“…The vast range of morphological variation (from tiny herbs to large trees) and ecological adaptation (from coastal sand dunes to montane forests) pose challenges for resolving phylogenetic relationships using taxonomic methods (Drummond et al, 2012). Comparisons of nuclear and chloroplast DNA sequences (Ainouche and Bayer, 1999;Wink and Mohamed, 2003;Ainouche et al, 2004;Ree et al, 2004;Drummond and Hamilton, 2007;Drummond, 2008;Eastwood et al, 2008b;Drummond et al, 2012) have made some progress toward resolving Lupinus phylogeny, but ambiguities still remain. Current efforts are underway to sample large gene sets obtained by whole transcriptome sequencing across New World Lupinus (C. Hughes, G. Atchison, D. Filatov, personal communication), which should definitively answer these remaining questions.…”