On the post-glacial spread of human commensal Arabidopsis thaliana

Cheng-Ruei Lee,Detlef Weigel,Hannes Svardal,Moises Exposito-Alonso,Polina Novikova,Magnus Nordborg,Wei Ding,Carlos Alonso-Blanco,Ashley Farlow

doi:10.1038/ncomms14458

Abstract

Recent work has shown that Arabidopsis thaliana contains genetic groups originating from different ice age refugia, with one particular group comprising over 95% of the current worldwide population. In Europe, relicts of other groups can be found in local populations along the Mediterranean Sea. Here we provide evidence that these ‘relicts’ occupied post-glacial Eurasia first and were later replaced by the invading ‘non-relicts’, which expanded through the east–west axis of Eurasia, leaving traces of admixture in the north and south of the species range. The non-relict expansion was likely associated with human activity and led to a demographic replacement similar to what occurred in humans. Introgressed genomic regions from relicts are associated with flowering time and enriched for genes associated with environmental conditions, such as root cap development or metal ion trans-membrane transport, which suggest that admixture with locally adapted relicts helped the non-relicts colonize new habitats.

Highlights

Recent work has shown that Arabidopsis thaliana contains genetic groups originating from different ice age refugia, with one particular group comprising over 95% of the current worldwide population
The best-known example comes from humans: anatomically modern humans migrated from Africa and replaced existing forms such as Neanderthals and Denisovans, in what is effectively a ‘genomewide sweep’—the genomes of one population rapidly replace those of others
Note that the process differs from a classical genetic sweep in that it is effectively genome-wide, and in that the driving force may not be genetics, but an environmental advantage: neutral variants can be swept to fixation not because they are linked to selectively advantageous alleles at particular loci, but because they are associated with an environment that has a large reproductive advantage

Summary

Introduction

Recent work has shown that Arabidopsis thaliana contains genetic groups originating from different ice age refugia, with one particular group comprising over 95% of the current worldwide population. Simple comparison of genetic distances identified several accessions that are distantly related to the majority These accessions were only found in the southern edge of the known species distribution and formed four geographically and genetically distinct groups (Cape Verde, Iberia, Sicily and Lebanon). We first identify the traces of hybridization between relicts and non-relicts and investigate whether the pattern of introgression appears to have been associated with adaptation to the local environment. Our overall conclusion is that A. thaliana of today is the product of a dramatic series of range expansions, admixture, and local adaptation, and the current pattern of A. thaliana genomic variation is very different from that before the last ice age

Methods

Results

Conclusion