Friday, January 26, 2018

Humans Left Africa About 185,000 Years Ago

It may have taken tens of thousands of years after leaving Africa for modern humans to establish permanent settlements beyond Southwest Asia, but modern humans left Africa at least about 185,000 years ago. And, even then, the range expansion appears to have been driven by technological advances.
To date, the earliest modern human fossils found outside of Africa are dated to around 90,000 to 120,000 years ago at the Levantine sites of Skhul and Qafzeh. A maxilla and associated dentition recently discovered at Misliya Cave, Israel, was dated to 177,000 to 194,000 years ago, suggesting that members of the Homo sapiens clade left Africa earlier than previously thought. This finding changes our view on modern human dispersal and is consistent with recent genetic studies, which have posited the possibility of an earlier dispersal of Homo sapiens around 220,000 years ago. The Misliya maxilla is associated with full-fledged Levallois technology in the Levant, suggesting that the emergence of this technology is linked to the appearance of Homo sapiens in the region, as has been documented in Africa.
Israel Hershkovitz, "The earliest modern humans outside Africa" 359 (6374) Science 456-459  (January 26, 2018) DOI: 10.1126/science.aap8369

Wednesday, January 24, 2018

The Genetics Of Conversos In Latin America

Latin American was colonized just as Jews were being expelled from Spain, and many converted to Christianity and migrated to the New World even though this was illegal. A new genetic study demonstrates that these "Conversos" made up a larger share of early migrants to Latin America than had generally been believed. The rest of the findings generally support the prevailing paradigm and historical record of migration to Latin America.

The paper also demonstrates the unsurprising finding that your genetic ancestry impacts your physical appearance.

A deeper issue is what this means to people emotionally and personally (which, of course, a genetics paper can't answer). While some Conversos maintained a connection to their ancestral religion, especially at first, five hundred years later, the vast majority of them let those ties fade away and assimilated into Latin American Catholicism, and in most cases, they did so before the lives of the people recorded in the oldest available recollections and genealogical records available to modern Latin Americans.

As a Brazilian or Mexican with hundreds of years of Catholic ancestors, who is now Catholic or Pentecostal or secular, who has never observed any aspect of a Jewish ancestry, does it matters that you have Sephardic Jewish ancestry?

If so, what does it mean to you and what does the prevalence of this ancestry across Latin America means to your whole society's understanding of itself and its past?

The paper is also a good quantitative example of the extent to which population structure decays over time. This happens significantly more slowly than it would under the hypothesis of panmixia which would have caused Sephardic ancestry to almost reach fixation in these countries. But, the decay of population structure is still strong enough of a tendency that only 23 people in a sample of 6,500 who did not have grandparents or more recent a ancestors who immigrated to Latin America (there were 19 recent immigrants in the sample) were more than 25% Sephardic, despite the fact that about 1500 people in the sample had a least 5% Sephardic ancestry. The average percentages of Sephardic ancestry by country in the study were: Brazil (1%), Chile (4%), Colombia (3%), Mexico (3%) and Peru (2%).

Razib Khan also has a decent post on the paper including its broader social importance.

The abstract from the paper, a citation to it, and some excerpts from the body text of the paper, with my emphasis added, follows below the fold.

Monday, January 22, 2018

Brahui Origins

The latest paper on Brahui origins, by Pagani, et al., purports to be interdisciplinary while flatly ignoring the linguistic and historical evidence contrary to the paper's own conclusion in what is, quite frankly, a shoddy piece of scholarship, despite doing solid work on the population genetic side of the analysis (although that too is uninformed by the ancient DNA necessary for the paper to make such a sweeping conclusion).
Pakistan is a part of South Asia that modern humans encountered soon after they left Africa ~50 - 70,000 years ago. Approximately 9,000 years ago they began establishing cities that eventually expanded to represent the Harappan culture, rivalling the early city states of Mesopotamia. The modern state constitutes the north western land mass of the Indian sub-continent and is now the abode of almost 200 million humans representing many ethnicities and linguistic groups. Studies utilising autosomal, Y chromosomal and mitochondrial DNA markers in selected Pakistani populations revealed a mixture of Western Eurasian-, South- and East Asian-specific lineages, some of which were unequivocally associated with past migrations. Overall in Pakistan, genetic relationships are generally predicted more accurately by geographic proximity than linguistic origin. The Dravidian-speaking Brahui population are a prime example of this. They currently reside in south-western Pakistan, surrounded by Indo-Europeans speakers with whom they share a common genetic origin. In contrast, the Hazara share the highest affinity with East Asians, despite their Indo-European linguistic affiliation. In this report we reexamine the genetic origins of the Brahuis, and compare them with diverse populations from India, including several Dravidian-speaking groups, and present a genetic perspective on ethnolinguistic groups in present-day Pakistan. Given the high affinity of Brahui to the other Indo-European Pakistani populations and the absence of population admixture with any of the examined Indian Dravidian groups, we conclude that Brahui are an example of cultural (linguistic) retention following a major population replacement.
Pagani L, Colonna V, Tyler-Smith C, Ayub Q., "An Ethnolinguistic and Genetic Perspective on the Origins of the Dravidian-Speaking Brahui in Pakistan." 97(1) Man India. 267-278 (2017) (Open Access).

I would have argued for elite driven language shift, rather than major population replacement as at least as plausible if not more so. (Hat Tip Razib Khan.)

In particular, the shallow analysis of the conclusion ignores a key point. The paper states (link added editorially):
Formally, two models could be considered. In model 1, the ancestors of the Brahui people were a pre-existing Dravidian-speaking group in Pakistan, who were gradually assimilated by the Indo-European migrants, who arrived ~3,000 years ago, while their language was preserved. In model 2, the Brahui ancestors were Indo-European speakers, who later adopted a Dravidian language. No historical or linguistic data support model 2, so model 1 provides the best explanation for the unique characteristics of the Brahui.
This is simply wrong.

Pagani could have argued that there was dispute in the historical and linguistic data and grappled with it, but instead Pagani simply ignores what was really the conventional wisdom in the linguistic discipline about Brahui.

The reality is that the linguistic data support a migration date after 1,000 CE (for what it is worth about the same time frame as the migration of the ancestors of the European Roma a.ka. gypsies and about two hundred years after the Parsi arrive in India) and the Brahui case follows a pattern common to the other North Dravidian dialects. Many North Dravidian communities also have oral histories that include a migration myth consistent with this kind of origin. This time frame also makes a pre-historic population replacement scenario far less plausible. As the linked Wikipedia page explains (with solid references):
Although in modern times speakers of the various Dravidian languages have mainly occupied the southern portion of India, in earlier times they probably were spoken in a larger area. After the Indo-Aryan migrations into north-western India, starting ca. 1500 BCE, and the establishment of the Kuru kingdom ca. 1100 BCE, a process of Sanskritisation started, which resulted in a language shift in northern India. Southern India has remained majority Dravidian, but pockets of Dravidian can be found in central India, Pakistan, Bangladesh and Nepal. 
The Kurukh and Malto are pockets of Dravidian languages in central India, spoken by people who may have migrated from south India. They do have myths about external origins.[66] The Kurukh have traditionally claimed to be from the Deccan Peninsula,[67] more specifically Karnataka. The same tradition has existed of the Brahui,[68][69] who call themselves immigrants.[70] Holding this same view of the Brahui are many scholars [71] such as L. H. Horace Perera and M. Ratnasabapathy.[72]
The Brahui population of Pakistan's Balochistan province has been taken by some as the linguistic equivalent of a relict population, perhaps indicating that Dravidian languages were formerly much more widespread and were supplanted by the incoming Indo-Aryan languages.[73][74][75] However, it has been argued that the absence of any Old Iranian (Avestan) loanwords in Brahui suggests that the Brahui migrated to Balochistan from central India less than 1,000 years ago. The main Iranian contributor to Brahui vocabulary, Balochi, is a western Iranian language like Kurdish, and arrived in the area from the west only around 1,000 AD.[76] Sound changes shared with Kurukh and Malto also suggest that Brahui was originally spoken near them in central India.[77]
[66] P. 83 The Quest for the Origins of Vedic Culture: The Indo-Aryan Migration Debate by Edwin Bryant
[67] P. 18 The Orāons of Chōtā Nāgpur: their history, economic life, and social organization. by Sarat Chandra Roy, Rai Bahadur; Alfred C Haddon
[68] P. 12 Origin and Spread of the Tamils By V. R. Ramachandra Dikshitar
[69] P. 32 Ideology and status of Sanskrit : contributions to the history of the Sanskrit language by Jan E M Houben
[70] P. 45 The Brahui language, an old Dravidian language spoken in parts of Baluchistan and Sind by Sir Denys Bray
[71] Ancient India; Culture and Thought By M. L. Bhagi
[72] P. 23 Ceylon & Indian History from Early Times to 1505 A.D. By L. H. Horace Perera, M. Ratnasabapathy
[73] Mallory (1989), p. 44.
[74] Elst (1999), p. 146.
[75] Trask (2000), p. 97 "It is widely suspected that the extinct and undeciphered Indus Valley language was a Dravidian language, but no confirmation is available. The existence of the isolated northern outlier Brahui is consistent with the hypothesis that Dravidian formerly occupied much of North India but was displaced by the invading Indo-Aryan languages, and the presence in the Indo-Aryan languages of certain linguistic features, such as retroflex consonants, is often attributed to Dravidian substrate influence."
[76] Elfenbein, Josef (1987). "A periplus of the 'Brahui problem'". Studia Iranica. 16 (2): 215–233. doi:10.2143/SI.16.2.2014604.
[77] Krishnamurti (2003), pp. 27, 142.
Note that the linguistic evidence of a 1,000 CE origin for the Brahui branch of Dravidian is also corroborated by the lack of Dravidian toponyms in Northern India and Pakistan. There are Dravidian place-names throughout the regions of Sindh, Gujarat and Maharashtra according to George Erdösy (1995), The Indo-Aryans of ancient South Asia: Language, material culture and ethnicity, p. 271 and Edwin Bryant, Laurie L. Patton (2005), The Indo-Aryan controversy: evidence and inference in Indian history, p. 254. But, those place names do not extend further north than these regions.  The Brahui are located beyond the range where Dravidian place-names are found.

A similar case of probable language shift in a North Dravidian population (the Gonds) also exists, although in that case, the original language of the Gonds was probably a Munda language.

A time depth of 3,000 years is also almost as great as the linguistically ascertained age of the Dravidian language family itself (arguably even older), so it is hard to see why Brahui wouldn't have a more basal position in the Dravidian language family than it does if it were really this old. And, it is harder to see why Brahui would have managed to persist for 3,000 years in a linguistic sea of Indo-European neighbors, than it is to see how it could have done so far less than 1,000 years.

In short, Pagani is guilty of shoddy cross-disciplinary research at a really elementary level that impacts the conclusion of the paper. This glaring error should have never made it past peer review.

Thursday, January 18, 2018

Maybe b quark decays aren't weird after all

Some indications that lepton universality (i.e. the propositions that leptons are identical to each other in their weak force decay behavior except that they are different in mass), is violated in b quark decays, which shouldn't happen in the Standard Model of Particle Physics, has created the latest cottage industry of "new physics" models that could explain this phenomena. But, it turns out that most of these models are tightly constrained or ruled out entirely by other data. 

Also, more accurate calculations of the Standard Model prediction in the "non-perturbative" regime governed by lattice QCD make the observed anomalies appear smaller than they had seemed using only perturbative QCD Standard Model predictions near the edge of their domain of applicability. 

One of the latest papers reviewing these constraints, from a month ago, has the following abstract:

"Many new physics models that explain the intriguing anomalies in the b-quark flavour sector are severely constrained by Bs-mixing, for which the Standard Model prediction and experiment agreed well until recently. New non-perturbative calculations point, however, in the direction of a small discrepancy in this observable. Using up-to-date inputs to determine ΔMSMs, we find a severe reduction of the allowed parameter space of Z and leptoquark models explaining the B-anomalies. Remarkably, in the former case the upper bound on the Z mass approaches dangerously close to the energy scales already probed by the LHC. We finally identify some model building directions in order to alleviate the tension with Bs-mixing."

Luca Di Luzio, Matthew Kirk and Alexander Lenz, "One constraint to kill them all?" (December 18, 2017).

Another paper from two weeks ago also constrains potential remedies for these anomalies by another means:

B decays proceeding via bcν transitions with =e or μ are tree-level processes in the Standard Model. They are used to measure the CKM element Vcb, as such forming an important ingredient in the determination of e.g. the unitarity triangle; hence the question to which extend they can be affected by new physics contributions is important, specifically given the long-standing tension between Vcb determinations from inclusive and exclusive decays and the significant hints for lepton flavour universality violation in bcτν and bs decays. We perform a comprehensive model-independent analysis of new physics in bcν, considering vector, scalar, and tensor interactions, including for the first time differential distributions of BDν angular observables. We show that these are valuable in constraining non-standard interactions. Specifically, the zero-recoil endpoint of the BDν spectrum is extremely sensitive to scalar currents, while the maximum-recoil endpoint of the BDν spectrum with transversely polarized D is extremely sensitive to tensor currents. We also quantify the room for e-μ universality violation in bcν transitions, predicted by some models suggested to solve the bcτν anomalies. Specific new physics models, corresponding to all possible tree-level mediators, are also discussed. As a side effect, we present Vcb determinations from exclusive B decays, both with frequentist and Bayesian statistics, leading to compatible results. The entire numerical analysis is based on open source code, allowing it to be easily adapted once new data or new form factors become available.

Martin Jung, David M. Straub, "Constraining new physics in b→cℓν transitions" (January 3, 2018).

In short, the evidence continues to mount that the observed b decay anomalies are a fluke or arise either from experimental errors or inaccuracies in theoretical Standard Model predictions, rather than from "new physics."