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Population structure and local selection yield high genomic variation in Mimulus guttatus.

Publication ,  Journal Article
Puzey, JR; Willis, JH; Kelly, JK
Published in: Molecular ecology
January 2017

Across western North America, Mimulus guttatus exists as many local populations adapted to site-specific environmental challenges. Gene flow between locally adapted populations will affect genetic diversity both within demes and across the larger metapopulation. Here, we analyse 34 whole-genome sequences from the intensively studied Iron Mountain population (IM) in conjunction with sequences from 22 Mimulus individuals sampled from across western North America. Three striking features of these data address hypotheses about migration and selection in a locally adapted population. First, we find very high levels of intrapopulation polymorphism (synonymous π = 0.033). Variation outside of genes is likely even higher but difficult to estimate because excessive divergence reduces the efficiency of read mapping. Second, IM exhibits a significantly positive genomewide average for Tajima's D. This indicates allele frequencies are typically more intermediate than expected from neutrality, opposite the pattern observed in many other species. Third, IM exhibits a distinctive haplotype structure with a genomewide excess of positive associations between rarer alleles at linked loci. This suggests an important effect of gene flow from other Mimulus populations, although a residual effect of population founding might also contribute. The combination of multiple analyses, including a novel tree-based analytic method, illustrates how the balance of local selection, limited dispersal and metapopulation dynamics manifests across the genome. The overall genomic pattern of sequence diversity suggests successful gene flow of divergent immigrant genotypes into IM. However, many loci show patterns indicative of local adaptation, particularly at SNPs associated with chromosomal inversions.

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Published In

Molecular ecology

DOI

EISSN

1365-294X

ISSN

0962-1083

Publication Date

January 2017

Volume

26

Issue

2

Start / End Page

519 / 535

Related Subject Headings

  • Selection, Genetic
  • North America
  • Mimulus
  • Haplotypes
  • Genotype
  • Genome, Plant
  • Genetics, Population
  • Gene Frequency
  • Gene Flow
  • Evolutionary Biology
 

Citation

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Puzey, J. R., Willis, J. H., & Kelly, J. K. (2017). Population structure and local selection yield high genomic variation in Mimulus guttatus. Molecular Ecology, 26(2), 519–535. https://doi.org/10.1111/mec.13922
Puzey, Joshua R., John H. Willis, and John K. Kelly. “Population structure and local selection yield high genomic variation in Mimulus guttatus.Molecular Ecology 26, no. 2 (January 2017): 519–35. https://doi.org/10.1111/mec.13922.
Puzey JR, Willis JH, Kelly JK. Population structure and local selection yield high genomic variation in Mimulus guttatus. Molecular ecology. 2017 Jan;26(2):519–35.
Puzey, Joshua R., et al. “Population structure and local selection yield high genomic variation in Mimulus guttatus.Molecular Ecology, vol. 26, no. 2, Jan. 2017, pp. 519–35. Epmc, doi:10.1111/mec.13922.
Puzey JR, Willis JH, Kelly JK. Population structure and local selection yield high genomic variation in Mimulus guttatus. Molecular ecology. 2017 Jan;26(2):519–535.
Journal cover image

Published In

Molecular ecology

DOI

EISSN

1365-294X

ISSN

0962-1083

Publication Date

January 2017

Volume

26

Issue

2

Start / End Page

519 / 535

Related Subject Headings

  • Selection, Genetic
  • North America
  • Mimulus
  • Haplotypes
  • Genotype
  • Genome, Plant
  • Genetics, Population
  • Gene Frequency
  • Gene Flow
  • Evolutionary Biology