Monday, March 12, 2018

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.


DDeden said...

"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." The after-effects would have been more damaging to shade-intolerant grassland & woodland dwellers & rainforest canopy arborealists than to AMHs living on the mottled forest floor, where shade-tolerant vegetation would have remained healthy, food abundant & large leaves used to shingle domiciles getting sufficient sunlight to survive. Similarly, many coastal foods would have returned soon due to currents movie g nutrients.

DDeden said...

movie g nutrients -> moving nutrients. (auto-mis-correct)
Re. wild potatoes in Utah, I wonder if the name for those tubers was similar to the Ute/Shoshoni word for wild carrots: Yampai, which I link to yam@English: (orange) tuber, nyama@Fulani: eat, and njama@Proto-Bantu: meat, and nyama@Mbuti: animal, all related to the chewing and mashing of food.
An important finding IMO: At Laetoli during A afarensis (Lucy) era, arboreal forest monkeys, not savannah grassland monkeys, dominated the simian niche. Per new article in Journal of Human Evolution.