Friday, March 16, 2018

Edo Era Ainu Genetics

The Ainu people of Japan are descendants of the Jomon fishing-gathering people of prehistoric Japan, but also have significant Siberian ancestry.
The Ainu, the indigenous people living on the northernmost island of Japan, Hokkaido, have long been a focus of anthropological interest because of their cultural, linguistic, and physical identity. A major problem with genetic studies on the Ainu is that the previously published data stemmed almost exclusively from only 51 modern-day individuals living in Biratori Town, central Hokkaido. To clarify the actual genetic characteristics of the Ainu, individuals who are less influenced by mainland Japanese, who started large-scale immigration into Hokkaido about 150 years ago, should be examined. Moreover, the samples should be collected from all over Hokkaido. 
Materials and methods 
Mitochondrial DNA haplogroups of 94 Ainu individuals from the Edo era were successfully determined by analyzing haplogroup-defining polymorphisms in the hypervariable and coding regions. Thereafter, their frequencies were compared to those of other populations. 
Our findings indicate that the Ainu still retain the matrilineage of the Hokkaido Jomon people. However, the Siberian influence on this population is far greater than previously recognized. Moreover, the influence of mainland Japanese is evident, especially in the southwestern part of Hokkaido that is adjacent to Honshu, the main island of Japan. 
Our results suggest that the Ainu were formed from the Hokkaido Jomon people, but subsequently underwent considerable admixture with adjacent populations. The present study strongly recommends revision of the widely accepted dual-structure model for the population history of the Japanese, in which the Ainu are assumed to be the direct descendants of the Jomon people.
Noboru Adachi, et al., "Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data" American Journal of Physical Anthropology (October 11, 2017).

Hat tip to the Linear Population Model blog.

Thursday, March 15, 2018

Ancient North African DNA

The biggest surprise of new Mesolithic ancient DNA samples from Morocco is that they lack any European hunter-gatherer ancestry, instead deriving from a mix of Levantine hunter-gatherers and sub-Saharan Africans. Sub-Saharan African admixture was not unexpected, but the proportion of sub-Saharan African ancestry in this ancient DNA is higher than expected, implying early, pre-Neolithic contact between the populations.
North Africa is a key region for understanding human history, but the genetic history of its people is largely unknown. We present genomic data from seven 15,000-year-old modern humans from Morocco, attributed to the Iberomaurusian culture. We find a genetic affinity with early Holocene Near Easterners, best represented by Levantine Natufians, suggesting a pre-agricultural connection between Africa and the Near East. We do not find evidence for gene flow from Paleolithic Europeans into Late Pleistocene North Africans. The Taforalt individuals derive one third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West and East Africans. Thus, we provide direct evidence for genetic interactions between modern humans across Africa and Eurasia in the Pleistocene.
Marieke van de Loosdrecht, et al.,"Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations" Science (March 15, 2018).

A related account of the find is aimed at an educated lay audience. It notes that:
DNA in hand, paleogeneticists Marieke van de Loosdrecht and Johannes Krause of the Max Planck Institute for the Science of Human History in Jena, Germany, sequenced it. They were able to analyze genetic material from the cell’s nucleus in five people and the maternally inherited mitochondrial DNA from seven people. But they found no genetic tie to ancient Europeans. Instead, the ancient Iberomaurusians appear to be related to Middle Easterners and other Africans: They shared about two-thirds of their genetic ancestry with Natufians, hunter-gatherers who lived in the Middle East 14,500 to 11,000 years ago, and one-third with sub-Saharan Africans who were most closely related to today’s West Africans and the Hadza of Tanzania. 
The Iberomaurusians lived before the Natufians, but they were not their direct ancestors: The Natufians lack DNA from Africa, Krause says. This suggests that both groups inherited their shared DNA from a larger population that lived in North Africa or the Middle East more than 15,000 years ago, the team reports today in Science. 
As for the sub-Saharan DNA in the Iberomaurusian genome, the Iberomaurusians may have gotten it from migrants from the south who were their contemporaries. Or they may have inherited the DNA from much more ancient ancestors who brought it from the south but settled in North Africa where some of the earliest members of our species, Homo sapiens, have been found at Jebel Irhoud in Morocco.

Fun With Archaic Admixture Analysis

Archaegenetics is not a reductionist field and the more we know the more intricate the tapestry of human ancestry becomes.
Anatomically modern humans interbred with Neanderthals and with a related archaic population known as Denisovans. Genomes of several Neanderthals and one Denisovan have been sequenced, and these reference genomes have been used to detect introgressed genetic material in present-day human genomes. Segments of introgression also can be detected without use of reference genomes, and doing so can be advantageous for finding introgressed segments that are less closely related to the sequenced archaic genomes. 
We apply a new reference-free method for detecting archaic introgression to 5,639 whole-genome sequences from Eurasia and Oceania. We find Denisovan ancestry in populations from East and South Asia and Papuans. Denisovan ancestry comprises two components with differing similarity to the sequenced Altai Denisovan individual. This indicates that at least two distinct instances of Denisovan admixture into modern humans occurred, involving Denisovan populations that had different levels of relatedness to the sequenced Altai Denisovan.

All of these Eurasian and New World populations have a bottom right cluster in the images below that corresponds to Neanderthal ancestry.

The Papuan (bottom right in the image below) sample also has a center-left cluster that corresponds to Deniovan ancestry. A less pronounced center-left cluster indicating a smaller amount of ancestry from the same population is found in East Asia, Southeast Asia and South Asian individuals middle two rows of the image below. 

The big reveal in this study is that the East Asian individuals, in particular, seem to have two distinct clusters of Denisovan ancestry, with a small secondary top left cluster in each suggesting a second admixture event with genetically diverged Denisovan populations.

Denisovan ancestry is absent, however, in European individuals (top row) and in New World individuals (bottom row except the Papuan). Pontus Skoglund also notes that:
There is an undiscussed but potentially explosive implication of this paper: the 2nd Denisovan gene flow signal in East Asia seems to be absent from Native American ancestry--could Denisovans have survived after the isolation of these lineages <30 kya??
For what it is worth, I don't think that Skoglund's hypothesis is correct. I think it is more likely that the primary Denisovan admixture event reflects admixture of Southern route modern human migrants with Denisovans and that the secondary Denisovan admixture event (which is absent in Papuans) reflects admixture of a subset of Northern route modern human migrants who followed more or less what is now known as the Silk Road, and was distinct from the small founding population of the Americas.

This data point also strengthens the hypothesis that very old, non-Homo erectus hominin remains found in China with a mix of archaic and modern features are either Denisovan or hybrid Denisovan-modern human individuals.

Figure 4: Contour Density Plots of Match Proportion of Introgressed Segments to the Altai Neanderthal and Altai Denisovan Genomes

The match proportion is the proportion of putative archaic-specific alleles in a segment that match the given archaic genome, excluding alleles at positions masked in the archaic genome sequence. Segments with at least ten variants not masked in the Neanderthal genome and at least ten variants not masked in the Denisovan genome are included. Numbers inside the plots indicate the height of the density corresponding to each contour line. Contour lines are shown for multiples of 1 (solid lines). In addition, contour lines for multiples of 0.1 between 0.3 and 0.9 (dashed lines) are shown for additional detail. European populations are given in the first row, East Asian populations in the second row, South Asian populations in the third row, and American and SGDP Papuan populations in the final row. Additional information about the populations can be found in Table 1.

Wednesday, March 14, 2018

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.

More Trouble For Dark Matter

An analysis of ambient radio wave activity at particular frequencies provides a window into the nature and temperature of the universe very early in its existence. What does it show?
The profile is largely consistent with expectations for the 21-centimetre signal induced by early stars; however, the best-fitting amplitude of the profile is more than a factor of two greater than the largest predictions. 
This discrepancy suggests that either the primordial gas was much colder than expected or the background radiation temperature was hotter than expected. Astrophysical phenomena (such as radiation from stars and stellar remnants) are unlikely to account for this discrepancy; of the proposed extensions to the standard model of cosmology and particle physics, only cooling of the gas as a result of interactions between dark matter and baryons seems to explain the observed amplitude. The low-frequency edge of the observed profile indicates that stars existed and had produced a background of Lyman-α photons by 180 million years after the Big Bang. The high-frequency edge indicates that the gas was heated to above the radiation temperature less than 100 million years later.
Of course, the (literally) defining property of dark matter in the standard model of cosmology (called ΛCDM for a cosmological constant with "cold dark matter") is that dark matter is completely or almost collisionless with respect to ordinary baryonic matter . . . . dots that this abstract refrains from connecting.

What correctly predicts what is observed?

A universe with no dark matter where the matter in the universe is entirely made up of baryonic matter (i.e. a modified gravity hypothesis), as explained in a readable two page (exclusive of references) paper supplementing the paper in the journal Nature linked above, that accepts virtually all of its data, theoretical framework and equations. It merely connects the dots that the paper in Nature didn't. They money language:
Equation 1 then predicts a maximum absorption of  
T21, max = −0.24 K for fb = 0.16; (2)  
T21, max = −0.60 K for fb = 1. (3)  
The observed value is T21 ≈ −0.5 K (Bowman et al. 2018), and appears from their Fig. 2 to be closer to −0.55 K. Such a strong signal is expected in a baryonic universe, but is unobtainable in ΛCDM. 
Figure 1 of the supplemental paper shows that a naive, unmodified ΛCDM prediction (as opposed to the maximal possible variation of it) is T21 ≈ −0.05 K, about 9% of the observed value, as opposed to 92% of the value predicted in a purely baryonic scenario (the exact margin of error isn't stated).

Once again, modified gravity theorists have correctly predicted the results of future experimental observations and dark matter theories made the wrong prediction, on a matter independent of previous predictions that have been confirmed.

McGaugh's linked supplement paper also makes some further predictions that new data can test:
1. Strong 21cm absorption will also be observed during the dark ages (z > 30).  
2. The 21cm power spectrum will show pronounced baryonic features.  
3. Large galaxies and the cosmic web emerge earlier than anticipated in ΛCDM (Sanders 1998; McGaugh 2015).  
The first two predictions stem simply from a universe made of baryons. Only the third prediction is model-specific; some hints of large early structures already exist (e.g., Steinhardt et al. 2016; Franck & McGaugh 2016). This implies that structure grows nonlinearly, erasing baryonic features at late times through mode mixing (McGaugh 1999).

UPDATE March 16, 2018: A completely separate paper constrains dark matter models via metal enrichment in very old galaxies. 

Tuesday, March 13, 2018

Sabine Hossenfelder (and others) On Naturalness

A Power Point presentation (converted to pdf form) on Naturalness from a recent conference presentation by Sabine Hossenfelder explains why Naturalness is not a legitimate hypothesis generator in physics. The straight forward reasoning is solid and she's right. Eventually, the rest of the discipline should come around, although they've wasted a generation ignoring this common sense.

Another presenter (Fred Jegelehner) at the same conference explains how, from other perspectives than the conventional one, there is nothing unnatural about the Higgs boson mass and the conventional "hierarchy problem" is misguided.

Meanwhile Jester comes out of a long hibernation at his blog to say this:
The clear message from the LHC is that the dominant paradigms about the physics at the weak scale were completely misguided. The Standard Model seems to be a perfect effective theory at least up to a few TeV, and there is no indication at what energy scale new particles have to show up. . . . The naturalness problem of the cosmological constant and of the Higgs mass may suggest some fundamental misunderstanding of quantum field theory on our part.
He offers sensible suggestions about new directions that experimenters and theorists in physics should consider as a result - something many of us have been preaching as voices in the wilderness for some time now. 

He cites Sabine's blog, a pre-print on the "Post-Naturalness" era, and an article at the Economist citing people including Woit (of "Not Even Wrong" fame).

Monday, March 12, 2018


For what it's worth, the analytics for this blog indicate that there has been some SEO mischief going on, although I can't figure out what it is really trying to accomplish, or how it is done. I police comment spam quite thoroughly, so whoever you are out in cyberspace screwing around with this, you have nothing to gain here.

Quick Hits

Europe and Northern Asia

* From Davidski at Eurogenes: 
the remains of this individual (sampled by Mathieson et al. 2018, see here) are from a cemetery of the Sredny Stog culture, which, based on historical linguistics and archaeological data, has already been posited to have been a Proto-Indo-European (PIE) culture. . . Ukraine_Eneolithic I6561 is the oldest recorded individual belonging to Y-haplogroup R1a-M417 . . . Ukraine_Eneolithic I6561 is the oldest sample with UDG-treated genome-wide data to carry the 13910*T lactase persistence allele, which reaches its maximum frequency in Northwestern Europe, and is also relatively common amongst Indo-European-speaking South Asians, but not Middle Easterners . . . based on historical linguistics data, the Proto-Indo-Europeans are generally regarded to have been foragers turned pastoralists, rather than farmers, but nevertheless, pastoralists familiar with farming, and indeed Ukraine_Eneolithic I6561 appears to be mostly a mixture of Eastern European and Caucasus Hunter-Gatherers (EHG and CHG, respectively), but with around 30% input from early European farmers.
Somebody has to be the first Indo-European-like ancient genome. But, this case offers a potential resolution of a key disputed historical mystery. Did the 13910*T lactase persistence allele arise in Indo-Europeans (in whom it was later strongly selected for) or in situ in Northwest Europe? 

This find strongly makes the case for a proto-Indo-European Ukrainian origin.

This doesn't refute the evidence of strong selective fitness for the LP allele, but the fitness coefficient doesn't have to be nearly as high if you start with an allele that is present at low frequency in a source population that is already growing rapidly for other reasons which may have strong founder effects, as it does if you start from a single mutation in Northwest Europe's early European farmer population that is otherwise shrinking or stagnating.

* I continue to think that the role of Vitamin D may be critical for the role of LP allele selection in Europe. "Normal" vitamin D consumption can reduce early death from cardiovascular disease by 30%, reduces vulnerability to TB, prevent chronic lung diseaseprevents osteomalacia in adults, seasonal flu and cold vulnerability (same link with sources linked therein), seasonal affective disorder vulnerability (same link), and really importantly (same link) prevents pre-eclampsia, gestational diabetes mellitus, preterm birth and first-trimester miscarriage. The health benefits for adults and especially pregnant women of not having a Vitamin D deficiency which is especially common in high latitudes where there is less sunlight much of the year in an already growing population with above average levels of the allele could be great.

Lot of deaths during famines are really compound with dietary deficiency leading to vulnerability to diseases that well nourished people would weather, which leads to death whose cause is really both disease and malnutrition. Also, an appearance of lower vulnerability to non-deadly diseases is something that sexual selection can also act upon. A guy (or gal) who more often suffers from colds and flus and is down emotionally in winter months is less sexy and less attractive as a mate.

* A lengthy lay audience oriented paper on Finnish genetic origins in Finnish.

It has been widely accepted that the Finno-Ugric Hungarian language, originated from proto-Uralic people, was brought into the Carpathian Basin by the Hungarian Conquerors. From the middle of the 19th century this view prevailed against the deep-rooted Hungarian Hun tradition, maintained in folk memory as well as in Hungarian and foreign written medieval sources, which claimed that Hungarians were kinsfolk of the Huns. 
In order to shed light on the genetic origin of the Conquerors we sequenced 102 mitogenomes from early Conqueror cemeteries and compared them to sequences of all available databases. We applied novel population genetic algorithms, named Shared Haplogroup Distance and MITOMIX, to reveal past admixture of maternal lineages. 
Phylogenetic and population genetic analysis indicated that more than one third of the Conqueror maternal lineages were derived from Central-Inner Asia and their most probable ultimate sources were the Asian Huns. The rest of the lineages most likely originated from the Bronze Age Potapovka-Poltavka-Srubnaya cultures of the Pontic-Caspian steppe, which area was part of the later European Hun empire. Our data give support to the Hungarian Hun tradition and provides indirect evidence for the genetic connection between Asian and European Huns. Available data imply that the Conquerors did not have a major contribution to the gene pool of the Carpathian Basin, raising doubts about the Conqueror origin of Hungarian language.
I am inclined to think that the linguistic and interpretative gloss placed on the genetic data in this bioXriv preprint is weak, even though the genetic data do accurately indicate a more complex population history of the Conquerors than had been previously been acknowledged. The failure of the study to take a more interdisciplinary approach to an event in the historic era is also disappointing.

Africa, Middle East and Southern Asia

* Sheep and goats were domesticated close in time and place to each other.

* Turkey started as early Anatolian but had multiple waves of introgression, most recently a moderate Turkish one, but earlier Greek and Armenia ones with the Greeks having somewhat more impact.

* Ancient artifacts and structure in Nubian funerary complexes reveal a blending of Egyptian and local traditions, and a strong role for women as bearers of family reputations and extended family identity.

* The Toba eruption did not cause a volcanic winter in East Africa and hence wasn't a push factor for migration Out of Africa which some genetic data hints should have taken place around then. But, this doesn't resolve the question of whether the eruption may have thinned jungles and local hominin populations that could have prevented modern human migration out of India until then. There is documented modern human associated tool use both before and after the Toba eruption in India. More analysis of this issue from a South African perspective is found in a new article at Nature.

* Paleoclimate and East African hominin evolution.

* Climate change in India relevant to Harappan civilization:
Our record reveals that relatively wet conditions prevailed at the northern edge of Rajasthan from ~5.1 ± 0.2 ka BP, during the beginning of the agricultural-based Early Harappan phase of the Indus Civilization. Monsoon rainfall intensified further between 5.0 and 4.4 ka BP, during the period when Indus urban centres developed in the western Thar Desert margin and on the plains of Haryana to its north. Drier conditions set in sometime after 4.4 ka BP, and by ~3.9 ka BP an eastward shift of populations had occurred. Our findings provide evidence that climate change was associated with both the expansion and contraction of Indus urbanism along the desert margin in northwest India.
* The climate change associated with its impact on the decline of Harappan civilization was fairly gradual. More on the timing of the death of the mighty Sarasvati River here. More research on this question (not necessarily mainstream in its conclusions).

* The Painted Gray Ware culture in NW India may be older than conventionally assumed.

* Steppe, Harappan and BMAC cultures compared.

* There were diverse, probably contemporaneous cemetery practices in Harappan society at a single cemetery.

* Indus seals probably regulated ownership and control of high value goods rather than being used for routine ration system administration. IVC script was probably written right to left.

* Does the Rig Veda recount Indian Ocean navigation at an earlier date than attested in existing Greco-Roman sources? Indus pottery has been found in Oman.

* What was the range of Neanderthals in South Asia?

* Were there Mousterian tools in North China briefly during the Upper Paleolithic era?

New World

Native Americans in California used nicotine: "the Ohlone tribe in San Francisco Bay to extract plaque from the teeth of eight individuals, buried between 6,000 and 300 years ago, and analyze it for nicotine. . . . Among the samples they analyzed, two tested positive for nicotine, demonstrating for the first time that the drug can survive in detectable amounts in ancient plaque. One of these individuals, an adult man, was also buried with a pipe. A surprise came from the molar of an older woman, which also tested positive for nicotine.The individuals who used it were pre-Columbian. The paper is: Jelmer W. Eerkens, et al. "Dental calculus as a source of ancient alkaloids: Detection of nicotine by LC-MS in calculus samples from the Americas." 18 Journal of Archaeological Science: Reports 509 (2018).

* If you've read Jared Diamond's classic "Guns, Germs and Steel", you know that there were a number of independently domesticated crops in what is now the American South, which went into disuse when a better package of crops developed in Meso-America reached the area. Researchers have unearthed evidence of the cultivation of that first wave of American original domesticates from 2000 years ago. The story follows the not uncommon path of a result that is well known in local museums disconnected from larger scientific networks finally connecting with the larger scientific discourse.

* Using new LIDAR tools, researchers have found evidence that a densely populated classical Mayan civilization full of cities had 10-15 million people in an area comparable to medieval England at its peak around 800 CE, which is two to three time the most optimistic earlier estimates, in places whose habitability had been doubted because it is currently so swampy.

* People were eating wild potatoes in Utah (and processing it into potato flour) ca. 10,900 years ago.

Friday, March 9, 2018

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.

Monday, March 5, 2018

Termites Are Social Cockroaches

Ten and a half year after a scientific paper reached this conclusion the U.S. scientific body that handles the naming of insect species has agreed that termites are a social sub-type of cockroach. As Science News explains:
The Entomological Society of America is updating its master list of insect names to reflect decades of genetic and other evidence that termites belong in the cockroach order, called Blattodea. 
As of February 15, “it’s official that termites no longer have their own order,” says Mike Merchant of Texas A&M University in College Station, chair of the organization’s common names committee. Now all termites on the list are being recategorized. 
The demotion brings to mind Pluto getting kicked off the roster of planets, says termite biologist Paul Eggleton of the Natural History Museum in London. He does not, however, expect a galactic outpouring of heartbreak and protest over the termite downgrade. Among specialists, discussions of termites as a form of roaches go back at least to 1934, when researchers reported that several groups of microbes that digest wood in termite guts live in some wood-eating cockroaches too. 
Once biologists figured out how to use DNA to work out genealogical relationships, evidence began to grow that termites had evolved as a branch on the many-limbed family tree of cockroaches. In 2007, Eggleton and two museum colleagues used genetic evidence from an unusually broad sampling of species to publish a new tree of these insects (SN: 5/19/07, p. 318). Titled “Death of an order,” the study placed termites on the tree near a Cryptocercus cockroach. 
The paper that spurred this reassessment is:

D. Inward, G. Beccaloni and P. Eggleton. Death of an order: a comprehensive molecular phylogenetic study confirms that termites are eusocial cockroaches. 3 Biology Letters 331 (June 22, 2007) doi: 10.1098/rsbl.2007.0102.

Coming Attractions

A number of really good anthropology and genetic papers have crossed my computer screen recently, but I have been out of pocket with work commitments, and also not quite sure what take to give them.

Sometimes soon, I will either cave and just do a "quick hits" post to acknowledge the new developments for future reference, or will put together some of them into a richer post with more analysis.

Friday, March 2, 2018

The Dynamics Of The Crater II Dwarf Satellite Galaxy Are Inconsistent With The Dark Matter Hypothesis

Crater II is a dwarf galaxy that orbits the Milky Way at a distance of about 360,000 light years, which while distant, is still within the gravitational field of the Milky Way. It is the "coldest" galaxy ever observed.

In the current iteration of MOND, its velocity dispersion was predicted to be 4 km/s if it were isolated in space away from any gravitational effect.

But, due to an "External Field Effect" of the current iteration of MOND, which violates the "Strong Equivalence Principle" of General Relativity that arises from the fact that it is still in the Milky Way's gravitational field in MOND, its velocity dispersion was predicted in advance of a measurement of this quantity to be 1.5 km/s to 3.0 km/s.
Crater II is an unusual object among the dwarf satellite galaxies of the Local Group in that it has a very large size for its small luminosity. This provides a strong test of MOND, as Crater II should be in the deep MOND regime (gin34km2s2kpc1a0=3700km2s2kpc1). Despite its great distance (120 kpc) from the Milky Way, the external field of the host (gex282km2s2kpc1) comfortably exceeds the internal field. Consequently, Crater II should be subject to the external field effect, a feature unique to MOND. This leads to the prediction of a very low velocity dispersion: σefe=2.1+0.90.6kms1.

This is a big deal because under a wide range of dark matter hypotheses, the velocity dispersion could have been no lower than 5 km/s and was expected to be more like 11 km/s to 24 km/s.

The actual velocity dispersion of Crater II was measured with the latest and greatest telescopes in a result first announced six and a half weeks after this prediction was made on December 19, 2016. What did they find?

A velocity dispersion of 2.4 km/s to 3.0 km/s. 

This was perfectly consistent with MOND adjusted for the external field effect at the one sigma level.

It is inconsistent with MOND without the external field effect by about four sigma

It is inconsistent at more than 7 sigma with even the most conservative estimate based upon dark matter, and is inconsistent at the 27 sigma level with a prediction at the low end of more typical dark matter assumptions.

Crater II is a rejection of the dark matter hypothesis that is particularly notable because it is independent of pretty much all of the other empirical evidence that shows that the dark matter hypothesis is inconsistent with the data, and because it is a very clean measurement that the dark matter hypothesis once again has failed to predict accurately.

I'll sum up all of the leading ways that the dark matter hypothesis contradicts empirical evidence in future post recapping the state of the dark matter debate when you consider Crater II with all of the over evidence. But, for now, the take away point is that multiple rejections of the cold dark matter hypothesis by multiple different methods makes the conclusion that the cold dark matter hypothesis is wrong much more robust and reliable. 

Incidentally, while the "external field effect" has no place in conventional general relativity as it violates the strong equivalence principle,* it makes lots of sense in a graviton based quantum gravity theory where there is a physical difference (a higher density of gravitons per cubic meter of space)  between the situation when there is an external field than when there is not an external field.

* as the link explains, general relativity arguably does not perfectly honor the strong equivalence principle either, but the deviation is negligible in weak gravitational fields with objects moving slowly relative to the speed of light which is the regime which Crater II inhabits. But see here (arguing that conventional general relativity does obey the strong equivalence principle).

In particular, this difference of graviton density could have an effect as a consequence of the fact that the importance of graviton self-interactions (which are the source of MOND-like effects in Deur's work) relative to the overall strength of the graviton field.

It will take time for the conclusion that dark matter phenomena are due to some form of gravity modification relative to conventional applications of classical general relativity, probably associated with quantum gravity effects that only manifest in weak gravitational fields. This modified/quantum gravity explanation is a better fit than some new undiscovered form of non-baryonic matter, possibly in association with some new undiscovered force that exists only in interactions involving this non-baryonic matter with other non-baryonic matter and/or between non-baryonic matter and ordinary matter.

Realistically, a generation of astrophysicists are going to have to die before MOND receives universal acceptance.

But, the evidence is already there and is already sufficiently weighty to make it clear that some form of MOND and not some form of dark matter and dark forces, is the answer. What is left is the sociology of science, not the science itself.

MOND will probably be the leading explanation of dark matter phenomena by the time I have grandchildren old enough to study the topic in a serious and scientific way, at the very least. I'm confident of this because, unlike high energy physics, astronomy data continues to produce torrents of new data, and when scientists have data rather than speculation and theory to help them answer a question, they usually get the right answer sooner or later.