Genome sequence analysis provides first evidence that linked, locally adapted alleles exist first, and subsequently are captured within a new, selectively-favored inversion.
The Science
A team of scientists investigated the pathway by which chromosomal inversions – in which a segment of the chromosome was removed, flipped and then re-inserted – contribute to speciation in nature.
For this study, researchers planted a test population in a mountain-top meadow near the Lost Trail Pass ski resort in the mountains of Montana. To water these transplants, they lugged nine empty garbage cans up the mountain and filled them with snow to water the plants throughout the summer. (Tom Mitchell-Olds)
The Impact
This study offers the first direct evidence showing that QTLs, genome regions on chromosomes to which genetic traits can be mapped, are a driving force behind speciation. While it’s known that chromosomal inversions contribute to speciation, it had not been clear whether or not this occurs due to: 1) a slow accumulation of mutations on older inversions; or, 2) young inversions that capture QTLs during the beginning stages of speciation.
Summary
On the slopes of the Northern Rocky Mountains, the flowering mustard plant Boechera stricta is undergoing a quiet transformation – that is, evolving into a fitter species better adapted to its local environment. Led by Thomas Mitchell-Olds of Duke University, a team including researchers at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, analyzed the mechanisms by which Boechera stricta living in a hybrid zone in the Northern Rocky Mountains experienced positive directional selection.
Creek-side habitat near Lost Trail Pass ski resort in Montana. (Tom Mitchell-Olds)
As part of the DOE JGI’s Community Science Program and Emerging Technologies Opportunity Program, the researchers sequenced and analyzed the genome of Boechera stricta, a relative of the model plant Arabidopsis. With the genome in hand, they used techniques including gene mapping and chromosome painting methods to identify a major chromosomal inversion that controls ecologically important traits in the plant. They tested for QTLs—regions of the genome where the DNA codes for genetic traits—in Boechera stricta’s chromosomal inversion. They found several linked QTLs that changed ecologically important characteristics of the plant such as flowering time and plant size, enabling it to adapt to its local environment, which in turn increased its fitness.
“Here, in Boechera stricta we are capturing that moment of selection – the moment when the subpopulation with the inversion takes over from the pre-inversion genotype and outcompetes it,” said DOE JGI Plant Program Head Jeremy Schmutz, a co-author on the study. “The inversion fixes a set of alleles in the population. Here the set of fixed alleles improves survivability over the previous genotypes.”
The knowledge gained from this study, published in the April 3, 2017 issue of the journal Nature Ecology & Evolution, “gives evolutionary biologists experimental evidence showing how chromosomal changes contribute to adaptation and speciation. Furthermore, the genome sequence will help us understand how Boechera species are able to reproduce asexually by seeds, a process that can be used by farmers to speed up crop improvement practices,” said senior author and DOE JGI collaborator Thomas Mitchell-Olds of Duke University.
Contacts
Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
daniel.drell@science.doe.gov
Jeremy Schmutz
Plant Program Head
DOE Joint Genome Institute
jschmutz@hudsonalpha.com
Funding
- DOE Office of Science
- National Science Foundation
- EMBO
- Taiwan Ministry of Science and Technology
- Swedish Research Council
- Czech Science Foundation
- National Institutes of Health
- AXA Research Fund
- Arizona Genomics Institute, University of Arizona
Publications
- Lee CR et al. “Young inversion with multiple linked QTLs under selection in a hybrid zone.” Nat. Ecol. Evol. (2017) doi: 10.1038/s41559-017-0119
Related Links
- Boechera stricta study on plant flowering time: http://jgi.doe.gov/soil-microbiomes-can-set-plant-flowering-time/
- Boechera stricta genome on Phytozome: https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Bstricta
- Community Science Program: http://jgi.doe.gov/user-program-info/community-science-program/
- Emerging Technologies Opportunities Program: http://jgi.doe.gov/doe-joint-genome-institute-expands-capabilities-via-new-partnerships/