Low Prevalence of Lactase Persistence in Bronze Age Europe Indicates Ongoing Strong Selection over the Last 3,000 Years

Bürger, Joachim; Link, Vivian; Blöcher, Jens; Schulz, Anna; Sell, Christian; Pochon, Zoé; Diekmann, Yoan; Žegarac, Aleksandra; Hofmanová, Zuzana; Winkelbach, Laura; Reyna-Blanco, Carlos S.; Bieker, Vanessa C.; Orschiedt, Jörg; Brinker, Ute; Scheu, Amelie; Leuenberger, Christoph; Bertino, Thomas S.; Bollongino, Ruth; Lidke, Gundula; Stefanović, Sofija; Jantzen, Detlef; Kaiser, Elke; Terberger, Thomas; Thomas, Mark G.; Veeramah, Krishna R.; Wegmann, Daniel

doi:10.1016/j.cub.2020.08.033

Cited by 66 publications

(62 citation statements)

References 88 publications

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“…The allele associated with lactase persistence was not found in any of the analyzed ancient samples, consistent with an increase in frequency of these alleles at a later stage 31 . However, early farmers already show allele frequencies similar to contemporary Europeans for 6 out of 7 SNPs of the FADS1/2 gene complex, potentially selected in populations with plant-based diet 32,33 (see Suppl.…”

Section: Resultssupporting

confidence: 75%

Demogenomic modeling of the timing and the processes of early European farmers differentiation

Marchi

Winkelbach

Schulz

et al. 2020

Preprint

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SummaryWhile the Neolithic expansion in Europe is well described archaeologically, the genetic origins of European first farmers and their affinities with local hunter-gatherers (HGs) remain unclear. To infer the demographic history of these populations, the genomes of 15 ancient individuals located between Western Anatolia and Southern Germany were sequenced to high quality, allowing us to perform population genomics analyses formerly restricted to modern genomes. We find that all European and Anatolian early farmers descend from the merging of a European and a Near Eastern group of HGs, possibly in the Near East, shortly after the Last Glacial Maximum (LGM). Western and Southeastern European HG are shown to split during the LGM, and share signals of a very strong LGM bottleneck that drastically reduced their genetic diversity. Early Neolithic Central Anatolians seem only indirectly related to ancestors of European farmers, who probably originated in the Near East and dispersed later on from the Aegean along the Danubian corridor following a stepwise demic process with only limited (2-6%) but additive input from local HGs.Our analyses provide a time frame and resolve the genetic origins of early European farmers. They highlight the impact of Late Pleistocene climatic fluctuations that caused the fragmentation, merging and reexpansion of human populations in SW Asia and Europe, and eventually led to the world's first agricultural populations.

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Section: Resultssupporting

confidence: 75%

Demogenomic modeling of the timing and the processes of early European farmers differentiation

Marchi

Winkelbach

Schulz

et al. 2020

Preprint

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“…Fluctuating milk availability could have created the need to transform it into a storable product. Milk was likely processed already in the earliest stages of the history of dairying, in line with widespread lactose intolerance among adults 68 , 69 , but also simply for preservation. Fresh milk that cannot be consumed within a few hours has to be handled to avoid microbial growth.…”

Section: Discussionmentioning

confidence: 99%

Seasonal calving in European Prehistoric cattle and its impacts on milk availability and cheese-making

Balasse

Gillis

Živaljević

et al. 2021

Sci Rep

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Present-day domestic cattle are reproductively active throughout the year, which is a major asset for dairy production. Large wild ungulates, in contrast, are seasonal breeders, as were the last historic representatives of the aurochs, the wild ancestors of cattle. Aseasonal reproduction in cattle is a consequence of domestication and herding, but exactly when this capacity developed in domestic cattle is still unknown and the extent to which early farming communities controlled the seasonality of reproduction is debated. Seasonal or aseasonal calving would have shaped the socio-economic practices of ancient farming societies differently, structuring the agropastoral calendar and determining milk availability where dairying is attested. In this study, we reconstruct the calving pattern through the analysis of stable oxygen isotope ratios of cattle tooth enamel from 18 sites across Europe, dating from the 6th mill. cal BC (Early Neolithic) in the Balkans to the 4th mill. cal BC (Middle Neolithic) in Western Europe. Seasonal calving prevailed in Europe between the 6th and 4th millennia cal BC. These results suggest that cattle agropastoral systems in Neolithic Europe were strongly constrained by environmental factors, in particular forage resources. The ensuing fluctuations in milk availability would account for cheese-making, transforming a seasonal milk supply into a storable product.

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“…Lactase persistence, or the continued ability to digest lactose into adulthood, is the most strongly selected single-gene trait over the last 10,000 years in multiple human populations 65 , believed to have spread amongst humans with the advent of animal domestication and the culturally transmitted practice of dairying 66 . In our study, as in previous work 4,6,7,11,12 , the association of LCT variants with Actinobacteria , more specifically Bifidobacterium , is by far the most statistically significant, suggesting a profound interaction between Actinobacteria and the human gut, in line with their reported keystone activities 30 .…”

Section: Discussionmentioning

confidence: 99%

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

Qin

Havulinna

Liu

et al. 2020

Preprint

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Co-evolution between humans and the microbial communities colonizing them has resulted in an intimate assembly of thousands of microbial species mutualistically living on and in their body and impacting multiple aspects of host physiology and health. Several studies examining whether human genetic variation can affect gut microbiota suggest a complex combination of environmental and host factors. Here, we leverage a single large-scale population-based cohort of 5,959 genotyped individuals with matched gut microbial shotgun metagenomes, dietary information and health records up to 16 years post-sampling, to characterize human genetic variations associated with microbial abundances, and predict possible causal links with various diseases using Mendelian randomization (MR). Genome-wide association study (GWAS) identified 583 independent SNP-taxon associations at genome-wide significance (p<5.0×10-8), which included notable strong associations with LCT (p=5.02×10-35), ABO (p=1.1×10-12), and MED13L (p=1.84×10-12). A combination of genetics and dietary habits was shown to strongly shape the abundances of certain key bacterial members of the gut microbiota, and explain their genetic association. Genetic effects from the LCT locus on Bifidobacterium and three other associated taxa significantly differed according to dairy intake. Variation in mucin-degrading Faecalicatena lactaris abundances were associated with ABO, highlighting a preferential utilization of secreted A/B/AB-antigens as energy source in the gut, irrespectively of fibre intake. Enterococcus faecalis levels showed a robust association with a variant in MED13L, with putative links to colorectal cancer. Finally, we identified putative causal relationships between gut microbes and complex diseases using MR, with a predicted effect of Morganella on major depressive disorder that was consistent with observational incident disease analysis. Overall, we present striking examples of the intricate relationship between humans and their gut microbial communities, and highlight important health implications.

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Low Prevalence of Lactase Persistence in Bronze Age Europe Indicates Ongoing Strong Selection over the Last 3,000 Years

Cited by 66 publications

References 88 publications

Demogenomic modeling of the timing and the processes of early European farmers differentiation

Demogenomic modeling of the timing and the processes of early European farmers differentiation

Seasonal calving in European Prehistoric cattle and its impacts on milk availability and cheese-making

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

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