Friday, March 16, 2018

Edo Era Ainu Genetics

The Ainu people of Japan are descendants of the Jomon fishing-gathering people of prehistoric Japan, but also have significant Siberian ancestry.
The Ainu, the indigenous people living on the northernmost island of Japan, Hokkaido, have long been a focus of anthropological interest because of their cultural, linguistic, and physical identity. A major problem with genetic studies on the Ainu is that the previously published data stemmed almost exclusively from only 51 modern-day individuals living in Biratori Town, central Hokkaido. To clarify the actual genetic characteristics of the Ainu, individuals who are less influenced by mainland Japanese, who started large-scale immigration into Hokkaido about 150 years ago, should be examined. Moreover, the samples should be collected from all over Hokkaido. 
Materials and methods 
Mitochondrial DNA haplogroups of 94 Ainu individuals from the Edo era were successfully determined by analyzing haplogroup-defining polymorphisms in the hypervariable and coding regions. Thereafter, their frequencies were compared to those of other populations. 
Our findings indicate that the Ainu still retain the matrilineage of the Hokkaido Jomon people. However, the Siberian influence on this population is far greater than previously recognized. Moreover, the influence of mainland Japanese is evident, especially in the southwestern part of Hokkaido that is adjacent to Honshu, the main island of Japan. 
Our results suggest that the Ainu were formed from the Hokkaido Jomon people, but subsequently underwent considerable admixture with adjacent populations. The present study strongly recommends revision of the widely accepted dual-structure model for the population history of the Japanese, in which the Ainu are assumed to be the direct descendants of the Jomon people.
Noboru Adachi, et al., "Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data" American Journal of Physical Anthropology (October 11, 2017).

Hat tip to the Linear Population Model blog.

Thursday, March 15, 2018

Ancient North African DNA

The biggest surprise of new Mesolithic ancient DNA samples from Morocco is that they lack any European hunter-gatherer ancestry, instead deriving from a mix of Levantine hunter-gatherers and sub-Saharan Africans. Sub-Saharan African admixture was not unexpected, but the proportion of sub-Saharan African ancestry in this ancient DNA is higher than expected, implying early, pre-Neolithic contact between the populations.
North Africa is a key region for understanding human history, but the genetic history of its people is largely unknown. We present genomic data from seven 15,000-year-old modern humans from Morocco, attributed to the Iberomaurusian culture. We find a genetic affinity with early Holocene Near Easterners, best represented by Levantine Natufians, suggesting a pre-agricultural connection between Africa and the Near East. We do not find evidence for gene flow from Paleolithic Europeans into Late Pleistocene North Africans. The Taforalt individuals derive one third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West and East Africans. Thus, we provide direct evidence for genetic interactions between modern humans across Africa and Eurasia in the Pleistocene.
Marieke van de Loosdrecht, et al.,"Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations" Science (March 15, 2018).

A related account of the find is aimed at an educated lay audience. It notes that:
DNA in hand, paleogeneticists Marieke van de Loosdrecht and Johannes Krause of the Max Planck Institute for the Science of Human History in Jena, Germany, sequenced it. They were able to analyze genetic material from the cell’s nucleus in five people and the maternally inherited mitochondrial DNA from seven people. But they found no genetic tie to ancient Europeans. Instead, the ancient Iberomaurusians appear to be related to Middle Easterners and other Africans: They shared about two-thirds of their genetic ancestry with Natufians, hunter-gatherers who lived in the Middle East 14,500 to 11,000 years ago, and one-third with sub-Saharan Africans who were most closely related to today’s West Africans and the Hadza of Tanzania. 
The Iberomaurusians lived before the Natufians, but they were not their direct ancestors: The Natufians lack DNA from Africa, Krause says. This suggests that both groups inherited their shared DNA from a larger population that lived in North Africa or the Middle East more than 15,000 years ago, the team reports today in Science. 
As for the sub-Saharan DNA in the Iberomaurusian genome, the Iberomaurusians may have gotten it from migrants from the south who were their contemporaries. Or they may have inherited the DNA from much more ancient ancestors who brought it from the south but settled in North Africa where some of the earliest members of our species, Homo sapiens, have been found at Jebel Irhoud in Morocco.

Fun With Archaic Admixture Analysis

Archaegenetics is not a reductionist field and the more we know the more intricate the tapestry of human ancestry becomes.
Anatomically modern humans interbred with Neanderthals and with a related archaic population known as Denisovans. Genomes of several Neanderthals and one Denisovan have been sequenced, and these reference genomes have been used to detect introgressed genetic material in present-day human genomes. Segments of introgression also can be detected without use of reference genomes, and doing so can be advantageous for finding introgressed segments that are less closely related to the sequenced archaic genomes. 
We apply a new reference-free method for detecting archaic introgression to 5,639 whole-genome sequences from Eurasia and Oceania. We find Denisovan ancestry in populations from East and South Asia and Papuans. Denisovan ancestry comprises two components with differing similarity to the sequenced Altai Denisovan individual. This indicates that at least two distinct instances of Denisovan admixture into modern humans occurred, involving Denisovan populations that had different levels of relatedness to the sequenced Altai Denisovan.

All of these Eurasian and New World populations have a bottom right cluster in the images below that corresponds to Neanderthal ancestry.

The Papuan (bottom right in the image below) sample also has a center-left cluster that corresponds to Deniovan ancestry. A less pronounced center-left cluster indicating a smaller amount of ancestry from the same population is found in East Asia, Southeast Asia and South Asian individuals middle two rows of the image below. 

The big reveal in this study is that the East Asian individuals, in particular, seem to have two distinct clusters of Denisovan ancestry, with a small secondary top left cluster in each suggesting a second admixture event with genetically diverged Denisovan populations.

Denisovan ancestry is absent, however, in European individuals (top row) and in New World individuals (bottom row except the Papuan). Pontus Skoglund also notes that:
There is an undiscussed but potentially explosive implication of this paper: the 2nd Denisovan gene flow signal in East Asia seems to be absent from Native American ancestry--could Denisovans have survived after the isolation of these lineages <30 kya??
For what it is worth, I don't think that Skoglund's hypothesis is correct. I think it is more likely that the primary Denisovan admixture event reflects admixture of Southern route modern human migrants with Denisovans and that the secondary Denisovan admixture event (which is absent in Papuans) reflects admixture of a subset of Northern route modern human migrants who followed more or less what is now known as the Silk Road, and was distinct from the small founding population of the Americas.

This data point also strengthens the hypothesis that very old, non-Homo erectus hominin remains found in China with a mix of archaic and modern features are either Denisovan or hybrid Denisovan-modern human individuals.

Figure 4: Contour Density Plots of Match Proportion of Introgressed Segments to the Altai Neanderthal and Altai Denisovan Genomes

The match proportion is the proportion of putative archaic-specific alleles in a segment that match the given archaic genome, excluding alleles at positions masked in the archaic genome sequence. Segments with at least ten variants not masked in the Neanderthal genome and at least ten variants not masked in the Denisovan genome are included. Numbers inside the plots indicate the height of the density corresponding to each contour line. Contour lines are shown for multiples of 1 (solid lines). In addition, contour lines for multiples of 0.1 between 0.3 and 0.9 (dashed lines) are shown for additional detail. European populations are given in the first row, East Asian populations in the second row, South Asian populations in the third row, and American and SGDP Papuan populations in the final row. Additional information about the populations can be found in Table 1.