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Neanderthal Ancestry Drives Evolution of Lipid Catabolism in Contemporary Europeans

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Neanderthal Ancestry Drives Evolution of Lipid Catabolism in Contemporary Europeans ARTICLE Received 27 Sep 2013 | Accepted 7 Mar 2014 | Published 1 Apr 2014 DOI: 10.1038/ncomms4584 OPEN Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans Ekaterina E. Khrameeva1,2, Katarzyna Bozek1,3, Liu He1, Zheng Yan1, Xi Jiang1, Yuning Wei1, Kun Tang1, Mikhail S. Gelfand2,4, Kay Prufer3, Janet Kelso3, Svante Paabo3, Patrick Giavalisco5, Michael Lachmann3 & Philipp Khaitovich1,3 Although Neanderthals are extinct, fragments of their genomes persist in contemporary humans. Here we show that while the genome-wide frequency of Neanderthal-like sites is approximately constant across all contemporary out-of-Africa populations, genes involved in lipid catabolism contain more than threefold excess of such sites in contemporary humans of European descent. Evolutionally, these genes show significant association with signatures of recent positive selection in the contemporary European, but not Asian or African populations. Functionally, the excess of Neanderthal-like sites in lipid catabolism genes can be linked with a greater divergence of lipid concentrations and enzyme expression levels within this pathway, seen in contemporary Europeans, but not in the other populations. We conclude that sequence variants that evolved in Neanderthals may have given a selective advantage to anatomically modern humans that settled in the same geographical areas. 1 CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China. 2 Research and Training Center on Bioinformatics, Institute for Information Transmission Problems, RAS, Moscow 127994, Russia. 3 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. 4 Department of Bioengineering and Bioinformatics, Moscow State University, Moscow 119992, Russia. 5 Molecular Physiology Department, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany. Correspondence and requests for materials should be addressed to P.G. (email: [email protected]) or to M.L. (email: [email protected]) or to P.K. (email: [email protected]). NATURE COMMUNICATIONS | 5:3584 | DOI: 10.1038/ncomms4584 | www.nature.com/naturecommunications 1 & 2014 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms4584 he ancestors of Neanderthals and modern humans catabolism changes specific to Europeans, we measured lipidome diverged from a common ancestral population B800– and transcriptome compositions of the brain tissue in con- T400 thousand years ago (KYA)1–5. Subsequently, temporary humans of European, East Asian and African descent, Neanderthals evolved in Europe and Central Asia and possibly as well as in chimpanzees representing the ancestral state. In spread further east into the Asian continent6. The first successful agreement with observations made at the genome level, we show migration of modern humans out of Africa can be traced back in significant excess of lipid concentration and gene expression the archaeological and genetic records to B70–60 KYA7. After divergence in lipid catabolism pathways in Europeans, but not the that, modern humans spread quickly across all continents and other population groups. Furthermore, lipid catabolism genes could have coexisted with Neanderthals in Europe and Central showing increased expression divergence in Europeans contain an Asia for thousands of years before the Neanderthal extinction even higher proportion of Neanderthal sites than other lipid 45–30 KYA7,8. Studies comparing the complete nuclear genome catabolism genes. Taken together, these observations indicate that sequences of Neanderthals and contemporary modern humans lipid catabolism of contemporary Europeans was partially shaped indicate that out-of-Africa human populations, but not sub- by the genetic variants shared with Neanderthals. We further Saharan African populations, contain genomic regions with speculate that these variants provided European ancestors with unusually high similarity to the Neanderthal genome9,10. In each adaptations to the geographic environment where Neanderthals individual, these regions were reported to occupy 1–4% of had evolved and where Neanderthals and archaic Europeans later the total genome sequence10. This phenomenon implies the coexisted. occurrence of gene flow from Neanderthals into those human populations that migrated from the African continent11,12. In this study, we asked whether genomic regions with high Results sequence similarity to the Neanderthal genome are distributed Neanderthal ancestry in contemporary human populations.We randomly across the genomes of contemporary modern humans. searched for regional similarities to the Neanderthal genome in If certain regions in the modern human genome show a decreased the genomes of 11 contemporary human populations, which have Neanderthal gene flow, these regions may contain genetic changes the best genome coverage in the 1,000 genomes project: three essential to the modern human phenotype that are undergoing populations of African ancestry—HapMap African ancestry purifying selection against the Neanderthal alleles. By contrast, individuals from South West of the United States (ASW), Luhya the presence of genomic regions experiencing excessive gene flow individuals (LWK) and Yoruba individuals (YRI); three popula- from Neanderthal may indicate that genetic changes that evolved tions of East Asian ancestry—Han Chinese in Beijing (CHB), Han in Neanderthals gave modern humans carrying the Neanderthal Chinese from South China (CHS) and Japanese (JPT); and five genotype a selective advantage. populations of European ancestry—CEPH individuals (CEU), We show that genetic variants shared between modern humans HapMap Finnish individuals from Finland (FIN), British indivi- and Neanderthals, but distinct from chimpanzees, are specifically duals from England and Scotland (GBR), Iberian populations in enriched in genes involved in lipid catabolism in contemporary Spain (IBS) and Toscan individuals (TSI)13. For each pair of the humans of European, but not East Asian descent. Excess of human populations, the human genome sequences were Neanderthal variants in lipid catabolism genes was further compared with the Neanderthal and the chimpanzee genome associated with signatures of recent positive selection. To assess sequences. We used the high-coverage Neanderthal genome whether Neanderthal variants resulted in adaptive lipid sequence, obtained from the bone of one individual excavated in FIN GBR ABBA: CEU CHB TSI IBS BABA: JPT CHS ASW GW LCP GW LCP GW LCP 0.25 YRI 0.20 LWK 0.15 0.10 0.05 Proportion of NLS 0.00 AF AS EU Figure 1 | Proportions of NLS in contemporary human populations. (a) Schematic representation of genomic distance calculations between contemporary human populations and Neanderthals. The genomes of out-of-Africa individuals were compared with the genomes of individuals of purely African ancestry (YRI). Single nucleotide differences from the Neanderthal genotype in an African genome were referred to as ‘ABBA’, while sites with the Neanderthal genotype in an out-of-Africa genome were referred to as ‘BABA’. (b) Average proportions of NLS in contemporary African (AF), European (EU) and Asian (AS) populations calculated based on sequence data from the 1,000 genomes project13; blue: genome wide (n ¼ 1,158,559 sites), red: LCP genes (n ¼ 498 sites). The error bars show the s.d. of the NLS proportion estimates. (c) Genomic distances between 11 contemporary human populations and Neanderthals; blue, genome wide; red, LCP genes. The maximal bar length corresponds to a NLS frequency of 30%. Placement of ASW and CEU individuals in sub-Saharan Africa and Western Europe, respectively, reflects their approximate historical geographical origins rather than their present location. 2 NATURE COMMUNICATIONS | 5:3584 | DOI: 10.1038/ncomms4584 | www.nature.com/naturecommunications & 2014 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | DOI: 10.1038/ncomms4584 ARTICLE 2008 in the east gallery of Denisova Cave in the Altai mountains 5.9±0.08% genome wide (two-sided t-test, Po0.0001, n ¼ 379 (Altai)14,15, combined with the low-coverage Neanderthal Europeans and n ¼ 246 Africans; Fig. 1b,c, red bars; genome sequence, obtained from three individuals (Vindjia)10, Supplementary Table 4; Supplementary Fig. 1). Further, among to reconstruct a consensus Neanderthal genome sequence by examined out-of-Africa human populations, the excess of NLS in excluding all sites with sequence variation among individuals. We LCP genes was only observed in individuals of European descent: further used the reference chimpanzee genome in combination the average NLS frequency in Asians is 6.7±0.7% in LCP genes with genome sequence data from 10 chimpanzees16 to exclude versus 6.2±0.06% genome wide (Supplementary Table 4). sites variable among chimpanzees. Only single nucleotide sites The excess of NLS observed in LCP genes for populations of displaying sequence differences between the chimpanzee16,17 and European descent was based on a large number of sites (n ¼ 498), the two reference Neanderthal genomes10,15 were used in the and was robust to bootstrapping across sites (Po0.01, 1,000 analysis (n ¼ 1,158,559). bootstraps, Supplementary Table 5; Supplementary Fig. 2). Similar to Green et al.10, we used the D statistic to detect Notably, NLS were located in 23 independent genomic regions. potential Neanderthal gene flow. For each pair of
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