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Title: A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species
Authors: Kubota, Shosei
Iwasaki, Takaya
Hanada, Kousuke
Nagano, Atsushi J.
Fujiyama, Asao
Toyoda, Atsushi
Sugano, Sumio
Suzuki, Yutaka
Hikosaka, Kouki
Ito, Motomi
Morinaga, Shin Ichi
Author's alias: 永野, 惇
Issue Date: 14-Jul-2015
Publisher: Public Library of Science
Journal title: PLOS Genetics
Volume: 11
Issue: 7
Thesis number: e1005361
Abstract: Adaptive divergence at the microgeographic scale has been generally disregarded because high gene flow is expected to disrupt local adaptation. Yet, growing number of studies reporting adaptive divergence at a small spatial scale highlight the importance of this process in evolutionary biology. To investigate the genetic basis of microgeographic local adaptation, we conducted a genome-wide scan among sets of continuously distributed populations of Arabidopsis halleri subsp. gemmifera that show altitudinal phenotypic divergence despite gene flow. Genomic comparisons were independently conducted in two distinct mountains where similar highland ecotypes are observed, presumably as a result of convergent evolution. Here, we established a de novo reference genome and employed an individual-based resequencing for a total of 56 individuals. Among 527, 225 reliable SNP loci, we focused on those showing a unidirectional allele frequency shift across altitudes. Statistical tests on the screened genes showed that our microgeographic population genomic approach successfully retrieve genes with functional annotations that are in line with the known phenotypic and environmental differences between altitudes. Furthermore, comparison between the two distinct mountains enabled us to screen out those genes that are neutral or adaptive only in either mountain, and identify the genes involved in the convergent evolution. Our study demonstrates that the genomic comparison among a set of genetically connected populations, instead of the commonly-performed comparison between two isolated populations, can also offer an effective screening for the genetic basis of local adaptation.
Rights: © 2015 Kubota et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
DOI(Published Version): 10.1371/journal.pgen.1005361
PubMed ID: 26172569
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