Genetic Genealogy and Ancient DNA in the News

[rozenfeld]

https://www.eurekalert.org/pub_relea...-oeo110118.php

Oldest evidence of dairying on the East Asian Steppe

Dairying of cattle, sheep, and goats was established in northern Mongolia by 1300 BC -- despite limited genetic interactions with Western Steppe herders

Max Planck Institute for the Science of Human History

http://www.pnas.org/content/early/2018/10/31/1813608115

Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe

Choongwon Jeong, Shevan Wilkin, Tsend Amgalantugs, Abigail S. Bouwman, William Timothy Treal Taylor, Richard W. Hagan, Sabri Bromage, Soninkhishig Tsolmon, Christian Trachsel, Jonas Grossmann, Judith Littleton, Cheryl A. Makarewicz, John Krigbaum, Marta Burri, Ashley Scott, Ganmaa Davaasambuu, Joshua Wright, Franziska Irmer, Erdene Myagmar, Nicole Boivin, Martine Robbeets, Frank J. Rühli, Johannes Krause, Bruno Frohlich, Jessica Hendy, and Christina Warinner

PNAS published ahead of print November 5, 2018
https://doi.org/10.1073/pnas.1813608115

Significance

Since the Bronze Age, pastoralism has been a dominant subsistence mode on the Western steppe, but the origins of this tradition on the Eastern steppe are poorly understood. Here we investigate a putative early pastoralist population in northern Mongolia and find that dairy production was established on the Eastern steppe by 1300 BCE. Milk proteins preserved in dental calculus indicate an early focus on Western domesticated ruminants rather than local species, but genetic ancestry analysis indicates minimal admixture with Western steppe herders, suggesting that dairy pastoralism was introduced through adoption by local hunter-gatherers rather than population replacement.

Abstract

Recent paleogenomic studies have shown that migrations of Western steppe herders (WSH) beginning in the Eneolithic (ca. 3300–2700 BCE) profoundly transformed the genes and cultures of Europe and central Asia. Compared with Europe, however, the eastern extent of this WSH expansion is not well defined. Here we present genomic and proteomic data from 22 directly dated Late Bronze Age burials putatively associated with early pastoralism in northern Mongolia (ca. 1380–975 BCE). Genome-wide analysis reveals that they are largely descended from a population represented by Early Bronze Age hunter-gatherers in the Baikal region, with only a limited contribution (∼7%) of WSH ancestry. At the same time, however, mass spectrometry analysis of dental calculus provides direct protein evidence of bovine, sheep, and goat milk consumption in seven of nine individuals. No individuals showed molecular evidence of lactase persistence, and only one individual exhibited evidence of >10% WSH ancestry, despite the presence of WSH populations in the nearby Altai-Sayan region for more than a millennium. Unlike the spread of Neolithic farming in Europe and the expansion of Bronze Age pastoralism on the Western steppe, our results indicate that ruminant dairy pastoralism was adopted on the Eastern steppe by local hunter-gatherers through a process of cultural transmission and minimal genetic exchange with outside groups.

Table S4. Uniparental haplogroups of the Khövsgöl individuals. 
We determined mitochondrial haplogroups for 19 of 20 individuals, and Y haplogroups for all 12 males.

ID	Sex	MT-haplogroup	Y-haplogroup 1
ARS001	M	D4		Q1a2a1c (Q-L334;Q-L330)
ARS002	F	D4j5		-
ARS003	M	U5a2d1		N1c1a (N-M178)
ARS004	M	F2a		Q1a2 (Q-L942;Q-M346)
ARS005	M	D4e1		Q1a2a1 (Q-L54)
ARS006	F	C4a1a+195	-
ARS007	M	A+152+16362	Q1a2a (Q-L475;Q-L53)
ARS008	M	C4a2c		Q1a2a1c (Q-L330)
ARS009	F	D5a2a		-
ARS011	M	n/d		Q1a2 (Q-L56;Q-M346)
ARS012	F	C4a2a1		-
ARS013	F	C		-
ARS014	F	C4a2c1		-
ARS015	M	G3a		Q1a1 (Q-Y706;Q-F1096)
ARS016	M	A+152+16362+16189	Q1a2a1c (Q-L334;Q-L330)
ARS017	F	G2a		-
ARS018	M	B5b1		Q1a (Q-M1117;Q-L472)
ARS024	F	C4a1a1		-
ARS025	M	D4b1a2a		Q1a2a (Q-L475;Q-L53)
ARS026	M	C4a1a+195	R1a1a1b2a2a (R-Z2123)

Notes: 1 Due to incomplete coverage of informative Y chromosome SNPs, Y haplogroup assignment has not gone down to the tip for some individuals. The assigned haplogroup is the most downstream one supported by the presence of derived alleles.

[Eterne]

https://www.cell.com/cell/fulltext/S...674(18)31380-1 - Reconstructing the Deep Population History of Central and South America

Highlights

Genome-wide analysis of 49 Central and South Americans up to ∼11,000 years old
Two previously unknown genetic exchanges between North and South America
Distinct link between a Clovis culture-associated genome and the oldest South Americans
Continent-wide replacement of Clovis-associated ancestry beginning at least 9,000 years ago

Summary

We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.

[Eterne]

http://science.sciencemag.org/conten...cience.aav2621 - Early human dispersals within the Americas

Abstract

Studies of the peopling of the Americas have focused on the timing and number of initial migrations. Less attention has been paid to the subsequent spread of people within the Americas. We sequenced 15 ancient human genomes spanning Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans, including an Ancient Beringian individual, and two morphologically distinct “Paleoamericans.” We find evidence of rapid dispersal and early diversification, including previously unknown groups, as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, and a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America.

[epoch]

http://science.sciencemag.org/conten...cience.aav2621

Early human dispersals within the Americas

Abstract

Studies of the peopling of the Americas have focused on the timing and number of initial migrations. Less attention has been paid to the subsequent spread of people within the Americas. We sequenced 15 ancient human genomes spanning Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans, including an Ancient Beringian individual, and two morphologically distinct “Paleoamericans.” We find evidence of rapid dispersal and early diversification, including previously unknown groups, as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, and a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America.

A Australasian signal found in 10k ya Brazilian samples. Nowhere else. Pretty spectacular, I'd say.

EDIT: Eterne beat me to it. I need to learn to refresh before submitting.

[rozenfeld]

And one more:

http://advances.sciencemag.org/content/4/11/eaau4921

The genetic prehistory of the Andean highlands 7000 years BP though European contact

John Lindo1,2,*, Randall Haas3, Courtney Hofman4,5, Mario Apata6, Mauricio Moraga6,7, Ricardo A. Verdugo6,8,*, James T. Watson9, Carlos Viviano Llave10, David Witonsky2, Cynthia Beall11, Christina Warinner4,5,12, John Novembre2, Mark Aldenderfer13,* and Anna Di Rienzo2,*

Science Advances 08 Nov 2018:

DOI: 10.1126/sciadv.aau4921

Abstract

The peopling of the Andean highlands above 2500 m in elevation was a complex process that included cultural, biological, and genetic adaptations. Here, we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7000 calendar years before the present (BP), and compare them to 42 new genome-wide genetic variation datasets from both highland and lowland populations. We infer three significant features: a split between low- and high-elevation populations that occurred between 9200 and 8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact. We do not find selective sweep signals related to known components of the human hypoxia response, which may suggest more complex modes of genetic adaptation to high altitude.

[Boreas]

Understanding 6th-century barbarian social organization and migration through paleogenomics
https://www.nature.com/articles/s41467-018-06024-4

[Camulogène Rix]

Morts néolithiques: 8 novembre 2018 Carcassonne, France:
* Vincent Ard et Muriel Gandelin - Analyse ADN et recrutement funéraire : réflexions autour de projets en cours entre Atlantique et Méditerranée
* Samantha Brunel et Mélanie Pruvost - Diversité génétique des populations néolithiques françaises : aperçu des premiers résultats du projet ANCESTRA.
* Aurore Fromentier - Characterizing the Mesolithic-Neolithic transition in Central and Southern Italy using Human ancient genome-wide data.
* Marie-France Deguilloux - Projet INTERACT, Interactions durant la transition Mésolithique-Néolithique en Europe de l’Ouest au travers de la double perspective des échanges biologiques et culturels.
* Nancy Saenz-Oyhéréguy - Étude paléogénétique des deux sépultures collectives du Néolithique récent, Le Mont Aime I et II (Bassin parisien).
* Andaine Seguin Orlando - NEO, Living in Europe in the late Neolithic: A transdisciplinary perspective.

Any news from the 'Ancestra Project' (on French ancient DNA) which has been presented in Carcassonne a few days ago? it seems that some information had been posted on AG and then deleted...

[Bernard]

Someone posts some informations on the French forum about the thesis of Samantha Brunel from Institut Jacques Monod, Paris. Samantha defended her thesis last week: Paléogénomique des dynamiques des populations humaines sur le territoire Français entre 7000 et 2000 and Jool was here. He wrote the summary of the Brunel thesis results on the French forum:

A
Ils ont une bonne centaine d’échantillons qui proviennent du nord, d’Alsace et de la côte méditerranéenne, du mésolithique à l’âge de fer.
Il n’y a pas de surprise majeure par rapport au reste de l’Europe. Sur le PCA plot, les mésolithiques sont avec les WHG, les early neolithics avec les premiers fermiers tout près des anatoliens. Puis il y a une petite résurgence des chasseurs cueilleurs qui déplace les middle néolithics un peu plus proches des WHG.
A l’age de bronze, ils ont 5 échantillons avec de l’ADN autosomal, tous en contexte archéologique Bell Beaker, qui sont très étalés sur le PCA. Un échantillon très haut vers les Yamnaya, un peu au-dessus des Corded Ware, deux échantillons en plein dans les Bell Beakers d’europe centrale, un assez bas juste au-dessus du paquet néolithique, et un dernier en plein dans le paquet. Le point le plus saillant était que les chromosomes Y de leurs 12 échantillons de l’âge de bronze (tous bell beaker) sont tous R1b, alors qu’il n’y avait aucun R1b dans les échantillons néolithiques.
Enfin ils ont des échantillons de l’âge de fer qui sont rassemblés sur le PCA plot dans la moyenne âge de bronze / France actuelle. Ils n’ont pas pu déterminer s’il y a continuité avec l’âge de bronze, ou un remplacement partiel par une population assez proche génétiquement.
Des résultats sur un signal de sélection chez les néolithiques a été mentionné pendant les questions mais n’ont pas été montré pendant la soutenance.

This is the translation:

They have a good hundred samples from the North, Alsace and the Mediterranean coast, from the Mesolithic to the Iron Age.
There is no major surprise compared to the rest of Europe. On the PCA plot, the Mesolithic are with the WHG, the early neolithics with the first farmers close to the Anatolians. Then there is a small resurgence of hunter-gatherers that moves the middle neolithics a little closer to the WHGs.
At the bronze age, they have 5 samples with autosomal DNA, all in Bell Beaker archaeological context, which are very spread on the PCA. A very high sample close to the Yamnaya, a little above the Corded Ware, two samples right in the Central European Bell Beakers, a fairly low just above the Neolithic package, and one last full in the package. The most salient point was that the Y chromosomes of their 12 Bronze Age samples (all bell beaker) are all R1b, whereas there was no R1b in the Neolithic samples.
Finally they have samples of the Iron Age that are collected on the PCA plot close to the Bronze Age samples. They could not determine if there is continuity with the Bronze Age, or a partial replacement by a genetically close population.

My comments:
* French Bell Beakersare derived from a genetic mixture between a steppe population (sample located with Yamnaya in the PCA) and a local Neolithic population (sample located with Neolithic farmers)
* The steppe population comes directly from the steppes (and not from Central Europe) otherwise we would not have a Bell Beaker sample that is located with the Yamnaya. So the Bell Beaker culture is not an emanation of the Corded Ware culture
* 100% of paternal lineages are R1b and come from the steppes (R1b is absent in the Neolithic) => this migration from the steppe to Western Europe is therefore composed mainly of men who take local women

[Eterne]

* The steppe population comes directly from the steppes (and not from Central Europe) otherwise we would not have a Bell Beaker sample that is located with the Yamnaya. So the Bell Beaker culture is not an emanation of the Corded Ware culture

Thanks for the information on this project. I'd just add I'm not sure about this part of your comment though because it doesn't seem unimaginable that you could see outliers of migration into Bell Beaker cultures from steppe-ancestry rich areas, even if most of the migration was from ancestors who were already admixed with EEF in Central Europe. A steppe outlier is not necessary representing the earliest stage of the culture. Plus steppe groups could be living in Central Europe for a few generations without admixing much.

[Generalissimo]

The steppe population comes directly from the steppes (and not from Central Europe) otherwise we would not have a Bell Beaker sample that is located with the Yamnaya.

But it's not located with the Yamnaya.

Here's your quote...

A very high sample close to the Yamnaya, a little above the Corded Ware.

Sounds like Corded Ware with excess WHG, no?