title: Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence.
abstract: Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ∼36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10⁻¹⁵). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant FST (p = 0.00003) and positive Tajima's D (p = 0.00285) statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human-Neandertal divergence and is evolving under balancing selection, especially among European populations.
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America.
authors.forename: Omer
authors.initials: O
authors.lastname: Gokcumen
authors.forename: Qihui
authors.initials: Q
authors.lastname: Zhu
authors.forename: Lubbertus C F
authors.initials: LC
authors.lastname: Mulder
authors.forename: Rebecca C
authors.initials: RC
authors.lastname: Iskow
authors.forename: Christian
authors.initials: C
authors.lastname: Austermann
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Scharer
authors.forename: Towfique
authors.initials: T
authors.lastname: Raj
authors.forename: Jeremy M
authors.initials: JM
authors.lastname: Boss
authors.forename: Shamil
authors.initials: S
authors.lastname: Sunyaev
authors.forename: Alkes
authors.initials: A
authors.lastname: Price
authors.forename: Barbara
authors.initials: B
authors.lastname: Stranger
authors.forename: Viviana
authors.initials: V
authors.lastname: Simon
authors.forename: Charles
authors.initials: C
authors.lastname: Lee
mesh_terms: D000483:Alleles; D000818:Animals; D001483:Base Sequence; D005006:Ethnicity / Q000235:genetics; D014644:Genetic Variation; D005828:Genetics, Population; D015894:Genome, Human; D006239:Haplotypes; D006801:Humans; D059125:Neanderthals / Q000235:genetics* / Q000502:physiology; D002679:Pan troglodytes / Q000235:genetics; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D017384:Sequence Deletion / Q000235:genetics*; D044465:White People