10.5061/DRYAD.B5MKKWHFP
Marciniak, Stephanie
0000-0002-0052-8919
Pennsylvania State University
Bergey, Christina
Rutgers, The State University of New Jersey
Silva, Ana Maria
University of Coimbra
Hałuszko, Agata
University of Wrocław
Furmanek, Mirosław
University of Wrocław
Veselka, Barbara
Vrije Universiteit Brussel
Velemínský, Petr
National Museum, Prague
Vercellotti, Giuseppe
The Ohio State University
Wahl, Joachim
University of Tübingen
Zarina, Gunita
University of Latvia
Longhi, Cristina
Soprintendenza Archeologia, Belle Arti e Paesaggio
Kolář, Jan
Masaryk University
Garrido-Pena, Rafael
Autonomous University of Madrid
Flores-Fernández, Raúl
Independent archaeologist
Herrero-Corral, Ana M.
Complutense University of Madrid
Simalcsik, Angela
Olga Necrasov Center for Anthropological Research
Müller, Werner
University of Neuchâtel
Sheridan, Alison
National Museums Scotland
Miliauskienė, Žydrūnė
Vilnius University
Jankauskas, Rimantas
Vilnius University
Moiseyev, Vyacheslav
Peter the Great's Museum of Anthropology and Ethnography
Köhler, Kitti
Hungarian Academy of Sciences
Király, Ágnes
Hungarian Academy of Sciences
Gamarra, Beatriz
Rovira i Virgili University
Cheronet, Olivia
University of Vienna
Szeverényi, Vajk
Hungarian Academy of Sciences
Kiss, Viktória
Hungarian Academy of Sciences
Szeniczey, Tamás
Eötvös Loránd University
Kiss, Krisztián
Eötvös Loránd University
Zoffmann, Zsuzsanna K.
Hungarian Natural History Museum
Koós, Judit
Ottó Herman Museum
Hellebrandt, Magdolna
Ottó Herman Museum
Maier, Robert M.
Harvard University
Domboróczki, László
István Dobó Castle Museum, Eger
Virag, Cristian
Satu Mare County Museum, Satu Mare
Novak, Mario
Institute for Anthropological Research
Reich, David
Harvard University
Hajdu, Tamás
Eötvös Loránd University
von Cramon-Taubadel, Noreen
University at Buffalo, State University of New York
Pinhasi, Ron
University of Vienna
Perry, George H.
Pennsylvania State University
Data from: An integrative skeletal and paleogenomic analysis of stature
variation suggests relatively reduced health for early European farmers
Dryad
dataset
2022
FOS: Biological sciences
2022-03-30T00:00:00Z
2022-03-30T00:00:00Z
en
https://doi.org/10.1101/2021.03.31.437881
9072871833 bytes
4
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
1. ReadMe file 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>T and G>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 2. VCF and index files containing the imputed genotypes for 167 ancient individuals with and without filtering for deamination. 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 3. VCF and index files containing the imputed genotypes for 167 ancient individuals filtered for a minimum genotype probability of 0.99. 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