Genome-Wide Analysis of Colonization History and Concomitant Selection in Arabidopsis lyrata

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.

Cold tolerance in the genus Arabidopsis

“…Thus, although some measures of cold tolerance may reveal a latitudinal cline in A. lyrata , our results do not. Unlike populations of A. thaliana and A. kamchatica , A. lyrata populations are highly differentiated (Wright et al., ; Mattila et al., ), and they show strong local climate adaptation (Leinonen et al., , , ; Hämälä et al., ; Lucek et al., ). The counter‐adaptive effects of gene flow or recent divergence are not a likely explanation for the lack of a latitudinal cline in A. lyrata .…”

“…lyrata , on the other hand, has higher cold tolerance than is needed, even at the northern edge of its range. This subspecies was recently derived in North America by a founder event from European A. lyrata subsp petraea (Wright et al., ; Mattila et al., ). It appears to have retained its ancestral high levels of cold tolerance and should have the capacity to expand northward.…”

Local adaptation and ecological differentiation under selection, migration, and drift inArabidopsis lyrata*

“…To supplement our data, we used six whole‐genome sequences from GER and NC, as well as five from J3 (bringing the number of individuals from that population to 12), published previously by Mattila et al. (). Therefore, our total dataset consisted of 44 resequenced individuals from six populations.…”

“…; Mattila et al. ) and phenotypically differentiated in life‐history and morphological traits (Kärkkäinen et al. ; Quilot‐Turion et al.…”

Impact of demography on linked selection in two outcrossing Brassicaceae species

“…Indeed, the recent colonization history of A. lyrata especially in northern Europe has likely been associated with strong population bottlenecks or effective population size reduction (Mattila, Tyrmi, Pyhäjärvi, & Savolainen, 2017;Pyhäjärvi, Aalto, & Savolainen, 2012;Ross-Ibarra et al, 2008;Savolainen & Kuittinen, 2011), which is in contrast to the large and relatively stable population of C. grandiflora (Douglas et al, 2015;Slotte, Foxe, Hazzouri, & Wright, 2010;Slotte et al, 2013;St. We chose these species because they have similar mating systems (both are self-incompatible outcrossers) and genome structure, and because previous research suggests considerable differences in the demographic histories of some populations.…”