Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae)

Lexer, Christian; Wüest, R. O.; Mangili, Sophia; Heuertz, Myriam; Stölting, Kai N.; Pearman, Peter B.; Forest, Félix; Salamin, Nicolas; Zimmermann, Niklaus E.; Bossolini, Eligio

doi:10.1111/mec.12870

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Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae)

Lexer, Christian Unit of Ecology & Evolution, Department of Biology, University of Fribourg, Switzerland
Wüest, R. O. Landscape Dynamics Unit, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland - Univ. Grenoble Alpes, LECA, Grenoble, France - CNRS, LECA, Grenoble, France
Mangili, Sophia Unit of Ecology & Evolution, Department of Biology, University of Fribourg, Switzerland
Heuertz, Myriam Unit of Ecology & Evolution, Department of Biology, University of Fribourg, Switzerland - INIA Forest Research Centre, Madrid, Spain
Stölting, Kai N. Unit of Ecology & Evolution, Department of Biology, University of Fribourg, Switzerland
Pearman, Peter B. Landscape Dynamics Unit, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
Forest, Félix Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, U.K
Salamin, Nicolas Department of Ecology & Evolution, University of Lausanne, Switzerland - Swiss Institute of Bioinformatics, Lausanne, Switzerland
Zimmermann, Niklaus E. Landscape Dynamics Unit, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
Bossolini, Eligio Unit of Ecology & Evolution, Department of Biology, University of Fribourg, Switzerland - Bayer CropScience, Gent, Belgium

01.09.2014

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Molecular Ecology. - 2014, vol. 23, no. 17, p. 4373–4386

English Understanding the drivers of population divergence, speciation and species persistence is of great interest to molecular ecology, especially for species-rich radiations inhabiting the world's biodiversity hotspots. The toolbox of population genomics holds great promise for addressing these key issues, especially if genomic data are analysed within a spatially and ecologically explicit context. We have studied the earliest stages of the divergence continuum in the Restionaceae, a species-rich and ecologically important plant family of the Cape Floristic Region (CFR) of South Africa, using the widespread CFR endemic Restio capensis (L.) H.P. Linder & C.R. Hardy as an example. We studied diverging populations of this morphotaxon for plastid DNA sequences and >14 400 nuclear DNA polymorphisms from Restriction site Associated DNA (RAD) sequencing and analysed the results jointly with spatial, climatic and phytogeographic data, using a Bayesian generalized linear mixed modelling (GLMM) approach. The results indicate that population divergence across the extreme environmental mosaic of the CFR is mostly driven by isolation by environment (IBE) rather than isolation by distance (IBD) for both neutral and non-neutral markers, consistent with genome hitchhiking or coupling effects during early stages of divergence. Mixed modelling of plastid DNA and single divergent outlier loci from a Bayesian genome scan confirmed the predominant role of climate and pointed to additional drivers of divergence, such as drift and ecological agents of selection captured by phytogeographic zones. Our study demonstrates the usefulness of population genomics for disentangling the effects of IBD and IBE along the divergence continuum often found in species radiations across heterogeneous ecological landscapes.

Faculty

Faculté des sciences et de médecine

Department

Département de Biologie

Language