The Precursors In America Failed To Thrive

There is pretty strong evidence (especially, well dated footprints from 22,000 to 30,000 years ago) of modern humans in North America, at least prior to and during the Last Glacial Maximum ca. 20,000 years ago, long before the Founding population of the Americas should have arrived around 15,000 years ago.

West Hunter considers conditions that would fit their "failure to thrive" in the New World, as evidenced by a complete lack of human remains, few and marginal possibly human made tools, and a lack of mass extinctions, in "virgin territory" without competition from other hominins. He notes:

The problem with the idea of an early, pre-Amerindian settlement of the Americas is that (by hypothesis, and some evidence) it succeeded, but (from known evidence) it just barely succeeded, at best. Think like an epidemiologist (they’re not all stupid) – once humans managed to get past the ice, they must have had a growth factor greater than 1.0 per generation – but it seems that it can’t have been a lot larger than that . . . .

A saturated hunter-gatherer population inhabiting millions of square miles leaves a fair number of artifacts and skeletons per millennium – but we haven’t found much. We have, so far, found no skeletons that old. I don’t think we have a lot of totally convincing artifacts, although I’m no expert at distinguishing artifacts from geofacts. (But these were modern humans – how crude do we expect their artifacts to be?)

For-sure footprints we’ve got, and intriguing genetic data.

A priori, I would expect hunter-gatherers entering uninhabited America to have done pretty well, and have high population growth rates, especially after they become more familiar with the local ecology. There is good reason to think that early Amerindians did: Bayesian skyline analysis of their mtDNA indicates fast population growth. They were expert hunters before they ever arrived, and once they got rolling, they seem to have wiped out the megafauna quite rapidly.

But the Precursors do not seem to have become numerous, and did not cause a wave of extinctions (as far as I know. check giant turtles.).

I've underlined some thoughts that I don't agree with fully. It looks like the Younger Dryas was a much bigger factor in mass extinctions relative to the overkill hypothesis than we previously expected. 

And then there is the genetic evidence. Unlike Cochran, I am quite convinced that it is basically mathematically impossible for this pre-Founding population to have been the source of "Paleo-asian" autosomal DNA in South America, which is much more likely to have arrived ca. 1200 CE via Oceanians (although other possibilities in that time frame could work as well). The frequency of the Paleo-Asian component is just too variable. And, any population that stayed isolated population genetically for more than 14,000 years to finally burst out into South America would be incredibly genetically distinctive (much like the Kalash people who are incredibly genetically distinctive after their small population was isolated for much less long a time period than that).

Statistical artifacts of the methods used and/or selective pressure against some Oceanian distinctive genes that make the remaining component look Onge rather than Papuan-like, could explain the closer f-test statistical matches to these populations. A relict non-Oceanian Paleo-asian population from Northeast Asia arriving in that time frame could work also but seems less plausible. Loss of distinctive Oceanian autosomal DNA during periods of stable population with low effective population size or during periods of shrinking populations during times of adverse conditions could also purge so statistically important genetic identifiers in what is already a small share of the total genome in the people who have it.

Further, some of the more convincing earlier pre-14,000 year ago finds of arguable stone tool making and fire use in the Americas were in North America (including Mesoamerica) or northeastern South America, not in the greater Amazon jungle basin where Paleo-asian ancestry has been found. 

But the points he makes about a "Precursor" (I like Cochran's choice of words here) population's lack of success are still valid. There shouldn't have been Malthusian limits to their population in the New World that allowed them to sustain their population, but population growth would have had to be exceedingly slight in the long run to be consistent with the available evidence. He considers some possibilities and I underline the ones that I think are too implausible to take seriously:

What might have limited their biological success?

Maybe they didn’t have atlatls. The Amerindians certainly did.

Maybe they arrived as fishermen and didn’t have many hunting skills. Those could have been developed, but not instantaneously. An analogy: early Amerindians visited some West Coast islands and must have had boats. But after they crossed the continent and reached the Gulf of Mexico, they had lost that technology and took several thousand years to re-develop it and settle the Caribbean. Along this line, coastal fishing settlements back near the Glacial Maximum would all be under water today.

Maybe they fought among themselves to an unusual degree. I don’t really believe in this, am just throwing out notions.

Maybe their technology and skills set only worked in a limited set of situations, so that they could only successfully colonize certain niches. Neanderthals, for example, don’t seem to have flourished in plains, but instead in hilly country. On the other hand, we don’t tend to think of modern human having such limitations.

One can imagine some kind of infectious disease that made large areas uninhabitable. With the low human population density, most likely a zoonosis, perhaps carried by some component of the megafauna – which would also explain why it disappeared.

What do I think?

In a nutshell, the Precursor population was probably just slightly below the tipping point that they needed to thrive, in terms of population size, knowledge, and the resources they brought with them, but just large enough to establish a community that was marginally sustainable in the long run with inbreeding depression and degraded technology.

I think the that Precursors were probably derived from one or more small expeditions from a population close to the ultimate Founding population of the Americas rooted in Northeast Asia that survived where many who left no trace at all died, as something of a fluke. 

A Kon-Tiki style transpacific route,  or trans-Atlantic Solutrean hypothesis route would be anachronistic technologically at 22,000 years ago or more and is disfavored by other evidence, including genetic evidence, as well. Claims of hominins in the Americas 130,000 years ago, are likewise not credible.

The Precursors probably had no dogs or other domesticated animals on their boat(s). But dogs were, in my opinion, probably a major fitness enhancing technology for the post-Papuan/Australian aborigine wave of modern humans in mainland Asia (the Papuan/Australian wave didn't have dogs), and for the Founding population of the Americas.

They probably had  a small founding population that suffered technological degradation similar to what Tasmania experienced when it separated from Australia for 8,000 years, including the loss of maritime travel technology needed to reunite with kin left behind in Asia or Beringia. See Joseph Henrich, "Demography and Cultural Evolution", 69(2) American Antiquity 197-214 (April 2004) but see Krist Vaesen, "Population size does not explain past changes in technological complexity" PNAS (April 4, 2016) (disputing this conclusion, unconvincingly IMHO).

For example, as Cochran notes, they may have known how to fish and hunt from boats, but not how to make boats, or how to hunt terrestrially, at first. 

The effective population size of the Founding population of the Americas was ca. 200-300 people; Henrich's hypothesis sees major degradations in technology as the population size falls significantly below 100, which would have been a typical size for a one-off exploratory expedition that was stranded and unable to return.  Once technology is lost, it can be recovered or rebuilt over time, but it takes much longer to innovate than to preserve culture transmitted from previous generations or to imitate neighboring civilizations. 

The loss of technology may not simply have been a matter of raw numbers either. Vaesen's counter-examples are very small, stable, complete hunter-gather communities. But an exploratory expedition may have consisted of bold young people not fully trained in reproducing their culture's technologies, even if they had enough raw numbers of people to do so, rather than the tribe or band's skill craftspeople.

They probably suffered inbreeding depression greater than the main founding population of the Americas due to a smaller founding population size. A scientific report in Nature (March 5, 2019) notes that:

Franklin has proposed the famous 50/500 rule for minimum effective population size, which has become the threshold to prevent inbreeding depression. This rule specifies that the genetic effective population size (N(e)) should not be less than 50 in a short term and 500 in a long term.

The possibility that the Precursors derived from one or more expeditions with an effective population size less than 50 in the short term, regardless of its long term size, seems plausible. Even if there were several dozen men on the expedition, it is very plausible that there could have been fewer than twenty-five reproductive age women on the expedition at the outset needed to avoid short run inbreeding depression, and many of them were probably cousin and/or siblings. 

These inbreeding depression effects could have lasted many, many generations without input from an outside population source, leaving a much less smart, much less fit group in the next few generations than in their first generation.

They probably faced challenges to thriving at hunting and gathering due to the ice age that caused the Last Glacial Maximum that their degraded technology didn't help them to overcome. They may have landed in North American fairly near to the glacial area that was particularly impaired.

They probably did go extinct in all, or almost all, of their range, after not too many generations. They may not have reached South America until after the Last Glacial Maximum at all, and if they did, may not have penetrated very far into it, sticking to the Gulf Coast.

To the extent that they didn't go extinct, they probably lost many of their uniparental genetic markers during sustained periods of stable low populations or population busts, as opposed to the preservation of the markers usually found in expanding populations. 

They also probably weren't all that genetically distinct from the Founding population of the Americas from which they were only separated for a few thousand years. A small effective population takes many generations to generate distinct mutations and both the Founding population of the Americas and the Precursors would have had small effective populations for most of the Last Glacial Maximum ice age.

The Founding population, due to a larger founding population, better technology retention, less inbreeding, dogs, and better climate conditions, expanded rapidly.  When the much more advanced Founding population arrived, the remnants of the Precursors that remained, if any, would have been diluted almost invisibly into the very genetically similar Founding population and may have died out from competition, or at least, shed any of its distinctive uniparental markers, with it as well.

Footnote

"Failure to thrive" is a phrase most commonly used in medicine to describe phenomena without a specific and well-determined cause of a child's lack of development at the pace of normal children in health environments. Usually, it is attributed to poor nutrition either in quality or quantity.

How Did One Language Family Come To Dominate Australia Prior To European Contact?

It remains a mystery how Pama–Nyungan, the world’s largest hunter-gatherer language family, came to dominate the Australian continent. Some argue that social or technological advantages allowed rapid language replacement from the Gulf Plains region during the mid-Holocene. Others have proposed expansions from refugia linked to climatic changes after the last ice age or, more controversially, during the initial colonization of Australia. Here, we combine basic vocabulary data from 306 Pama–Nyungan languages with Bayesian phylogeographic methods to explicitly model the expansion of the family across Australia and test between these origin scenarios. We find strong and robust support for a Pama–Nyungan origin in the Gulf Plains region during the mid-Holocene, implying rapid replacement of non-Pama–Nyungan languages. Concomitant changes in the archaeological record, together with a lack of strong genetic evidence for Holocene population expansion, suggests that Pama–Nyungan languages were carried as part of an expanding package of cultural innovations that probably facilitated the absorption and assimilation of existing hunter-gatherer groups.

Remco R. Bouckaert, Claire Bowern & Quentin D. Atkinson "The origin and expansion of Pama–Nyungan languages across Australia" Nature Ecology & Evolution (March 12, 2018).

Skepticism is in order because New Zealander Quentin D. Atkinson has a history of relying on math that fails to honor existing linguistic knowledge resulting in clearly wrong predictions. But, his hypothesis here is, at least, strongly conventional wisdom confirming.

My strong suspicion is that the key cultural innovation was the integration of the Dingo into Australian society after ca. 50,000-60,000 previous years without dogs. The epicenter of this expansion coincides perfectly with the expected location of an introduction of the Dingo into Australia, and the Dingo is also known to have resulted in a second wave of mass extinctions of local fauna in Australia.

The Demographic History Of Southeast Asia

Analysis of uniparental DNA clades and linguistic evidence in modern Southeast Asian populations and archaeology had supported this conclusion a decade ago. The migrationist paradigm continues to rule. Now, ancient DNA confirms it. 

Two distinct population models have been put forward to explain present-day human diversity in Southeast Asia. The first model proposes long-term continuity (Regional Continuity model) while the other suggests two waves of dispersal (Two Layer model). 

Here, we use whole-genome capture in combination with shotgun sequencing to generate 25 ancient human genome sequences from mainland and island Southeast Asia, and directly test the two competing hypotheses. 

We find that early genomes from Hoabinhian hunter-gatherer contexts in Laos and Malaysia have genetic affinities with the Onge hunter-gatherers from the Andaman Islands, while Southeast Asian Neolithic farmers have a distinct East Asian genomic ancestry related to present-day Austroasiatic-speaking populations. 

We also identify two further migratory events, consistent with the expansion of speakers of Austronesian languages into Island Southeast Asia ca. 4 kya, and the expansion by East Asians into northern Vietnam ca. 2 kya. These findings support the Two Layer model for the early peopling of Southeast Asia and highlight the complexities of dispersal patterns from East Asia.

Hugh McColl, et al., "Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia" BioRxiv (March 8, 2018).

Some first blush thoughts.

Two(+2) early waves or three (+2)?

Was there are distinct pre-Hoabinhian wave of pre-Papuan/Australian folk whom Onge-like hunter-gatherers (largely) replaced? If there was a replacement, what gave the newcomers an edge and when did that replacement happen?

The first paragraph of the paper impliedly raises this question but it doesn't seem to get resolved. It says:

The population history of Southeast Asia (SEA) has been shaped by interchanging periods of isolation and connectivity. Anatomically modern humans first colonized SEA at least 70,000 years ago. Within SEA, the complex topography and changes in sea level promoted regional expansions and contractions of populations. By the late Pleistocene/early Holocene, a pan-regional lithic technological culture was established across mainland SEA, named Hoabinhian. Hoabinhian foragers are thought to be the ancestors of present-day SEA hunter-gatherers, sometimes referred to as ‘Negritos’ because of their comparatively darker skin colour and short stature. Today, however, the majority of people in SEA are believed to be descendants of rice and millet farmers with varying degrees of East Asian phenotypic affinity, suggesting that human diversity in SEA was strongly influenced by population expansions from the north. Yet, the extent to which the movements from East Asia (EA) impacted on the genetic and cultural makeup of the people of SEA remains controversial.

The early Holocene is 10,000 years ago, leaving a 60,000 year gap between the first settlers and the Hoabinhian culture. There are limits to what the ancient DNA can do to resolve this because the ancient DNA samples in the study are not too old (the oldest is no more than 8,000 years old at more than two sigma). But, on closer examination, it appears that this question was examined but not resolved.

Unlike all other ancient samples, the two Hoabinhian samples (which also happen to be the oldest samples in our study) - Pha Faen, Laos (La368 - 14 140 C 7,888 ± 40) and Gua Cha, Malaysia (Ma911 - 14 C 4,319 ± 64) - designated as Group 1, cluster distantly from most East and Southeast Asians in the PCA and position closely to present-day Onge (Figure 1A). Group 1 individuals also contain a mixture of several different ancestral components in the fastNGSadmix plot, including components shared with Onge, the Pahari and Spiti from India, Papuans and Jehai (a Malaysian ‘Negrito’ group), which are markedly different from the other SEA ancient samples. This possibly results from our modeling of ancient populations as a mixture of components inferred in present-day populations, via fastNGSadmix, and from the fact the ancient samples are likely poorly represented by a single present-day group. 

The rest of the ancient samples are defined primarily by East and Southeast Asian components that are maximised in present-day Austroasiatic (Mlabri and Htin), Austronesian (Ami) and Hmong (indigenous to the mountainous regions of China, Vietnam, Laos and Thailand) populations, along with a broad East Asian component. . . . 

We used D-statistics of the form D(Papuan,Tianyuan,X,Mbuti), where X is a test population, to explore the relatedness of ancient and present-day Southeast Asians to two highly differentiated groups: Papuans and an ancient northern East Asian individual (Tianyuan - a 40 kya-old sample from Northeastern China). The values of this D-statistic are consistent with present-day and ancient SEA mainland samples being more closely related to Tianyuan than to Papuans. This applies to present-day northern EA populations, and - more weakly - to most populations of ancient and present-day SEA. However, this D-statistic is not significantly different from 0 in present-day Jehai, Onge, Jarawa and Group 1 - the ancient Hoabinhians. While the Onge’s relationship with Papuans and Tianyuan is unclear, D-statistics of the form D(Onge,Tianyuan,X,Mbuti), where X is a test population, show that Jarawa, Jehai and the ancient Group 1 share more ancestry with Onge than with Tianyuan. Like the Onge, both Group 1 samples carry mtDNA haplogroups from the M lineage, thought to represent the coastal migration to Australasia. 

To assess the diversity among the remaining ancient individuals, we computed a new PCA including only EA and SEA populations that did not have considerable Papuan or Ongelike  ancestry. . . . 

Group 2 samples from Vietnam, Laos, and the Malay Peninsula are the oldest samples after Group 1, and range in age from 4.2 to 2.2 kya. 

At K=6, Group 2 individuals, the present-day Mlabri and a single Htin individual are the only MSEA samples in the fastNGSadmix analysis to lack the broad EA component (dark green) maximised in northern EA , with the exception of the Malaysian ‘Negritos’ and ‘Proto-Malays’ (Temuan). 

At K=7, a bright green component is maximised in these populations, and this component is also found in present-day Indonesian samples west of Wallace’s Line. The two ancient Indonesian samples (Group 5; 2.2 to 1.9 kya) represent a mix of Austronesian- and Austroasiatic-like ancestry, similar to present-day western Indonesians. Indeed, after Mlabri and Htin, the closest populations to Group 2 based on outgroup-f3 statistics are the western Indonesian samples (from Bali and Java) reported to have the highest amounts of ancestry from mainland SEA. 

These lines of evidence suggest Group 2 are possible descendants of an “Austroasiatic” migration that expanded southward across MSEA and into island SEA (ISEA) by 4 kya. We also observe a gradient in “Austronesian-like” vs. “Austroasiatic-like” ancestry in the PCA: while PC1 separates populations found in SEA and those found in northern EA, PC2 distinguishes population based on their amounts of Austronesian-like ancestry (pink component in Figure 1 - lower panel) versus Austroasiatic-like ancestry (bright green component in Figure 1 - lower panel).

The Supplemental Materials note that:

Relationship between Papuan, Tianyuan and EA/SEA/Ancients

We find support for Australians and Bougainville islanders forming a clade with Papuans, to the exclusion of Tianyuan (Table S14). In turn, many EA and SEA form a clade with Tianyuan, to the exclusion of Papuan (Table S13). Onge, Jarawa and Jehai do not form a clade with either Papuans or Tianyuan (Table S13, S14), but have a stronger affinity to Papuans than to Tianyuan (Z = 3 - 4.2, for D(Onge/Jarawa/Jehai, Tianyuan; Papuan, Mbuti)).

Relationship between Onge, Tianyuan and SEA

We find Onge, Jarawa and Jehai form a clade with Onge to the exclusion of Tianyuan, but no other EA or SEA population form a clade with Onge, to the exclusion of Tianyuan (Table S17).

Relationship to Surui and Mixe

We tested for a specific affinity in the Surui to our ancient samples, as was previously detected in Papuans, Onge and Tianyuan. For the 2240k panel, we find that D-statistics of the form D(Mixe, Surui, Group 1 individual, Mbuti) are high but non-significant (Z = -2.18 and -2.5, using Ma911 and La368, as the Group 1 representative, respectively) (Table S19).

Relevant data is also contained in a paper looking at the genetics of modern Indonesia.

What cultural and technological and ecological impact did each of these waves have? Were there climate or other events that drove these transitions?

One plausible possibility in my mind is that the Tianyuan individual, the Onge, Mainland Southeast Asian Negritos, and pre-admixture Ancestral South Asians are all part of a wave of Asian migration after an initial pre-Papuan wave ca. 70,000 years ago, but at least somewhat before the Tianyuan individual ca. 40,000 years ago. In that scenario, these second wave hunter-gatherers may have been able to conquer pre-Papuan first wave hunter-gatherers by virtue of the fact that they had domesticated dogs at their disposal, while the pre-Papuans did not (or if they did, didn't bring them with them on their maritime colonization journey). Certainly, we know that the founding population of the Americas which would have arrived in Beringia more than 20,000 years ago had dogs (a conclusion that tends to trump estimates for dog domestication at just 15,000 years ago or less). I previously explored this hypothesis at greater length here as a way to help explain the dilution of Denisovan ancestry in mainland Southeast Asia and parts of Island Southeast Asia that were previously part of Sundaland.

This time frame is a fairly good fit the genetically and archaeologically estimated time frame in which dog were domesticated: One scholar has argued at book length that dog domestication was a key factor in the Upper Paleolithic revolution and also in giving modern humans an edge over the Neanderthals in Europe. See also here. There have even been some studies that located the domestication of the dog event (if there was just one primary one) in Southeast Asia, although there is not a consensus on that point.

It also isn't too far afield from estimates of wave of Asian migration in the Upper Paleolithic based upon analysis of the phylogeny of uniparental markers in modern populations in light of known mutation rates.

Archaic hominins in Southeast Asia

We know that archaic Homo erectus was present in Southeast Asia before any modern humans. We know that Homo floresiensis was present in Southeast Asia before any modern humans. We are quite confident that Homo floresiensis were not Denisovans because their physical anthropology is too archaic even relative to Homo erectus.

In the modest straightforward scenario by which Papuan/Australian folk receive Denisovan admixture, there were Denisovans in Southeast Asia before any modern humans.

We don't know with any great confidence which archaic hominins were present to have first contact with modern humans, although Denisovans must have been among them.

The paper has this to say about Denisovan admixture:

We find that the genetic diversity found in present day SEA populations derives from at least four prehistoric population movements by the Hoabinhians, an “Austroasiatic-like” population, the Austronesians and, finally, additional EA populations into MSEA. We further show that the ancient mainland Hoabinhians (Group 1) shared ancestry with present-day Onge of the Andaman Islands and the Jehai of peninsular Malaysia. These results, together with the absence of significant Denisovan ancestry in these populations, suggest that the Denisovan admixture observed in Papuans occurred after their ancestors split from the ancestors of the Onge, Jehai and the ancient Hoabinhians. This is also consistent with the presence of substantial Denisovan admixture in the Mamanwa from the Philippines, which are best modeled as resulting from an admixture between Austronesians and Papuans, not Onge.

I think a model in which Papuans comes first, and entirely separate wave of modern humans akin to the Onge arrive next is a better description of the most plausible inference, even though they may be technically equivalent.

Why don't researchers integrate more kinds of evidence?

I remain puzzled by the reluctance of investigators to more heavily integrate distinct evidence from the modern mix of human uniparental markers, modern autosomal DNA in humans, ancient and modern plant genetics, ancient DNA, linguistics, and archaeology into a single comprehensive analysis which would be so much more powerful. It isn't as if these are lone wolf investigators who can't play well with others. These papers are done by large teams with lots of well informed feet on the ground. Some of this may flow from the incentives to publish in the smallest publishable unit and to have relatively short papers in science relative to the humanities or law. But, one can get much more powerful conclusions by integrating all of the available evidence.

The paper does outline that "Two layer model" that its data eventually confirms:

[T]he Two Layer model advocates for two major dispersal waves into SEA, where EA farmers replaced the original Hoabinhian inhabitants across SEA through a major demographic southward expansion ca. 4 kya. The exception to this would be the isolated populations of the Andaman Islands, peninsular Thailand/Malaysia and the Philippines which are considered the primary descendants of Hoabinhian hunter-gatherers. Under this model, the migratory wave of farmers originated in present-day China, where rice and millet were fully domesticated in the Yangtze and Yellow River valleys between 9-5.5 kya, and paddy fields developed by 4.5 kya. Farming practices are thought to have accompanied these populations as they spread southward through two main routes – an inland wave associated with the expansion of Austroasiatic languages, and an island-hopping route associated with Austronesian languages which eventually reached the Pacific. Within mainland SEA (MSEA), exchanges with EA appear to have continued in the recent past, however, the extent to which these expansions had a genetic impact on the indigenous populations is unknown.

Some of this gap is filled in with efforts like Razib's excellent post on the topic which contextualizes this paper's findings in a larger cultural context and also ties it in to relevant aspects of South Asian pre-history like the origins of the Munda people of India. With respect to the two waves of migration after the "first farmers" ca. 4 kya, he explains:

The authors also detect migrations into Southeast Asia besides that of the Austro-Asiatics and Austronesians. One element seems correlated with the Tai migrations, and another with Sino-Tibetan peoples, most clearly represented in Southeast Asia by the Burmans. The excellent book, Strange Parallels: Volume 1, Integration on the Mainland: Southeast Asia in Global Context, c.800–1830, recounts the importance of the great migrations of the Tai people into Southeast Asia ~1000 A.D. Modern-day Thailand was once a flourishing center of Mon civilization, an Austro-Asiatic people related to the Khmers of Cambodia. The migrations out of the Tai highlands of southern China reshaped the ethnography of the central regions of mainland Southeast Asia. The Tai also attempted to take over the kingdoms of the Burmans. Though they failed in this, the Shan states of the highlands are the remnants of these attempts (tendrils of the Tai migrations made it to India, the Ahom people of Assam were Tai). Vietnam, shielded by the Annamese Cordillera, came through this period relatively intact. It is also well known that Cambodia’s persistence down to the present has much to do with the shielding it received from France in the 19th century in the wake of Thai expansion.

What Does This Mean For South Asian Pre-History?

With respect to the Munda of India, Razib notes that:

They detect shared drift between Austro-Asiatic people and tribal populations in northeast India. This is not surprising. A 2011 paper found that Munda speaking peoples, whose variant of Austro-Asiatic is very different from that of Southeast Asia, are predominant carriers of Y chromosome O2a. This is very rare in Indo-European speaking populations, and nearly absent in Dravidian speaking groups. Additionally, their genome-wide patterns indicate some East Asian admixture, albeit a minority, while they carry the derived variant of EDAR, which peaks in Northeast Asia. 

One debate in relation to the Munda people is whether they are primal and indigenous, or whether they are intrusive. The genetic data strongly point to the likelihood that they are intrusive. An earlier estimate of coalescence for O2a in South Asia suggested a deep history, but these dates have always been sensitive to assumptions, and more recent analysis of O2a diversity suggests that the locus is mainland Southeast Asia. 

Now that archaeology and ancient DNA confirm Austro-Asiatic intrusion into northern Vietnam ~4,000 years ago, I think it also sheds light on when these peoples arrived in India. That is, they arrived < 4,000 years ago. As widespread intensive agriculture came to Burma ~3,500 years ago, I think that makes it likely that Munda peoples arrived in South Asia around this period. 

I now believe it is likely that the presence of Austro-Asiatic, Dravidian, and Indo-Aryan languages in India proper was a feature of the period after ~4,000 years ago. None of the languages of the hunter-gatherer populations of the subcontinent remain, with the possible exception of isolates such as Nihali and Kusunda.

The recent origins of Austro-Asiatic, Indo-Aryan and Tibeto-Burmese languages in India are all established beyond what I would consider to be reasonable doubt through multiple lines of evidence.

The case of Dravidian, which is correlated, especially in lower caste populations, with Ancestral South Indian genetics that autochthonous to India and for whom the closest modern population is the Onge population of the Andaman Islands, is trickier, and one I've explored before. 

At a minimum, the close linguistic relations between the Dravidian languages suggest that this language family underwent a linguistic bottleneck, possibly sometime after the arrival of the Indo-Aryan invasion of India, from which all modern Dravidian languages derive, even if the pre-agricultural people of India spoke languages that were part of a family that includes proto-Dravidian.

It is also very plausible that the rise of the Dravidian languages, whether or not my bottleneck conjecture for the Dravidian languages is correct, is associated with the South Indian Neolithic revolution ca. 4500 years ago (i.e. around 2500 BCE), only a thousand years or less before the Indo-Aryan invasion. There is ample precedent of language replacement in favor of a dominant farmer language in association with the expansion of a newly food producing culture. 

This would be a few centuries older than Razib's casual estimate, but still reflects the same basic theme that the pre-agricultural hunter-gatherer languages of India are probably now entirely lost or are represented by only a couple of nearly moribund language isolates while untold scores or hundreds of other hunter-gatherer languages of pre-agricultural India (since hunter-gatherer civilizations appear to have had more linguistic diversity than early farmer civilizations in the fertile areas that first adopted farming) have been forever lost.

It is far less obvious, however, whether Dravidian's ultimate source (possibly a source prior to a bottleneck that impairs the usual linguistic methods of dating it) was home grown, becoming dominant while stamping out its neighbors, or if Dravidian has its source in the same population that brought the crops that made the South Indian Neolithic revolution possible as none of the core crops in that food production package are native to India. Some of those crops have origins in the Fertile Crescent and others arose in the wild and were domesticated in the African Sahel.

I've also explored potential genetic markers of an outside source for Dravidian, with Y-DNA T looking like a particularly promising marker in light of its geographical distribution within India, the fact that it is almost certainly invasive to India, and the fact that it was present in a place that would have been on the path of African Sahel crops to India, but I don't have data good enough to confirm or rule out those hypotheses definitively. Without more detailed sub-haplogroups of Dravidian Y-DNA T bearers, it is hard to date their antiquity, their diversity, and the place from which they made an invasive appearance in India. If it is a distinctly Indian and very basal clade of Y-DNA T, my hypothesis that it arrived with African Sahel crops is probably wrong. If it shows affinities in particular to clades of Y-DNA found in Yemen and Somalia and Ethiopia, and shows a star-like pattern of sub-haplotypes specific to India around 2500 BCE (per this paper by Dorian Fuller), it would strongly confirm my hypothesis.

The much anticipated ancient Harappan DNA evidence that should appear in published work any day now won't be much help because, as I have recent argued at length elsewhere, the Harappan language was unlikely to be a Dravidian language and while it may have shared some areal linguistic features with Dravidian, may not have even been in the same language family.

Did Bell Beaker People Introduce Modern European Dogs?

Dogs similar to modern European dog breeds start to appear in Europe in about the same time and places as the Bell Beaker people and in at least one instance, accompanying a Bell Beaker man in his burial.

All About Animals

* The ability of a horse to have a gait called an "amble" which is a very useful thing if you ride horses, is tied to a single gene (based on this paper). A subsequent paper with overlapping authors, looked into the origins of this mutation.

The researchers analyzed DNA from 90 ancient horses dating to over 5,000 years ago, and found the first instance of the mutation occurred in two horses from the York Archaeological Collection, dated to between 850 and 900 A.D. 

The horses originated in medieval England, they say, and were likely taken to Iceland by the Vikings, where they were interbred to produce a population of the gaited variety. From there, these superior comfortable horses spread across Europe, resulting in the wide distribution and diversity of gaits evident today. . . Today, horse breeds ranging from the North American Saddlebred to the Indian Kathiawari possess the ability to amble.

* More progress is being made in understanding the linguistic nature of communications between dolphins.  The article doesn't acknowledge, however, that previous attempts to decode dolphin communication have concluded that an exceptionally large share of the dolphin vocabulary compared to human spoken languages, consists of proper names. A paper discussing a dolphin's complex brain structure is here.

* There is such a thing as a "patchwork virus" in animals as well as plants and fungi.  

Scientists found a virus that is made out of 4 to 5 separate components - it infects mosquitos, and they have to catch at least four of those components to get infected, the smallest, fifth component is optional. For plants and fungi, similar viruses were known before, but (at least according to the study) this is the first example in animals studied in detail. 

Original publication

News report

The one discovered doesn't affect humans, but a similar virus seems to be present in Ugandan monkeys. More generally patchwork type rearrangements of chunks of genetic material that are already part of the human genome, are important in human genetics and evolution.

* The first genome of the ocean sunfish has been sequenced in the following paper:

Hailin Pan et. al. "The genome of the largest bony fish, ocean sunfish (Mola mola), provides insights into its fast growth rate." GigaScience 5:36 (9 Sept 2016).

It is the world's largest bony fish and grows fast from a tiny size.

Wrinkled and colored a sickly shade of gray, the sunfish doesn't exactly shimmer. However, its pallor isn't nearly as distracting as its awkward shape -- the fish is usually taller than it is long. Moreover, the sunfish's mouth is constantly agape, granting it a dumbfounded look of everlasting surprise. With that gaping maw, the sunfish primarily consumes jellies, a less-than-sumptuous prey. Yet it is on this slimy diet that sunfish can attain weights of over 1,000 kilograms and lengths of nearly six feet. The largest sunfish weighed in at 2,300 kilograms and extended over ten feet in length! Not bad for a fish that, as a baby, begins life measuring just four millimeters across. . . . Researchers recorded a captive sunfish ballooning 880 pounds in fifteen months, an average of 1.8 pounds per day. That's far, far above other ray-finned fish, even ones that are similar in size to the sunfish.

* While dinosaurs were basically wiped out 66 million years ago (except for birds), mammals didn't have an easy time either.  About 93% of mammal species were wiped out at that time as well.  But, those that did make rapidly filled the many niches left vacant by extinct dinosaurs in a period of rapid speciation.

The biggest animals to survive on land would have been no larger than a cat. The fact that that most mammals were small helps explain why they were able to survive. 

Yet the researchers found that mammals also recovered more rapidly than previously thought, not only gaining back the lost diversity in species quickly but soon doubling the number of species found before the extinction. The recovery took just 300,000 years, a short time in evolutionary terms.

The paper is:

N.R. Longrich, J. Scriberas, M.A. Wills. "Severe extinction and rapid recovery of mammals across the Cretaceous-Paleogene boundary, and the effects of rarity on patterns of extinction and recovery." Journal of Evolutionary Biology, 2016.

A nice account of that event is found here.

* One of the placental mammals that survived that event was the solenodon, a venomous insectivore (who knew there were any venomous mammals?), which diverged from other mammals around 78 million years ago. It mitochondrial genome was the last to be sequenced of the major branches of placental mammals. It is now an endangered species. The paper is:

Adam L. Brandt, et al., "Mitogenomic sequences support a north–south subspecies subdivision withinSolenodon paradoxus." Mitochondrial DNA Part A (2016).

* Ancient Moose DNA thousands of years old was found and sequenced in Western Siberia where that clade went extinct in the last glacial maximum.

* Empirical evidence supports breed specific laws related to dogs.  Half of dog fatalities are due to pit bulls and a small number of other breed account for an outsized share of the rest. The source for the article is here.

* A highly contagious dog disease is spreading across the country and killing some of the dogs that get it, but not nearly enough for my liking.

* A new specimen of a newly discovered species of type of rodent that went extinct 18 million years ago, called a gundi or "comb-rat", was identified from remains found in Israel.

* The world's largest rabbit is 4'4" and "three and a half stones" (i.e. about 49 pounds) in weight, but may soon be surpassed by an even bigger son.

Did Dogs Originate In Mongolia Or Tibet?

Dog genetics are most diverse in Mongolia and Tibet and show a roughly clinal trend towards less diversity with distance away from that area, suggesting that the domesticated dog may have originated there. But, there are conflicting indications from different kinds of data.

Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups—a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we conducted a large-scale survey of autosomal, mitochondrial, and Y chromosome diversity in 4,676 purebred dogs from 161 breeds and 549 village dogs from 38 countries. Geographic structure shows both isolation and gene flow have shaped genetic diversity in village dog populations. Some populations (notably those in the Neotropics and the South Pacific) are almost completely derived from European stock, whereas others are clearly admixed between indigenous and European dogs. Importantly, many populations—including those of Vietnam, India, and Egypt—show minimal evidence of European admixture. These populations exhibit a clear gradient of short-range linkage disequilibrium consistent with a Central Asian domestication origin.

L. Shannon et al., Genetic structure in village dogs reveals a Central Asian domestication origin, PNAS (Published online October 19, 2015).

Did Dogs Drive The UP?

A new book entitled "The Invaders" by Pat Shipman, argues that the domestication of dogs was key to the Middle Paleolithic-Upper Paleolithic transition and to the demise of Neanderthals. The theory is reasonably plausible.

Rethinking Madagascar's Prehistory

There are archaeological traces of villages of mixed Indonesian and East African heritage dating back to at least 500 CE in Madagascar, a date that roughly coincides with megafauna extinctions on the island.[1]  The Malagasy language spoken in Madagascar is closely related to a particular Austronesian language spoken in a particular river valley of Borneo from which about 90% of the words in Malagasy are derived.[5]  The remaining Malagasy lexicon is derived from a number of other Southeast Asian and South Asian languages, and from the African Bantu language.[5]

Linguistic and cultural evidence, strongly supported by archaeological evidence, population genetic evidence, evidence of Indonesian plants that appeared in Africa with Austronesian names around that time (e.g. the banana is native to Southeast Asia, not to Africa), and evidence of Austronesian seamanship in Oceania that make such a journey plausible, all combine to make the settlement of Madagascar one of the most well established and remarkable long distance migrations of a whole people in pre-modern human history.

The story from the genetic evidence

A number of studies have been done of the non-recombining Y-DNA population genetics, mtDNA population genetics, and autosomal population genetics of the Malagasy people.[2][3][4][5][6][7][8].  These studies show significant (but differing) relative proportions of Asian and African genetic origins in Y-DNA, mtDNA, and autosomal DNA.  Only a small portion of Malagasy individuals are entirely Asian or entirely African as measured by their Y-DNA, mtDNA and autosomal DNA.[3]  The vast majority of the Asian genetic contribution to this population is consistent with origins in Southern Borneo.[2][4][5][6]  Based on the mtDNA diversity in the Asian part of the mtDNA of the Malagasy people, it is estimated that there were only about thirty women in the Indonesian founding population of the island.[6]

The African component of the population genetic makeup of the Malagasy people is a better match, in Y-DNA, mtDNA and autosomal genetics, to East African Bantus, such as the Luhya people, than to any other modern African population.

The African component of the uniparental and autosomal components of Malagasy population genetics.  As a percentage of the total mtDNA mix in the Malagasy population, the African haplogroup breakdown in one study was as follows [5]:
L* 5%
L2b1b 2%
L3b1 28%
L3e1a 4%
Total: 37%
Asian: 63%

Of these mtDNA haplogroups, all are very typical of Bantu populations except L* (which may in this context mean L not elsewhere classified rather than maximally basal form of haplogroup L).[12]

As a percentage of the total Y-DNA mix in the Malagasy population, the African haplogroup breakdown was comprised mostly of E3a (36% of the total), with smaller amounts of E2b, E1b1a, and B2.[5] These are mostly characteristic Bantu Y-DNA haplogroups.[11]

Genetics blogger Razib Khan compared the whole genomes of two Malagasy individuals to a number of reference populations.[8][9]  He used software that does a best fit of the data from the reference populations and subjects to ten hypothetical source populations using what amounts to eigenvector analysis of the data sets.  With this software, he was able to estimate the percentage of the African component in the Malagasy individuals attributable to each of the source populations, and to compare the mix of African autosomal genetic components in these individuals to those in his African reference populations.

The largest African component in each Malagasy individual was a component which makes up about 90% to 95% of the Mandenka and Yoruba populations, which a Bantu peoples from near the Nigeria-Cameroon border where the Bantu people originated.  There was also small contributions of from other African autosomal genetic components:

*About 3-4% (of the total) of a component that is modal in the pastoralist Nilo-Saharan Maasi of East Africa and in Ethiopian Jews.  This contribution made up about the same share of the African autosomal genetics of both Malagasy individuals, but in each case was smaller relative to the Bantu contribution than in the East African Bantu Luhya reference population.

*About 2-4% (of the total) of the various components that are predominant in Biaka Pygmies, Mbuti Pygmies, the San people, and the Sandawe people of Africa (all of whom are relict hunter-gatherer populations in Africa).  The proportion of these components in the Malagasy individuals relative to the size of their Bantu genetic component was very similar to that seen in the East African Bantu Luhya reference population.

*There was no evidence of admixed contributions from Yemen Jews (a SW Asian reference population) or a European reference population, although there were both SE Asian and South Asian autosomal components of the Asian part of their autosomal genetics.

In sum, Razib Khan's detailed, nuts and bolts autosomal genetic analysis of Malagasy individuals shows that the African contribution to their autosomal DNA looks very much like that of East African Bantu Luhya people, except that the East African Bantus show more Nilo-Saharan admixture.

History may explain the discrepancy.  It is likely that a group of Africans joined a group of Borneans with some minor South Asian admixture to make the trip to Madagascar and settled there at around this earliest archaeologically supported data for an Indonesian presence in Madagascar around 500 CE.  There is historical and prehistory evidence (including Maasai oral histories) to suggest that  the Maasai people and other Nilo-Saharan peoples migrated through East Africa from North to South starting around the 1400s CE.  If this contact resulted in some level of admixture in the hundred of years between then and the present, we would expect modern East African Bantus to have more Nilo-Saharan admixture today than they did in the 500s CE at the time of the fusional proto-Malay ethnogenesis.

Other autosomal genetic studies of the Malagasy people have likewise concluded that the African component of the Malagasy autosomal gene pool is basically Bantu in character.[2][3]  And, the uniparental genetic studies have similarly been congruent with a predominantly East African Bantu source for the African component of the Malagasy gene pool.[3][4][5]

Notably, the only study of which I am aware of the autosomal population genetics of Mozambique, the Southeastern African country closest to the island of Madagascar specifically noted that the Bantu people of Mozambique are not genetically similar to any of the three reference populations that Razib Khan compared to the two Malagasy individuals for whom he had whole genome data:  the Mandenka and Yoruba populations, and the East African Bantu Luhya people.[9] The population genetics of the Bantus of Mozambique show far less population replacement and far more assimilation of an indigenous pre-Bantu population that is genetically distant from any of the extant relict hunter-gather "Paleo-African" populations of Africa that are extant today.[9]

The studies of autosomal genetics in Madagascar that have been done to date either showed no sign at all of a Mozambique component to the gene pool of the Malagasy people,[2][7][8], although one uniparental study did see some sign of a trace and secondary contribution of Mozambique or the vicinity.[5]  That 2009 high resolution uniparental genetics study stated:

The pattern of diffusion of uniparental lineages was compatible with at least two events: a primary admixture of proto-Malay people with Bantu speakers bearing a western-like pool of haplotypes, followed by a secondary flow of Southeastern Bantu speakers unpaired for gender (mainly male driven) and geography (mainly coastal).

Thus, a small number of Malagasy people have Y-DNA haplotypes associated with coastal Mozambique or the vicinity, and an even smaller number of individuals have mtDNA haplogroups that are distinctively from there.

The new evidence

A study released this summer complicates this neat and simple narrative.

The new study finds clearly modern human microlithic stone tools and other artifacts in layers of two long occupied terrestrial forager villages in Madagascar dating back to about 2000 BCE, about 2500 years before the earliest solid evidence of proto-Malagasy settlement in Madagascar.[1]  These settlements also greatly predate the megafauna extinctions that occurred in Madagascar when the mix of Borneans and East African Bantus who gave rise to the Malagasy people arrived.[1]

This first wave of settlers must have been either entirely replaced or swamped demographically by the proto-Malay people who arrived around 500 CE. The people who were in the first wave of human settlers of Madagascar could not have been Bantus, because the Bantu expansion, which began about 2000 BCE in West Africa near the Nigeria-Cameroon border, did not reach the East African coast until ca. 1000 BCE.[10]  But, the African genetic component of the Malagasy people is East African Bantu which is very different from that of all coastal populations of Africa around 2000 BCE, so this genetic contribution to the Malagasy people must have arrived later, probably in the same boats that the Austronesians did.  The absence of non-Eastern Bantu genes in the Malagasy gene pool, establishes that these indigenous foragers of Madagascar did not contribute much to the modern gene pool, either because they were entirely replaced, or because their contribution was so small in proportion to the newcomers that it has left almost no discernible mark on the modern gene pool in Madagascar.

Alternatively, the foragers could have been relocated to continental Africa by the Austronesians, in a manner similar to the relocation of Native Americans to reservations in early American history, although this seems like a possibility with fewer historical precedents in the expansion histories of the Austronesian and Bantu peoples who made up the proto-Malays.

The data interpreted as a subsequent and secondary wave of male dominated migration from Mozambique in the high resolution uniparental genetic data [5] could really be, at least in part, a relict of pre-Malay African foragers in Madagascar.  But, the fact that the Southeast African uniparental genetic haplogroups are male dominated disfavors a relict population as the primary source of these Southeast African uniparental genetic haplogroups in the Malagasy gene pool.  Generally, when an indigenous substrate population is demographically swamped by a newly arrived dominant superstrate population, more matriline transmitted mtDNA survives in the resulting gene pool from the substate population than Y-DNA.

So, the maximum contribution of a relict population to the Malagasy gene pool is probably some fraction of the distinctively Southeast African contribution that was observed in [5] and the data are not inconsistent with a total replacement of the first wave humans of Madagascar by the proto-Malays that left no surviving genetic trace of this first wave forager population (i.e. with genocide).

Why didn't first wave human settlers of Madagascar cause a mega-fauna extinction?

Equally important, why didn't the arrival of African foragers ca. 2000 BCE result in a mega-fauna extinction in Madagascar as hunter-gatherer migrations into Australia and Papua New Guinea, into the Americas, in Europe and into Siberia did tens of thousands of years earlier with presumably more primitive technology?

This is also not a case comparable to that of continental Africa where the local wildlife co-evolved with modern humans and their hominin predecessors and hence learned to survive in spite of them for tens of thousands of years.

How could this be possible?

Here is one speculative narrative that could explain this new discovery.

The arrival of this first wave of African foragers may have been a one way trip by a small population made possible only by luck and pluck that wasn't repeated.  If these foragers had been able to reliably navigate to Madagascar and back at the time, presumably, they would have engaged in trade with mainland Africa.  But, there is no archaeological evidence of ongoing trade between Madagascar and continental African prior to 500 CE, which would have been highly distinctive in the archaeological record because it contained species of flora and fauna found nowhere in mainland Africa.

In a case similar to that of the people of Tasmania, once separated from their continental African communities, they may have regressed technologically (e.g. in terms of hunting effectiveness) as their population fell below critical mass to sustain this knowledge, if not immediately, after some mishap or bad foraging season or disease outbreak at a latter time.  They may have held on to enough cultural capital to be a sustainable population, but may not have been a large enough community to sustain the level of excellence in hunting and gathering practices that made them a dominant species in Africa and Eurasia and the Americas.

Since Madagascar's flora and fauna are so distinct from those of continental Africa, it may also have been the case in which the knowledge the first wave African foragers brought with them from continental Africa may have been of limited usefulness in this new ecology. Since they were not farmers or herders, they would have brought no familiar plants or animals to feed themselves with them.  The need to rapidly develop new gathering skill sets could have given this first wave of modern humans on the island a rocky start, causing their population to fall before eventually recovering as they learned to adapt to local conditions.  This could have caused them to regress culturally, in part from their loss of important hunting and gathering knowledge. Without the cultural capital shared by other Upper Paleolithic peoples who brought about mega-fauna extinctions (and contributed to the demise of the Neanderthals), they may have lost the capacity to become so dominant as hunters and gatherers who could cause mega-fauna extinctions.

There also isn't even any sign that they brought domesticated dogs with them.  Dogs were first domesticated around 30,000 years ago and were widespread by ca. 2000 BCE, even into Australia where they weren't initially present for tens of thousands of years but appeared about 4000 years ago. Perhaps the relevance of domesticated dogs that modern humans brought with them has been underestimated, which could also explain why Southeast Asia, which is a point of origin of many species of domestic dogs, has so less mega-fauna extinction since Southeast Asian fauna co-evolved with these dogs.

Even if the first wave of humans in Madagascar eventually recovered technologically and cultural, centuries later, their recovery may have been gradual enough to be less disruptive to the local ecology.

These disadvantages wouldn't burden later proto-Malays who brought food sources with them, had reliable sea transportation that permitted them to colonize Madagascar at populations in excess of the critical mass needed to sustain their population, and thus didn't need detailed knowledge of how to turn indigenous plants and animals into food and didn't suffer the cultural regression that may have been experienced by first wave foragers on the island twenty-five centuries earlier.

References

1. Robert E. Deward et al., "Stone tools and foraging in northern Madagascar challenge Holocene extinction models.", PNAS (2013).[doi:10.1073/pnas.1306100110] (Mr. Deward died on April 8, 2013.)

2. Regueiro, et al., "Austronesian genetic signature in East African Madagascar and Polynesia.", Journal of Human Genetics (2008) 53, 106–120; doi:10.1007/s10038-007-0224-4

3. Poetsch, et al., "Determination of population origin: a comparison of autosomal SNPs, Y-chromosomal and mtDNA haplogroups using a Malagasy population as example.", European Journal of Human Genetics (24 April 2013) doi:10.1038/ejhg.2013.51

4. Hurles, et al. "The dual origin of the malagasy in island southeast Asia and East Africa: evidence from maternal and paternal lineages.", Am J Hum Genet. 2005;76;894-901. PMID: 15793703

5. Tofanelli, et al., "On the origins and admixture of Malagasy: new evidence from high-resolution analyses of paternal and maternal lineages.", Mol. Biol. Evol. 26, 2109–2124 (2009) (doi:10.1093/molbev/msp120)

6. Cox, et al., "A small cohort of Island Southeast Asian women founded Madagascar", Proc. R. Soc. B. (21 March 2012) doi: 10.1098/rspb.2012.0012

7. Razib Khan, "The Betsileo of Madagascar are Malay and Bantu.", Gene Expression (October 23, 2011). (Supplemental materials: here).

8. Razib Khan, "The Merina of Madagascar are Malay and Bantu.", Gene Expression (September 9, 2011).

9. Sikora, et al., "A genomic analysis identifies a novel component in the genetic structure of sub-Saharan African populations.", European Journal of Human Genetics (2011) 19, 84–88; doi:10.1038/ejhg.2010.141.

10.  Wikipedia entry on "Bantu Expansion" (the Bantu reach the East African coast sometime after 1500 BCE and before 500 BCE; and there is no evidence of Bantu seafaring activity independent of assistance from other cultures such as the Austronesians).

11.  Gemma Berniell-Lee, et al., "Genetic and demographic implications of the Bantu expansion: insights from human paternal lineages.", Molecular Biology and Evolution (April 2009) doi:10.1093/molbev/msp069 (quoted at Dienekes' Anthropology Blog)("these lineages have been associated either to Bantu-speaking people - E1b1a (E3a according to The Y Chromosome Consortium (2002)), B2a, and E2 - or to Pygmy populations (haplogroup B2b).").

12.  Salas, et al., "The Making of the African mtDNA Landscape",  Am J Hum Genet. 71(5): 1082–1111.(November 2002) PMCID: PMC385086. ("L2b, L2c, and L2d appear to be largely confined to West and western Central Africa (and African Americans), with only minor occurrences of a few derived types in the southeast. . . . [L3b is a] major southeastern haplogroups of clear West African origin. . . .  L3e1 is distributed throughout sub-Saharan Africa, but it is especially common in southeastern Africa. This clade appears to have a west Central African origin and is rare among West Africans, although it is well represented among African Americans. Several southeastern African types are shared with East African Bantu-speaking Kikuyu from Kenya. This suggests that L3e1 may have spread into Kenya via the eastern stream from a Cameroon source population (best represented in this data set by Bioko and São Tomé) or from some Central African source. It subsequently dispersed into the southeast (although, with so little data, back migration into Kenya cannot be ruled out). The African American types may be the result of direct transportation from Mozambique, given the lack of West African representatives. One L3e1a type is also present at elevated frequency in the Khwe, but, since it matches two Herero and also has a direct derivative in the southeast, this again appears to have been the result of gene flow from Bantu speakers, even though the type has not been sampled in that group.")

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.