Dairying, diseases and the evolution of lactase persistence in Europe:

In European and many African, Middle Eastern and southern Asian populations, lactase persistence (LP) is the most strongly selected monogenic trait to have evolved over the past 10,000 years1. Although the selection of LP and the consumption of prehistoric milk must be linked, considerable uncertainty remains concerning their spatiotemporal configuration and specific interactions2,3. Here we provide detailed distributions of milk exploitation across Europe over the past 9,000 years using around 7,000 pottery fat residues from more than 550 archaeological sites. European milk use was widespread from the Neolithic period onwards but varied spatially and temporally in intensity. Notably, LP selection varying with levels of prehistoric milk exploitation is no better at explaining LP allele frequency trajectories than uniform selection since the Neolithic period. In the UK Biobank4,5 cohort of 500,000 contemporary Europeans, LP genotype was only weakly associated with milk consumption and did not show consistent associations with improved fitness or health indicators. This suggests that other reasons for the beneficial effects of LP should be considered for its rapid frequency increase. We propose that lactase non-persistent individuals consumed milk when it became available but, under conditions of famine and/or increased pathogen exposure, this was disadvantageous, driving LP selection in prehistoric Europe. Comparison of model likelihoods indicates that population fluctuations, settlement density and wild animal exploitation—proxies for these drivers—provide better explanations of LP selection than the extent of milk exploitation. These findings offer new perspectives on prehistoric milk exploitation and LP evolution.

Two issues

1) Doesn’t seem to explain why LP started becoming common in Britain before the continent

2) Why are the alleles not in HWE? There’s not really any assortative mating.

Two preprints/papers.

Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals:

Admixture has played a prominent role in shaping patterns of human genomic variation, including gene flow with now-extinct hominins like Neanderthals and Denisovans. Here, we describe a novel probabilistic method called IBDmix to identify introgressed hominin sequences, which, unlike existing approaches, does not use a modern reference population. We applied IBDmix to 2,504 individuals from geographically diverse populations to identify and analyze Neanderthal sequences segregating in modern humans. Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date.

Basically, this paper concludes that Eurasian back-migration related to Europeans/West Asians seems to be around 30% of Sub-Saharan African ancestry. They carry about 30% of the Neanderthal ancestry of Eurasians.

Then, a preprint that uses a pretty sophisticated method, Ancient Admixture into Africa from the ancestors of non-Africans:

Genetic diversity across human populations has been shaped by demographic history, making it possible to infer past demographic events from extant genomes. However, demographic inference in the ancient past is difficult, particularly around the out-of-Africa event in the Late Middle Paleolithic, a period of profound importance to our species’ history. Here we present SMCSMC, a Bayesian method for inference of time-varying population sizes and directional migration rates under the coalescent-with-recombination model, to study ancient demographic events. We find evidence for substantial migration from the ancestors of present-day Eurasians into African groups between 40 and 70 thousand years ago, predating the divergence of Eastern and Western Eurasian lineages. This event accounts for previously unexplained genetic diversity in African populations and supports the existence of novel population substructure in the Late Middle Paleolithic. Our results indicate that our species’ demographic history around the out-of-Africa event is more complex than previously appreciated.

This paper estimates 35-40% back-migration from the ancestral proto-Eurasian population, with less (~20%) in African hunter-gatherers. This paper didn’t detect Neanderthal ancestry and argues that the back-migration predates the West vs East Eurasian split. It plausibly argues African effective population sizes are inflated by the admixture event.

The two results here clearly contradict the details.

Ancient genomes from the last three millennia support multiple human dispersals into Wallacea:

Previous research indicates that the human genetic diversity found in Wallacea – islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves – has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Here, we provide new insights into this region’s demographic history based on genome-wide data from 16 ancient individuals (2600-250 yrs BP) from islands of the North Moluccas, Sulawesi, and East Nusa Tenggara. While the ancestry of individuals from the northern islands fit earlier views of contact between groups related to the Austronesian expansion and the first colonization of Sahul, the ancestry of individuals from the southern islands revealed additional contributions from Mainland Southeast Asia, which seems to predate the Austronesian admixture in the region. Admixture time estimates for the oldest individuals of Wallacea are closer to archaeological estimates for the Austronesian arrival into the region than are admixture time estimates for present-day groups. The decreasing trend in admixture times exhibited by younger individuals supports a scenario of multiple or continuous admixture involving Papuan- and Asian-related groups. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.

This paper is hard to parse. But here are my takeaways

– the samples in this study do not seem particularly closely related to the 7,000 years old sample from Sulawesi

– there was likely an earlier mainland migration into Wallacea of Austro-Asiatic speaking people

– gene flow seems to have been reoccurrent from the east, in western Melanesia, as well as from Austronesians to the northeast

I have been staring and this figure and rereading Ancient West African foragers in the context of African population history. The Shum Laka sample from this paper, dating to four to eight thousand years ago, have drawn my attention, and I’m just looking at them a lot.

It seems ridiculous I’ve been using Nigerians as my “African reference” for decades. Most African populations, including Pygmies and Khoisan, have Eurasian admixture from the last 10,000 years. And what about deeper back-to-Africa ancestry? That seems likely and is hinted at in the above paper.

Modern human lineages have a deep history in Africa and the Near East. I think we’re going to have a transformation of our understanding of what happened in these regions in the near future.

The New Yorker has a long feature that explores the strange results from the paper last year, Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India. Basically, they found a bunch of Indians who died 1,000 years ago, and, a bunch of Greeks who died a few centuries ago. They were buried naturally in a very isolated lake high in the Himalayas. There are all sorts of hypotheses regarding the Greeks, whose bones indicate a Mediterranean diet, and the closest match to individuals in Crete. My personal experience is that “mainland Greeks” tend to be a bit Northern European shifted, so these individuals may have been Anatolian or Aegean Greeks.

Stuart Fidel, who sometimes comments on this weblog, suggests these were Armenian traders. But David Reich correctly points out Armenians are very distinct genetically from Greeks (though the two are not entirely different obviously!). Another hypothesis is a bone mix-up, but the issue here is there are a lot of individuals who are of the same population and seem to have lived in the same region. How could bone mix-ups produce so many systematic errors?

Ultimately there’s no final answer in the piece, though hopefully, someone will present a reasonable conjecture.

Because the piece has Reich and his lab spotlighted, they allude to the controversy around him. This is ultimately going to be the legacy of the hit-piece from a few years back. He’s now a “controversial figure,” which is, to be frank not a bad thing in the eyes of some of the Reich lab’s scientific rivals. Most media treatments that aren’t purely about his research (i.e., Carl Zimmer’s column in The New York Times covering the Reich lab publications) will mention this now.

Here’s why he’s a mensch:

Still, some anthropologists, social scientists, and even geneticists are deeply uncomfortable with any research that explores the hereditary differences among populations. Reich is insistent that race is an artificial category rather than a biological one, but maintains that “substantial differences across populations” exist. He thinks that it’s not unreasonable to investigate those differences scientifically, although he doesn’t undertake such research himself. “Whether we like it or not, people are measuring average differences among groups,” he said. “We need to be able to talk about these differences clearly, whatever they may be. Denying the possibility of substantial differences is not for us to do, given the scientific reality we live in.”

This is, in 2020, is an old-fashioned view. There are now young American researchers who frankly express disquiet and discomfort at the idea of studying human population genetic variation, period.  Including people who themselves have studied topics such as polygenic adaptation in humans. This would be a very strange view for older researchers, but it’s not totally out of the norm today, so expect someone like Reich to be viewed as quite the dinosaur in a decade. It seems ridiculous to say, but I do wonder if we’re seeing the end of the “humans as a model organism” era. Lots of ppl are not happy with the new atmosphere, but lots of people just keep quiet and go along.