Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex FEDERICO RODA,* LUKE AMBROSE,* GREGORY M. WALTER,* HUANLE L. LIU,* ANDREA SCHAUL,* ANDREW LOWE, ‡ § PIETER B. PELSER, ¶ PETER PRENTIS, † LOREN H. RIESEBERG** †† and DANIEL ORTIZ-BARRIENTOS* *School of Biological Sciences, The University of Queensland, St. Lucia, Qld 4072, Australia, †School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Qld 4001, Australia, ‡Australian Centre for Evolutionary Biology and Biodiversity, School of Earth and Environmental Science, University of Adelaide, Adelaide, SA, Australia, §Science Resource Centre, Department for Environment and Natural Resources, North Terrace, Adelaide, South Australia, Australia, ¶School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand, **Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC,V6T 1Z4, Canada, ††Biology Department, Indiana University, 1001 E Third Street, Bloomington, IN 47405, USA Abstract Instances of parallel ecotypic divergence where adaptation to similar conditions repeat- edly cause similar phenotypic changes in closely related organisms are useful for studying the role of ecological selection in speciation. Here we used a combination of traditional and next generation genotyping techniques to test for the parallel diver- gence of plants from the Senecio lautus complex, a phenotypically variable groundsel that has adapted to disparate environments in the South Pacific. Phylogenetic analysis of a broad selection of Senecio species showed that members of the S. lautus complex form a distinct lineage that has diversified recently in Australasia. An inspection of thousands of polymorphisms in the genome of 27 natural populations from the S. lautus complex in Australia revealed a signal of strong genetic structure independent of habitat and phenotype. Additionally, genetic differentiation between populations was correlated with the geographical distance separating them, and the genetic diver- sity of populations strongly depended on geographical location. Importantly, coastal forms appeared in several independent phylogenetic clades, a pattern that is consistent with the parallel evolution of these forms. Analyses of the patterns of genomic differ- entiation between populations further revealed that adjacent populations displayed greater genomic heterogeneity than allopatric populations and are differentiated according to variation in soil composition. These results are consistent with a process of parallel ecotypic divergence in face of gene flow. Keywords: adaptation, parallel evolution, RAD genotyping, Senecio, speciation Received 15 June 2012; revision received 10 February 2013; accepted 14 February 2013 Introduction Natural selection can replicate the evolution of forms and functions and create similarities between distantly related species (Schluter et al. 2004; Elmer & Meyer 2011; Wake et al. 2011). Traditional examples include the repeated evolution of melanism in mammals, reptiles and birds (Nachman et al. 2003; Mundy 2005; Rosenblum & Harmon 2011), and the independent adaptation to serpentine soils in flowering plants (Bergl- und et al. 2004; Brady et al. 2005; Bratteler et al. 2006; Turner et al. 2010). The repeated and independent evolution of forms can also occur amongst taxa sharing a recent common ancestor and similar biology. For instance, in freshwater populations where predators are rare, Canadian stickleback fish have repeatedly evolved smaller defensive structures when compared with their Correspondence: Daniel Ortiz-Barrientos, Fax: (61)7 3365 1656; E-mail: d.ortizbarrientos@uq.edu.au Molecular Ecology (2013) 22, 2941–2952 doi: 10.1111/mec.12311 © 2013 John Wiley & Sons Ltd