The datasets created and employed in population genetic and demographic analyses will also be used to test specific phylogenetic and gene genealogical hypotheses of allele, gene, and species/lineage divergence times. For further comparison of the effect of adaptive evolution on genomewide patterns of sequence diversity, we will estimate ‘empirical null distributions’ of estimated sequence diversity and divergence parameters for all three species pairs and compare these to expected distributions for alternative demographic models such as population structure, gene flow, and population size changes for the three species pairs. Because of the recency of the speciation events, we expect many of the loci sampled to exhibit incomplete lineage sorting within species-pair comparisons, particularly in the more recently-derived species pairs (Friar et al. 2006)

Additionally, because HSA species are allopolyploids, homoeologous duplicate gene pairs derived from separate California tarweed progenitor genome lineages will also be sequenced and examined for patterns of diversity of divergence since genome duplication timed to the origin of this adaptive radiation ~ 5 mya (Lawton-Rauh 2003, Lawton-Rauh et al. 2003). Altogether, this group of analyses, coupled with the population analyses listed on the previous page, will help us to detect the differences between gene-specific events due to forces of natural selection and genome-wide events (as estimated using the baseline loci as a multi-locus approach) due to demographic factors most likely resulting from the dynamic environmental and geological processes shaping the Hawaiian archipelago.

• Lawton-Rauh, AL (2003)  Evolutionary dynamics of duplicated genes in plants.  Molecular Phylogenetics and Evolution 29:396-409
• 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 60:1777-92.
• Friar, EA, Cruse-Sanders, JM, McGlaughlin, ME (2007) Gene flow in Dubautia arborea and D. ciliolata: the roles of ecology and isolation by distance in maintaining species boundaries despite ongoing hybridization. Molecular Ecology, in press.
• Lawton-Rauh, AL, Robichaux, RH, Purugganan, MD (2007)  Diversity and divergence patterns in regulatory genes suggest differential gene flow in recently-derived species of the Hawaiian silversword alliance adaptive radiation.  Molecular Ecology, in press