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Mattila TM, Tyrmi J, Pyhäjärvi T, Savolainen O. Genome-Wide Analysis of Colonization History and Concomitant Selection in Arabidopsis lyrata. Mol Biol Evol 2017; 34:2665-2677. [PMID: 28957505 DOI: 10.1093/molbev/msx193] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The high climatic variability in the past hundred thousand years has affected the demographic and adaptive processes in many species, especially in boreal and temperate regions undergoing glacial cycles. This has also influenced the patterns of genome-wide nucleotide variation, but the details of these effects are largely unknown. Here we study the patterns of genome-wide variation to infer colonization history and patterns of selection of the perennial herb species Arabidopsis lyrata, in locally adapted populations from different parts of its distribution range (Germany, UK, Norway, Sweden, and USA) representing different environmental conditions. Using site frequency spectra based demographic modeling, we found strong reduction in the effective population size of the species in general within the past 100,000 years, with more pronounced effects in the colonizing populations. We further found that the northwestern European A. lyrata populations (UK and Scandinavian) are more closely related to each other than with the Central European populations, and coalescent based population split modeling suggests that western European and Scandinavian populations became isolated relatively recently after the glacial retreat. We also highlighted loci showing evidence for local selection associated with the Scandinavian colonization. The results presented here give new insights into postglacial Scandinavian colonization history and its genome-wide effects.
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Affiliation(s)
- Tiina M Mattila
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Jaakko Tyrmi
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Tanja Pyhäjärvi
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Outi Savolainen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
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Mattila TM, Aalto EA, Toivainen T, Niittyvuopio A, Piltonen S, Kuittinen H, Savolainen O. Selection for population-specific adaptation shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post-glacial colonization. Mol Ecol 2016; 25:581-97. [PMID: 26600237 DOI: 10.1111/mec.13489] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 12/20/2022]
Abstract
Spatially varying selection can lead to population-specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location-specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine populations of the perennial herb Arabidopsis lyrata, which has a wide but patchy distribution in temperate and boreal regions of the northern hemisphere. The populations differ in their recent population demographic and colonization histories and current environmental conditions, especially in the growing season length. We searched for population-specific molecular signatures of directional selection by comparing a set of candidate flowering time loci with a genomic reference set within each population using multiple approaches and contrasted the patterns of different populations. The candidate loci possessed approximately 20% of the diversity of the reference loci. On average the flowering time loci had more rare alleles (a smaller Tajima's D) and an excess of highly differentiated sites relative to the reference, suggesting positive selection. The strongest signal of selection was detected in photoperiodic pathway loci in the colonizing populations of Northwestern Europe, whereas no evidence of positive selection was detected in the Central European populations. These findings emphasized the population-specific nature of selection and suggested that photoperiodic adaptation was important during postglacial colonization of the species.
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Affiliation(s)
- Tiina M Mattila
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Esa A Aalto
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Tuomas Toivainen
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland.,Biocenter Oulu, University of Oulu, 90014, Oulu, Finland
| | - Anne Niittyvuopio
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Susanna Piltonen
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Helmi Kuittinen
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Outi Savolainen
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland.,Biocenter Oulu, University of Oulu, 90014, Oulu, Finland
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