Visualizing phylogenetic trees of ancient DNA in a map

haplogroup-r1b-v88-v2219-phylogenetic

Yesterday the Eaton Lab at Columbia University announced on Twitter a nifty little tool by Carlos Alonso Maya-Lastra called TreeToM, which accepts Newick trees and CSV latitude/longitude data to explore phylogeny and geography interactively, with no coding required.

I thought it could complement nicely my All Ancient DNA Dataset, particularly for those newly described SNPs (FTDNA private variants, etc.) that have not been incorporated yet into SNP Tracker.

Here are two examples with snippets to copy&paste to the appropriate boxes in TreeToM. Feel free to add others in the comments:… Read the rest “Visualizing phylogenetic trees of ancient DNA in a map”

The expansion of Indo-Europeans in Y-chromosome haplogroups

yamnaya-corded-ware-y-dna-haplogroups

I have compiled for two years now the reported Y-DNA and mtDNA haplogroups of ancient DNA samples published, including also SNPs from analysis of the BAM files by hobbyists.

Y-DNA timeline

Here is a video with a timeline of the evolution of Indo-European speakers, according to what is known today about reconstructed languages, prehistoric cultures and ancient DNA:

NOTE. The video is best viewed in HD 1080p (1920×1080) with a display that allows for this or greater video quality, and a screen big enough to see haplogroup symbols, i.e. tablet or greater. The YouTube link is here. The Read the rest “The expansion of Indo-Europeans in Y-chromosome haplogroups”

A multidisciplinary approach to Neolithic life reconstruction

france-neolithic

Open access A Multidisciplinary Approach to Neolithic Life Reconstruction, by Goude et al. J Archaeol Method Th (2018).

Abstract (emphasis mine):

The expansion of Neolithic stable isotope studies in France now allows distinct regional population-scale food patterns to be linked to both local environment influences and specific economic choices. Carbon and nitrogen isotope values of more than 500 humans and of animal samples also permit hypotheses on sex-biased human provenance. To advance population scale research, we here present the first study that draws together carbon (C), nitrogen (N), sulphur (S) and strontium (Sr), dental calculus, aDNA, and palaeoparasitology analysis

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FADS1 and the timing of human adaptation to agriculture

fads1-farmers

Open access FADS1 and the timing of human adaptation to agriculture, by Sara Mathieson & Iain Mathieson, bioRxiv (2018).

Abstract:

Variation at the FADS1/FADS2 gene cluster is functionally associated with differences in lipid metabolism and is often hypothesized to reflect adaptation to an agricultural diet. Here, we test the evidence for this relationship using both modern and ancient DNA data. We document pre-out-of-Africa selection for both the derived and ancestral FADS1 alleles and show that almost all the inhabitants of Europe carried the ancestral allele until the derived allele was introduced approximately 8,500 years ago by Early Neolithic farming

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Phylogeny of leprosy, relevant for prehistoric Eurasian contacts

leprosy-medieval-europe

Some interesting studies were published at roughly the same time as Damgaard et al. (Nature 2018 and Science 2018), and that’s probably why they got little attention (at least by me).

Monica H. Green (also in Academia.edu), specialized in History of Medicine, summed up their relevance in Twitter quite well (her text is edited here for clarity):

I’ve been disappointed that three recent exceptional studies of one of the world’s most historically important diseases, leprosy, have gotten so little notice from the science communication. It will take me a few hours to lay out their significance. But

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Ancient nomadic tribes of the Mongolian steppe dominated by a single paternal lineage

The genome of an ancient Rouran individual reveals an important paternal lineage in the Donghu population, by Li et al. Am J Phys Anthropol (2018), 1–11.

Abstract (emphasis mine):

Objectives
Following the Xiongnu and Xianbei, the Rouran Khaganate (Rouran) was the third great nomadic tribe on the Mongolian Steppe. However, few human remains from this tribe are available for archaeologists and geneticists to study, as traces of the tombs of these nomadic people have rarely been found. In 2014, the IA‐M1 remains (TL1) at the Khermen Tal site from the Rouran period were found by a Sino‐Mongolian joint

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The uneasy relationship between Archaeology and Ancient Genomics

Allentoft Corded Ware

News feature Divided by DNA: The uneasy relationship between archaeology and ancient genomics, Two fields in the midst of a technological revolution are struggling to reconcile their views of the past, by Ewen Callaway, Nature (2018) 555:573-576.

Interesting excerpts (emphasis mine):

In duelling 2015 Nature papers6,7the teams arrived at broadly similar conclusions: an influx of herders from the grassland steppes of present-day Russia and Ukraine — linked to Yamnaya cultural artefacts and practices such as pit burial mounds — had replaced much of the gene pool of central and Western Europe around

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David Reich on the influence of ancient DNA on Archaeology and Linguistics

An interesting interview has appeared on The Atlantic, Ancient DNA Is Rewriting Human (and Neanderthal) History, on the occasion of the publication of David Reich’s book Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past.

Some interesting excerpts (I have emphasized some of Reich’s words):

On the efficiency of the Reich Lab

Zhang: How much does it cost to process an ancient DNA sample right now?

Reich: In our hands, a successful sample costs less than $200. That’s only two or three times more than processing them

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