Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria

Veeramah, Krishna R.; Rott, Andreas; Groß, Melanie; Dorp, Lucy van; López, Saioa; Kirsanow, Karola; Sell, Christian; Blöcher, Jens; Wegmann, Daniel; Link, Vivian; Hofmanová, Zuzana; Peters, Joris; Trautmann, Bernd; Gairhos, Anja; Haberstroh, Jochen; Päffgen, Bernd; Hellenthal, Garrett; Haas-Gebhard, Brigitte; Harbeck, Michaela; Bürger, Joachim

doi:10.1073/pnas.1719880115

Cited by 77 publications

(71 citation statements)

References 43 publications

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“…We collected published aDNA data from 1071 ancient individuals from Western Eurasia (west of 50° E), dated to between 38,000 and 1100 years before present (BP) (27, 29, 30, 32–57). Using GWAS summary statistics for height from the UK Biobank (generated and made available by the Neale lab: http://nealelab.is/), we computed height PRS for each individual, using a P-value cutoff of 10 −6 , clumping variants in 250kb windows, and replacing missing genotypes with the mean across individuals (Methods).…”

Section: Resultsmentioning

confidence: 99%

Genetic contributions to variation in human stature in prehistoric Europe

Cox¹,

Ruff

Maier

et al. 2019

Preprint

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11The relative contributions of genetics and environment to temporal and geographic variation in 12 human height remain largely unknown. Ancient DNA has identified changes in genetic ancestry 13 over time, but it is not clear whether those changes in ancestry are associated with changes in 14 height. Here, we directly test whether changes over the past 38,000 years in European height 15 predicted using DNA from 1071 ancient individuals are consistent with changes observed in 16 1159 skeletal remains from comparable populations. We show that the observed decrease in 17 height between the Early Upper Paleolithic and the Mesolithic is qualitatively predicted by 18 genetics. Similarly, both skeletal and genetic height remained constant between the Mesolithic 19and Neolithic and increased between the Neolithic and Bronze Age. Sitting height changes 20 much less than standing height-consistent with genetic predictions-although genetics predicts 21 a small Bronze Age increase that is not observed in skeletal remains. Geographic variation in 22 stature is also qualitatively consistent with genetic predictions, particularly with respect to 23 latitude. Finally, we hypothesize that an observed decrease in genetic heel bone mineral 24 density in the Neolithic reflects adaptation to the decreased mobility indicated by decreased 25 femoral bending strength. This study provides a model for interpreting phenotypic changes 26 predicted from ancient DNA and demonstrates how they can be combined with phenotypic 27 measurements to understand the relative contribution of genetic and developmentally plastic 28 responses to environmental change. 29 30 Significance 31 Measurements of prehistoric human skeletal remains provide a record of changes in height and 32 other anthropometric traits, over time. Often, these changes are interpreted in terms of plastic 33 developmental response to shifts in diet, climate or other environmental factors. These 34changes can also be genetic in origin but, until recently, it has been impossible to separate the 35 effects of genetics and environment. Here we use ancient DNA to directly estimate genetic 36 changes in phenotypes and to identify changes driven not by genetics, but by environment. We 37show that changes over the past 35,000 years are largely predicted by genetics, but also 38 identify specific shifts that are more likely to be environmentally driven. 39 40 7 ) difference between EUP and LUP-Neolithic and a 0.27 SD (1.8cm; P=3.6x10 -5 ) difference 127 between LUP-Neolithic and post-Neolithic. Broad patterns of change in stature over time are 128 therefore consistent with genetic predictions. 129 130Additionally, we fit a piecewise linear model allowing PRS to decrease from the EUP to the 131 Neolithic and then increase and change slope in the post-Neolithic (Fig. 1d-f). In this model, 132 PRS(GWAS) decreases by about 1.8´10 -5 SD/year (P=0.014) from EUP to Neolithic, and increases 133 by 2.0´10 -4 SD/year (P=0.001) post-Neolithic (Fig. 1d). PRS(GWAS/sib) decreases by about 134 1.6´10 -5 SD...

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Section: Resultsmentioning

confidence: 99%

Genetic contributions to variation in human stature in prehistoric Europe

Cox¹,

Ruff

Maier

et al. 2019

Preprint

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“…It is interesting to compare our neutral set of SNPs to another previously defined set of neutral regions of the human genome that has been used as a reference for demographic inferences in a series of studies (e.g. Gronau et al, 2011 ; McManus et al, 2015 ; King and Wakeley, 2016 ; Veeramah et al, 2018 ). Gronau et al (2011) have identified a set of 37,574 potentially neutral regions of 1 kb in length with carefully chosen properties (e.g.…”

Section: Discussionmentioning

confidence: 99%

“…We finally retrieved 37,574 potentially neutral regions of 1 kb (e.g. Gronau et al, 2011 ; McManus et al, 2015 ; King and Wakeley, 2016 ; Veeramah et al, 2018 ) from http://compgen.cshl.edu/GPhoCS/data.php to make comparisons between our neutral set of SNPs to another possible sets.…”

Section: Methodsmentioning

confidence: 99%

Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences

Pouyet

Aeschbacher

Thiéry

et al. 2018

eLife

130

168

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Disentangling the effect on genomic diversity of natural selection from that of demography is notoriously difficult, but necessary to properly reconstruct the history of species. Here, we use high-quality human genomic data to show that purifying selection at linked sites (i.e. background selection, BGS) and GC-biased gene conversion (gBGC) together affect as much as 95% of the variants of our genome. We find that the magnitude and relative importance of BGS and gBGC are largely determined by variation in recombination rate and base composition. Importantly, synonymous sites and non-transcribed regions are also affected, albeit to different degrees. Their use for demographic inference can lead to strong biases. However, by conditioning on genomic regions with recombination rates above 1.5 cM/Mb and mutation types (C↔G, A↔T), we identify a set of SNPs that is mostly unaffected by BGS or gBGC, and that avoids these biases in the reconstruction of human history.

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“…Dependent on the analysis, target Migration Period samples were analyzed individually (to avoid the effects of relatedness) or together (using a set of unrelated individuals that maximized SNP number) Population Assignment Analysis. PAA was conducted as described in Veeramah et al 25 using the POPRES and HellBus datasets. Spatial Ancestry Analysis.…”

Section: Dna Isolation Screening Sequencing and Bioinformatic Procementioning

confidence: 99%

Understanding 6th-Century Barbarian Social Organization and Migration through Paleogenomics

Amorim

Vai

Posth

et al. 2018

Preprint

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Despite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies, we obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards , a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized around one large pedigree, suggesting that biological relationships played an important role in these early Medieval societies. Moreover, we identified genetic structure in each cemetery involving at least two groups with different ancestry that were very distinct in terms of their funerary customs.Finally, our data was consistent with the proposed long-distance migration from Pannonia to Northern Italy.

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Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria

Cited by 77 publications

References 43 publications

Genetic contributions to variation in human stature in prehistoric Europe

Genetic contributions to variation in human stature in prehistoric Europe

Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences

Understanding 6th-Century Barbarian Social Organization and Migration through Paleogenomics

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