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PLoS Genet. 2015 Jul 14;11(7):e1005361. doi: 10.1371/journal.pgen.1005361. eCollection 2015 Jul.

A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species.

Author information

1
Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo, Japan; College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan. skubota44@gmail.com.
2
Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo, Japan.
3
Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan; Frontier Research Academy for Young Researchers, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
4
Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
5
Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan.
6
Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
7
CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan; Graduate School of Life Sciences, Tohoku University, Sendai, Miyagai, Japan.
8
College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.

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.

PMID:
26172569
PMCID:
PMC4501782
DOI:
10.1371/journal.pgen.1005361
[Indexed for MEDLINE]
Free PMC Article

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