlands. Hill societies do produce “a surplus”, but they do not use that surplus to support kings and monks. Distinction of status and wealth abound in the hills, as in the valleys. The difference is that in the valleys they tend to be enduring, while in the hills they are both unstable and geographically confined. . . .

Southeast Asian expert Victor Lieberman agrees that the highland people crafted their own social worlds in response to the political and natural environments that they encountered, . . . [but] argues that Scott is overestimating the importance of manpower as a determinant in military success. While the bulk of Scott’s argument lies on the efforts of lowland states to dominate the highlands, Lieberman shows the importance of maritime commerce as an equally contributing factor. . . . Lieberman, however, argues that the highland peoples of Borneo/Kalimantan had virtually the same cultural characteristics as the Zomians, such as the proliferation of local languages and swidden cultivation, which were all developed without a lowland predatory state.

Zomia As A Divider Between Geographic Regions

From the perspective of someone whose primary interest is studying population genetics, historical linguistics, ecology, and hominin prehistory and ancient history, the concept of Zomia is also a useful way to help understand why there are natural geographic clusters in Asia in genetics, language, politics and ecology between South Asia, Southeast Asia, and East Asia, respectively. The highlands of Zomia separate them and by discouraging long distance travel, prevent culturally and genetic exchange. Mountains, jungles, deserts and even modest open water distances were some of the main forces to divide populations in prehistory, while river basins and to a lesser extent, open plains or undivided mesas tended to unite them.

Zomia As A Classic Refugium

Zomia shares important social, political, cultural and linguistic similarities with other highland refugia around the world such as the Caucusas Mountains, the Alps, the Mountains near the Volga River which are home to the Mountain Mari people, the Altai, the Nuba Mountain area, the Himalayas, Tibet and the Tarim Basin, the Papuan Highlands, and perhaps isolated areas of Anatolia and Persia.

These regions are often highly balkanized politically and linguistically, are often home to relict populations and cultures that have more effectively resisted assimilation by low land populations, are characterized ecologically by distinctive species of flora and fauna restricted to microenvironmental niches, and often have different food producing methods than the low lands often involving either pastoralism or different kinds of farming than the types found in the lowlands.

In the early Neolithic era in Mesopotamia, the oldest available historical record of these interactions, the herders lived in the nearby hills, while the farmers lived in the lowland river valleys.

The archaeological evidence and one of several theories advanced by classical Roman historians, while not entirely unequivocal, tends to show that the linguistically non-Indo-European language speaking Etruscan people of hilly central Italy derived from an Alpine population described as Rhaetic (although not related except by the area in which it was spoken to the modern language in Switzerland known as Rhaetic). According the their own histories of the ancient Rhaetic people were a relict population that made their way to an Alpine refugium from the South of France fleeing from the Gauls.

Zomia is no doubt home to histories, not widely known in the West (and certainly not well known to me) of similar patterns of highland-lowland interaction and of similarly exiled or relict populations.

Zomia and Mesolithic Expansion Into Asia

One interesting possibility in the Out of Africa and Paleolithic era, is that the more ecologically flexible modern humans, rather than taking a coastal route, may have skirted around archaic hominins like Neanderthals and Homo Erectus as previously supposed, may have been more or less confined to lowland areas by their less flexible subsistence patterns.

One plausible way to test this hypothesis would be to look at a detailed distribution of archaeological evidence such as pre-Out of Africa stone tools in Mousterian and Aterian lithic traditions, and, of course, the detailed geographic distribution of archaic hominin skeletal remains. Large area summary maps often interpolate a hominin species or tool culture's range over a broad geographic area. But, if all actual archaic hominin relic and remain finds are actually confined to lowlands, at least until the appearance of modern humans in the area forced them to flee, then the hypothesis that these species were not "naturally" found in highlands would be supported.

The range confinement of archaic hominins mostly to relatively low altitude environments would seem to be consistent with an apparent absence of arachic hominins in arctic or near arctic climate regions in Scandinavia and northern Sibera. This may have had a very simple explanation. In order to live someplace that gets really cold for long periods of time, you need to be able to build decent semi-permanent shelters (at least away from places where there are naturally occuring caves) and decent clothing. It doesn't appear that either Neanderthals or other Eurasian archaic hominins had this level of architectural and sartorial sophistication. These highlands may have also been ill suited to a subsistence pattern centered around hunting herds of big game like mammoths that may have preferred wide open spaces to tight mountain terrains.

Modern humans may have only ventured further into archaic hominin territory at opportune moments when archaic hominin populations were struggling, perhaps due to shifts in climate or major disasters like volcanic eruptions that were disruptive and caused population decline even if those climate shifts and eruptions in the absence of competition from another hominin species, weren't themselves sufficient to cause them to go extinct. In addition to the pull factor of an increasingly lightly populated fertile destination, modern humans at these times of climate change and/or disaster triggered effects may have faced the push factor of an increasingly inhospitable territory that encouraged them to seek greener pastures despite the presence of some existing hominins occupying that territory.

Zomia and the Distribution of Y-DNA Haplogroup D

The Mesolithic Southern Mountain route "into Asia" scenario described above could provide one way to reconcile the disconnect between Y-DNA haplogroup D. Y-DNA haplogroup D is very old on a mutation dated basis, and has a patchwork mountainous and island distribution that is seemingly suggestive of a previously wider distribution, but is very thinly present outside of the refugium areas where it is found. One would expect a once widely distributed first wave population to leave more of a genetic substrate trace in lowland areas. One would also expect a first wave modern human population in Southeast Asia to have some level of Denisovian admixture, which, in fact, Y-DNA haplogroup D carriers uniformly lack.

The analysis above offers an alternate hypothesis to the theory that Y-DNA haplogroup D carriers were a second migration wave (a hypothesis consistent with its distribution, but not its mutation rate dated antiquity) that could explain the pattern of Denisovian admixture, could be that archaic hominins in Southeast Asia and East (probably all descended from Homo Erectus) without an absolute genocide on the mainland that produced no hybrid descendants outside mainland Asia. Archaic hominins in Asia may have characteristically fled from incoming modern human populations, rather than sticking around to admix as Neanderthals apparently did, until they ultimately reached a final dead end in some Denisovian caves from which they had no further route of retreat.

In this scenario, modern traces of Denisovian admixture are confined to populations of Island Southeast Asia because the archaic hominins on these islands, lacking reliable means of maritime transportation at that time, had no ability to flee incoming modern humans and once forced to co-exist with the newcomers, admixed to a signficant extent with them.

How did this happen?

Perhaps the original distribution of the Y-DNA haplogroup D people was one designed to avoid archaic hominins, rather than one due to being pushed out by or skirting around different waves of modern human populations. Then, new waves of modern humans swept in to replace archaic hominins in areas where the archaics died out before the people with Y-DNA haplogroup D then quite ensconced in their mountain lifestyle could swoop in and lay claim to the lowlands.

Thus, Y-DNA haplogroup D people may never have co-exististed in close proximity to archaic homins in Asia (after the initial Out of Africa admixture with Neanderthals), and may not have experienced serious population pressure from lowland modern humans until the post-Last Glacial Maximum era.

Was Asian Archaic Admixture Influenced By Archaic Hominin IQ?

Commenters at this blog, like Terry, have made the point here and at other blogs, that circumstantial evidence from Neanderthal brain case size, for example, tends to suggest that Neanderthals (who share a common ancestor with modern humans perhaps 800,000 years ago) were comparable in intelligence to modern humans. Populations of species like the Neanderthals with comparable intelligence to modern humans may have felt that they had decent odds of holding their own without fleeing the newcomers into a land to which they had developed more specialized anatomical adaptations. And, indeed, the Neanderthal did not go completely extinct until something on the order of 80,000 years after their first Eurasian contact with modern humans in the Levant, and were the dominant hominin species in Europe for more than 50,000 years after modern humans left Africa, until the Upper Paleolithic revolution took hold in modern humans (roughly coincident with the Aurginacian archaeological culture and the point at which we see evidence of deep sea fishing in Island Southeast Asia and modern humans crossing the Wallace line).

In contrast, known examples of Homo Erectus species had smaller brain cases than either Neanderthals or early modern humans relative to their body size. Their lithic tool cultures in Asia were also even more static than that of the Neanderthals, showing almost no innovations in the archaeological record from the initial arrival of Homo Erectus in Asia around 1,800,000 years ago through the disappearance of this Acheulean tool culture around 100,000 years ago when they too disappeared. This could have been due to the fact that their African tool set was better adapted to their semi-tropical or tropical Asian territory and thus needed no improvement to be optimal, or due to archaic hominin use of bamboo tools in preference to stone tools that left no relics for us to find today.

Map of Range of Archaic Hominin Lithic Tool Cultures. Map source: Wikipedia (recent analysis and an original source map from 2010 found here supports the continued viability of the geographic distinction shown in this map originally proposed in the late 1960s and suggests that that East Asia and Southeast Asian shaded areas represent an independent and more primative development).

But, maybe they were just cognitively incapable of much innovation even relative to Neanderthals whose lithic tool set was much more static and narrow than that of modern humans, at least, by about 75,000 years ago where modern human bone tools, harpoons, and post-Mousterian lithic tools began to appear in the archaeological record (and perhaps any modern human intellectual advantages relative to Neanderthals date only from that time period) (critical analysis of this hypothesis can be found, for example, here). Thus, archaic hominins in Asia may have viewed themselves as more clearly out matched by incoming modern humans making flight in the face of their arrival a more clearly desirable option.

Another, perhaps further reason that there may have been less archaic hominin admixture in mainland Asia relative to areas of modern human co-existence with Neanderthals, may have been that less intelligent archaic hominins in Asia may have seemed like less desirable mates than more intelligence and modern human-like Neanderthals who also had less genetic distance from modern humans.

A Neanderthal admixture event may have seemed to the participants like an extreme case of interracial sex. Admixture with what I have hypothesized were less intelligent Asian archaic hominins may have seemed more like instances of bestality analogous today to sex with a chimpanzee or monkey or oragatang (none of which are popular even within the subculture of pornographic fetish writing). Many modern humans who cohabit with these primates eat them (it is called "bush meat"); none of the modern human populations of which I am aware that cohabit with other primate species have a tradition (even covert or taboo) of sexual relations with primates. Even rampaging lawless soldiers who seem to rape every woman they encounter in places like the recent horrible wars in the Congo, are not known to go about raping females of the primate species they encounter in their travels.

Sunda, Sahul, and the Wallace Line, from Wikipedia

The existence of Homo Flores, the "hobbits" of Flores island, could explain why this is different in Melanesian and Australian Aboriginal populations, whose ancestors almost certain had to pass through Flores en route to Melanesia and Australia. Flores is the third island to the East of the Wallace line, about 40 miles from the Bali which is the eastward most island that was part of mainland Asia during the last glacial maximum, at which point the distance across the Wallace line was about twenty-miles. The next two steps would have been from Lombok and Sumbawa, which is about 8 miles, and between Sumbawa and Flores which is about 12 miles.

The leading explanation of Homo Flores is that they were Homo Erectus individuals who experienced the common phenomena of island dwarfism in their evolution. Intelligence is a function of brain size relative to body size, so evolutionary changes that reduce the body size of a species tend, all other things being equal, to increase its intelligence. Their smaller size would also make them cuter and less threating. It also isn't inconceivable that island dwarfism may have in some way contributed to making it possible for hybrid children to be carried to term.

Mainland Asian archaic hominins at the end point of their trail of exile from a core territory in mainland Southeast Asia and East Asia found in bones in a cave in Denisovia may have been only 100,000 to 200,000 years diverged from Homo Flores and drawn from the same population, so genetically Homo Flores, late mainland Asian Homo Erectus, and the Denisovians whose remains date from a time period when that species would have been moribund (and may perhaps have even hybrid Neanderthal-Erectus individuals in a population that no longer existed as a pure type at that point), would have been no more genetically distinct from each other the most genetically distant clades of modern humans that exist today.

The point at which modern humans crossed the Wallace line, by far the most formidable biogeographic barrier that expanding modern humans had yet encountered, may also have been the moment at which these populations faced their most serious population genetic bottle neck, thus making it possible for a quite small number of instances of admixture with archaic humans to have a maximal effect, and would likewise be a point at which the proto-Melanesians may have had their most dire gender imbalance leaving either men or women as the case might be, short of partners.

Flores as the source of all Denisovian admixture in modern humans is supported because it is the only place where there seems to be some credible archaeological signs that modern humans and archaic hominins were sometimes part of the same community on a sustained basis (with Homo Flores possibly serving as servants in some instances), or at least where the two species appear to have engaged in sustained trade relationships with each other for thousands of years. Homo Flores and modern humans probably co-existed from not later than circa 45,000 years ago until perhaps as late as 12,000 years ago and was probably the last archaic hominin species to go extinct. Thirty-three thousand years of co-existence is a long time, and the extinction of Homo Flores comes not long after the period when the Western islands of Indonesia would have been joined to the mainland as part of the Sunda penninsula, bringing in new peoples and ideas which may have been disruptive to the fragile harmony that modern humans had reached with Homo Florensis there. There are even some linguistic hints that Flores may have had an unexpectly large population of non-native language learners or people with reduced linguistic abilities (perhaps the hobbits) that is not found in the related languages of neighboring islands in Indonesia.

Everywhere else (except possibly in the Levant from the initial arrival of modern humans there about 100,000 years ago until about 75,000 years ago when modern humans disappeared from the region for a couple of dozen millenia), co-existence in one particular geographic location of two separate hominin species appears to have been short lived (probably not more than 1,000 years in any one place; perhaps less, since the fuzziness in dating technologies account for some of the duration of the maximal period of overlap in any given location).

This timing shows some consistency with the timing of the baseline levels of Neanderthal admixture in modern humans which seems to take place at the peak moment of a proto-Eurasian modern human population bottleneck around 75,000 years ago in the Near East. Interspecies admixture may have been something that modern humans intentionally refrained from resorting except in times of extreme shortages of reproductive alternatives during population bottlenecks.

The bottom line is that it isn't inconceivable to me that almost all "Denisovian" admixture in modern humans is actually traceable to a dozen or two instance of admixture with members of the species Homo Flores on the island of Flores, and that a strong flight instinct of Homo Erectus population members who did not experience dwarfism and had someplace to which they could flee, together with a modern human perception of those who did not experience dwarfism as more primate than fellow hominin, could have meant that there was no meaningful amount of archaic hominin admixture anywhere else in Southeast Asia or East Asia (with a possible exception probably involving even fewer instances of admixture relative to the founding population in the Philippines).

Monday, August 20, 2012

Modern Human SE Asian Skull 63,000 Years Old

There are other modern human fossils in China or in Island Southeast Asia that may be around the same age but they either are not well dated or they do not show definitively modern human features. This skull is very well dated and shows very conclusive modern human features," . . . Researchers at Illinois used uranium/thorium dating to determine the age of the skull [in the Annamite Mountains in northern Laos], which they determined was about 63,000 years old.

Research fellow Kira Westaway, of Macquarie University in Australia (who dated the soils around the famous "hobbit" fossil found on Flores Island in Indonesia in 2003), conducted the luminescence analyses. These techniques measure the energy retained in crystalline particles in the soil to determine how much time has elapsed since the soil was last exposed to heat or solar radiation. She found that the layer of soil surrounding the fossil had washed into the cave between 46,000 and 51,000 years ago.

"Those dates are a bit younger than the direct date on the fossil, which we would expect because we don't know how long the body sat outside the cave before it washed in," Shackelford said.

From here.

The time frame at this location between South Asia and Australia is in accord with an oldest South Asian archaelogical relic associated with modern humans shortly predating the Toba erruption circa 75,000 years ago, and with evidence from old human remains and megafauna extinctions of modern humans in Australia circa 45,000 years ago. The data also is the right order of magnitude to fit the oldest wave of migration to Southeast Asia visible in genetic data.

It is also notable because this location is decidedly not a coastal one.

Experimental Constraints On Dark Matter Theories

A preprint released Friday by Matts Roos summarizes the experimental constraints upon, and evidence for, dark matter phenomena. The abstract of the thirty-nine page paper entitled, "Astrophysical and cosmological probes of dark matter" explains:

Dark matter has been introduced to explain mass deficits noted at different astronomical scales, in galaxies, groups of galaxies, clusters, superclusters and even across the full horizon. Dark matter makes itself felt only through its gravitational effects. This review summarizes phenomenologically all the astrophysical and cosmological probes that have been used to give evidence for its existence.

Friday, August 17, 2012

Notable New Physics Preprints

A Reasonable Ab Initio Cosmological Constant Without Holography by Aaron D. Trout (Submitted on 15 Aug 2012)

We give a well-motivated explanation for the origin of dark energy, claiming that it arises from a small residual negative scalar-curvature present even in empty spacetime. The vacuum has this residual curvature because spacetime is fundamentally discrete and there are more ways for a discrete geometry to have negative curvature than positive. We explicitly compute this effect in the well-known dynamical triangulations (DT) model for quantum gravity and the predicted cosmological constant . . . agrees with observation.

A similar analysis explains the non-integer magnetic moment of the electron.

Structural Aspects Of Gravitational Dynamics And The Emergent Perspective Of Gravity by T. Padmanabhan (Submitted on 7 Aug 2012))

I describe several conceptual aspects of a particular paradigm which treats the field equations of gravity as emergent. These aspects are related to the features of classical gravitational theories which defy explanation within the conventional perspective. The alternative interpretation throws light on these features and could provide better insights into possible description of quantum structure of spacetime.


On the physical mechanism underlying Asymptotic Safety by Andreas Nink and Martin Reuter (Submitted on 31 Jul 2012)

We identify a simple physical mechanism which is at the heart of Asymptotic Safety in Quantum Einstein Gravity (QEG) according to all available effective average action-based investigations. Upon linearization the gravitational field equations give rise to an inverse propagator for metric fluctuations comprising two pieces: a covariant Laplacian and a curvature dependent potential term. By analogy with elementary magnetic systems they lead to, respectively, dia- and paramagnetic-type interactions of the metric fluctuations with the background gravitational field. We show that above 3 spacetime dimensions the gravitational antiscreening occurring in QEG is entirely due to a strong dominance of the ultralocal paramagnetic interactions over the diamagnetic ones that favor screening. (Below 3 dimensions both the dia- and paramagnetic effects support antiscreening.) The spacetimes of QEG are interpreted as a polarizable medium with a "paramagnetic" response to external perturbations, and similarities with the vacuum state of Yang-Mills theory are pointed out. As a by-product, we resolve a longstanding puzzle concerning the beta function of Newton's constant in 2+ε dimensional gravity.

Thursday, August 16, 2012

The State of Linguistic Diversity

The Earth’s population of seven billion people speaks roughly 7,000 languages, a statistic that would seem to offer each living language a healthy one million speakers, if things were equitable. In language, as in life, things aren’t. Seventy-eight percent of the world’s population speaks the 85 largest languages, while the 3,500 smallest languages share a mere 8.25 million speakers. . .  some 85 percent of languages have yet to be documented.
From National Geographic.

Wednesday, August 15, 2012

Hawks Refutes African Population Structure Theory

John Hawks, an American anthropologist whose research focus includes Neanderthals, has made a post at his blog strongly refuting the just released paper by Eriksson and Manica at PNAS.  Their paper argued for an African population structure model of Neanderthal contributions to the modern human genome that I discussed yesterday, as opposed to a more recent interspecies mating model.
[T]he idea of Neandertal ancestry has been challenged by several papers that haven't performed any new empirical comparisons at all. . . .We have an unparalleled ability to explore the genomes of humans and Neandertals, and we should believe a computer model with no empirical data?

I've been assessing the Neandertal similarity of 1000 Genomes Project samples here on my blog (e.g., "Which population in the 1000 Genomes Project samples has the most Neandertal similarity?"). This is ongoing research here in my group, but we've been making it open because it tells us immediately that some hypotheses about Neandertal similarity must be wrong. 
For example, our comparisons quickly refute the hypothesis that Neandertal similarity comes only from ancient population structure in Africa. That hypothesis predicts much more heterogeneity within Africans in Neandertal similarity than exists today. We've shown that the heterogeneity in Africans is basically the same as within Europeans or Asians, and that the variance among African populations so far is quite small. Those are very simple observations, which are consistent with what Yang and colleagues [2] concluded on the basis of the frequency spectrum of Neandertal alleles in large samples of living people. Even though many Neandertal-shared SNP alleles came from incomplete lineage sorting, the signature of excess Neandertal sharing outside Africa must come mostly from recent introgression. In Ewen Callaway's article about this research, David Reich dismissed the new paper by Eriksson and Manica as "obsolete". I agree. The paper describes a model without carrying out any new empirical comparisons, and so has fallen behind where the science has gone. . .
Earlier this year, the genome of Ötzi the Tyrolean Iceman was reported by Andreas Keller and colleagues [4]. Aaron Sams and I downloaded the data and have been carrying out several different kinds of comparisons. . . . The European and Asian samples are substantially greater than either African sample (here, Luhya and Yoruba ...). If we took as a baseline that Europeans have an average of 3.5 percent Neandertal, Ötzi would have around 5.5 percent (...the actual percentage would be highly model-dependent). He has substantially greater sharing with Neandertals than any other recent person we have ever examined. . . . I can share the abstract of the conference paper I'll be presenting in September at the meeting of the European Society of Human Evolution in Bordeaux:
Evaluating recent evolution, migration and Neandertal ancestry in the Tyrolean Iceman
Paleogenetic evidence from Neandertals, the Neolithic and other eras has the potential to transform our knowledge of human population dynamics. Previous work has established the level of contribution of Neandertals to living human populations. Here, I consider data from the Tyrolean Iceman. The genome of this Neolithic-era individual shows a substantially higher degree of Neandertal ancestry than living Europeans. This comparison suggests that early Upper Paleolithic Europeans may have mixed with Neandertals to a greater degree than other modern human populations. I also use this genome to evaluate the pattern of selection in post-Neolithic Europeans. In large part, the evidence of selection from living people’s genetic data is confirmed by this specimen, but in some cases selection may be disproved by the Iceman’s genotypes. Neolithic-living human comparisons provide information about migration and diffusion of genes into Europe. I compare these data to the situation within Neandertals, and the transition of Neandertals to Upper Paleolithic populations – three demographic transitions in Europe that generated strong genetic disequilibria in successive populations.


 From John Hawks weblog (italics in original, emphasis in bold faced body text mine).
Does a lack of heterogeneity in modern Africa populations prove that much?
While I agree with the conclusion reached by John Hawks.  He somewhat overstates the relevance of the fact that the African population structure model calls heterogeneity within Africans in Neanderthal similarity than is seen in modern populations, at least within the data that his group has used in its analysis.

An African population structure model of Neanderthal genome similarity requires considerable heterogeneity within Africans in the Out of Africa era about 100,000 years ago.  But, the African population structure model does not require that this heterogeneity continue to the present.

The genetic evidence in Africa strong supports a model in which the population ancestral to the Yoruba of West Africa, i.e. the proto-Niger-Congo language family speakers, underwent a massive population expansion long after the Out of Africa era and through a combination of dilution and replacement of prior populations became (probably sometime in the last 20,000 years, and possibly considerably more recently) the dominant source of genetic ancestry in West Africa, and later, during Bantu expansion (sometime within the last 3000 years), for which the Luhya, an East African Bantu population is typical, in the rest of sub-Saharan African.  Yet, despite the fact that these two populations are a very narrow subset of even the African genetic diversity that is present today because they derive mostly from a population that expanded much more recently than the out of Africa era, even the variation in Neanderthal genome similarity within these relatively homogeneous African populations is still greater than the variation in Neanderthal genome similarity found among the entire gene pool of Europeans and Asians combined.

There are exceptions to rule that most Africans derive a large part of their genetic ancestry from the proto-Niger-Congo population.  The proto-Niger-Congo populations did not predominantly replace the linguistically non-Niger-Congo language family speakers of Africa in North Africa, the Sahel or East Africa, nor did they erase the genetic traces of relict populations like the Khoisan, the Hazda, and the Pygmies (even though the Pygmies now speak Bantu languages and their pre-Bantu languages are dead and were never committed to writing).  But, no individuals from any of these groups were included in the analysis done by Hawks' group that are discussed in posts at his blog.
But, even these cases don't necessarily capture Out of Africa levels of genetic diversity and population structure in Africa.  There is linguistic evidence (the shared presence of click languages), and genetic evidence, to support the claim that the existing relict pre-Bantu population of the Southern Africa (the Khoisan) has origins shared with relict East African hunter-gatherer populations like the Hazda, possibly long Africa the Out of Africa era.  North African and East African populations show evidence of "recent" (i.e. within the last twenty-thousand years or so, and to a considerable extent, much more recent) introgression of back migrating populations from the Near East into Africa.  The African component of North Africa and East Africa is generally speaking East African in character.  Madagascar's Indonesian genetic component probably arrived in Africa within the last 1,500 to 3,000 years and Madagascar's African component looks a lot like the East African Bantu Luhya population.  There are no pre-Bantu ancient DNA samples from anywhere in Africa and there is precious little Mesolithic modern human skeletal evidence to analyze in Africa outside of East Africa (something partially due to poor conditions for preservation of these kinds of remains).

In short, there is every reason to believe that a small number of population genetically more successful founding populations in Africa, most of which have antecedents either somewhere ion East Africa, or among the proto-Niger-Congo speakers whose ancestral place of origin prior to their expansion is sketchy, are the ancestors of virtual all modern Africans. 

All of these populations may be traceable to someplace that is geographically quite close to the probable ancestral home of the population that is ancestral to all non-Africans.  They may have lived perhaps a few hundred miles away over territory that was passable to early modern human hunter-gatherers, instead of a few thousand miles away across geographic barriers that would have been nearly impossible for early modern human hunter-gatherers, a scenario that was not inconsistent with the available evidence not so long ago.

It is very plausible that these more successful African populations brought about the extinction of, or dilution beyond recognition of, most of other genetic populations that existed in the Out of Africa era when they expanded much later on.  In the process, these expanding populations likely destroyed much of the genetic heterogeneity within Africans that existed in the Out of Africa era.

The African populations that are included in the analysis posted done by Hawks' group might be compared to using a Han Chinese population and a linguistically Chinese speaking modern Taiwanese population as a stand in for all of Asia.  This is clearly a good place to start, because in each case this accurately captures of the genetics of the modal population of the continent in question.  But, it is not a good place to look if you are interested in estimating how much genetic diversity there was on that continent in the Mesolithic.

Hawks' conclusion is very likely correct anyway.

Still, the model emerging from multiple lines of evidence including the Ötzi and 1000 Genomes genetic data, is one in which Upper Paleolithic modern humans have more Neanderthal admixture than other Out of Africa populations.   In this model, this excess admixture was then diluted by later episodes of migration into Europe after Neanderthals went extinct.  Thus, the European excess admixture attributable to continued interspecies mating in Europe that continued after admixture with Neanderthals by the ancestors of modern Asian populations is difficult to distinguish in the data, although not invisible if there is enough data and the right methods are used.

How can agree with Hawks' despite thinking that his first and primary argument based on a lack of heterogeneity within Africans? 

The quibbles I outline above with the weight that Hawks' gives to one particular line of evidence that he uses to support the conclusion that African population structure is not the source of differences in genetic similarity to Neanderthals in modern humans does not mean that his bottom line conclusion is wrong.  This piece of evidence standing alone wouldn't prove the point.  But, this piece of evidence doesn't stand alone.  When it is taken together with other evidence, important parts of which he himself played an important part in bringing into being (and the rest of which he is intimately familar with), the total mosaic picture created emphatically supports his conclusion.

Indirect Arachaic Admixture Evidence

For example, one point that he doesn't mention, but that I find convincing, is that studies using the same indirect methods (which I won't describe in detail in this post) that predicted the amount of Neanderthal admixture observed in non-Africans before a direct comparison with ancient Neanderthal DNA was made in 2010, and that also predicted the presence of an excess of ancient admixture in Papuans and Aboriginal Australians before a direct comparison was made between their genomes and ancient Denisovian archaic hominin DNA, has revealed low levels of archaic admixture (perhaps 1-2% or so) in modern Khoisan and Pygmy populations.  These indirect measures imply that this archaic hominin admixture in Africans probably happened sometime in the Upper Paleolithic era (i.e. well after the Out of Africa era).  These indirect traces of archaic hominin admixture in African relict populations don't match either the Neanderthal or the Denisovian ancient DNA samples, so they were probably one or two different species of archaic hominins than either Neanderthals or Denisovians or modern humans. 

This, in turn, suggests that even if there was far more genetic heterogeneity within Africans and population structure in Africa in the Out of Africa era than is today, that it probably didn't follow the kind of North-South cline in Neanderthal genome similarity that could fit the African population structure model.  It also suggests that there is not a huge amount of ancient African population structure not seen in Luhya and Yoruba populations that could be teased out of an analysis of African relict populations that would favor an African population structure model over a Neanderthal admixture in the Out of Africa era model.

This indirect archaic admixture evidence suggests that there isn't a huge amount of undiscovered archaic admixture out there in either non-Africans, or in the predominant African populations that isn't explained by a model that includes only Neanderthal and Denisovian admixture, even though that probably doesn't fully capture every bit of the story of archaic admixture in Africa.  There are no meaningful traces of non-Neanderthal archaic admixture on the side of the Africans that include almsot all Niger-Congo language family speakers (other than Pygmies), Nilo-Saharan language speakers, and Afro-Asiatic language speakers (perhaps 98%+ of all Africans), as opposed to the branch of African populations that includes the Pygmies and Khoisan peoples.  And, the Neanderthal archaic admixture in Africans that do have Neanderthal admixture closely tracks the overall level of Eurasian admixture attributable to backmigration from Eurasia in the last 20,000 years or so in these individuals.

The pattern of specific possibly Neanderthal gene frequency observed in particular populations.

Another couple of important data points that he has observed in his prior posts on Neanderthal DNA patterns in modern Eurasians are that (1) the particular loci of Neanderthal DNA in Asian and European populations don't overlap much, and (2) while most of these loci show a pattern consistent with genes that are neutral from a genetic fitness perspective, that a small number of these genes show clear signs of having their frequency enhanced because they have imparted increased genetic fitness to people who have the genes sometimes after the Out of Africa migration.  These data points strongly favor an interspecies admixture model over an African population structure model.
It would be difficult to get such a clear split in the particular Neanderthal genes inherited by Asians and Europeans respectively from the schism of a small population migrating Out of Africa around 100,000 years ago, and then spliting into distinct subpopulations sometime not more recent than 50,000 years ago, in a model where apparent Neanderthal admixture arose from African population structure derived from a common ancestor of modern humans and Neanderthals at least 350,000 years ago.  If that was the case, the archaic components of the modern human genome in the African subpopulation that migrated out of Africa would have long prior to that point reached fixation in that subpopulation, so the mix of seemingly Neanderthal genes in both Europeans and Asians should have been much more similar, even considering founder effects.

Also, even if the African population structure model could explain the mix of fitness neutral derived Neanderthal SNPs in non-Africans, it could not easily explain how genetic fitness enhancing derived Neanderthal SNPs that are present at highly elevated levels in non-Africans managed to stay so rare in other modern humans in different African subpopulations not all that geographically distant from the homeland of the subpopulation of Africans that is ancestral to all non-African modern humans.  Genetic fitness enhancing genes spread like wildfire even between populations with very low levels of gene exchange (e.g., one instance of gene exchange per generation between the two populations).  Moreover, some of the environments where the genetic fitness enhancing genes also found in Neanderthals are common aren't that different from Africa.

Recent Relevant Archaeological Discoveries

My statement that the Out of Africa subpopulation was "not all that geographically distant" from the ancestors of other known African populations is also far less hypothetical than it would have been a couple of years ago.  This year, for the first time, anthropologists have linked archaeological relics from some of the earliest modern humans in the interior of Arabia in the Out of Africa era to contemporaneous modern humans in Sudan and the Nile basin. 
Likewise, considerable progress has been made in the last few years in determining from archaeological evidence:

(1) when modern humans reached Southern India (sometime after Out of Africa and before the Toba volcano exploded about 75,000 years ago),

(2) when and where populations that used characteristically Neanderthal tools were present in South Asia,

(3) that there were very ancient modern human populations in the interior of Arabia as far back as 75,000 years ago who were in cultural continuity with early Levantine modern humans (during a climate phase when the interior of Arabia was wetter there than it is now),

(4) the precise time frame during which the first modern humans arrived in Europe (about 43,000 years ago and spreading to the entire region faster than had previously been assumed), and

(5) more clearly the archaeological demarkations between Neanderthal and modern human sites in Europe during the period when the two hominin species co-existed in Europe - this disfavors the possibility that the two species ever used identical lithic tool sets and material cultures at the same time and is contrary to prior knowledge which would have allowed for that possibility and greater cultural sharing between the two species.

Not So Recent Data Points

This list of data points to support the conclusions being reached by John Hawks' group and others isn't exhaustive and is pretty much limited to evidence available for the first time in the last few years.  For example, we have known for many decades that the earliest modern humans in the Levant co-existed at first with Neanderthals in the same region around 100,000 to 75,000 years ago.  And, we have known for at least a decade the general outlines of the evolutionary tree of modern human genetic diversity that is rooted by every measure in Africa, with Eurasians generally having closer phylogenetic links to genetic markers, such as mtDNA haplogroup L3, that are now most common within Africa in East Africa.  Similarly, we have known for a decade or so, the gist of how East Eurasians, in general, differ genetically from West Eurasians.

Bottom Line: Lots Of Old Models Are Now Ruled Out

The facts have firmed up enough to rule out a lot of models that were previously believed to be consistent with all available evidence in the last decade or so. This has been mostly due to analysis of large and rich DNA sampling from large numbers of people who include representatives of almost all significantly distinct populations in the world, the availability and analysis of a large number of ancient DNA samples, improved paleoclimate data, and recent archaeological relic discoveries.

The bottom line point is that when you piece together multiple, at least somewhat independent, pieces of genetic and archaeological evidence at our disposal, they hang together in the kind of model modern human population history that I spelled out in my post yesterday which includes Neanderthal and Denisovian admixture outside Africa.  In contrast, these puzzle pieces aren't a good fit for an African population structure model even if individual pieces of the evidence could be fit to that model.  Likewise, a model in which the Neolithic revolution in Europe (or pretty much anywhere else) took place predominantly via cultural diffusion has been pretty definitively ruled out.  The story of human prehistory and genetic ancestry isn't seemless and complete.  But, it is much better defined by the available hard evidence than it was when I graduated from college in 1992, for example.

Evidence From Regional Differences In Neanderthal Admixture

The gap in the number of shared Neanderthal derived SNPs between the two African populations, on one hand, and the Asian and European individuals on the other, is about three times as great as the range of variation in the number of shared Neanderthal derived SNPs among Africans, and among the combined Asian and European population, respectively.  There is no overlap at all between the number of SNPs in the two African populations examined and the number of SNPs in the non-African individuals.

The number of shared Neanderthal derived SNPs in Asian individuals and in European individuals does overlap, although the mean number of SNPs in slightly higher in the European individuals for whom data is available from the 1000 Genomes project and the Asian individuals.  Also, the highest number of SNPs in the 1000 Genomes project is found in Europeans, while the lowest number of SNPs in Eurasians in the 1000 Genomes project is found in Asians. 

The magnitude of the difference between the Asian and European individuals is about what my back in napkin estimates in yesterday's post suggested, a barely discernable fraction of a percentage point that is less than the standard deviation of the differences within each of the respective populations.

The Ötzi genome as evidence of demic diffusion

Indeed, the Ötzi genome is at least as powerful in establishing the theory that the Neolithic era came to Europe a heavily demic migration model, as it is in establishing that Neanderthal admixture is attributable to interspecies mating rather than African population structure.  In the demic migration model, existing European hunter-gatherer populations provide only a minority contribution to the modern European gene pool, because farming and herding came to Europe mostly through the migration of farmers and herders from elsewhere who moved into Europe after their people became herders and farmers.  This is in contrast to the now largely discredited model, popular in the 1970s, in which existing European hunter-gatherers adopted farming and herding methods, crops, and animals ultimately from Fertile Crescent Neolithic sources, with minimal population replacement or dilution.

Ötzi, in the early Neolithic, in Southern Europe, had a less diluted European hunter-gatherer component to his genome than anyone living today whose whole genome has been sequenced.  The Ötzi genetic data is corroborated by ancient DNA data showing stark genetic differences between ancient DNA from European hunter-gatherers and ancient DNA from early Neolithic individuals (and from both, in turn, relative to modern European populations) in uniparental genetic markers.  It is also corroborated by physical anthropology data that show stark differences apparent in skeletal remain dimensions between European hunter-gathers populations and Neolithic individuals. 

The Upper Paleolithic modern human hunter-gatherers of Europe and the Neolithic migrants who moved into Europe would have looked as different from each other on the Neolithic revolution's frontier as Australian Aborigines looked from the English colonists who later migrated to Australia (and would have been genetically distinct from each other to a similar degree).

Also, I note here, as I did in my previous post, the European hunter-gatherer population at the dawn of the Neolithic revolution in Europe had probably already been infused with significant amounts of migration from outside Europe after the Neanderthals went extinct, particularly during the time period when Europe was repopulated from the South as the glaciers retreated.

Given Ötzi's age and location not so far from the boundary between Europe and parts of Western Asia that were inhabited by modern humans long before they reached Europe, its is reasonable to infer that the Ötzi genome with something on the order of 5.5% Neanderthal admixture probably had less Neanderthal admixture than Cro-Magnons in Northern Europe prior to the Last Glacial Maximum around 20,000 years ago did. 

In light of Ötzi, I am beginning to think that a level of Neanderthal admixture with Cro-Magnons that reached something around 8% (the estimated level of peak admixture in the population that was the source of Denisovian admixture in Melanesian and Aboriginal Australians), is a fairly realistic estimate.  My best guess (and admittedly no more than an educated guess) would be that Ötzi was perhaps half or a quarter Cro-Magnon by descent and probably had a West Asian paternal grandfather given his Y-DNA haplogroup.

This is huge.  By comparison, this is about the same amount of introgressed Neanderthal ancestry in early modern human European hunter-gatherers as the amount of introgressed Turkic genetic ancestry found in modern day Turkey.  (The original Turks who brought their language to Turkey originated someplace a bit to the Northeast of Mongolia and arrived in Turkey in the first millenium of the common era; for at least twenty-five hundred years before that (some would argue much longer than that, although I would disagree), most Anatolians spoke Indo-European languages of one kind or another).

A peak Cro-Magnon level of Neanderthal admixture of 8% would also imply that my back of napkin estimate in yesterday's post materially overestimated the percentage of modern European ancestry that is traceable to Cro-Magnons.  The actual percentage of Cro-Magnon ancestry must have been closer to half of my previous rough estimate, perhaps 4%-5% rather than the 10% that I previously estimated, in the vast majority of European populations, although more in a select minority of European populations with a larger European hunter-gatherer component.

This would also disfavor, for example, a Basque population that not dervive from European hunter-gatherers to a greater extent than most Indo-European linguistic family populations of Europe, because they do not have a particularly elevated level of Neanderthal admixture compared to Indo-European language speaking populations that are more widely assumed to have thoroughly replaced pre-existing hunter-gatherer populations.  Basque genetic roots predominantly in the early Neolithic or copper age, or at the very least, in the Epipaleolithic, are a better fit to this data point.