Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose since the last glaciation and subsequently reached local high frequency in a hybrid speciation zone. Furthermore, the inversion shows signs of positive directional selection. To test whether the inversion could have captured existing, linked QTLs, we crossed standard, collinear haplotypes from the hybrid zone and found multiple linked phenology QTLs within the inversion region. These findings provide the first direct evidence that linked, locally adapted QTLs may be captured by young inversions during incipient speciation.

Arizona Genomics Institute and BIO5 Institute School of Plant Sciences University of Arizona Tucson Arizona 85721 USA

Biosystematics Group Wageningen University and Research Center Droevendaalsesteeg 1 6708PB Wageningen The Netherlands

Department of Biology Colorado State University Fort Collins Colorado 80523 USA

Department of Biology Duke University Box 90338 Durham North Carolina 27708 USA

Department of Energy Joint Genome Institute Walnut Creek California 94598 USA

Department of Plant Ecology and Genetics Uppsala University Norbyvägen 18D SE 752 36 Uppsala Sweden

HudsonAlpha Institute for Biotechnology Huntsville Alabama 35806 USA

Institute of Ecology and Evolutionary Biology and Institute of Plant Biology National Taiwan University Taipei 10617 Taiwan ROC

Phyzen Genomics Institute Phyzen Inc Seoul 151 836 South Korea

Plant Cytogenomics Group Central European Institute of Technology Masaryk University Kamenice 5 Brno CZ 62500 Czech Republic

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Nat Ecol Evol. 2017 Oct;1(10):1585. doi: 10.1038/s41559-017-0310-8. PubMed

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How Important Are Structural Variants for Speciation?

Chromosomal Evolution and Apomixis in the Cruciferous Tribe Boechereae

Young inversion with multiple linked QTLs under selection in a hybrid zone