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PLoS Genet. 2018 Feb 12;14(2):e1007155. doi: 10.1371/journal.pgen.1007155. eCollection 2018 Feb.

The rate and potential relevance of new mutations in a colonizing plant lineage.

Author information

1
Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
2
Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
3
Institute of Archaeological Sciences, University of Tübingen, Tübingen, Germany.
4
Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, Germany.
5
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
6
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America.
7
Institute of Tibet Plateau Research, Chinese Academy of Sciences, Beijing, China.
8
Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada.
9
Department of Archeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.

Abstract

By following the evolution of populations that are initially genetically homogeneous, much can be learned about core biological principles. For example, it allows for detailed studies of the rate of emergence of de novo mutations and their change in frequency due to drift and selection. Unfortunately, in multicellular organisms with generation times of months or years, it is difficult to set up and carry out such experiments over many generations. An alternative is provided by "natural evolution experiments" that started from colonizations or invasions of new habitats by selfing lineages. With limited or missing gene flow from other lineages, new mutations and their effects can be easily detected. North America has been colonized in historic times by the plant Arabidopsis thaliana, and although multiple intercrossing lineages are found today, many of the individuals belong to a single lineage, HPG1. To determine in this lineage the rate of substitutions-the subset of mutations that survived natural selection and drift-, we have sequenced genomes from plants collected between 1863 and 2006. We identified 73 modern and 27 herbarium specimens that belonged to HPG1. Using the estimated substitution rate, we infer that the last common HPG1 ancestor lived in the early 17th century, when it was most likely introduced by chance from Europe. Mutations in coding regions are depleted in frequency compared to those in other portions of the genome, consistent with purifying selection. Nevertheless, a handful of mutations is found at high frequency in present-day populations. We link these to detectable phenotypic variance in traits of known ecological importance, life history and growth, which could reflect their adaptive value. Our work showcases how, by applying genomics methods to a combination of modern and historic samples from colonizing lineages, we can directly study new mutations and their potential evolutionary relevance.

PMID:
29432421
PMCID:
PMC5825158
DOI:
10.1371/journal.pgen.1007155
[Indexed for MEDLINE]
Free PMC Article

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