Assessing the Presence of Recent Adaptation in the Human Genome With Mixture Density Regression

Diego F. Salazar-Tortosa, Yi Fei Huang, David Enard

Research output: Contribution to journalArticlepeer-review

Abstract

How much genome differences between species reflect neutral or adaptive evolution is a central question in evolutionary genomics. In humans and other mammals, the presence of adaptive versus neutral genomic evolution has proven particularly difficult to quantify. The difficulty notably stems from the highly heterogeneous organization of mammalian genomes at multiple levels (functional sequence density, recombination, etc.) which complicates the interpretation and distinction of adaptive versus neutral evolution signals. In this study, we introduce mixture density regressions (MDRs) for the study of the determinants of recent adaptation in the human genome. MDRs provide a flexible regression model based on multiple Gaussian distributions. We use MDRs to model the association between recent selection signals and multiple genomic factors likely to affect the occurrence/detection of positive selection, if the latter was present in the first place to generate these associations. We find that an MDR model with two Gaussian distributions provides an excellent fit to the genome-wide distribution of a common sweep summary statistic (integrated haplotype score), with one of the two distributions likely enriched in positive selection. We further find several factors associated with signals of recent adaptation, including the recombination rate, the density of regulatory elements in immune cells, GC content, gene expression in immune cells, the density of mammal- wide conserved elements, and the distance to the nearest virus-interacting gene. These results support the presence of strong positive selection in recent human evolution and highlight MDRs as a powerful tool to make sense of signals of recent genomic adaptation.

Original languageEnglish (US)
Article numberevad170
JournalGenome biology and evolution
Volume15
Issue number10
DOIs
StatePublished - Oct 1 2023

Keywords

  • human evolution
  • mixture distributions
  • recent adaptation
  • recombination rate
  • selection determinants

ASJC Scopus subject areas

  • General Medicine

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