To begin identifying the genes responsible for adaptive differentiation in the Hawaiian silversword alliance (HSA), we will examine whether candidate genes show patterns of intraspecific and interspecific variation consistent with divergent selection. Our hypothesis is that at least some positional candidate genes identified in the QTL analysis will show patterns consistent with divergent selection in the Dubautia reticulata/Dubautia menziesii pair, and that some of these genes may show similar patterns in the other two species pairs. Such patterns would provide evidence that these genes may be at least partially responsible for the detected QTL effects. Moreover, functional candidates not associated with D. reticulata/D. menziesii QTLs may be responsible for differentiation in one of the other species pairs. Homoeologous copies of 34 “baseline” loci plus at least 20 functional candidate genes will be sequenced from at least 10 individuals from each sampled population (two populations/species).  The baseline loci will be used to estimate ‘empirical null distributions’ of nucleotide diversity, haplotype diversity, and levels and ranges of linkage disequilibrium, which will be used to test hypotheses of historical demographic and selection events. Such empirical distributions of genetic diversity indices are vital to have enough power to detect significant differences in genetic variation in functional candidate loci (Schmid et al. 2005) and will also permit examination of genome dynamics.

In addition to testing for differences among empirical null distributions between species (thus indicating differences in genome-wide patterns of variation associated with differences in demographic effects), these comparisons will also be used to test whether candidate genes show genetic patterns consistent with involvement in trait differences between D. menziesii and D. reticulata. These comparisons will be powerful due to the minimal genetic differentiation between these two species (Friar et al. 2006) which occurs with high levels of haplotype diversity and high rates of effective recombination (Lawton-Rauh et al. in press). We will also examine whether the loci exhibit similar genetic patterns in the additional pairwise species comparisons. These analyses will indicate if the three species pairs within the HSA have “taken the same path” towards ecological and genomic differentiation.

• Schmid, K. J., S. Ramos-Onsins, H. Ringys-Beckstein, B. Weisshaar, and T. Mitchell-Olds. 2005. A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism. Genetics 169:1601-15.
• Friar, E. A., L. M. Prince, E. H. Roalson, M. E. McGlaughlin, J. M. Cruse-Sanders, S. J. De Groot, and J. M. Porter.  2006.  Ecological speciation in the East Maui-endemic Dubautia (Asteraceae) species. Evolution Int J Org Evolution 60:1777-92.