Does selection occur at the intermediate zone of two insufficiently isolated populations? A whole-genome analysis along an altitudinal gradient

Abstract

Adaptive divergence would occur even between the insu ciently isolated populations when there is a great difference in the environments between their habitats. The individuals present in the intermediate zone of the two divergent populations are expected to have an admixed genetic structure due to gene ow. A selective pressure that acts on the genetically admixed individuals may limit the gene ow and promote the adaptive divergence. Here, we addressed a question whether the selection occurs in the genetically admixed individuals between the divergent populations and assessed its effects on the population divergence. We obtained the whole-genome sequences of a perennial montane plant, Arabidopsis halleri, which has clear phenotypic dimorphisms between altitudes, along an altitudinal gradient of 359-1,317 m with a high spatial resolution (mean altitudinal interval of 20 m). We found the zone where the highland and lowland genes were mixing (intermediate subpopulation). We sought genetic variants that had been selected in the intermediate subpopulation. In the intermediate subpopulation, we identi ed 9 and 22 genetic regions, which included 7 and 19 genes, had a high frequency of alleles that are accumulated in highland and lowland subpopulations, respectively, suggesting that these genes have been selected in the admixed zone. This selection might limit the gene ow and contribute to the adaptive divergence along the altitudes. We also identi ed a genetic region that contains different alleles from those in both highland and lowland subpopulations, though the variants were not included in encoded genes. We also identi ed 7 genetic regions had low heterozygote frequencies in the intermediate subpopulation. We could not nd any genetic regions whose heterozygote frequency was higher than theoretical expectation. We conclude that different types of selection in addition to gene ow occur at the intermediate altitude and shape the genetic structure across altitudes.

Population genomics reveals demographic history and climate adaptation in JapaneseArabidopsis halleri

“…While there have been a few studies on population structure in Japanese A. halleri , they relied on a limited number of loci and sampling locations (Sato and Kudoh, 2014) or focused on a microgeographic scale (Kubota et al, 2015; Yoshida et al, 2023). In this study, by using full-genome re-sequencing data from region-wide samples, we revealed a population structure that showed a clear geographic pattern (Fig.…”

“…This study focused on Arabidopsis halleri, a perennial herb distributed in East Asia and Europe. This species has been used extensively for evolutionary and ecological studies (reviewed in Honjo and Kudoh, 2019; Koch, 2018), such as self-incompatibility (Castric and Vekemans, 2004; Durand et al, 2020), heavy metal hyperaccumulation (Krämer, 2010; Stein et al, 2017), and adaptation to high altitudes (Kubota et al, 2015; Yoshida et al, 2023; Yumoto et al, 2021). Five subspecies are recognized in A. halleri : A. halleri subsp.…”

“…Given its wide distribution in the diverse climates across the Japanese archipelago, A. halleri can serve as a model species to study how plant populations are locally adapted to diverse climates and their changes during glacial cycles. Population structure and demographic histories are the fundamental basis for studying local adaptation, but the information is currently limited except for a few studies, including the one based on microsatellite markers (Sato and Kudoh, 2014) or the one on a microgeographic scale (Kubota et al, 2015; Yoshida et al, 2023).…”

“…The copyright holder for this preprint this version posted April 11, 2024. ; https://doi.org/10.1101/2024.04.08.588504 doi: bioRxiv preprint incompatibility (Castric and Vekemans, 2004;Durand et al, 2020), heavy metal hyperaccumulation (Krämer, 2010;Stein et al, 2017), and adaptation to high altitudes (Kubota et al, 2015;Yoshida et al, 2023;Yumoto et al, 2021). Five subspecies are recognized in A.…”