Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

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

View ORCID ProfileSean Stankowski, View ORCID ProfileMadeline A. Chase, View ORCID ProfileAllison M. Fuiten, View ORCID ProfileMurillo F. Rodrigues, View ORCID ProfilePeter L. Ralph, View ORCID ProfileMatthew A. Streisfeld
doi: https://doi.org/10.1101/342352
Sean Stankowski
1Institute of Ecology and Evolution, 335 Pacific Hall 5289, University of Oregon, Eugene, OR 97405, USA
2Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sean Stankowski
Madeline A. Chase
1Institute of Ecology and Evolution, 335 Pacific Hall 5289, University of Oregon, Eugene, OR 97405, USA
3Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Madeline A. Chase
Allison M. Fuiten
1Institute of Ecology and Evolution, 335 Pacific Hall 5289, University of Oregon, Eugene, OR 97405, USA
4Department of Dermatology, Oregon Heath and Science University, L468R Portland, OR, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Allison M. Fuiten
Murillo F. Rodrigues
1Institute of Ecology and Evolution, 335 Pacific Hall 5289, University of Oregon, Eugene, OR 97405, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Murillo F. Rodrigues
Peter L. Ralph
1Institute of Ecology and Evolution, 335 Pacific Hall 5289, University of Oregon, Eugene, OR 97405, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Peter L. Ralph
Matthew A. Streisfeld
1Institute of Ecology and Evolution, 335 Pacific Hall 5289, University of Oregon, Eugene, OR 97405, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Matthew A. Streisfeld
  • For correspondence: mstreis@uoregon.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

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 recent radiation of monkeyflowers. After inferring the phylogenetic relationships among the nine 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 (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. Thus, combined with existing evidence for adaptation in this system, we conclude that the correlation in FST among these taxa informs us about the genomic basis of adaptation and speciation in this system.

Author summary What can patterns of genome-wide variation tell us about the speciation process? The answer to this question depends upon our ability to infer the evolutionary processes underlying these patterns. This, however, is difficult, because many processes can leave similar footprints, but some have nothing to do with speciation per se. For example, many studies have found highly heterogeneous levels of genetic differentiation when comparing the genomes of emerging species. These patterns are often referred to as differentiation ‘landscapes’ because they appear as a rugged topography of ‘peaks’ and ‘valleys’ as one scans across the genome. It has often been argued that selection against deleterious mutations, a process referred to as background selection, is primarily responsible for shaping differentiation landscapes early in speciation. If this hypothesis is correct, then it is unlikely that patterns of differentiation will reveal much about the genomic basis of speciation. However, using genome sequences from nine emerging species of monkeyflower coupled with simulations of genomic divergence, we show that it is unlikely that background selection is the primary architect of these landscapes. Rather, differentiation landscapes have probably been shaped by adaptation and gene flow, which are processes that are central to our understanding of speciation. Therefore, our work has important implications for our understanding of what patterns of differentiation can tell us about the genetic basis of adaptation and speciation.

Footnotes

  • Taking into account reviewer comments and feedback from other people.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted May 22, 2019.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
Sean Stankowski, Madeline A. Chase, Allison M. Fuiten, Murillo F. Rodrigues, Peter L. Ralph, Matthew A. Streisfeld
bioRxiv 342352; doi: https://doi.org/10.1101/342352
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
Sean Stankowski, Madeline A. Chase, Allison M. Fuiten, Murillo F. Rodrigues, Peter L. Ralph, Matthew A. Streisfeld
bioRxiv 342352; doi: https://doi.org/10.1101/342352

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Evolutionary Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4683)
  • Biochemistry (10361)
  • Bioengineering (7675)
  • Bioinformatics (26337)
  • Biophysics (13529)
  • Cancer Biology (10686)
  • Cell Biology (15440)
  • Clinical Trials (138)
  • Developmental Biology (8497)
  • Ecology (12821)
  • Epidemiology (2067)
  • Evolutionary Biology (16860)
  • Genetics (11399)
  • Genomics (15478)
  • Immunology (10617)
  • Microbiology (25219)
  • Molecular Biology (10223)
  • Neuroscience (54472)
  • Paleontology (401)
  • Pathology (1668)
  • Pharmacology and Toxicology (2897)
  • Physiology (4342)
  • Plant Biology (9247)
  • Scientific Communication and Education (1586)
  • Synthetic Biology (2558)
  • Systems Biology (6781)
  • Zoology (1466)