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Cited by 134Genetic diversity and population structureChromosomal and Genetic VariationsEvolution and Genetic Dynamics

Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers

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Stankowski, Sean, Chase, Madeline A., Fuiten, Allison M., Rodrigues, Murillo F., Ralph, Peter L., Streisfeld, Matthew A.·2019·PLOS Biology
DOI 10.1371/journal.pbio.3000391PMC PMC6660095

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Abstract

Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic "landscape" of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use whole-genome sequencing and simulations to shed light on the processes that have shaped the genomic landscape during a radiation of monkeyflowers. After inferring the phylogenetic relationships among the 9 taxa in this radiation, we show that highly similar diversity (π) and differentiation (FST) landscapes have emerged across the group. Variation in these landscapes was strongly predicted by the local density of functional elements and the recombination rate, suggesting that the landscapes have been shaped by widespread natural selection. Using the varying divergence times between pairs of taxa, we show that the correlations between FST and genome features arose almost immediately after a population split and have become stronger over time. Simulations of genomic landscape evolution suggest that background selection (BGS; i.e., selection against deleterious mutations) alone is too subtle to generate the observed patterns, but scenarios that involve positive selection and genetic incompatibilities are plausible alternative explanations. Finally, tests for introgression among these taxa reveal widespread evidence of heterogeneous selection against gene flow during this radiation. Combined with previous evidence for adaptation in this system, we conclude that the correlation in FST among these taxa informs us about the processes contributing to adaptation and speciation during a rapid radiation.

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  • In nine Mimulus species, FST was negatively correlated with genetic diversity as well as tree concordance.

    “They found that FST was negatively correlated with genetic diversity as well as tree concordance.”

    From Genomics of plant speciation (2023) · cites this paper as Stankowski et al. (2019)

    In Results and discussion, “Common genomic landscapes have been shaped by heterogeneous indirect selection” (page unavailable), the paper reports that lower diversity was associated with higher FST, supporting that part of the claim. It also reports that lower diversity was associated with higher tree concordance—not that FST was negatively correlated with tree concordance. The analysis covered nine taxa, not nine species. (LLM, conf=0.90)

    Experimental — accuracy not yet measured

  • Simulations using only background selection showed only modest variation in the differentiation landscape, suggesting that background selection was not the primary driver of the differentiation landscape observed in Stankowski et al. (2019).

    “simulations using only background selection showed only modest variation in the differentiation landscape, suggesting that background selection was not the primary driver of the differentiation landscape observed.”

    From Genomics of plant speciation (2023) · cites this paper as Stankowski et al. (2019)

  • Functional analyses are time consuming and technically challenging even in model species and can be complicated by the polygenic architecture of RI and by the diversity of possible mutations underlying RI.

    “This is time consuming and technically challenging even in model species and can be further complicated by the polygenic architecture of RI seen in many systems (e.g., Zuellig and Sweigart 2018; Stankowski et al., 2019) and by the diversity of possible mutations underlying RI, which range from amino acid substitutions to regulatory changes to SVs (Rieseberg and Blackman, 2010).”

    From Genomics of plant speciation (2023) · cites this paper as Stankowski et al., 2019

  • In Mimulus, MaMyb2, an R2R3-MYB transcription factor identified as a candidate gene for differences in floral pigmentation, has been shown to locate in a sharp peak of genomic differentiation.

    “In Mimulus, an R2R3-MYB transcription factor, MaMyb2, which was identified as a candidate gene for differences in floral pigmentation (Streisfeld et al., 2013), has been shown to locate in a sharp peak of genomic differentiation (Stankowski et al., 2019).”

    From Genomics of plant speciation (2023) · cites this paper as Stankowski et al., 2019

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Cited by

Sorted by citations

  • Genomics of plant speciation

    Bock, D. G., Cai, Z., Elphinstone, C., González-Segovia, E., Hirabayashi, K., Huang, K., Keais, G. L., Kim, A., Owens, G. L., & Rieseberg, L. H. (2023) · Plant Communications · doi:10.1016/j.xplc.2023.100599 · Cited by 84 · see citing works

    “This is time consuming and technically challenging even in model species and can be further complicated by the polygenic architecture of RI seen in many systems (e.g., Zuellig and Sweigart 2018; Stankowski et al., 2019) and by the diversity of possible mutations underlying RI, which range from amino acid substitutions…”

Authors
Stankowski, S., Chase, M. A., Fuiten, A. M., Rodrigues, M. F., Ralph, P. L., & Streisfeld, M. A.
Affiliations
University of Oregon (US)
Corresponding author
  • Stankowski, Sean
  • Streisfeld, Matthew A.
ORCID
Venue
PLOS Biology
Publisher
Public Library of Science (PLoS)
Published
2019-07-24
Volume
17
Issue
7
Pages
e3000391
ISSN
  • 1544-9173 (ISSN-L)
  • 1545-7885
DOI
10.1371/journal.pbio.3000391
PMC
PMC6660095
OpenAlex
W2963913467
Cited by
134
References
6
Citations by year
2026: 13 · 2025: 12 · 2024: 20 · 2023: 18 · 2022: 20 · 2021: 24 · 2020: 22 · 2019: 5
FWCI
10.70
Type
journal article
Language
en
Update notices
new_version (2019-07-26)
Open access
Licence
Locations
  • PLoS Biology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Figshare (submittedVersion, cc-by)
Funders
National Science Foundation (DEB-1258199)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords
monkeyflowers, Convolvulaceae, speciation, genomic landscape, natural selection, background selection, positive selection, genetic incompatibility, gene flow, introgression, recombination rate, functional elements, population divergence, adaptive radiation, chromosome-level genome assembly
MeSH terms
Adaptation, Physiological, Genetics, Population, Phylogeny, Selection, Genetic, Genetic Variation, Genome, Plant, Genomics, Mimulus, Genetic Speciation, Gene Flow

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