Genetic Genealogy and Ancient DNA in the News

[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?

[GASKA]

Some (I6542 dated to 2500 BC-1750 BC is haplogroup F) of the samples that I posted above have a radio-carbon date that goes well past 4000 years ago, i.e they date from 2500 BC to 1750 BC. Nonetheless, the only way to make such a strong assertion of 100% replacement rate, is to have numerous samples from the period post 2000 BC and have all of them in the Iberian peninsula be R1b-P312, we know from modern and ancient data this is not the case. Otherwise, this would imply that all the non-R1b-P312 lineages found in modern Iberians came post-Iron Age to present. This is impossible, since Neolithic lineages such as G2a and I-M26 are found at non-trivial frequencies both in modern and some of the ancient Iberians. Reich is over-stepping in claiming 100%, and I think he will be met with the proper criticism, because the only way to make such a strong claim is to have a large enough sample size and show that all of them are R1b-P312. In the upcoming Olalde study the sample size spanning from Mesolithic down to Iron Age is 154. Thus Reich should know better than to claim that. Perhaps R1b-P312 reached majority status in the time frame of post 4000 years ago, but anyone with a descent knowledge of statistics knows the dangers of drawing conclusions from very small samples sizes. Right now what we have 4000 years in terms of Iberia is:


Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia

Table S4.1


esp005 Cueva de los lagos/South 2.36 480.40XY1.31 [0.78-1.84] 0.0334 K1a R1b-DF27 Not C14 Bronze Age
pir001 El Pirulejo/South 0.21 214.27XY0.77 [0.16-1.38] 0.0105 K1a13 R1b-M269 Not C14 Bronze Age

From the study about Portugal:

3585 ybp Monte do Gato de Cima 3 Portugal R1b1a2a1a2
3585 ybp Torre Velha 3 Portugal R1b1a2a1a2
3585 ybp Torre Velha 3 Portugal R1b1a2

We also have the remains from Aldaieta Cementary dated to 600 AD, as you can see they have some lineages that belong to I, likely being I-m26.

Obviously Reich's statement is an error or an exaggeration, the majority haplogroups in the Iberian Neolithic (38 samples I2, 14 samples G2) have been maintained with percentages up to 10% of the current Spanish population-I2-M438, I2a1a-I2a1b-M423, I2a2a-M223, I-M284, I-Z161, G2a, G2a1, G2a2, G2a2a1, G2a2b-L30, G-M201, G2a2b2b........ We also have E-V13 in Cova Avellaner (Neolitic Epi-Cardial, 5.000 BC). This haplogroup is actually 4.2% of men (province of Huelva, Andalucia) and 1% of men (province of Granada, Andalucia). It seems clear that it was not an absolute substitution.

[cacarlos]

Un échantillon très haut vers les Yamnaya, un peu au-dessus des Corded Ware

Very interesting, thank you. I guess that puts this sample very close to (probably above) Yamna Hungary EBA1 from Wang et al. (2018), and it (unexpectedly) extends the high variability of "steppe ancestry" from late Yamna in Hungary to expanding East Bell Beakers in south-central Europe. I would also guess this one is an early sample from Alsace or maybe northern France near the Rhine, but not from the Mediterranean, based on the available samples from Olalde et al. (2018)...

PCA-yamna-hungary.jpg

[Generalissimo]

Very interesting, thank you. I guess that puts this sample very close to (probably above) Yamna Hungary EBA1 from Wang et al. (2018), and it (unexpectedly) extends the high variability of "steppe ancestry" from late Yamna in Hungary to expanding East Bell Beakers in south-central Europe. I would also guess this one is an early sample from Alsace or maybe northern France near the Rhine, but not from the Mediterranean, based on the available samples from Olalde et al. (2018)...

How's the Corded Ware = Uralic theory coming along?

Have you actually managed to convince anyone except yourself with your crazy maps?