The genomic basis of high-elevation adaptation in wild house mice (Mus musculus domesticus) from South America

• Published in: Genetics (Austin) Vol. 220; no. 2
• Main Authors: Beckman, Elizabeth J, Martins, Felipe, Suzuki, Taichi A, Bi, Ke, Keeble, Sara, Good, Jeffrey M, Chavez, Andreas S, Ballinger, Mallory A, Agwamba, Kennedy, Nachman, Michael W
• Format: Journal Article
• Language: English
• Published: United States Oxford University Press 04.02.2022; Genetics Society of America
• Subjects: Acclimatization; Adaptation; Adaptation, Physiological - genetics; Alleles; Animals; Gene frequency; Genes; Genetics; Genomics; Hypoxia; Investigation; Mammals - genetics; Mice; Mus musculus domesticus; Natural populations; Oxygen; Phylogeny; Single-nucleotide polymorphism; South America; Andes; high elevation; adaptive evolution; parallelism; Mus musculus domesticus
• ISSN: 1943-2631; 0016-6731; 1943-2631
• DOI: 10.1093/genetics/iyab226

Abstract Understanding the genetic basis of environmental adaptation in natural populations is a central goal in evolutionary biology. The conditions at high elevation, particularly the low oxygen available in the ambient air, impose a significant and chronic environmental challenge to metabolically active animals with lowland ancestry. To understand the process of adaptation to these novel conditions and to assess the repeatability of evolution over short timescales, we examined the signature of selection from complete exome sequences of house mice (Mus musculus domesticus) sampled across two elevational transects in the Andes of South America. Using phylogenetic analysis, we show that house mice colonized high elevations independently in Ecuador and Bolivia. Overall, we found distinct responses to selection in each transect and largely nonoverlapping sets of candidate genes, consistent with the complex nature of traits that underlie adaptation to low oxygen availability (hypoxia) in other species. Nonetheless, we also identified a small subset of the genome that appears to be under parallel selection at the gene and SNP levels. In particular, three genes (Col22a1, Fgf14, and srGAP1) bore strong signatures of selection in both transects. Finally, we observed several patterns that were common to both transects, including an excess of derived alleles at high elevation, and a number of hypoxia-associated genes exhibiting a threshold effect, with a large allele frequency change only at the highest elevations. This threshold effect suggests that selection pressures may increase disproportionately at high elevations in mammals, consistent with observations of some high-elevation diseases in humans. To examine the process of adaptation to a novel environment, Beckman, Martins et al. sequence exomes from house mice sampled across two elevational transects in the Andes, finding that house mice in Ecuador and Bolivia colonized high elevation independently. The response to selection at high elevation was largely transect-specific, with a small subset of genes under parallel selection. They find a number of hypoxia-associated genes that exhibited a threshold effect–a large shift in allele frequency at the highest elevations.