Adaptive radiations such as the Darwin finches in the Galapagos or the cichlid fishes from the Eastern African Great Lakes have been a constant source of inspiration for biologists and a stimulus for evolutionary thinking. A central concept behind adaptive radiation is that of evolution by niche shifts, or ecological speciation. Evidence for adaptive radiations generally requires a strong correlation between phenotypic traits and the environment. But adaptive traits are often cryptic, hence making this phenotype-environment approach difficult to implement. Here we propose a procedure for detecting adaptive radiation that focuses on species’ ecological niche comparisons. It evaluates whether past ecological disparity in a group fits better a neutral Brownian motion model of ecological divergence or a niche shift model. We have evaluated this approach on New Zealand rockcresses (Pachycladon) that recently radiated in the New Zealand Alps. We show that the pattern of ecological divergence rejects the neutral model and is consistent with that of a niche shift model. Our approach to detect adaptive radiation has the advantage over alternative approaches that it focuses on ecological niches, a key concept behind adaptive radiation. It also provides a way to evaluate the importance of ecological speciation in adaptive radiations and will have general application in evolutionary studies. In the case of Pachycladon, the high estimated diversification rate, the distinctive ecological niches of species, and the evidence for ecological speciation suggest a remarkable example of adaptive radiation.

R scriptsR scripts to perform the analyses performed in the paper.Joly&al_SystBiol_R_scripts.R*Beast analysis xml filexml file used to perform the species tree analysis.*Beast_analysis_ConstantPopSize.xmlbpp Species Delim Control Filecontrol file used to perform the BP&P species delimitation analysis.bpp_SpeciesDelimControlFile.ctlSupplementary figuresSupplementary figures 1, 2, and 3.Supp_figures.pdfSupplementary table 1Table S1TableS1.docxSupplementary table 2Table S2TableS2.docxSupplementary table 3Table S3TableS3.docx