1. Ellinghaus, D. et al. Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci. Nat Genet 48, 510-518 (2016).
2. Caruso, R., Lo, B. C. & Núñez, G. Host-microbiota interactions in inflammatory bowel disease. Nat Rev Immunol 20, 411-426 (2020).
3. Hampe, J. et al. A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet 39, 207-211 (2007).
4. Corona, E., Dudley, J. T. & Butte, A. J. Extreme evolutionary disparities seen in positive selection across seven complex diseases. PLoS One 5, e12236 (2010).
5. Jostins, L. et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 491, 119-124 (2012).
6. Nakagome, S. et al. Crohn’s disease risk alleles on the NOD2 locus have been maintained by natural selection on standing variation. Mol Biol Evol 29, 1569-1585 (2012).
7. Cagliani, R. et al. Crohn’s disease loci are common targets of protozoa-driven selection. Mol Biol Evol 30, 1077-1087 (2013).
8. Raj, T. et al. Common risk alleles for inflammatory diseases are targets of recent positive selection. Am J Hum Genet 92, 517-529 (2013).
9. Mesbah-Uddin, M., Elango, R., Banaganapalli, B., Shaik, N. A. & Al-Abbasi, F. A. In-silico analysis of inflammatory bowel disease (IBD) GWAS loci to novel connections. PLoS One 10, e0119420 (2015).
10. Karlsson, E. K., Kwiatkowski, D. P. & Sabeti, P. C. Natural selection and infectious disease in human populations. Nat Rev Genet 15, 379-393 (2014).
11. Quintana-Murci, L. Understanding rare and common diseases in the context of human evolution. Genome Biol 17, 225 (2016).
12. Domínguez-Andrés, J. et al. Evolution of cytokine production capacity in ancient and modern European populations. Elife 10, e64971 (2021).
13. Marciniak, S. & Perry, G. H. Harnessing ancient genomes to study the history of human adaptation. Nat Rev Genet 18, 659-674 (2017).
14. Cox, S. L., Ruff, C. B., Maier, R. M. & Mathieson, I. Genetic contributions to variation in human stature in prehistoric Europe. Proc Natl Acad Sci U S A 116, 21484-21492 (2019).
15. Marnetto, D. et al. Ancestral genomic contributions to complex traits in contemporary Europeans. Curr Biol 32, 1412-1419.e3 (2022).
16. Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499-503 (2015).
17. Richards, M. P., Schulting, R. J. & Hedges, R. E. Archaeology: sharp shift in diet at onset of Neolithic. Nature 425, 366 (2003).
18. Lipson, M. et al. Parallel palaeogenomic transects reveal complex genetic history of early European farmers. Nature 551, 368-372 (2017).
19. Immel, A. et al. Genome-wide study of a Neolithic Wartberg grave community reveals distinct HLA variation and hunter-gatherer ancestry. Commun Biol 4, 113 (2021).
20. Hedjoudje, A. et al. rs2476601 polymorphism in PTPN22 is associated with Crohn’s disease but not with ulcerative colitis: a meta-analysis of 16,838 cases and 13,356 controls. Ann Gastroenterol 30, 197-208 (2017).
21. Rabaneda-Bueno, R. et al. PTPN22 gene functional polymorphism (rs2476601) in older adults with frailty syndrome. Mol Biol Rep 48, 1193-1204 (2021).
22. Armitage, L. H., Wallet, M. A. & Mathews, C. E. Influence of PTPN22 Allotypes on Innate and Adaptive Immune Function in Health and Disease. Front Immunol 12, 636618 (2021).
23. Zhang, C., Wang, W., Zhang, H., Wei, L. & Guo, S. Association of FCGR2A rs1801274 polymorphism with susceptibility to autoimmune diseases: A meta-analysis. Oncotarget 7, 39436-39443 (2016).
24. López-Martínez, R. et al. The FCGR2A rs1801274 polymorphism was associated with the risk of death among COVID-19 patients. Clin Immunol 236, 108954 (2022).
25. Abdollahi, E., Tavasolian, F., Momtazi-Borojeni, A. A., Samadi, M. & Rafatpanah, H. Protective role of R381Q (rs11209026) polymorphism in IL-23R gene in immune-mediated diseases: A comprehensive review. J Immunotoxicol 13, 286-300 (2016).
26. Riemenschneider, M. et al. A functional polymorphism within plasminogen activator urokinase (PLAU) is associated with Alzheimer’s disease. Hum Mol Genet 15, 2446-2456 (2006).
27. Swaminathan, B. et al. Fine mapping and functional analysis of the multiple sclerosis risk gene CD6. PLoS One 8, e62376 (2013).
28. Ma, C. et al. Critical Role of CD6highCD4+ T Cells in Driving Th1/Th17 Cell Immune Responses and Mucosal Inflammation in IBD. J Crohns Colitis 13, 510-524 (2019).
29. Zhernakova, A. et al. Evolutionary and functional analysis of celiac risk loci reveals SH2B3 as a protective factor against bacterial infection. Am J Hum Genet 86, 970-977 (2010).
30. Lahiri, A., Hedl, M., Yan, J. & Abraham, C. Human LACC1 increases innate receptor-induced responses and a LACC1 disease-risk variant modulates these outcomes. Nat Commun 8, 15614 (2017).
31. Kaplan, G. G. & Windsor, J. W. The four epidemiological stages in the global evolution of inflammatory bowel disease. Nat Rev Gastroenterol Hepatol 18, 56-66 (2021).
32. Sankararaman, S. et al. The genomic landscape of Neanderthal ancestry in present-day humans. Nature 507, 354-357 (2014).
33. Marchi, N. et al. The genomic origins of the world’s first farmers. Cell 185, 1842-1859.e18 (2022).
34. Münster, A. et al. 4000 years of human dietary evolution in central Germany, from the first farmers to the first elites. PLoS One 13, e0194862 (2018).
35. Schulting, R. Dietary shifts at the Mesolithic-Neolithic transition in Europe: An overview of the stable isotope data in The oxford handbook of the archaeology of diet (eds Lee-Thorp, J. A. & Katzenberg, M. A., Oxford Academic, 2018).
36. Simmons, A. H. The Neolithic revolution in the Near East: transforming the human landscape (University of Arizona Press, 2011).
37. Bellwood, P. First farmers: The origins of agricultural societies (Wiley-Blackwell, 2004).
38. Ferguson, L. R. et al. IL23R and IL12B SNPs and haplotypes strongly associate with Crohn’s Disease risk in a New Zealand population. Gastroenterol Res Pract 2010, 539461 (2010).
39. Gerosa, F. et al. Differential regulation of interleukin 12 and interleukin 23 production in human dendritic cells. J Exp Med 205, 1447-1461 (2008).
40. Reay, W. R. & Cairns, M. J. Advancing the use of genome-wide association studies for drug repurposing. Nat Rev Genet 22, 658-671 (2021).
41. Spalinger, M. R. et al. PTPN22 regulates NLRP3-mediated IL1B secretion in an autophagy-dependent manner. Autophagy 13, 1590-1601 (2017).
42. Larabi, A., Barnich, N. & Nguyen, H. T. T. New insights into the interplay between autophagy, gut microbiota and inflammatory responses in IBD. Autophagy 16, 38-51 (2020).
43. Consuegra-Fernández, M. et al. Genetic and experimental evidence for the involvement of the CD6 lymphocyte receptor in psoriasis. Cell Mol Immunol 15, 898-906 (2018).
44. Larsen, C. S. et al. Bioarchaeology of Neolithic Çatalhöyük reveals fundamental transitions in health, mobility, and lifestyle in early farmers. Proc Natl Acad Sci U S A 116, 12615-12623 (2019).
45. Latham, K. J. Human health and the Neolithic revolution: An overview of impacts of the agricultural transition on oral health, epidemiology, and the human body. Nebraska Anthropologist 28, 95-102 (2013).
46. Dietrich, L. et al. Investigating the function of Pre-Pottery Neolithic stone troughs from Göbekli Tepe–An integrated approach. J Archaeol Sci Rep 34, 102618 (2020).
47. Evershed, R. P. et al. Dairying, diseases and the evolution of lactase persistence in Europe. Nature 608, 336-345 (2022).
48. Rosen, A. M. & Rivera-Collazo, I. Climate change, adaptive cycles, and the persistence of foraging economies during the late Pleistocene/Holocene transition in the Levant. Proc Natl Acad Sci U S A 109, 3640-3645 (2012).
49. Sebald, S. V., Papathanasiou, A. & Grupe, G. Changing subsistence economies in the course of the Neolithic transition: Isotopic sourcing of collagen isotopic ratios in human skeletons from early Neolithic Anatolia and Greece. J Archaeol Sci Rep 43, 103450 (2022).
50. Martino, C. et al. Acetate reprograms gut microbiota during alcohol consumption. Nat Commun 13, 4630 (2022).
51. Crittenden, A. N. & Schnorr, S. L. Current views on hunter-gatherer nutrition and the evolution of the human diet. Am J Phys Anthropol 162 Suppl 63, 84-109 (2017).
52. Kılınç, G. M. et al. The demographic development of the first farmers in Anatolia. Curr Biol 26, 2659-2666 (2016).
53. Kılınç, G. M. et al. Archaeogenomic analysis of the first steps of Neolithization in Anatolia and the Aegean. Proc Biol Sci 284, 20172064 (2017).
54. Furholt, M. Mobility and social change: Understanding the european neolithic period after the archaeogenetic revolution. J Archaeol Res 29, 481-535 (2021).
55. Graham, D. B. & Xavier, R. J. Pathway paradigms revealed from the genetics of inflammatory bowel disease. Nature 578, 527-539 (2020).
56. Susat, J. et al. Yersinia pestis strains from Latvia show depletion of the pla virulence gene at the end of the second plague pandemic. Sci Rep 10, 14628 (2020).
57. Haller, M. et al. Mass burial genomics reveals outbreak of enteric paratyphoid fever in the Late Medieval trade city Lübeck. iScience 24, 102419 (2021).
58. Meadows, J. et al. High-precision Bayesian chronological modeling on a calibration plateau: the Niedertiefenbach gallery grave. Radiocarbon 62, 1261-1284 (2020).
59. Rinne, C., Drummer, C. & Hamann, C. Collective and individual burial practices. Changing patterns at the beginning of the third millennium BC: The megalithic grave of Altendorf. Journal of Neolithic Archaeology 21, 75-88 (2019).
60. Raetsel-Fabian, D. Der nordwestliche Nachbar: Neue Aspekte zur Wartbergkultur. Kolloquien Des Instituts Für Ur Und Frühgeschichte Erlangen 1, 26-28 (1999).
61. Raetzel-Fabian, D. Absolute Chronologie. Die Kollektivgräber-Nekropole Warburg IV. Bodenaltertümer Westfalens 34, 165-178 (1997).
62. Pechtl, J., Hanöffner, S., Staskiewicz, A. & Obermaier, H. Die linienbandkeramische Gräbergruppe von Niederpöring-”Leitensiedlung”, Gde. Oberpöring, Lkr. Deggendorf in Vorträge des 36. Niederbayerischen Archäologentages Leidorf, Marie, 2018).
63. Biel, J. Ein bandkeramischer Friedhof in Fellbach-Oeffingen, Rems-Murr-Kreis in Excavaciones arqueológicas en Baden-Württemberg (ed Theiss, K., Theiss, Konrad, 1987).
64. Trautmann, I. & Wahl, J. Leichenbrände aus linearbandkeramischen Gräberfeldern Südwestdeutschlands-Zum Bestattungsbrauch in Schwetzingen und Fellbach-Oeffingen. Fundberichte aus Baden-Württemberg 28, 7-18 (2005).
65. Müller, J. Zur Belegungsabfolge des Gräberfeldes von Trebur: Argumente der typologieunabhängigen Datierungen. Prachistorische Zeitschrifte 77, 148-158 (2002).
66. Krause-Kyora, B. et al. Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans. Nat Commun 9, 1569 (2018).
67. Buniello, A. et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res 47, D1005-D1012 (2019).
68. Jun, G., Wing, M. K., Abecasis, G. R. & Kang, H. M. An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data. Genome Res 25, 918-925 (2015).
69. Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987-2993 (2011).
70. Fay, M. P. Confidence intervals that match Fisher’s exact or Blaker’s exact tests. Biostatistics 11, 373-374 (2010).
71. Kassambara, A. & Mundt, F. Factoextra: extract and visualize the results of multivariate data analyses. R package version (2020).
72. Ulgen, E., Ozisik, O. & Sezerman, O. U. pathfindR: An R Package for comprehensive identification of enriched pathways in omics data through active subnetworks. Front Genet 10, 858 (2019).
73. Alpaslan-Roodenberg, S. et al. Ethics of DNA research on human remains: five globally applicable guidelines. Nature 599, 41-46 (2021).