Zomia

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).

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.

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.

and

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.

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.

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.

References

1. Eriksson A, and Manica A. 2012. Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Proceedings of the National Academy of Sciences.
2. Yang MA, Malaspinas A-S, Durand EY, and Slatkin M. 2012. Ancient structure in Africa unlikely to explain Neanderthal and non-African genetic similarity. Molecular biology and evolution.
3. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, et al. 2010. A Draft Sequence of the Neandertal Genome. Science [Internet] 328:710–722. Available from: http://dx.doi.org/10.1126/science.1188021
4. Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, Maixner F, Leidinger P, Backes C, Khairat R, Forster M, et al. 2012. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nature communications 3:698.

 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.

Neanderthals Ties, A Tree Or An Ewok Village?

There is a significant (about 2.5%-4% of all non-Africans) overlap between the Neanderthal genome and the modern human genome.  Why? 

Theory One: Ancient African Population Structure

It could be due to a shared common ancestor, Homo heidelbergensis, which could have split into Neanderthal population in the North and early modern humans in Africa around 350,000 to 500,000 years ago.  In this scenario the differences in the amount of apparent Neanderthal admixture between non-Africans and Africans was due to population structure in Africa, with the Out of Africa population drawing on a different part of the genetic diversity of modern humans at the time than the population which in ancestral to most Africans today. 

Keep in mind that much of the population diversity present at the Out of Africa moment in Africa was found in populations that subsequently left no descendants or are survived only by relic populations like the Pygmies and Khoisan today, or only have ancestors who slightly introgressed into other, more successful African populations. 

Different African and Eurpean hominid populations around 100,000 years ago could have had different levels of relatedness to each other, presumably on a North to South cline, with the populations closest to Europe being most similar to Neanderthals and the populations most distant from Europe being least similar.  If many of the intermediate hominin populations descended from Homo heidelbergensis between Northeastern African modern humans who were necessarily the ancestors of non-Africans on one hand, and the Southern African or Western African modern humans, on the other, subsequently went extinct, the genetic trace that would be left in modern humans would look a lot like an admixture model, but without the hot interspecies sex.  Likewise, hominin populations intermediate between Northeastern African modern humans (pre-Out of Africa), and Neanderthals, in the Levant, would also have left no genetic traces.  Fans of Jean M. Auel's Clan of the Cave Bear series wouldn't be vindicated after all.

This is the essence of the argument made by Andrea Manica and Anders Eriksson in a paper in the Proceedings of the National Academy of Sciences, which was acknowledged by viewed a less parsimonious in the seminal Neanderthal admixture paper.  (Archaeogenetics blogger Dienekes is a fan of this theory.)

Theory Two: Neanderthal Admixture

Or, it could it be that the sexier theory that Homo neanderthalensis interbred in small numbers with some of the earliest ancestors of all non-African modern humans is correct? 

This is the proposal of Svante Pääbo "who led the sequencing of the Neanderthal genome in 2010 and has championed the idea that modern humans interbred with Neanderthals[.]"

Pääbo has co-authored a paper, which is yet to undergo peer-review, to further support his thesis that humans and Neanderthals did in fact interbreed. "We find that the last gene flow from Neanderthals (or their relatives) into Europeans likely occurred 37,000-86,000 years before the present, and most likely 47,000-65,000 years ago," he writes. "This supports the recent interbreeding hypothesis, and suggests that interbreeding may have occurred when modern humans carrying Upper Paleolithic technologies encountered Neanderthals as they expanded out of Africa."

These Admixture Dates, If Recalibrated, Fit An Early Out of Africa In The Levant That Lived

If the dates are calibrated to fit archaeological suggestions of date that make sense, to be longer by a factor of 1.6, as I have advocated in previous posts (the difference mostly reflects a probably inaccurate mutation rate used to develop the estimate of the number of years ago that genetic populations became distinct), one gets a date range of 75,200 to 104,000 years ago. 

This neatly coincides with the earliest time period in which there is archaeological evidence of Neanderthal and modern human co-existence in the Levant, after which modern humans reappear in the Levant about 50,000 years ago.

The adjusted date range would be powerful evidence that the first Out of Africa period in the Levant was not "Out of Africa that failed", but instead, was the source of the population that is the dominant ancestral population for all non-African populations today.  In this scenario, rather than dying out, after which Eurasia was recolonized by a second wave of modern humans leaving Africa, the early Out of African Levantine population was dispersed around 75,000 years ago from the Levant to refugia (probably in a wetter interior of Arabia, in the less inundated Persian Gulf, in Iran, and/or in South Asia) that later rebounded and ultimately populated the rest of the Earth.

Why Don't Europeans Have More Neanderthal Admixture Than Asians?

How can one explain the similarity in levels of African admixture between Europe and Asia in an admixture theory, despite the fact that Neanderthals co-existed with Cro-Magnon modern humans in Europe for many thousands of years, but in Southeast Asia and East Asia for far shorter time periods? 

Did the propensity of modern humans to interbreed with Neanderthals decline in the Upper Paleolithic?  I don't think that it did.

The more likely scenario, I think, is that Neanderthal co-existence with modern humans in the Middle East ended far sooner than it did in Europe, and that most of that ancestry of Europeans today comes not from the Cro-Magnon population that had a prolonged period when there could have been admixture, but from Middle Eastern populations with less Neanderthal exposue.  These peoples repopulated Europe after the Last Glacial Maximum (around 20,000 years ago, long after the Neanderthals had gone extinct) and in subsequent waves of population expansion around the beginning of the Neolithic Revolution in Europe (plus or minus a few thousand years) and with Indo-European language expansion.  This would dilute the amount of excess Neanderthal admixture in Europe.


Since the level of Neanderthal admixture would have been modest even in populations with long periods of co-existence with Neanderthals relative to the non-African baseline, even in more admixed populations, it could be that these elevated Neanderthal admixture levels from Cro-Magnon populations are almost indistinguishable from background random noise in modern populations.

For example, suppose that later waves of populations from the Middle East provided 80% of the autosomal genetic source for modern Europeans (one number that has been seriously proposed based on assumptions made about uniparental genetic markers) and 20% of the autosomal genetic source for modern Europeans was Cro-Magnon.  Then, assume that the Middle Easterners were 4% Neanderthal admixed and that the Cro-Magnon were 8% Neanderthal admixed (half due to their remote Middle Eastern source ca. 43,000 years ago, and the other half from further admixture in Europe).  The end result would be a modern European population with 4.8% Neanderthal admixture on average, a percentage that has a standard deviation in Europe on the order of 0.5 percentage points in the data so far used to derive that figure.

More realistic numbers are something like this:

* The level of Neanderthal admixture may be somewhat higher in the minority of modern European populations, probably not more than 10% of all Europeans overall (mostly in the far Northeastern part of Europe), with the largest genetic contributions from the last European hunter-gatherers to convert to herding and farming, who might have, perhaps as much as 20%-30% of ancestry in these populations traceable to Cro-Magnons.   

* Don't forget that post-last glacial maximum relict European hunter-gatherer populations, even before the demic impact of Neolithic and metal age migrants, would not have been 100% Cro-Magnon.  Almost all of Northern Europe was 99.99% depopulated of modern humans because it was under glaciers (there may have been a warm protected valley or current warmed coastal area in a few isolated spots that could support a village or two), leaving relict populations mostly in Iberia, Italy and far Southeastern Europe.  When the glaciers retreated, some of the repopulation probably had its source not from these Cro-Magnon refugia, but from the Middle East.  By the time that the herders and farmers arrived, these source populations would have had at least several thousand years to reach something close to

* In contrast, most European populations, who make up perhaps 90% of all Europeans, might have on average 10% Cro-Magnon ancestry or less.

* The level of Neanderthal admixture in Cro-Magnon populations might have been 50% more than in Middle Easterners (i.e. Cro-Magnon populations might have been 6% Neanderthal), rather than twice as great.

* This would suggest an expected average level of European Neanderthal admixture of 4.23% relative to a baseline of 4% +/- circa 0.5%, and the existence of population structure in Europe would mean that the choice of sample individuals from which you made the estimate could skew the sample far more than the excess of the European average over the shared non-African baseline percentage of Neanderthal admixture.  Thus, the excess Neanderthal admixture would be almost invisible.

Why Is There No Neanderthal mtDNA or Y-DNA in modern humans?

There are also plausible models that can account for the absence of Neanderthal mtDNA or Y-DNA in any modern humans. 

In these models, a principle called Haldane's law insures that almost all of the fertile Neanderthal-modern human hybrids were probably female in the first generation, accounting for the lack of Neanderthal Y-DNA.  Haldane's law says that mixed sex chromosome interspecies hybrids (XY males in the case of hominins) tend not to be born, or to be infertile if they are born, relative to homogeneous sex chromosome interspecies hybrids (XX females in the case of hominins).

Neanderthal mtDNA's absence is explained by the theory that hybrid children grew up with a tribe made up of the species of the mothers rather than the fathers, and that the hybrid children born into Neanderthal tribes died out with the rest of the Neanderthal population, while the hybrid children born into modern human tribes have descendants who are alive today.  In this scenario, there could have been just as many hybrid children with Neanderthal mothers as there were with modern human mothers, and yet have no Neanderthal mtDNA in modern humans.

Of course, in both the Y-DNA and mtDNA cases, isolated exceptions to the rule could wash out of the gene pools due to genetic drift.

Horticulture Naturally Encourages Carpentry

Pre-Pottery Neolithic A (PPNA) and Pre-Pottery Neolithic B (PPNB) [:] Agriculture and domesticated plants and animals appear only in PPNB. . . . Within PPNA, humans remained gatherers but lived in more permanent settlements for the first time. . . . Axes associated with this period are small and delicate, used for light carpentry but not suited for felling trees or other massive woodworking tasks. In PPNB, the tools have evolved to much larger and heavier axes. . . .  they were used to cut down trees and complete various building project. . . .The round and oval structures of earlier domiciles were replaced by rectangular structures in PPNB. . . "Evidence tells that us that for each home, approximately 10 wooden beams were needed. Prior to this, there were no homes with wooden beams."  

[I]n the Judean hills . . . changes during the PPNA–PPNB transition at the onset of the Levantine Moist Period (ca. 8000 cal B.C.) when conditions for agriculture improved. . . . villagers added heavy-duty axes to a toolkit they had used for carpentry and began to clear forests for fields and grazing lands. Sustainable forest management continued for the duration of the PPN until the cumulative effects of tree-felling and overgrazing seem to have led to landscape degradation at end of the Pre-Pottery Neolithic C (PPNC), when a cold, dry climatic anomaly (6600–6000 cal B.C.) may have accelerated the reduction of woodlands.

From here.

Much of what is loosely called the Neolithic revolution is really talking about the events that happened at the PPNA-PPNB transition point in the Near East.

It isn't entirely clear to me that populations that received the Neolithic revolution from incoming populations, rather than inventing it locally, experienced the PPNA phase at all.  These areas may have skipped directly from a hunter-gatherer society to a PPNB or higher level of technological development without passing through the intermediate PPNA stage.

One implication of this kind of stage skipping technological expansion is that less technologically distinct early PPNA populations in the Near East from which PPNB populations emerged may have been more able than early Neolithic populations from other regions to assimilate prior hunter-gather populations that didn't participate in developing the Neolithic technologies themselves.

In a scenario where civilizations that are culturally daughters of the Near Eastern Neolithic where food production and the associated technologies were developed skipped immediately to post-PPNA or maybe even post-PPNB stages, the extent to which the critical stage expanded in all directions almost simultaneously once it had reached the critical point where it was superior to hunting and gathering in a large swath of ecological niches, is accentuated. 

If, for example, the Egyptians and Indus River Valley start their Neolithic revolutions at PPNC, rather than PPNA, then PPNC reached them within just two hundred years or so of the time it emerges in the Near East and has a much clearer push factor to drive its emergence from the Near East to  new territories (the cold, dry climatic anomaly).  This is a series of mass migrations that would have been dramatic events of historic proportions in  the eyes of anyone experiencing them, on the scale of the Biblical book of Exodus, if anyone had been able to write them down or accurately recount them in oral histories.

In contrast, if you think about the Neolithic emerging in the Near East two thousand years before it appears elsewhere, the pace of its expansion seems veritably glacial and is has less of a well motivated climatic dynamic to push its expansion.  This looks more like the kind of rudderless diffusion and osmosis scenarios that many computer models generate, in which individually insignificant decisions of one household at a time to go over the the next hill from the one they grew up in only looks like a dramatic mass migration through someone with a time-lapse photography like perspective that no one actually participating in it would have realized was happening.

On the other hand, perhaps I have it backward.  Perhaps, a lot of what seems like late Upper Paleolithic hunter-gatherer activity that seem to have involved brought about major changes in both North African and Southern European population genetics are better described as PPNA than as late UP hunter-gatherers.  In these areas (which are geographically contiguous and similar in climate to the places where the PPNA emerged in the Near East), the PPNA rather than a later PPNB wave may have been the most powerfully formative population genetic source for later populations in the same region. 

An Upper Paleolithic to PPNB or PPNC leap with less admixture may have been something more particular to the Danubian Neolithic, where PPNA technologies outside the more narrow ecological niche where they emerged did not translate to new climates as well until they were more advanced, rather than representing a general feature of Neolithic expansion in Western Eurasia and North Africa.

The study is also notable for showing how an obvious archaeological feature (round v. rectangular buildings) could emerge naturally and independently from a less visible technological development (better axes), which in turn turns out to be intimately linked to more reliable and productive horticultural production that made it important to figure out how to efficiently clear land and hence to develop better tools to accomplish that end.  The end architectural impact was an indirect but inevitable unintended benefits of improving carpentry in general in order to make more room for farms by cutting down forests. 

This kind of apparent coincidence with fundamental technological sources can help explain why there are such striking architectural parallels between early Near Eastern and Anatolian Neolithic structures and structures that started to be built in the American Southwest by a totally independent maize and bean Neolithic food production system almost eight thousand years later in the New World.  The earliest stages of architectural development in Mesopotamia, for example, are very similar to the earliest stages of architectural development in a geographic region roughly within the boundaries Mexico as it existed in the early 19th century.  But, a Book of Moron style transmission of technologies via migrations across the ocean make no sense to explain these similarities when one considers that forms seen in the New World had been obsolete in the place where these architectural forms are seen first on the globe eight millenia earlier (in addition to having no archaeologically or genetically supported evidence to support it).

More deeply, it suggests that the technology and climate driven long term path of history is much more tightly constrained by the non-obvious universal implications of laws of physics and biology that drive engineering and horticulture than a naive, "anything can happen at any given point in history" conception where slight random differences in initial conditions and innovations can produce radically different end results apart from some of the cultural window dressing put on the largely universal tends.

In other worlds, absent outside intervention, technology may be constrained to a high level of probability to develop in a highly specific sequence with material cultures and forms of social organization that natural world limitations turn out to specify at a quite high level of detail.  For example, maybe there are similarly deep reasons why early metal age cultures are naturally predisposed to develop particular kinds of linguistic structures (like base twenty numbers), political systems led by priest-kings who preside over rituals involving animal and human sacrifice, and polytheistic religions that divided the forces of nature into portfolios of influence for various deities, even if they develop totally independently.  But, of course, the precise names of the polytheistic gods in question and most popular precise visual motifs that emerge to sheath this universal tendencies are pretty much chaotic (i.e. highly sensitive to random variations in initial conditions and inherently unpredictiable).  (Likewise, today, the technological developments that have given rise to the transition from industrial to post-industrial economies may have hidden and indirect drivers that encourage secularism and undermine the ceremonially oriented mainline monotheism that prevailed in the Industrial Age.)

In a related observation, it is also worth noting that emerging view that the large stone structures that are the diagnostic and nominative feature of the Megalithic culture are increasingly being interpreted not simply as outdoor astronomical calenders, but also as the most robust skeleton of what were actually large, predominantly timber buildings when they were erected.  These massive, precision timber structures align the Megalithic culture with a stage of technological development and material culture no earlier than PPNB.  And, in much of Western Europe, the Megalithic culture appears to have been the initial and original Neolithic culture in the region, coming immediately after a hunter-gatherer phase with no intermediate steps.  Notably, the Megalithic culture emerged at and beyond the fringes of the areas in the Mediterranean basin most similar to the Fertile Crescent areas where the Neolithic was invented by the people of PPNA.  The Megalithic culture was out of the sweet spot for the more fragile PPNA form of food production.  So, the expansion of the Megalithic culture, like the Danubian Neolithic, may have similarly been a technological stage skipping one rather than a more gradual and continuous one.

Cocktail Party Etiquette

The intricate non-verbal and pseduo-verbal dance of cocktail party communication, whose below the surface complexity is epic and whose rules are unwritten and mostly subconscious.  If you appreciate Neil Simon plays but know you could never write them or act in one, you appreciate this fact.  This dance is vividly depicted in all of its epic complexity in a collection of xkcd comic panels discussed in a Language Log post today. 

Anyway, why is it that things that are funny and things that are potentially embarassing, so often overlap?

What Now For High Energy Physics?

The Large Hadron Collider has many years of operations ahead of it, but it is increasingly looking likely that those experiments will continue to confirm that they have found a Standard Model Higgs boson, with this hypothesis becoming more and more certain with each coming year, and that they have not found any deviations from the Standard Model predictions, with the relevant parameters being pinned down with somewhat greater precision over time.  It is also quite likely that exclusion areas from the SUSY parameter space and of other beyond the Standard Model theories will be increasingly ruled out.

There will still be open questions in neutrino physics, since the LHC is ill suited to reveal the neutrino's mysteries (we lack basic parameters like the neutrino masses in absolute terms and accurate measurements of the values of the PMNS matrix), and there will still always be the possibility that some new physics is lurking at an energy scale beyond that observable at the LHC after a full run. 

As I've noted before, a particularly important parallel track of fundamental physics research involves the ongoing efforts to see, or exclude down to a certain production rate, neutrinoless double beta decay - I doubt that it is out there or that neutrinos have Majorana mass (which an obserbation of neutrinoless double beta decay would imply).  Equally important, a failure to find neutrinoless double beta decay below a sufficiently low rate of production, combined with a lack of direct detection of supersymmetric particles in the LHC's planned run, pretty much closes the door on all versions of SUSY that make sense and a fortori, falsifies String Theory.

If all of the leading alternatives to the Standard Model with a single Standard Model Higgs boson and Dirac mass neutrions are ruled out and the remaining neutrino related constants of the Standard Model are established more precisely, which could happen before my kids are old enough to take the early graduate school level classes where physis like this is taught, the possibility of a new physics "desert" all of the way up to the Grand Unification scale (which will probably never be tested in man made experiments) starts to look very plausible.

The one point of experimental evidence which has overconstrained theory, ruling out every possible explanation in one way or another, is the phenomena attributed to dark matter.  In the range of particle properties that could be consistent with what astronomers observe, high energy physicists have pretty much ruled out ever possible candidate particle (with the possible exception of sterile neutrinos).  But, modifications to the laws of gravity in weak fields, which can predict many of the same phenomena, also seem to be contradicted or rendered incomplete by seem key astronomy observations like the Bullet Cluster collision.

There is also progress being made in ironing out some of the quirks in the Standard Model.  Folks like Italian physicist Macro Frasca and Russian physicists I.M. Suslov are making inroads into fixing some of the technical anomolies key sets of equations like the Landau pole of Quantum Electrodynamics and non-trivial fixed points in pure Yang-Mills theory (which is essentially strong force physics before quarks are introduced into the mix). 

For work day to day at high energy physics experiments figuring out Standard Model backgrounds this doesn't matter too much, since the quirks manifest in the extreme high and low energy regimes of strong force physics that can't be directly observed due to lack of experiment scale and confinement respectively, and in QED has extremely short distances and extremely high energies.  But, these developments are critical in theoretical tasks like unifying the Standard Model forces into some kind of grand unified theory or even, if one includes quantum gravity as well, as so called "Theory of Everything."  They also give us greater confidence that existing equations are accurate up to arbitrarily high energy scales and allow us to revisit conjectures made with incorrect assumptions about the Higgs boson and the beta functions that govern the running of the respective coupling constants.

ATLAS Higgs Date Update

Today, the ATLAS experiment has updated its July 4, 2012 Higgs boson discovery result paper to reflect additional data, this time through 8 TeV of data in this detection channels, (1) ZZ to 4 charged lepton, (2) diphoton, and (3) WW to two charged leptons and two neutrinos.

More data confirms that they have discovered a new particle.

The combined result yields a 5.9 sigma significance level for the hypothesis that there is a Standard Model Higgs boson relative to the Standard Model without a Higgs boson null hypothesis (reduced to as little as 5.1 sigma with look elsewhere effects, which still unambiguously meets a scientific discovery threshold in physics). This is roughly a one sigma improvement over the five sigma significance standard for particle discovery it reported on July 4 and is really unsurprising and no big deal by itself.

The new particle is consistent with a Standard Model Higgs boson

Now that everyone knows that there is a Higgs boson (and really, most of us have been convinced since the "inconclusive" LHC results announced in November 2011 on that point), the big question remaining is whether what we have seen is really the Higgs boson predicted by the Standard Model or if its properties show beyond the Standard Model behavior. Refinements in its estimated mass are also interesting.

On that score, the important numbers are the deviations from the Standard Model with the right mass Higgs boson expectation. These numbers should average about 1 sigma in any given channel, and shouldn't be far in excess of two sigma, if the Standard Model is correct (results that are consistently too perfect across the board suggest data falsification to favor the theory advanced).

In the ZZ to 4 lepton channel, the fit to the SM with SM Higgs prediction is 1.4 +/- 0.6 sigma. In the diphoton channel the fit is 1.8 +/- 0.5 sigma and the mix of subtypes of collisions in which diphoton events are observed to the predicted value is also within 1.5 sigma of the Standard Model with Standard Model Higgs boson expection. In the WW to lvlv channel the fit is 1.4 +/- 0.3 sigma. Overall, the combined channels at a 1.4 +/- 0.3 sigma fit to the Standard Model (although the combined result is somewhat less meaningful in this kind of hypothesis testing than the individual channel results). Thus, overall, the experimental results in all three channels are very consistent with a Standard Model Higgs with no beyond the Standard Model physics and there are good statistical reasons to expect a bit of an excess over the expected number of non-Standard Model events right at the moment of discovery in highly diagnostic of a Higgs boson decay channels.

The best fit ATLAS has for the Higgs boson mass is 126.0 GeV +/- 0.4 GeV statistical, +/- 0.4 GeV systemic, which is based mostly on the four lepton and diphoton channels that have the highest mass resolutions. The qualitative results of the excess events arae also consistent with a neutral electrical charge, spin zero or spin two boson (the Standard Model Higgs boson has a neutral electrical charge and spin zero and no one seriously expects a spin two boson, of which the graviton is the only really strongly proposed example).

In conclusion, the new paper states:

The decays to pairs of vector bosons whose net electric charge is zero identify the new particle as a neutral boson. The observation in the diphoton channel disfavours the spin-1 hypothesis. Although these results are compatible with the hypothesis that the new particle is the Standard Model Higgs boson, more data are needed to assess its nature in detail.

These conclusions were not a sure thing on July 4. The initial excess in the diphoton channel was so great that it suggested that there might be beyond the Standard Model physics enhancing the signal in that channel, while the tau-tau channel was much weaker than the Standard Model with Standard Model Higgs boson expectation. The fact that additional data has not unduly exaggerated the diphoton or WW channel deviations from the Standard Model (and that the reanalyzed Tevatron data on the bb channel are also perfectly consistent with a 126 GeV Standard Model Higgs boson).

The new report does not address the deficit in the tau-tau channel which exactly matched the Standard Model with Standard Model Higgs expectation through December 2011, but was far below the expected level in the first half of 2012. But, the margin of error in that channel is quite high. Overall, the update from ATLAS is good news for the likelihood that the newly discovered particle is precisely a Standard Model Higgs boson with a mass of 126 GeV +/- 0.8 GeV, and bad news for proponents of beyond the Standard Model theories. Measured channels making up about 83% of the possible Higgs boson decays are within two sigma of the expected values, a channel representing about 1.2% of expected decays is perhaps lower by barely more than two sigma, and the remaining decay channels haven't been measured. This doesn't leave much room for the predicted branching ratios of a Standard Model Higgs boson to be wrong.

UPDATE (8/2/12):

The CMS paper (the other LHC experiment) reports a Higgs mass of 125.3 Gev  +/- 0.4 GeV statistical, +/- 0.5 GeV systematic and reports results for searches performed in five decay modes: diphoton, ZZ, WW, tau-tau, and bb. CMS reports an overall consistency of the results with the SM with a SM Higgs boson of 0.87 sigma +/- 0.23 sigma and a 5.0 sigma finding relative to the null hypothesis of the Standard Model without a Higgs boson considering look elsewhere effects.

Its results in the ZZ, WW, and bb channels are very close to the SM with a SM Higgs boson expectation.  The tau-tau result is about 1 sigma below the SM expectation.  The diphoton result is not quite two sigma above the Standard Model expectation.  Overall, this too is perfectly consistent with a Standard Model with Standard Model Higgs boson with no beyond the Standard Model physics. The average of the ATLAS and CMS predictions for the Higgs boson mass is 125.65 GeV and a mass range of 125.2-126.2 GeV is within one sigma of the predictions of both experiments (that is not the proper way to determine the standard deviation from the mean of the two results, but in this case hte actual combined margin of error assuming equal weighting of the results is pretty close to +/- 0.6 GeV, so it heavily overlaps with the combined one sigma bands, but is a bit wider). 


There really is very little room for this to be anything but a plain vanilla Standard Model Higgs boson, the result which is far better theoretically motivated than any other possibility.


The Expected Decay Width and Mean Lifetime of A Standard Model Higgs


 The expected decay width of a Standard Model Higgs boson (the reduced Planck's constant divided by decay width equal to mean particle lifetime, which is proportional to a particle's half-life) at the mass indicated by the LHC results is definitely less than 10 MeV and really closer to 1 MeV (compared to 1.4-2.7 GeV for a top quark which corresponds to a half-life of 5*10^-25 seconds see also 2011 estimates for top quark widths found here. ), and for the weak force bosons 2.495 GeV for the Z and 2.141 GeV for the W, implying lifetimes on the order of 3*10*-25 seconds. Thus, the lifetime of a Higgs boson should be on the order of at least 7*10^-23 seconds and probably closer to 7*10^-22 seconds. The mean life for a tau lepton is about 2.9*10^-13 seconds. The lifetime of most, but not all, composite two quark particles (mesons) and three quark particles (baryons) for which a mean lifetime duration is known is longer or about the same than the expected mean lifetime of a Standard Model Higgs boson. But, measurements so far at LHC may be hard pressed to bound the total decay width of the Higgs boson to being much less than something on the order of 100 MeV due to the limited precision of the LHC experiment in making this measurement, although the thousands of clever people involved might be able to find some way to do a bit better than that.


Conjectures And The Higgs Vacuum Expectation Value


The Higgs mass suggested by the equation 2H=2W+Z implies a mass of 125.988 +/- 0.015 GeV at current Particle Data Group estimates for the W and Z masses is a value that is within about 0.5 sigma of the averaged mass measurement of ATLAS and CMS, and the LHC is probably incapable of ever ruling out this value.  Even a proposed International Linear Collider (which would probably be the next big thing in particle physics if any major new colliders of any kind are built) would be hard pressed to rule it out.

The Higgs vacuum expectation value is often quoted as approximately 246 GeV, but is apparently known with greater precision although I can't find the value anywhere.  This is a value suggestively close to 2H minus the sum of the masses of all quarks lighter than the top quark.  The Higgs vev (which does not count as mass-energy for general relativity purposes) is not to be confused with cosmic microwave background radiation at 2.725 Kelvin which also fills the vacuum, or with "dark energy" aka the cosmological constant of general relativity.

Anatomy of A Crackpot

Razib has posted a nicely done profile of "human origins in the Americas" blogger and self-published author German Dziebel.  I've come across his posts at a number of prehistory and population genetics blogs and concur with Razib's assessment.