A Catalog of Single Nucleotide Changes Distinguishing Modern Humans from Archaic Hominins

Overview

Journal Sci Rep

Specialty Science

Date 2019 Jun 13

PMID 31186485

Citations 34

Authors

Martin Kuhlwilm

Cedric Boeckx

Affiliations

Soon will be listed here.

Abstract

Throughout the past decade, studying ancient genomes has provided unique insights into human prehistory, and differences between modern humans and other branches like Neanderthals can enrich our understanding of the molecular basis of unique modern human traits. Modern human variation and the interactions between different hominin lineages are now well studied, making it reasonable to go beyond fixed genetic changes and explore changes that are observed at high frequency in present-day humans. Here, we identify 571 genes with non-synonymous changes at high frequency. We suggest that molecular mechanisms in cell division and networks affecting cellular features of neurons were prominently modified by these changes. Complex phenotypes in brain growth trajectory and cognitive traits are likely influenced by these networks and other non-coding changes presented here. We propose that at least some of these changes contributed to uniquely human traits, and should be prioritized for experimental validation.

Citing Articles

Integrated analysis of the complete sequence of a macaque genome.

Zhang S, Xu N, Fu L, Yang X, Ma K, Li Y Nature. 2025; .

PMID: 40011769 DOI: 10.1038/s41586-025-08596-w.

A multi-layered integrative analysis reveals a cholesterol metabolic program in outer radial glia with implications for human brain evolution.

Moriano J, Leonardi O, Vitriolo A, Testa G, Boeckx C Development. 2024; 151(16).

PMID: 39114968 PMC: 11385646. DOI: 10.1242/dev.202390.

Enrichment of a subset of Neanderthal polymorphisms in autistic probands and siblings.

Pauly R, Johnson L, Feltus F, Casanova E Mol Psychiatry. 2024; 29(11):3452-3461.

PMID: 38760502 PMC: 11541192. DOI: 10.1038/s41380-024-02593-7.

A regulatory variant impacting TBX1 expression contributes to basicranial morphology in Homo sapiens.

Funato N, Heliovaara A, Boeckx C Am J Hum Genet. 2024; 111(5):939-953.

PMID: 38608674 PMC: 11080286. DOI: 10.1016/j.ajhg.2024.03.012.

Archaic Introgression Shaped Human Circadian Traits.

Velazquez-Arcelay K, Colbran L, McArthur E, Brand C, Rinker D, Siemann J Genome Biol Evol. 2023; 15(12).

PMID: 38095367 PMC: 10719892. DOI: 10.1093/gbe/evad203.

References

Camp J, Treutlein B . Human organomics: a fresh approach to understanding human development using single-cell transcriptomics. Development. 2017; 144(9):1584-1587. DOI: 10.1242/dev.150458. View

Gullard A, Gluhak-Heinrich J, Papagerakis S, Sohn P, Unterbrink A, Chen S . MEPE Localization in the Craniofacial Complex and Function in Tooth Dentin Formation. J Histochem Cytochem. 2016; 64(4):224-36. PMC: 4817730. DOI: 10.1369/0022155416635569. View

Boeckx C, Benitez-Burraco A . Globularity and language-readiness: generating new predictions by expanding the set of genes of interest. Front Psychol. 2014; 5:1324. PMC: 4243498. DOI: 10.3389/fpsyg.2014.01324. View

Camp J, Badsha F, Florio M, Kanton S, Gerber T, Wilsch-Brauninger M . Human cerebral organoids recapitulate gene expression programs of fetal neocortex development. Proc Natl Acad Sci U S A. 2015; 112(51):15672-7. PMC: 4697386. DOI: 10.1073/pnas.1520760112. View

Somel M, Liu X, Khaitovich P . Human brain evolution: transcripts, metabolites and their regulators. Nat Rev Neurosci. 2013; 14(2):112-27. DOI: 10.1038/nrn3372. View

Grote S, Prufer K, Kelso J, Dannemann M . ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain. Bioinformatics. 2016; 32(20):3201-3203. PMC: 5048072. DOI: 10.1093/bioinformatics/btw392. View

OBleness M, Searles V, Varki A, Gagneux P, Sikela J . Evolution of genetic and genomic features unique to the human lineage. Nat Rev Genet. 2012; 13(12):853-66. PMC: 4097811. DOI: 10.1038/nrg3336. View

Belyk M, Brown S . The origins of the vocal brain in humans. Neurosci Biobehav Rev. 2017; 77:177-193. DOI: 10.1016/j.neubiorev.2017.03.014. View

Bufill E, Blesa R, Augusti J . Alzheimer's disease: an evolutionary approach. J Anthropol Sci. 2013; 91:135-57. DOI: 10.4436/jass.91001. View

10.

Hublin J, Ben-Ncer A, Bailey S, Freidline S, Neubauer S, Skinner M . New fossils from Jebel Irhoud, Morocco and the pan-African origin of Homo sapiens. Nature. 2017; 546(7657):289-292. DOI: 10.1038/nature22336. View

11.

Posth C, Wissing C, Kitagawa K, Pagani L, van Holstein L, Racimo F . Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals. Nat Commun. 2017; 8:16046. PMC: 5500885. DOI: 10.1038/ncomms16046. View

12.

Ramirez Rozzi F, Bermudez de Castro J . Surprisingly rapid growth in Neanderthals. Nature. 2004; 428(6986):936-9. DOI: 10.1038/nature02428. View

13.

Simonti C, Vernot B, Bastarache L, Bottinger E, Carrell D, Chisholm R . The phenotypic legacy of admixture between modern humans and Neandertals. Science. 2016; 351(6274):737-41. PMC: 4849557. DOI: 10.1126/science.aad2149. View

14.

Kevenaar J, Bianchi S, van Spronsen M, Olieric N, Lipka J, Frias C . Kinesin-Binding Protein Controls Microtubule Dynamics and Cargo Trafficking by Regulating Kinesin Motor Activity. Curr Biol. 2016; 26(7):849-61. DOI: 10.1016/j.cub.2016.01.048. View

15.

Ardesch D, Scholtens L, Li L, Preuss T, Rilling J, van den Heuvel M . Evolutionary expansion of connectivity between multimodal association areas in the human brain compared with chimpanzees. Proc Natl Acad Sci U S A. 2019; 116(14):7101-7106. PMC: 6452697. DOI: 10.1073/pnas.1818512116. View

16.

Li Y, Muffat J, Omer A, Bosch I, Lancaster M, Sur M . Induction of Expansion and Folding in Human Cerebral Organoids. Cell Stem Cell. 2017; 20(3):385-396.e3. PMC: 6461394. DOI: 10.1016/j.stem.2016.11.017. View

17.

Han S, Andres A, Marques-Bonet T, Kuhlwilm M . Genetic Variation in Pan Species Is Shaped by Demographic History and Harbors Lineage-Specific Functions. Genome Biol Evol. 2019; 11(4):1178-1191. PMC: 6482415. DOI: 10.1093/gbe/evz047. View

18.

Jensen K, Dredge B, Stefani G, Zhong R, Buckanovich R, Okano H . Nova-1 regulates neuron-specific alternative splicing and is essential for neuronal viability. Neuron. 2000; 25(2):359-71. DOI: 10.1016/s0896-6273(00)80900-9. View

19.

Konopka G, Friedrich T, Davis-Turak J, Winden K, Oldham M, Gao F . Human-specific transcriptional networks in the brain. Neuron. 2012; 75(4):601-17. PMC: 3645834. DOI: 10.1016/j.neuron.2012.05.034. View

20.

Wynn T, Coolidge F . The expert Neandertal mind. J Hum Evol. 2004; 46(4):467-87. DOI: 10.1016/j.jhevol.2004.01.005. View