Saturday, April 21, 2018

The High Steppe

Drugs are not new to the human experience.
[T]he Yamnaya people, who swept out of Central Asia about 5000 years ago and left their genes in most living Europeans and South Asians, appear to have carried cannabis to Europe and the Middle East. In 2016, a team from the German Archaeological Institute and the Free University, both in Berlin, found residues and botanical remains of the plant, which originates in East and Central Asia, at Yamnaya sites across Eurasia. It's difficult to know whether the Yamnaya used cannabis simply to make hemp for rope or also smoked or ingested it. But some ancient people did inhale: Digs in the Caucasus have uncovered braziers containing seeds and charred remains of cannabis dating to about 3000 B.C.E.
From here.

Wednesday, April 18, 2018

Progress Made On 68 Year Old Math Problem

How many colours are needed to colour the plane so that no two points at distance exactly 1 from each other are the same colour? 
This quantity, termed the chromatic number of the plane or CNP, was first discussed (though not in print) by Nelson in 1950 (see [Soi]). Since that year it has been known that at least four and at most seven colours are needed. 
The lower bound was also noted by Nelson (see [Soi]) and arises because there exist 4-chromatic finite graphs that can be drawn in the plane with each edge being a straight line of unit length, the smallest of which is the 7-vertex Moser spindle [MM] (see Figure 7, left panel). 
The upper bound arises because, as first observed by Isbell also in 1950 (see [Soi]), congruent regular hexagons tiling the plane can be assigned seven colours in a pattern that separates all same-coloured pairs of tiles by more than their diameter. 
The question of the chromatic number of the plane is termed the Hadwiger-Nelson problem, because of the contributions of Nelson just mentioned and because the 7-colouring of the hexagonal tiling was first discussed (though in another context) by Hadwiger in 1945 [Had]. The rich history of this problem and related ones is wonderfully documented in [Soi]. Since 1950, no improvement has been made to either bound. 
From here.

The author, a professional scientist and amateur mathematician, proves in the linked pre-print that the lower bound is 5 and not 4.

So, the correct answer is now 5, 6 or 7, although we still don't know which of those three integers is the correct answer.

Saturday, April 14, 2018

Neanderthals And Modern Humans Experienced Hybrid Incompatability

Also know as Haldane's law, heterozygotes for sex determination genes are strongly disfavored as children of cross-species hybrids. And, the evidence is strong that this hybrid incompatibility prevented Neanderthal-human hybrids from being born. This is strong evidence that Neanderthals and modern humans were biologically separate species.

As the author explains in an open access summary:
After years of sequencing the genomes of female Neandertals, researchers have finally got their first good look at the Y chromosome of a male Neandertal—and found that it is unlike that of any other Y in modern humans living today. Even though Neandertals and modern humans interbred several times in the past 100,000 years, the DNA on the Y chromosome from a male Neandertal who lived at El Sidrón, Spain, 49,000 years ago has not been passed onto modern humans, researchers report today in The American Journal of Human Genetics. The finding fits with earlier studies that have found that although living Asians and Europeans have inherited 1% to 3% of their DNA from their ancestors’ interbreeding with Neandertals, they are missing chunks of Neandertal DNA on their Y chromosomes. This has suggested that female modern humans and male Neandertals were not fully compatible and that male Neandertals may have had problems with sperm production. The new study finds a clue to why: The El Sidrón Neandertal had mutations in three immune genes, including one that produces antigens that can elicit an immune response in pregnant women, causing them to reject and miscarry male fetuses with those genes. So even though male Neandertals and female modern humans probably hooked up more than once over the ages, they may have been unable to produce many healthy male babies (such as the reconstruction of this Neandertal boy from fossils from Gibraltar)—and, thus, hastened the extinction of Neandertals.
There are also no Neanderthal mtDNA sequences in modern humans. This is probably because the children of hybrid couples were probably raised in the tribe of the mother. Hybrid children with modern human mothers were raised in modern human tribes and left descendants who are alive today. Hybrid children with Neanderthal mothers were raised in Neanderthal tribes that ultimately went extinct. 

This inferred pattern of matrilocality for hybrid children, despite the fact that Neanderthals were predominantly patrilocal, also favors the possibility that hybrid children were largely a result of rape or brief encounters, rather than than marriage-like couple relationships. There is not a single example archaeologically of a hominin tribe containing both full blooded Neanderthal and full blooded modern human members.

Wednesday, April 11, 2018

Modern Humans At Monte Verde Ca. 18,500 Years Ago?

Two and a half years ago, a paper that I had missed announced strong evidence of a human presence in Monte Verde (in South America) about 18,500 years ago. This is about 4,000 years older than the next oldest reliably dated evidence (from the same site).

Less significantly, evidence of wild potato use in Utah (which was converted into flour) from 10,900 years ago.

Tuesday, April 10, 2018

Koreans v. Japanese v. Chinese Genetic Ancestry

A new paper purports to be able to distinguish almost perfectly between Koreans, the Japanese, and Chinese individuals based upon autosomal genetics. This is something that consumer genetic services such as 23andMe struggle with right now.

For example, 23andMe claims that my son has more Japanese ancestry than Korean ancestry, when, in fact, he probably has no recent Japanese ancestry and has entirely North Korean ancestry on his mother's side (something upon which we have very solid genealogical support from living memory back to his great-great grandparents because his last great-grandparent died just a few years ago at the age of 98).

In the case of 23andMe, this is probably because ancestry in Japanese people from Yayoi people (including mounted warriors) who invaded Japan from Korea ca. 1000 BCE is being classified as Japanese in origin, rather than Korean, despite the fact that these genetic component originated in Korea, because there are more Japanese individuals in their samples than there are Koreans. 

The paper also controversially suggests that these three populations have a common origin at about 1200 BCE (in the Shang Dynasty of China). 

Indeed, we are pretty much certain that this is not true in the case of the Japanese who have substantial Jomon ancestry that has a much greater time depth. 

The common origin hypothesis is also contrary to the hypothesis that the non-Jomon genetic component of the Koreans and Japanese has a significant "Altaic" component (also hypothesized linguistically) derived from Manchuria and Mongolia and the vicinity, in addition to substantial Chinese admixture in both Korean and Japanese populations, which is well documented historically at least in the case of the Japanese.

So, this 1200 BCE common origin date may be due to some methodological artifact (i.e. flaw) that might, perhaps, simply be measuring a common origin for the Chinese admixture component in all three populations that is significant in all of them, since this is around the time that the Chinese component of these nations would have diverged historically.

Both the linguistic and genetic origins of the Yayoi prior to their migration from Korea to Japan are disputed. Wikipedia (from the link above) notes that:
Origin 
There are several hypotheses about the origin of the Yayoi people. 
The most popular one is that they were the people who brought wet rice cultivation to Japan from the Korean peninsula and Jiangnan near the Yangtze River Delta in China.[1] This is supported by archeological researches and bones found in today southeastern China.[2] 
Another is that they are from Primorskaya Oblast or northern part of the Korean peninsula. It is because the human bones of the Doihigahama ruins resemble the ancient human bones of the northern part of the Korean peninsula, and pottery is similar to the "Engraved band sentence pottery", widely used during the Yayoi period, was discovered in the Sini-Gai culture in the southwestern coastal province of Primorskaya Oblast.[3] 
The theory that Yayoi people have multiple origins is suggested and influential.[4][5] 
It is estimated that Yayoi people mainly belonged to [Ed. Y-DNAHaplogroup O-M176 and Haplogroup O-M122 which are typical for East- and Southeast-Asians.[6] 
Language 
The Yayoi may have spoken an Austroasiatic language or Tai-Kadai language, based on the reconstructed Japonic terms *(z/h)ina-Ci 'rice (plant)', *koma-Ci '(hulled) rice', and *pwo 'ear of grain' which Vovin assumes to be agricultural terms of Yayoi origin. Vovin suggests that Japonic was in contact with Austronesian, before the migration from Southern China to Japan, pointing to an ultimate origin of Japonic in southern China.[7][8] Although Vovin (2014)[8]does not consider Japonic to be genetically related to Tai-Kadai, he suggests that Japonic was later in contact with Tai-Kadai, pointing to an ultimate origin of Japonic in southern China with possible genetic relation to Austroasiatic
There is typological evidence that Proto-Japonic may have been a monosyllabic, SVO syntax and isolating language; which are features that the Austroasiatic languages also famously exhibit.[8] 
A 2015 analysis using the Automated Similarity Judgment Program resulted in the Japonic languages being grouped with the Austroasiatic languages. The same analysis also showed a connection to Ainu languages, but this is possibly because of heavy influence from Japonic to Ainu.[9]
Many linguistic scholars, however, think that Japonic and Korean are distant members of the Altaic language family which also includes the Turkish, Mongolian and Manchurian (a.k.a. Tungistic) languages.

Japanese has borrowed heavily in the historic era from the Chinese language, without changing its underlying grammar and structure, and has virtually no linguistic connection to the Ainu language which was related to the language of the Jomon people who were invaded by the Yayoi. 

This lack of linguistic borrowing from the Jomon is the case even though Jomon genetic input into the modern Japanese gene pool was very substantial for a hunter-gatherer population, perhaps because hunter-gatherers who fish, like those in Japan, the Pacific Northwest and the Baltic-Finnish region, seem to have more staying power than terrestrial hunter-gatherers, vis-a-vis farmers and herders.

Rethinking The Survival Of The Flattest

In evolution, there is a tradeoff between genomes that are maximally fit but particularly vulnerable to deleterious mutations, and those that are more capable of ignoring deleterious mutations that are less maximally fit, a type of genome known as a "flat" genome. Hence, the notion "survival of the flattest". 

But, it turns out that the trade off is not a perfect one, so minimizing the load in a genome of deleterious mutations still confers improved fitness, according to a recent pre-print:
Populations exposed to a high mutation rate harbor abundant deleterious genetic variation, leading to depressed mean fitness. This reduction in mean fitness presents an opportunity for selection to restore adaptation through the evolution of mutational robustness. In extreme cases, selection for mutational robustness can lead to "flat" genotypes (with low fitness but high robustness) out-competing "fit" genotypes with high fitness but low robustness-a phenomenon known as "survival of the flattest". 
While this effect was previously explored using the digital evolution system Avida, a complete analysis of the local fitness landscapes of "fit" and "flat" genotypes has been lacking, leading to uncertainty about the genetic basis of the survival of the flattest effect.  
Here, we repeated the survival of the flattest study and analyzed the mutational neighborhoods of fit and flat genotypes. We found that flat genotypes, compared to the fit genotypes, had a reduced likelihood of deleterious mutations as well as an increased likelihood of neutral and, surprisingly, of lethal mutations. This trend holds for mutants one to four substitutions away from the wild-type sequence. We also found that flat genotypes have, on average, no epistasis between mutations, while fit genotypes have, on average, positive epistasis. 
Our results demonstrate that the genetic causes of mutational robustness on complex fitness landscapes are multifaceted. While the traditional idea of the survival of the flattest effect emphasized the evolution of increased neutrality, others have argued for increased mutational sensitivity in response to strong mutational loads. Our results show that both increased neutrality and increased lethality can lead to the evolution of mutational robustness. Furthermore, strong negative epistasis is not required for mutational sensitivity to lead to mutational robustness. Overall, these results suggest that mutational robustness is achieved by minimizing heritable deleterious variation.

A Notable Paper Potentially Falsifying String Theory

There are vast numbers of mathematically possible concrete theories called vacua within the class of theories that make up string theory. This makes finding the needle in the haystack that could match reality difficult. This has been one of the main obstacles to developing a string theory phenomenology that can be tested with experiments.

But, it turns out that all, or almost all, of the vacua are topologically inconsistent with observed reality which has a "de Sitter" topology:
De Sitter space and anti-de Sitter space are named after Willem de Sitter (1872–1934), professor of astronomy at Leiden University and director of the Leiden Observatory. Willem de Sitter and Albert Einstein worked in the 1920s in Leiden closely together on the spacetime structure of our universe. 
In the language of general relativity, de Sitter space is the maximally symmetric vacuum solution of Einstein's field equations with a positive cosmological constant (corresponding to a positive vacuum energy density and negative pressure). When n = 4 (3 space dimensions plus time), it is a cosmological model for the physical universe; see de Sitter universe
De Sitter space was also discovered, independently, and about the same time, by Tullio Levi-Civita.
The class of topologically inconsistent vacua are called the "Swampland" and if all or most String theory vacua are in the Swampland then the task of finding a String theory vacuum consistent with our reality, or ruling out String theory entirely becomes much easier.

Woit notes an important new pre-print on "Swampland" string theory vacua (paragraph breaks  and emphasis in bold added), which suggests that all of the Sting theory vacua are in the Swampland.
I haven’t paid much attention to the Swampland business since then, but noticed last night a new preprint with the title What if string theory has no de Sitter vacua?. The authors summarize their argument:
From this analysis we conclude that string theory has not made much progress on the problem of the cosmological constant during the last 15 years. There is a general agreement that the presence of dark energy should be an important clue to new physics. So far, string theory has not been up to the challenge. Or to be more precise, string theorists have not been up to the challenge. 
The well-motivated introduction of the anthropic principle and the multiverse, was a big relief. The mathematical standards were lowered, and unconstrained model building could set in exploring a wild and free landscape of infinite possibilities. But beyond this suggestive connection between a possible multiverse and the rich mathematical structures of string theory not much solid results have been achieved. 
We reviewed some fraction of the mounting evidence that most, if not all of this landscape, is a swampland and we refer to [14,16,149] for similar lines of thought. We believe it makes more sense to listen to what string theory is trying to tell us, then to try to get out of the theory what one would like to have. In recent years, especially with the program of the Swampland [14, 150–152], there is luckily a growing community that embraces this idea. Perhaps this program really already made its first prediction: no measurable tensor modes in the CMB. 
From what we have seen so far, we believe that the most sensible attitude is to accept there are no dS vacua at all because string theory conspires against dS vacua. 
The suggestion here is basically that effective field theories on a deSitter background are in the Swampland, so can’t be derived from string theory. Since we seem to live in a deSitter space, the obvious conclusion to draw from this is that string theory is falsified: it can’t be the fundamental theory we are looking for. The authors discuss various unconvincing ways to try and avoid this conclusion.
Physicists have been working on String Theory for basically my entire life. It has turned out to be a dead end and a distraction for the most part, although it has revealed some important mathematical insights including some relevant to quantum gravity. It is time to look for alternatives.

For what it is worth, it is also possible that gravity and the cosmological constant observed are not actually topological effects as in General Relativity, but are instead has a mechanism that involves the behavior of gravitons in a spacetime that is itself, fundamentally flat rather than being deSitter or anti-deSitter, even though that graviton behavior is similar to and in most circumstances almost exactly equivalent to, a topologically curved spacetime.

Monday, April 9, 2018

Ancient DNA From Patagonia Supports Paradigm

The latest ancient DNA study from South American, although the ancient DNA is just 500 years pre-Columbian, supports the existing paradigm of New World pre-historic demography. Notably, there do not seem to be any hints of Paleo-Asian DNA in these populations.
Significance 
Recent genomic studies of ancient and modern humans from the Americas have given a comprehensive view of the peopling of the continent. However, regional characterization of ancient and modern individuals is lacking, being key to unveiling fine-scale differences within the continent. We present genome-wide analyses of ancient and modern individuals from South America from Western Patagonia. We found a strong affinity between modern and ancient individuals from the region, providing evidence of continuity in the region for the last ∼1,000 years and regional genetic structure within Southern South America. In particular, the analysis of these ancient genomes helps address questions related to the maritime tradition in the region and its diversification posterior to the split from terrestrial hunter-gatherers. 
Abstract 
Patagonia was the last region of the Americas reached by humans who entered the continent from Siberia ∼15,000–20,000 y ago. Despite recent genomic approaches to reconstruct the continental evolutionary history, regional characterization of ancient and modern genomes remains understudied. Exploring the genomic diversity within Patagonia is not just a valuable strategy to gain a better understanding of the history and diversification of human populations in the southernmost tip of the Americas, but it would also improve the representation of Native American diversity in global databases of human variation. Here, we present genome data from four modern populations from Central Southern Chile and Patagonia (n = 61) and four ancient maritime individuals from Patagonia (∼1,000 y old). Both the modern and ancient individuals studied in this work have a greater genetic affinity with other modern Native Americans than to any non-American population, showing within South America a clear structure between major geographical regions. Native Patagonian Kawéskar and Yámana showed the highest genetic affinity with the ancient individuals, indicating genetic continuity in the region during the past 1,000 y before present, together with an important agreement between the ethnic affiliation and historical distribution of both groups. Lastly, the ancient maritime individuals were genetically equidistant to a ∼200-y-old terrestrial hunter-gatherer from Tierra del Fuego, which supports a model with an initial separation of a common ancestral group to both maritime populations from a terrestrial population, with a later diversification of the maritime groups.

Modern Human Remains In Arabia 86,000 Years Ago

Tools associated with modern humans in inland Arabia have suggested that modern humans arrived there ca. 125,000 years ago, but modern human remains are much more powerful evidence and the latest find on that front is from at least 86,000 years ago.
Understanding the timing and character of the expansion of Homo sapiens out of Africa is critical for inferring the colonization and admixture processes that underpin global population history. It has been argued that dispersal out of Africa had an early phase, particularly ~130–90 thousand years ago (ka), that reached only the East Mediterranean Levant, and a later phase, ~60–50 ka, that extended across the diverse environments of Eurasia to Sahul. However, recent findings from East Asia and Sahul challenge this model. Here we show that H. sapiens was in the Arabian Peninsula before 85 ka. We describe the Al Wusta-1 (AW-1) intermediate phalanx from the site of Al Wusta in the Nefud desert, Saudi Arabia. AW-1 is the oldest directly dated fossil of our species outside Africa and the Levant. The palaeoenvironmental context of Al Wusta demonstrates that H. sapiens using Middle Palaeolithic stone tools dispersed into Arabia during a phase of increased precipitation driven by orbital forcing, in association with a primarily African fauna. A Bayesian model incorporating independent chronometric age estimates indicates a chronology for Al Wusta of ~95–86 ka, which we correlate with a humid episode in the later part of Marine Isotope Stage 5 known from various regional records. Al Wusta shows that early dispersals were more spatially and temporally extensive than previously thought. Early H. sapiens dispersals out of Africa were not limited to winter rainfall-fed Levantine Mediterranean woodlands immediately adjacent to Africa, but extended deep into the semi-arid grasslands of Arabia, facilitated by periods of enhanced monsoonal rainfall.
H.S. Groucutt et al. "Homo sapiens in Arabia by 85,000 years ago." Nature Ecology & Evolution. (April 9, 2018) doi:10.1038/s41559-018-0518-2.

Commentary by the authors of the paper notes that:
According to the old textbook view, our species evolved in Africa about 200,000 years ago. Despite a brief, failed expansion to the edge of Eurasia about 100,000 years ago when humans first tried migrating to the lands at the eastern end of the Mediterranean (the Levant), we only successfully spread out of Africa around 60,000 to 50,000 years ago. 
Recent evidence suggests that much of this narrative is wrong. Findings in Africa, such as from the site of Jebel Irhoud in Morocco, suggest that Homo sapiens appeared early, more than 300,000 years ago. Our origin does not seem to have occurred in only one small area, but across much of Africa. 
Findings from the Levant, most recently the dating of a maxilla (upper jawbone) from Misliya Cave in Israel, suggest our species repeatedly expanded into the winter-rainfall fed, forested area just outside Africa. We don’t yet know if people survived long term in the Levant, which is a very small area. It seems more likely that there were repeated migrations from Africa. 
But what about the areas beyond the Levant? Recent findings suggest that our species got to East Asia and Australia much earlier than had been thought. But determining the hominin species present and the age of these sites have proven challenging. 
Our finger fossil gives us a more specific time range to work with, which correlates with other evidence. Stone tools from Al Wusta are similar to those from the Middle Palaeolithic (Stone Age) period in the Levant and north-east Africa. They suggest that our early spread into Eurasia was not associated with some kind of technological breakthrough, such as the invention of projectile technology as some have suggested
Together, these findings show that Homo sapiens had spread beyond the Levant much earlier than traditional accounts would have it. The Al Wusta phalanx is the oldest directly dated fossil of our species beyond Africa and the Levant and so represents a crucial reference point in understanding this topic.
Here is a link to images of arrowheads found by the same investigator.

Sunday, April 8, 2018

Quote Of The Day

Of course the scientific paper will not die any time soon. I know that because I've measured the approximate speed by which academia moves, and it's about 0.01 mm per millenium.
Sabine Hossenfelder‏ @skdh Apr 5, 2018

Thursday, April 5, 2018

Something Very Amiss In Archaic Admixture Presentation



A conference presentation on archaic admixture including Denisovan admixture purports to show an admixture date of 25,000 to 40,000 years ago, which isn't remotely plausible given existing archaeological knowledge (it should be more like 50,000 to 65,000 years ago). 

For what it's worth, I do like the "heart" icons for admixture events (even though my suspicion is that those admixture events were not actually long term romantic encounters, and may have been mostly rapes).

The abstract of the paper from 2016 discussed in the presentation is as follows:
The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama–Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25–40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10–32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.
Anna-Sapfo Malaspina, et al., "A genomic history of Aboriginal Australia" 538 Nature 207-214 (October 13, 2016) doi:10.1038/nature18299

More details about the sample, including uniparental haplotypes are available here. The main supplements are here. The dating is discussed in the S07 supplemental materials.

No subsamples of Aboriginal Australians (except three outlier individuals two of whom have known mixed Papuan and Australian ancestry) have greater than average genetic affinities to any particular Papuan population and no Papuans in the sample have greater than average genetic affinities to any particular Australian population. There is no significant difference in Denisovan admixture proportions between Papuans and Aboriginal Australians after controlling for recent Eurasian admixture. ANCESTRY software analysis supports a "shared genetic origin of Aboriginal Australians, Papuans and Bougainvilleans[.]" Various scenarios for one or two Out of Africa events and one or two Neanderthal admixture events, in addition to one Denisovan admixture event in all cases are nearly degenerate in their fit to the data.

The Denisovan related population that admixes with Papuans and Australian Aborigines is about 400,000 years diverged from the Altai Denisovans per S07 supplemental materials.

All Papuan and Australian populations in the study as well as the mainland Asian Dai population picked as representative, show a bottleneck in effective population size to 2,000 to 3,000 people from about 60,000 years ago to 40,000 years ago, preceded by falling effective population size back to the dawn of the species, followed by growing effective population sizes. But, several Australian sub-populations show a dip in effective population size from 10,000 years ago to 5,000 years ago.

Given the discussion in the abstract, it would be possible to reconcile the genetic based estimates and the archaeology if the archaic admixture actually took place coincident with divergence from Eurasians 51-72 kya. In that scenario, the 25-40 thousand years ago date could reflect the point at which Papuan and Aboriginal Australians ceased to be a common gene pool in Sahul because they ceased to exchange brides and/or husband with each other, perhaps as the last major ice age began to have an impact. A bottleneck event in Australia later (perhaps around the time of the Last Glacial Maximum or the Younger Dryas), or at about the same time, wiping out all other Australian populations and reducing the last one to a small founding population could then have occurred ca. 10-32 kya.

I remain skeptical, however, because other genetic studies have pointed to an almost immediate divergence of Papuans from Aboriginal Australians at about the same time as the two populations crossed the Wallace line and diverged from other Eurasians. Also, the archaeology suggests that there were little trade or interaction between the Papuans and the Aboriginal Australians, even during the time period when they could have interacted over a land bridge.

This Wikipedia summary regarding the ancient contours of Sahul states (omitting references to much later Austronesian contact in the Holocene era, i.e. less than 10,000 years ago):
Humans first populated eastern Wallacea (including Timor, which at the time was separated from mainland Sahul), the rest of Sahul, and the Bismarck Archipelago from Sunda around 45,000 years ago, by a founding population estimated to have been at least several hundred, and having had relatively sophisticated water craft.[44] There was little subsequent population mixing between Wallacea and Sahul for about 30,000 years, and indeed relatively little mixing between the north and south and the east and west of Sahul after the initial dispersal of the population. 
Indigenous Australians are the original inhabitants of the Australian continent and nearby islands who migrated from Africa to Asia around 70,000 years ago[45] and arrived in Australia around 50,000 years ago.[46] They are believed to be among the earliest human migrations out of Africa. . . .
The original inhabitants of the group of islands now named Melanesia were likely the ancestors of the present-day Papuan-speaking people. Migrating from South-East Asia, they appear to have occupied these islands as far east as the main islands in the Solomon Islands, including Makira and possibly the smaller islands farther to the east.[48]
Also, the estimate for arrival of humans in Australia is conservative. This linked Wikipedia article notes evidence of humans in Australia 65,000 years ago citing to: Clarkson, Chris, et al., "Human occupation of northern Australia by 65,000 years ago" 547 (7663) Nature 306–310 (July 19, 2017) doi:10.1038/nature22968.

A minority view that could explain the discrepancy between the genetic data and the archaeological data (which is admittedly thin before about 40,000 years before present), is that the first wave of modern humans in Australia could have gone extinct or become moribund only to be replaced by a second wave of settlers from Wallacea or Papua New Guinea that was also Denisovan admixed. As one Wikipedia footnote explains:
The dominant view among archaeologists and palaeoanthropologists is that the earliest humans in Australia were among the ancestors of modern Aborigines. There is some evidence to the contrary. For instance, among the Lake Mungo remains, the mtDNA of the remains known as LM3 do not indicate a close relationship to modern Aborigines, according to "Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins" (PNAS, volume 98, issue 2) by Adcock et al. This finding has not been widely accepted by the palaeoanthropological community.
There are certainly examples of first wave colonization efforts of new territory that failed (e.g., the Leif Erikson's Vikings in North America ca. 1000 CE, and Roanoke in what would become the United States, and Madagascar in the early 1st Millenium), only to be followed by colonizations that thrived later on, however. And, there are also examples of near total population replacement (e.g. Great Britain in the Bell Beaker era) in a place. So, this theory can't be entirely dismissed out of hand, so long as the resettling population also had Denisovan admixture.

Another possibility is that there is a problem with the methodology or assumptions of the 2016 paper. For example, that papers could be using inaccurate assumptions about effective population size or population structure or mutation rates or generation duration that distort the paper's estimates.


Saturday, March 31, 2018

Ancient DNA From Pakistan And The Vicinity

The big South Asian ancient DNA paper is finally out (in pre-print form) after many months of waiting and publication delays (purportedly for political reasons). UPDATE: This is not actually the long awaited Indian DNA paper, although it answers many of the same questions by using different ancient DNA data. END UPDATE.

The big news that we've been awaiting is the twelve ancient DNA samples from a cemetery in Pakistan. The gender, mtDNA, Y-DNA and Y-DNA classification of those samples follows. 

There are also hundreds other ancient DNA samples over a wide range of time from the vicinity included. I will update my analysis and the findings as time permits. The abstract, some key figures and lots of discussion in the comments is available at Eurogenes. Razib does a nice job of dissecting the pre-print.


M R30b1 L1a South Asian Private
M .. L1a South Asian Private
M W3a1b R1b1a1a2a1a1c2b2b1a2 R-M269/U106/Z381/S499
M W3a1b R2a South Asian Private
M U2e1'2'3 C1b1a1a1 SW Asia, Central Asia and South Asia
M M4 L1a South Asian Private
M M5a Q1b2 SW Asia
M U7a .. Female
F T2g1 .. Female
F U2c1 .. Female
F U3b1a1 .. Female
M T2g1 L1a South Asian Private

It strongly appears that Y-DNA L1a, R2a and Q1b2 al derive from Iranian farmers.

UPDATE April 4, 2018: I left this comment at Razib's blog:

“Also, the polytomy at the base of the eastern Eurasian human family tree, where all the major lineages diverge rapidly from each other, makes me wonder about gene flow vs. admixture. It seems possible that the polytomy may mask a phylogenetic tree topology which had gradually bifurcating nodes, if periodically a single daughter population replaced all its sister lineages in a local geographic zone. Much of history in human meta-populations may be characterized by isolation-by-distance and gene flow, erased by the extinction of most lineages and expansion of a favored lineage.”

This is a really interesting observation, and both possibilities, naively, seem pretty plausible.

It is almost unthinkable that there was complete genetic continuity and stasis in South Asia from prior to 65,000 BP to 6000 BP. All of the examples we have point to very sustained stasis as very rare, even though turnover may have happened less frequently among hunter-gatherers than among Holocene people at the continental level. The late modern history of hunter-gatherer tribes of Native Americans, for example, suggests that moderately long distance folk wanderings and exterminations of whole tribes were relatively common even on time scales of 1000 years or so.

There were probably at least two significant waves of migration and expansion after the one that gave rise to the Papuans in mainland Asia that greatly interrupted HG genetics there.

Y-DNA D people were probably a mid Upper Paleolithic Northern route arrival in Asia (although pre-LGM given Y-DNA D in the Andamanese) and were possibly male dominated (given that the Onge autosomally are close to AASI), that migrated to South Asia from Tibet to the South ultimately reaching Burma and the Andamans (since phylogeny-wise the Y-DNA D of India and the Andamans is closer to Siberian and Tibetan Y-DNA D than to Japanese Y-DNA D which splits at a very basal point from other Y-DNA D). Other Y-DNA D people take the Northern route to become the founding Jomon people of Japan. Most Y-DNA D people of Northern Asia in between are wiped out in the LGM.

Y-DNA C is remarkably rare and quite low if phylogenetic diversity in South Asia. This could simply mean that the coastal route theory for Y-DNA C is wrong, and that instead it took a clockwise northern route to reach East Asia, mainland SE Asia and Island SE Asia, and the lack of phylogenetic diversity of Y-DNA C in South Asia tends to support that reading of the data. But, another possibility, given the proportionately high level of C-M130* in South Asia relative to other Y-DNA C haplotypes is that Y-DNA C differentiated from Y-DNA CF in India, with lots of Y-DNA C people migrating east, but a few remaining, and that Y-DNA F people (including sister Y-DNA clade Y-DNA H people) subsequently wiped out most of the original Y-DNA C right population of South Asia, and that a lot of Y-DNA C people in India today are associated with a Y-DNA C1b1 back migration later in the Upper Paleolithic. The fact that autosomal ASI ancestry in India is pretty much proportional to Y-DNA C proportions in India, even though the proportions are low, also points to the antiquity of Y-DNA C in India, followed by later events.

In particular, the Y-DNA C people in India were probably marginalized by the expansions of Y-DNA F*, F1, F3 and H in India in the pre-Neolithic period, with other clades of F and daughter clades derived from F expanding into both West Eurasia and East Eurasia where the expanding clades became dominant. It is hard to know what gave the Y-DNA F/H people a decisive advantage over the Y-DNA C people in India and elsewhere, although forced to supply my best guess, I might suspect dog domestication or perhaps mastering how to turn wild grains into flour (flour predates the Neolithic revolution by at least ten or twenty thousand years).

It is also worth noting that ancient DNA suggests that in parallel with these developments in India, that Y-DNA C was once much more common than it is today in Europe, which definitely reflects Neolithic and Steppe driven replacement of remaining European HGs with Y-DNA C, but which may also reflect Mesolithic era replacement.

Similarly, in East Asia and SE Asia, Y-DNA O which is also a remote descendant of Y-DNA F, also sweeps those regions even before the Neolithic revolution.

If Indian nationalists want to discuss their basal and formative influence on the rest of the world, they would be well advised to de-emphasize the Bronze Age and to instead focus on how, on one hand, Y-DNA F is the dominant ancestor of modern Eurasian Y-DNA clades and that it probably originated in India (or at least had its first major expansion there), and how, on the the other hand, in the Iron Age, Buddhism, which also has its origins in India, came to be a profound and arguably dominant religious influence in East Asia.

Of course, the problem is that Indian Nationalism today is Hindu rather than Buddhist, which is a religious movement that India didn’t heavily export and which outside Bali didn’t have much staying power where it was exported, and which isn’t entirely home grown, even though much of it has local roots.

Similarly, the expansion of Y-DNA F people to become the predominant people of Eurasia (especially West Eurasia) is so remote and thinly attested archaeologically that it is hard to identify with those ancient hunter-gathers.

Friday, March 30, 2018

A Galaxy Without Dark Matter?

The Hubble Space telescope has observed an ultra diffuse galaxy which does not seem to have any dark matter or modified gravity effects. The abstract of the preprint states:
Studies of galaxy surveys in the context of the cold dark matter paradigm have shown that the mass of the dark matter halo and the total stellar mass are coupled through a function that varies smoothly with mass. Their average ratio M_{halo}/M_{stars} has a minimum of about 30 for galaxies with stellar masses near that of the Milky Way (approximately 5x10^{10} solar masses) and increases both towards lower masses and towards higher masses. The scatter in this relation is not well known; it is generally thought to be less than a factor of two for massive galaxies but much larger for dwarf galaxies. 
Here we report the radial velocities of ten luminous globular-cluster-like objects in the ultra-diffuse galaxy NGC1052-DF2, which has a stellar mass of approximately 2x10^8 solar masses. We infer that its velocity dispersion is less than 10.5 kilometers per second with 90 per cent confidence, and we determine from this that its total mass within a radius of 7.6 kiloparsecs is less than 3.4x10^8 solar masses. 
This implies that the ratio M_{halo}/M_{stars} is of order unity (and consistent with zero), a factor of at least 400 lower than expected. NGC1052-DF2 demonstrates that dark matter is not always coupled with baryonic matter on galactic scales.
Pieter van Dokkum, et al., "A galaxy lacking dark matter",  arXiv (March 27, 2018). A follow up paper by the same authors is here. It's abstract is as follows:
We recently found an ultra diffuse galaxy (UDG) with a half-light radius of R_e = 2.2 kpc and little or no dark matter. The total mass of NGC1052-DF2 was measured from the radial velocities of bright compact objects that are associated with the galaxy. Here we analyze these objects using a combination of HST imaging and Keck spectroscopy. Their average size is <r_h> = 6.2+-0.5 pc and their average ellipticity is <{\epsilon}> = 0.18+-0.02. From a stacked Keck spectrum we derive an age >9 Gyr and a metallicity of [Fe/H] = -1.35+-0.12. Their properties are similar to {\omega} Centauri, the brightest and largest globular cluster in the Milky Way, and our results demonstrate that the luminosity function of metal-poor globular clusters is not universal. The fraction of the total stellar mass that is in the globular cluster system is similar to that in other UDGs, and consistent with "failed galaxy" scenarios where star formation terminated shortly after the clusters were formed. However, the galaxy is a factor of ~1000 removed from the relation between globular cluster mass and total galaxy mass that has been found for other galaxies, including other UDGs. We infer that a dark matter halo is not a prerequisite for the formation of metal-poor globular cluster-like objects in high redshift galaxies.

This is an extreme outlier of a result, which, if true, poses serious issues for modified gravity theories and for theories about how dark matter usually ends up tightly correlated with baryonic matter if it exists.

There are several possibilities:

1. It could be the product of MOND with an external field effect. The paper notes that the MOND prediction is off by about a factor of two (which beats the factor of 400 problem with the expectation from dark matter theory noted in the abstract handily), but the calculation, at first glance, didn't appear to have considered the external field effect, which should tweak the result in the right direction. If MOND with an external field effect makes an accurate prediction it is a huge vindication of that particular theory (which obviously still have to be generalized to the relativistic case) and very close cousins of it. But, if the reality is contrary to the MOND with external field effect prediction, it could suggest that, at a minimum, MOND is not the right way to modify gravity. Specifically, the paper states with respect to what MOND would predict that:
For a MOND acceleration scale of a0 = 3.7 × 10^3 km^2 s^−2 kpc^−1, the expected velocity dispersion of NGC1052–DF2 is σM ≈ (0.05 GMstarsa0) 1/4 ≈ 20 km s^−1 , a factor of two higher than the 90% upper limit on the observed dispersion.
The external field effect reduces velocity dispersion in dwarf galaxies when present by an amount that appears to be about right on an order of magnitude basis.

This would happen if the gravitational field was NGC1052 at a range of 20 MPc was greater than a0 or greater than the gravitational field due to the dwarf galaxy.

2. It could be a function of a unique geometry that causes gravitational effects from dark matter and/or modified gravity to cancel out (or at least appear to cancel out for a viewer from our direction). In Deur's work, this happens when a galaxy or other structure is spherically symmetric or nearly so. In other cases, some geometries can cause force vectors from gravitational pulls in opposite directions from different masses to cancel out if they are arranged just so.

3. It could be a methodology problem. The calculation of the inferred dark matter and velocity dispersion is quite involved and there are lots of instrumental issues and calculation issues that could lead to such an extreme outlier result.

All three possibilities are supported by this description of the galaxy (emphasis added):
In terms of its apparent size and surface brightness it resembles dwarf spheroidal galaxies such as those recently identified in the M101 group at 7 Mpc, but the fact that it is only marginally resolved implies that it is at a much greater distance. Using the I814 band image we derive a surface brightness fluctuation distance of DSBF = 19.0 ± 1.7 Mpc (see Methods). It is located only 14' from the luminous elliptical galaxy NGC 1052, which has distance measurements ranging from 19.4 Mpc to 21.4 Mpc. We infer that NGC1052–DF2 is associated with NGC 1052, and we adopt D ≈ 20 Mpc for the galaxy.
For the Crater II galaxy, a distance of 120 kpc from the Milky Way galaxy led to a Milky Way gravitational field eight times larger than necessary to induce a strong external field effect, and while this dwarf galaxy is about 166 times further from the NGC 1052 as Crater II is from the Milky Way, elliptical galaxies are typically much larger than spiral galaxies, so they have stronger external fields at the same distance.

The Milky Way's mass is about 5.8*10^11 solar masses. NGC1052-DF2 appears to have a mass about 200 times smaller than the Milky Way. Giant elliptical galaxies have up to about 10^13 solar masses. But, the mass of this one has been measured to be only about 1.25 to 4 times larger than the Milky Way (up to almost 6x at two sigma). The estimated mass of NGC1052 (the parent galaxy) is as follows:
Using the kinematic information from the 16 GCs, we can estimate the mass enclosed within the radius of the GC system observed. We use the projected mass estimator (Evans et al. 2003), assuming isotropy and an r−4 distribution, to derive a mass of 1.7 ± 0.9 × 10^12M⊙ within 19 kpc (∼6.5re). The mass estimate error was calculated by bootstrapping the observed velocities and errors. van Gorkom et al. (1986) used HIkinematics to measure a mass of 3.1 × 10^11M⊙ within 23 kpc.
Given the only moderately greater mass and much greater distance, whether or not the external field effect applies here is close thing. If the greater distance reduces the external field strength by less than a factor of 18-54 (284 km/s for the Milky Way external field on Crater II v. 20 km/s for this galaxy scaled by the higher mass of this galaxy; up to about 81 at two sigma for the NGC1052 mass), then the external field effect should be present. But, a distance 166 times further from the dwarf galaxy should reduce the parent galaxy's gravitational field on the dwarf galaxy by more than a factor of 54 (or even the two sigma factor of 81). So, my back of napkin estimate, which could be flawed, suggests that there should be an external field effect from NGC1052 on NGC1052-DF2, or at least, not a full fledged one, unless there is some other source of a stronger external field acting on NGC1052-DF2.

So, spherical symmetry in the Deur paradigm looks like a more likely explanation than the external field effect in MOND, at first glance.

Another possibility is that an unusually rich interstellar gas/dust medium could increase a naive estimate of the strength of local gravitational fields in this system.

Still, this bears further investigation as it is a potentially extremely important data point, which is something I don't have the time to do in depth at the moment.

UPDATE April 2, 2018: This post suggests that the correctly calculated MOND prediction is 14+/- 4 and that the measured value is 8.4 with a 90% confidence interval upper limit of 10. So, it does not disprove MOND, the paper's calculation simply failed to consider the external field effect. The limited data points used in the calculation (ten) also suggests that the measured value is likely to be an underestimate as it was in FORNAX. And, the 20 mpc was distance from Earth, not distance from the dwarf to the elliptical which is about 80 kpc, which is the main reason that my calculation was off.

UPDATE April 3, 2018 (from the comments to the previous link by its author):
On closer reading, I notice in the details of their methods section that the rms velocity dispersion is 14.3 km/s. It is only after the exclusion of one outlier that the velocity dispersion becomes unusually low. As a statistical exercise rejecting outliers is often OK, but with only 10 objects to start it is worrisome to throw any away. And the outlier is then unbound, making one wonder why it is there at all. 
Consider: if they had simply reported the rms velocity dispersion, and done the MOND calculation correctly, they would have found excellent agreement. This certainly could be portrayed as a great success for MOND. Instead, tossing out just one globular cluster makes it look like a falsification. Just one datum, and a choice of how to do the statistics. Not a wrong choice necessarily, but a human choice… not some kind of statistical requirement.
UPDATE April 11, 2018

One of the authors addresses a variety of concerns (of the kind that quite honestly should have been addressed at a pre-print/peer review stage rather than post-publication) (hat tip Backreaction).

In particular, he justifies at great length his velocity dispersion calculation, although the paper really fails seriously in failing to address just how problematic and assumption prone it really is and the reasoning behind the choices made. The uncertainty due to fundamental assumption issues is greatly understated.

He acknowledges that he screwed up the MOND calculation and shifts attention from that mistake to a different dwarf galaxy (Dragonfly 44) where MOND might be off without conclusively showing that this is the case. He states:  "The whole MOND / alternative gravity discussion in the paper rests on a misunderstanding on my part."

He acknowledges the need for more and better data to get a more accurate measurement, some of which can be done quite easily (and really should have been done prior to publication in Nature).

He unconvincingly argues that "lacking" and "without" have different meanings while backpedaling on the "no" dark matter claim, although this criticism isn't honestly such a big deal since other language in the abstract does clarify the point (and indeed highlights that the dark matter a priori prediction was off by a factor of 100 v. a factor of about 0.4 at most for the correctly done MOND prediction).

Bottom line: Nature printed what was really a rough draft with some serious problems as a final and definitive work.

UPDATE April 14, 2018

A rebuttal paper.

Monday, March 26, 2018

Quantum Mechanical Interpretations

Woit reviews a new book discussing the different prevailing interpretations of quantum mechanics (Copenhagen, Many World, Bohmian, etc.) and in the process does something even more useful. He refers us to an arXiv pre-print, which he finds to be a better treatment of the subject, in addition to being shorter and free and instantly available. He describes the article this way:
For a . . . recent serious take on the issues involved, I’d recommend reading something by Wojciech Zurek, for instance this article, a version of which was published in Physics Today. Trying to figure out what “interpretation” Zurek subscribes to, I notice that he refers to an “existential interpretation” in some of his papers. I don’t really know what that means. Unlike most discussions of “interpretations”, Zurek seems to be getting at the real physical issues involved, so I think I’ll adopt his (whatever it means) as my chosen “interpretation”.
The article opens in this way:
Quantum principle of superposition decrees every combination of quantum states a legal quantum state. This is at odds with our experience (Fig. 1). 
Decoherence selects preferred pointer states that survive interaction with the environment. They are localized and effectively classical. They persist while their superpositions decohere. Decoherence marks the border between quantum and classical, alleviating concern about flagrant and manifestations of quantumness in the macroscopic domain. 
Here we consider emergence of ‘the classical’ starting at a more fundamental pre-decoherence level, tracing the origin of preferred pointer states and deducing their probabilities from the core quantum postulates. We also explore role of the environment as a medium through which observers acquire information. This mode of information transfer leads to perception of objective classical reality.
The arXiv says this about the eight page long pre-print:

Quantum Darwinism, Classical Reality, and the Randomness of Quantum Jumps

Tracing flows of information in our quantum Universe explains why we see the world as classical.
Comments:This manuscript, after cuts and edits to comply with Physics Today limits and style, was published last October. It may have some rough edges, but it also contains technical elaborations omitted from the published version for lack of space that may be of interest to some readers. Thus, while the essence is the same, but there are differences (starting with the title and abstract)
Subjects:Quantum Physics (quant-ph)
Journal reference:Physics Today, vol. 67, pp. 44-50 (2014).

Sunday, March 25, 2018

Was The Dali Skull A Denisovan?

Consider the Dali skull in China from 209,000 +/- 23,000 years ago. 



Was it a Denisovan? As one person in the linked twitter thread notes:

It is not a Neanderthal and and too recent for Homo heidelbergensis. It is almost as old as the oldest trace of modern humans in Africa, and it is about 100,000 years older than the oldest Out of Africa modern human known from any other source.

We don't have ancient DNA from this 1978 discovery or several other ill classified old hominin fossils from China.

Wikipedia notes that:
The Dali cranium is interesting to modern anthropologists as it is possibly a well-preserved example of archaic Homo sapiens; it has a mixture of traits from Homo erectus and Homo sapiens.The details of the face and skull are however distinct from European Neanderthals and earlier European hominids, such as remains found in Petralona cave and Atapuerca. . . . 
There has been considerable debate regarding how to classify the fossil in terms of species, with some anthropologists insisting it to be a regional variant of Homo heidelbergensis and others categorizing it as an early representative of Homo sapiens, and as such there is no current consensus on the species status of the Dali fossil. Some anthropologists, notably many Chinese representatives, cite the characteristics of the Dali cranium and other similar Chinese fossils of that era as evidence for genetic continuity in modern H. sapiens today, as Dali's traits are commonly found in modern Chinese H. sapiens populations. . . . 

An assortment of primitive Homo skulls have tentatively been placed with the Dali find. The Maba Man, a 120 to 140 000 year old fragmentary skull from Guangdong in China shows the same general contours of the forehead. A partial female skeleton with skull from Jinniushan (also China) seems to belong to the same group, characterized by a very robust skull cap but less robust skull base. A possibly fourth member could be the Narmada skull from the Madhya Pradesh in India, consisting of a single robust cranial vault
The Denisova hominin, represented by a very robust finger bone found in the Altai mountains in Russia is quoted as likely linked to the Dali people. DNA studies show the bone belong to a woman, with Mitochondrial DNA linking it to a very deep split in the human tree, at around 1 million years old. This would make the DNA erectus rather than heidelbergensis or other more recent splits. However, the analysis of the nuclear DNA points to a sister group relationship with the neanderthals.
Even one DNA match to Denisovans from any of the skulls in this category could make a very strong case for the classification of all of them.

A related question is whether Dali-hominins replaced Homo erectus in China, co-existed with Homo erectus in China, or evolved from Homo erectus in China. 

Thursday, March 22, 2018

The Impossible Early Galaxy Problem

This paper and its proposed solution is less notable than its discussion of the problem with the standard model of cosmology, which is known as the "impossible early galaxy problem". In general, modified gravity theories lead to earlier structure development in cosmology, so this problem favors such theories relative to dark matter, although modified gravity isn't necessarily the only possible solution.
To understand the formation and evolution of galaxies at redshifts z < 10, one must invariably introduce specific models (e.g., for the star formation) in order to fully interpret the data. Unfortunately, this tends to render the analysis compliant to the theory and its assumptions, so consensus is still somewhat elusive. 
Nonetheless, the surprisingly early appearance of massive galaxies challenges the standard model, and the halo mass function estimated from galaxy surveys at z > 4 appears to be inconsistent with the predictions of LCDM, giving rise to what has been termed "The Impossibly Early Galaxy Problem" by some workers in the field. A simple resolution to this question may not be forthcoming. 
The situation with the halos themselves, however, is more straightforward and, in this paper, we use linear perturbation theory to derive the halo mass function over the redshift range z < 10 for the R_h=ct universe. We use this predicted halo distribution to demonstrate that both its dependence on mass and its very weak dependence on redshift are compatible with the data. 
The difficulties with LCDM may eventually be overcome with refinements to the underlying theory of star formation and galaxy evolution within the halos. For now, however, we demonstrate that the unexpected early formation of structure may also simply be due to an incorrect choice of the cosmology, rather than to yet unknown astrophysical issues associated with the condensation of mass fluctuations and subsequent galaxy formation.
Manoj K. Yennapureddy, Fulvio Melia, "A Cosmological Solution to the Impossibly Early Galaxy Problem" (March 19, 2018).

A related issue is that we don't know how black holes got so big so fast under existing cosmology models.

Metal enrichment in the intergalactic medium in the very early universe also challenges our models.

Wednesday, March 21, 2018

More Archaic Admixture Data

More Ancient Neanderthal Genomes

An article in Nature provides great understanding of Neanderthal admixture by adding five new autosomal Neanderthal genomes to our pool of knowledge:
Although it has previously been shown that Neanderthals contributed DNA to modern humans, not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared. 
Our ability to retrieve DNA from a larger number of Neanderthal individuals has been limited by poor preservation of endogenous DNA and contamination of Neanderthal skeletal remains by large amounts of microbial and present-day human DNA. Here we use hypochlorite treatment6 of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five Neanderthals who lived around 39,000 to 47,000 years ago (that is, late Neanderthals), thereby doubling the number of Neanderthals for which genome sequences are available. 
Genetic similarity among late Neanderthals is well predicted by their geographical location, and comparison to the genome of an older Neanderthal from the Caucasus indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neanderthal history. We find that the bulk of Neanderthal gene flow into early modern humans originated from one or more source populations that diverged from the Neanderthals that were studied here at least 70,000 years ago, but after they split from a previously sequenced Neanderthal from Siberia around 150,000 years ago. Although four of the Neanderthals studied here post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.
The bottom line is that most Neanderthal admixture in modern humans can be traced to the Out of Africa era in a population that would have been basal to almost all non-African modern humans, even Papuans who together with Australian Aborigines who diverge from other non-African modern humans at the most basal point, probably around 65,000-70,000 years ago. If modern humans made it into Asia and Europe before then, and Altai Neanderthal admixture dated to ca. 100,000 years ago suggests that this did happen somewhere, they have not left much of a genetic trace in modern humans.

This makes sense. First wave modern humans in Europe and Siberia mostly went extinct in an ice age about 20,000 years ago, so any subsequent admixture in the Neanderthals European homeland would have been lost. By the time that modern humans recolonized Europe, Neanderthals were extinct.

Inferred Archaic Admixture In Africans

There is essentially no Neanderthal admixture or Denisovan admixture in sub-Saharan Africans that can't be traced to Eurasian back migration to Africa. But, that doesn't mean that the ancestors of today's sub-Saharan Africans didn't also experience admixture with archaic hominins. It just means that they admixed with different hominins from whom we have no ancient DNA, in part due to poor conditions for preserving it, and in part due to insufficient resources devote to looking for potential samples.

But, it is possible to reliably estimate ancient admixture from "ghost populations" of hominins by statistically analyzing patterns in the genomes of people who are alive today and these methods have been validated by comparing their results to those obtained from direct comparisons to ancient homin genomes.

What have scientists found?

According to a new preprint at bioarXiv that largely confirms a couple of prior studies along the same lines:
Analyses of Neanderthal and Denisovan genomes have characterized multiple interbreeding events between archaic and modern human populations. 
While several studies have suggested the presence of deeply diverged lineages in present-day African populations, we lack methods to precisely characterize these introgression events without access to reference archaic genomes. We present a novel reference-free method that combines diverse population genetic summary statistics to identify segments of archaic ancestry in present-day individuals.  
Using this method, we find that ~7.97±0.6% of the genetic ancestry from the West African Yoruba population traces its origin to an unidentified, archaic population (FDR [false discovery rate] ≤20%). We find several loci that harbor archaic ancestry at elevated frequencies and that the archaic ancestry in the Yoruba is reduced near selectively constrained regions of the genome suggesting that archaic admixture has had a systematic impact on the fitness of modern human populations both within and outside of Africa.
This admixture percentage rivals that of Papuans and aboriginal Australians. It is equivalent to a situation at the time shortly after archaic introgression had ceased, in which the average person had 1.5 great-grandparents who were archaic hominins. This is roughly four times the archaic admixture proportion found in Europeans, and a somewhat lower multiple of Asians who have no Papuan ancestry. It is similar to the total amount of archaic admixture in Papuans. 

But, in this case, it involves West Africans who, unlike early of of Africa modern human populations and proto-Papuan populations, did not experience a really severe population bottleneck in their demographic history that the other populations did.

The study controlled for admixture with highly diverged African populations like Biaka Pygmies.

It is kind of nuts that we can see this huge amount of archaic admixture, and yet have no meaningful idea what kind of hominin was those source of this admixture, just as it is pretty crazy that we can document Denisovan admixture so well while having no real idea what a Denisovan looked like.

As in other cases of archaic admixture, with Neanderthals and Denisovans, it also appears that natural selection has weeded out archaic ancestry from our genomes in areas where modern human genes provide a fitness advantage relative to archaic hominins, who were, on average, less fit than modern humans. But, as in other cases of archaic admixture, there are a few loci where archaic admixture is elevated, suggesting that the introgressed genes provided their descendants with selective advantages involving those loci.

Other studies have found a distinct source of archaic admixture in a different sub-Saharan African Paleo-African population.

While this method was superior in identifying particular loci where archaic introgression did or did not take place, unlike prior studies of this type, the paper does not expressly identify how deeply diverged the archaic population is from the modern humans who admixed (other than that they are much more diverged than the most divergent modern human populations), nor does it identity how long ago this admixture event probably took place, something that prior studies have put shortly before the Holocene era (i.e. more than 10,000 years ago, but not that much earlier than that; certainly in the Upper Paleolithic era).

A finding for the West African Yoruba has wide relevance to sub-Saharan Africa because almost all populations except for a handful of relicts, gained substantial Bantu admixture in the mid-Holocene era, and the Bantu have origins geographically close to that of the Yoruba.

Linguistic Analysis Argues For Expansion Of Proto-Dravidian With South Indian Neolithic


Languages attested in writing more than 950 years ago shown in bold.

A new linguistic analysis argues that the Dravidian languages arose ca. 2500 BCE, the same time as the South Indian Neolithic Revolution. This is one very plausible date, although other studies have argued for a more recent origin on linguistic grounds (and one study argued, implausibly, for a 13000 years BP date). If this is the date of origin it pre-dates the arrival of Indo-Europeans in India by 500-1000 years, and precedes the arrival of Indo-Europeans in the Dravidian linguistic area by a bit longer than that.

The study is an honest effort, but not necessarily terribly reliable as any study is only as good as its assumptions and methods, which aren't terribly convincing, and no serious effort is made in  the paper to validate the assumptions they use or even to clearly describe those assumptions. The methods used are fairly reliable for creating a branching phylogeny of the language family (something that has never been in serious doubt), but is less reliable for purposes of estimating time depth.

For example, the analysis puts all Dravidian languages on an equal footing based upon a Swaedesh vocabulary list, but really, to do it right, they should be limiting themselves to what can be determined from the historic content of the four Dravidian languages that are attested earliest. And, they should be pretty much ignoring North Dravidian languages for which there is a strong case to be made that they didn't arise until about 1000 CE, entirely.

Their own error bars are 1000 BCE to 4500 BCE, with the archaeology of the South Indian Neolithic used to support a mid-range value. The most reliable youngest possible date comes from Dravidian loan words in the Rig Veda:
There is clear evidence of Dravidian loanwords into Old-Indo-Aryan (1750–250 BCE) dating to the middle Rigvedic period (ca 1200 BCE) in a source area that might have been Sindh, contemporary Southwest Pakistan [6], [8, pp. 69ff, 88]. Southworth [8, p. 64] proposes Sindh, Gujarat and eastern Maharashtra as areas where Dravidian would have been spoken at earlier stages.
Thus a range of perhaps 1500 BCE to 2500 BCE is quite plausible.

But, many linguists have doubted that the amount of linguistic diversity really supports a 4500 years time depth, which could be consistent with a bottleneck effect of diversification from surviving dialects after the language family temporarily went extinct in a large part of its range. Indeed, it is very likely that the particular dialect of Dravidian that was the source of the Rig Vedic substrate is extinct.

The study is: Kolipakam et al. A Bayesian phylogenetic study of the Dravidian language family. Royal Society Open Science (2018).