Abstract
Colonization of new habitats is expected to require genetic adaptations to overcome environmental challenges. Here, we use full genome re-sequencing and extensive common garden experiments to investigate demographic and selective processes associated with colonization of Japan by Lotus japonicus over the past ~20,000 years. Based on patterns of genomic variation, we infer the details of the colonization process where L. japonicus gradually spread from subtropical conditions to much colder climates in northern Japan. We identify genomic regions with extreme genetic differentiation between northern and southern subpopulations and perform population structure-corrected association mapping of phenotypic traits measured in a common garden. Comparing the results of these analyses, we find that signatures of extreme subpopulation differentiation overlap strongly with phenotype association signals for overwintering and flowering time traits. Our results provide evidence that these traits were direct targets of selection during colonization and point to associated candidate genes.
Highlights
Colonization of new habitats is expected to require genetic adaptations to overcome environmental challenges
It has been suggested that combining population structure-corrected genome-wide association (GWA) analysis of phenotypic data from common garden experiments with purely genotype-based genome scans could be a powerful approach for studying local adaptation
If a potentially adaptive signal detected using a phenotype-independent genome scan for population differentiation overlaps with a GWA signal derived from common garden fitness data, the argument is that these signals would constitute two independent lines of evidence supporting local adaptation, one based on genomic and the other on phenotypic differentiation[5,6]
Summary
Colonization of new habitats is expected to require genetic adaptations to overcome environmental challenges. We identify genomic regions with extreme genetic differentiation between northern and southern subpopulations and perform population structure-corrected association mapping of phenotypic traits measured in a common garden. It has been suggested that combining population structure-corrected GWA analysis of phenotypic data from common garden experiments with purely genotype-based genome scans could be a powerful approach for studying local adaptation. A second study examined drought stress data from a laboratory experiment and observed marginally elevated FST levels for the top SNPs8, while a third showed evidence for an adaptive role of a sodium transporter by GWA analysis of ion accumulation coupled with investigation of gene expression and distances to saline soils[9]. Most of the relatively few potentially adaptive plant traits studied by GWA have not revealed clear signals of local adaptation, and the power of combining GWA analysis of common garden phenotype data with genotype-based genome scans for the study of local adaptation has not been systematically explored. It has a relatively small genome size of ~472 Mb and is found in diverse natural habitats across East and Central
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