title: The psoriasis-associated deletion of late cornified envelope genes LCE3B and LCE3C has been maintained under balancing selection since Human Denisovan divergence.
abstract: A common, 32kb deletion of LCE3B and LCE3C genes is strongly associated with psoriasis. We recently found that this deletion is ancient, predating Human-Denisovan divergence. However, it was not clear why negative selection has not removed this deletion from the population.
  
  
  
  Here, we show that the haplotype block that harbors the deletion (i) retains high allele frequency among extant and ancient human populations; (ii) harbors unusually high nucleotide variation (π, P < 4.1 × 10-3); (iii) contains an excess of intermediate frequency variants (Tajima's D, P < 3.9 × 10-3); and (iv) has an unusually long time to coalescence to the most recent common ancestor (TSel, 0.1 quantile).
  
  
  
  Our results are most parsimonious with the scenario where the LCE3BC deletion has evolved under balancing selection in humans. More broadly, this is consistent with the hypothesis that a balance between autoimmunity and natural vaccination through increased exposure to pathogens maintains this deletion in humans.
authors.affiliation: Department of Biological Sciences, University at Buffalo, Cooke 639, Buffalo, NY, 14260, USA.
authors.forename: Petar
authors.initials: P
authors.lastname: Pajic
authors.affiliation: Department of Biological Sciences, University at Buffalo, Cooke 639, Buffalo, NY, 14260, USA.
authors.forename: Yen-Lung
authors.initials: YL
authors.lastname: Lin
authors.affiliation: Department of Biological Sciences, University at Buffalo, Cooke 639, Buffalo, NY, 14260, USA.
authors.forename: Duo
authors.initials: D
authors.lastname: Xu
authors.affiliation: Department of Biological Sciences, University at Buffalo, Cooke 639, Buffalo, NY, 14260, USA. omergokc@buffalo.edu.
authors.forename: Omer
authors.identifier: 0000-0003-4371-679X
authors.initials: O
authors.lastname: Gokcumen
mesh_terms: D000483:Alleles; D055233:Cornified Envelope Proline-Rich Proteins / Q000235:genetics*; D019143:Evolution, Molecular; D017353:Gene Deletion; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D011565:Psoriasis / Q000235:genetics*; D017384:Sequence Deletion
chemical_list: D055233:Cornified Envelope Proline-Rich Proteins; C549748:LCE3B protein, human; C524768:LCE3C protein, human
keywords: Atopic dermatitis; Copy number variation; Defensins; Genomic structural variants; HLA; Human evolution; LCE3A; Neanderthal