Abstract: Genetic material sequenced from ancient samples is revolutionizing our understanding of the recent evolutionary past. However, ancient DNA is often degraded, resulting in low coverage, error-prone sequencing. Several solutions exist to this problem, ranging from simple approach such as selecting a read at random for each site to more complicated approaches involving genotype likelihoods. In this work, we present a novel method for assessing the relationship of an ancient sample with a modern population while accounting for sequencing error by analyzing raw read from multiple ancient individuals simultaneously. We show that when analyzing SNP data, it is better to sequencing more ancient samples to low coverage: two samples sequenced to 0.5x coverage provide better resolution than a single sample sequenced to 2x coverage. We also examined the power to detect whether an ancient sample is directly ancestral to a modern population, finding that with even a few high coverage individuals, even ancient samples that are very slightly diverged from the modern population can be detected with ease. When we applied our approach to European samples, we found that no ancient samples represent direct ancestors of modern Europeans. We also found that, as shown previously, the most ancient Europeans appear to have had the smallest effective population sizes, indicating a role for agriculture in modern population growth.Joshua Schraiber, Assessing the relationship of ancient and modern populations, bioRxiv, Posted March 4, 2017, doi: https://doi.org/10.1101/113779
Saturday, March 4, 2017
Modern-day Europeans: a post-Neolithic product
There's a new preprint at bioRxiv looking at the relationship between ancient and modern-day Europeans. I think it misses its mark, because the author concludes that the Neolithic transition created the modern-day European gene pool.
This is only partly true, because modern-day Europeans are in fact, by and large, the product of intense Indo-European expansions from the Late Neolithic to the Migration period.
Just take a look the Y-haplogroup landscape in much of Europe and you'll see that our direct ancestors did not mostly spring from Neolithic farming communities. If you want to find them in the ancient DNA record, then seek out post-Neolithic populations rich in R1b-L51, R1a-Z645 and I1-M253.
By the way, the author uses Mormons from Utah (also known as CEU) to represent Europeans. I don't know if this is a problem, it might well be, but in any case, why Utah Mormons? Why not a wide variety of actual Europeans all the way from the Atlantic to the Urals? They're freely available online nowadays.
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8 comments:
Your logic in this post is circular. I mean, shamelessly conclusory and circular.
You wouldn't know what logic is.
Using Mormons from Utah will be a big problem as a proxy for Europeans. The founding population for Utah Mormons is heavily slanted towards English origin Americans but also surprisingly also immigration from East Lancashire in the second waves. I know that my family history is typical in this.
Not totally clear on their model but this hasn't stopped me before, so...
The big problem I see here is "Similarly, we only consider a single ancient population at a time, albeit with multiple samples. Ideally, ancient samples would be embedded in complex demographic models that include admixture, detailing their relationships to each other and to modern populations [Patterson et al., 2012, Lipson and Reich, 2017]."
Clearly no single population is going to be ancestral to "Europeans" - CEU. Of those they test Bell Beaker Germany would likely be closest... but even then will this one Bronze Age set of samples have all the variants to converge with CEU's ancestors via their model? Heterozygosity will be higher in modern Europeans from pooling distinct isolated populations that existed at, e.g. Bronze Age time period (which may have been quite similar in terms of the major components we think about).
(To some extent I got an impression here (perhaps wrongly) that they were thinking of these populations as having broken off at some point from a single population who were the single true ancestors of CEU, and then to have gone through greater drift and smaller population than the real ancestors... but of course that wouldn't make any sense.)
Hey y'all, I'm the author of the preprint. You're absolutely right---the lack of signal of direct ancestry in Europe is primarily a result of the fact that modern Europeans are extremely mixed, so the result is really not super exciting. Frankly, the model is misspecified for Europeans, but Europe happens to be the place where there's the most ancient data so I thought it would the most interesting demonstration of the way the method works.
I also absolutely agree that CEU are not a particularly good stand-in for "all Europeans". I mostly chose them as an example in the paper because they are often used as the default European stand-in, and I couldn't figure out a nice way to present results from, e.g., all the 1000 Genomes EUR populations simultaneously.
I'll take the thoughts here into account and try to think of a better way to present the empirical results in a revision. Honestly, I'm a theoretician; the thing I think is the coolest in the manuscript is the diffusion theory in the methods :)
I think Palacista is correct. CEU is definitely English. The results will be favouring Bell Beaker genomes from an ancients standpoint.
@Joshua
Thanks for the comment.
@AWood
CEU is mostly of British Mormon origin, but also with individuals of wholly or largely Scandinavian, German and Polish ancestry. A few also have Italian and Sub-Saharan ancestry.
Wouldn't Bell Beakers & Corded Ware folks be closer to modern Europeans?
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