DOI: 10.5061/dryad.b5mkkwhfp
title: Data from: An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers

description: Human culture, biology, and health were shaped dramatically by the onset
 of agriculture ~12,000 years before present (BP). This shift is
 hypothesized to have resulted in increased individual fitness and
 population growth as evidenced by archaeological and population genomic
 data alongside a decline in physiological health as inferred from skeletal
 remains. Here, we consider osteological and ancient DNA data from the same
 prehistoric individuals to study human stature variation as a proxy for
 health across a transition to agriculture. Specifically, we compared
 ‘predicted’ genetic contributions to height from paleogenomic data and
 ‘achieved’ adult osteological height estimated from long bone measurements
 for 167 individuals across Europe spanning the Upper Paleolithic to Iron
 Age (~38,000-2,400 BP). We found that individuals from the Neolithic were
 shorter than expected (given their individual polygenic height scores) by
 an average of -3.82 cm relative to individuals from the Upper Paleolithic
 and Mesolithic (P=0.040) and -2.21 cm shorter relative to post-Neolithic
 individuals (P=0.068, with osteological vs. expected stature steadily
 increasing across the Copper (+1.95 cm relative to the Neolithic), Bronze
 (+2.70 cm), and Iron (+3.27 cm) Ages. These results were attenuated when
 we additionally accounted for genome-wide genetic ancestry variation, for
 example with Neolithic individuals -2.82 cm shorter than expected on
 average relative to pre-Neolithic individuals (P=0.120). We also
 incorporated observations of paleopathological indicators of non-specific
 stress that can persist from childhood to adulthood in skeletal remains
 into our model. Overall, our work highlights the potential of integrating
 disparate datasets to explore proxies of health in prehistory.
description: <strong>1. ReadMe
 file</strong> Description of the methods used to
 generate the imputed data sets. In brief, the 1000 Genomes Phase 3 genetic variants reference
 panel was used for genotyping and imputation, as provided by
 BEAGLE (ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/). UnifiedGenotyper was used to obtain genotypes and likelihood scores. Due to the potential for post-mortem damage impacting C&gt;T and G&gt;A allele changes, the per chromosome VCF files of the called genotypes were filtered for potential post-mortem damage. Genotype likelihoods were then estimated using the per-chromosome VCF files, followed by imputation of missing SNPs based on the genotype probability score using the 1000 Genomes phase 3 haplotypes (http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/) and GRCh37 genomic maps (http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/). Genotyping calling and imputation was repeated for data not subject to filtering for potential deamination signals. README_Marciniak_et_al_2022.txt <strong>2. VCF and index files containing the imputed genotypes for 167 ancient individuals with and without filtering for deamination.</strong> VCF (*.vcf.gz) and index (*.tbi) files of imputed genotypes for 167 ancient individuals (previously published and publicly available), with and without filtering for signals of deamination (prior to imputation). a) ALL_MERGED_CHRS_DEAM_n167.preGLfilter.vcf.gz, ALL_MERGED_CHRS_DEAM_n167.preGLfilter.vcf.gz.tbi; b) ALL_MERGED_CHRS_NODEAM_n167.preGLfilter.vcf.gz, ALL_MERGED_CHRS_NODEAM_n167.preGLfilter.vcf.gz.tbi <strong>3. VCF and index files containing the imputed genotypes for 167 ancient individuals filtered for a minimum genotype probability of 0.99.</strong> VCF (*.vcf.gz) and index (*.tbi) files of imputed genotypes for 167 ancient individuals (previously published and publicly available), with and without filtering for signals of deamination (prior to imputation) as well as filtered for a minimum genotype probably of 0.99. a) ALL_MERGED_CHRS_DEAM_n167.GL99.vcf.gz, ALL_MERGED_CHRS_DEAM_n167.GL99.vcf.gz.tbi; b) ALL_MERGED_CHRS_NODEAM_n167.GL99.vcf.gz, ALL_MERGED_CHRS_NODEAM_n167.GL99.vcf.gz.tbi