Creationism in Crisis - How Natural Selection Produced Modern Europeans

Creationism in Crisis

How Natural Selection Produced Modern Europeans

Pontus Skoglund

Creationism in Crisis

How Natural Selection Produced Modern Europeans

Tom Davy

Ancient genomes reveal immunity adaptation in early farmers | Crick

Reconstruction of Mesolithic 'Chaddar Man'

Credit: Dr Yoan Diekmann

About 8000 years ago, i.e. around about the time Creationists believe the Universe was created, humans had already diversified in Eurasia into several major cultural groups, each with its distinct genome, having adapted to the local environment including local pathogens like viruses and bacteria.

Evidence from archaeology shows that farmers, complete with their domesticated livestock, were migrating into Western Europe and mixing with the indigenous hunter-gatherers.

Until now, it had been assumed that close proximity to their domestic livestock would have meant that the incoming farmers would have a more developed immune system, having evolved immunity to the pathogens carried by their livestock. The genes associated with this immune system would be expected to be favoured by natural selection so should account for the largest part of the genes of modern Europeans.

However, that view fails to take into account that the farmers were migrating into a new environment with new environmental selectors.

So, the evidence produced by researchers at the Francis Crick Institute's Ancient Genomics Laboratory have shown that in fact, modern Europeans have inherited only about half their immunity genes from the incoming farmers and the other half from the hunter-gatherers, showing that the hunter-gatherers' genes for immunity were selected equally by natural selection. This evidence comes from comparing the genomes of 677 individuals spanning Mesolithic and Neolithic Europe.br>
The conclusion then is that hunter-gatherers had evolved immunity genes in response to local conditions and that those local conditions then influenced which of their genes the incoming farmers retained and which indigenous genes were retained. In fact, it was increased diversity which was favoured by natural selection, not specific immunity to specific pathogens.

By contrast, the genes for (lack of) skin pigmentation that the farmers brought with them from Central Asia were retained differentially to give modern Europeans their pale skin, probably as an adaptation to lower vitamin D in the diet, since vitamin D is produced by the action of sunlight on skin.

Why Europeans have pale skin.

The researchers' findings are published, open access, in Current Biology.

Here is how the Crick Institute news release explains it:

Research from the Francis Crick Institute published today in Current Biology has revealed that diversity in genes coding for immunity may have facilitated adaptation to farming lifestyles in prehistoric periods.

Researchers at the Ancient Genomics Laboratory at the Crick studied available genome-wide DNA from 677 individuals dating to Stone Age Europe, spanning the movement of Neolithic farmers from the Near East into Europe about 8000 years ago, where they mixed with Mesolithic hunter-gatherers already in Europe.

They were interested in whether any particular genes might have coded for adaptations important to early farming groups, and looked for evidence of rapid evolution in these populations.

Since about 20% of the ancestry of descendant late Stone Age people could be traced to the local European hunter-gatherers, the researchers also asked whether any particular genes showed evidence of more hunter-gatherer ancestry.

They found that a large genetic region responsible for immune responses to diseases – the major histocompatibility complex (MHC) – showed both the strongest evidence of rapid evolution, and more Mesolithic hunter-gatherer ancestry than expected, suggesting that genetic variants in the MHC region already present in Europe were passed down preferentially.

It was really exciting to see for the first time that immunity is important for the transition to farming in a prehistoric population. The later Neolithic people had far more farmer ancestry in general, so we expected to see the same at the MHC region, especially as many diseases have been linked to Neolithic periods. But we saw about 50:50 ancestry from Neolithic farmers and Mesolithic hunter-gatherers here, showing that natural selection favoured genes from the hunter-gatherers already in Europe.

At the moment we’re not quite sure why this happened, but a proposal is that the European hunter-gatherers had genetic variations which allowed them to fight Europe-specific diseases. Or picking up a variety of genes from both hunter-gatherers and farmers was beneficial because it resulted in lots of diversity at this major group of genes, allowing people to better fight off disease.

Tom Davy, lead author
PhD student
Ancient Genomics Laboratory
Francis Crick Institute, London, UK.

It has previously been thought that the transition to farming was associated with increased natural selection on immunity variants, as people started living closer to animals and eating more animal products. This research supports this view, but also shows that diversity in immune genes may be just as important as adaptation to lifestyle.

The research team speculates that either the hunter-gatherers already had genetic adaptations against bacteria, viruses or other microorganisms in Europe, or that having many different forms of the genes was advantageous.

The shift to farming was an important transition all over the world, resulting in changing diets and exposure to infectious disease.

Previous research has suggested that adaptation in genetic regions relating to immunity, such as the MHC, has been important in recent time periods, and this research now provides similar evidence for adaptation in prehistory. By growing the ancient genomic record, we will be able to better understand the role of immunity in other periods of the human past.

Pontus Skoglund
Group Leader
Ancient Genomics Laboratory
Francis Crick Institute, London, UK.

The team also confirmed results from previous studies, showing that genes coding for skin pigmentation showed the greatest representation for Neolithic farmer ancestry, with these variations coming into Europe from the Near East. This may be to maintain vitamin D levels when sources, such as diet and exposure to sunlight, change.

Figure 1. Admixture model and geographic distribution of Neolithic and Mesolithic individuals with genome-wide ancient DNA
(A) An illustration of the genetic history of the Neolithic-Mesolithic transition in Western Eurasia.
(B) “Casino-plot” of individuals included for analyses, colored by the ancestry group for which those individuals were used in this paper. For sites with multiple samples, we stack those individuals above the reported coordinates.

Source: Davy, T, et al. (2023)

Highlights

• Genomic evidence for adaptive admixture in Stone Age Europe
• Excess of Neolithic farmer ancestry around the pigmentation-associated gene SLC24A5
• Excess of hunter-gatherer ancestry in the major histocompatibility complex (MHC)
• Post-admixture selection occurred upon variants from both admixing ancestries

Summary

Ancient DNA has revealed multiple episodes of admixture in human prehistory during geographic expansions associated with cultural innovations. One important example is the expansion of Neolithic agricultural groups out of the Near East into Europe and their consequent admixture with Mesolithic hunter-gatherers.^1,2,3,4 Ancient genomes from this period provide an opportunity to study the role of admixture in providing new genetic variation for selection to act upon, and also to identify genomic regions that resisted hunter-gatherer introgression and may thus have contributed to agricultural adaptations. We used genome-wide DNA from 677 individuals spanning Mesolithic and Neolithic Europe to infer ancestry deviations in the genomes of admixed individuals and to test for natural selection after admixture by testing for deviations from a genome-wide null distribution. We find that the region around the pigmentation-associated gene SLC24A5 shows the greatest overrepresentation of Neolithic local ancestry in the genome (|Z| = 3.46). In contrast, we find the greatest overrepresentation of Mesolithic ancestry across the major histocompatibility complex (MHC; |Z| = 4.21), a major immunity locus, which also shows allele frequency deviations indicative of selection following admixture (p = 1 × 10⁻⁵⁶). This could reflect negative frequency-dependent selection on MHC alleles common in Neolithic populations or that Mesolithic alleles were positively selected for and facilitated adaptation in Neolithic populations to pathogens or other environmental factors. Our study extends previous results that highlight immune function and pigmentation as targets of adaptation in more recent populations to selection processes in the Stone Age.

Davy, Tom; Ju, Dan; Mathieson, Iain; Skoglund, Pontus
Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers
Current Biology (2023), DOI: 10.1016/j.cub.2023.02.049

Copyright: © 2023 The authors.
Published by Elsevier Inc. Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

What Creationists now need to explain is how the two populations that admixed in Western Eurasia had diversified genomically by 8000 years ago to such an extent that traces of the two genomes can be found in modern Europeans. Genetic diversification to that degree implies many thousands of years of relative genetic isolation.

They also need to explain why, if, as their cult leaders tell them, the Theory of Evolution by natural selection is being abandoned by mainstream biologists as not fit for purpose, it explains perfectly the facts as observed by this research group, who offer nothing but the TOE as the explanation for what they found.

But I doubt we'll ever get those explanations.

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Thank you for sharing!

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