Resolving deep relationships of PACMAD grasses : a phylogenomic approach
Cotton, Joseph L.
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The phylogenetically recognized PACMAD (Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, Danthonioideae) clade of grasses has been the subject of numerous phylogenetic studies that have made an attempt at determining subfamilial relationships of the clade (Clark et al., 1995, GPWGI, 2001, Duvall et al., 2007, GPWGII, 2012). The purpose of this thesis was to examine chloroplast genome sequences for 18 PACMAD species, and analyze them phylogenomically. These analyses were conducted to provide resolution of deep subfamilial relationships within the clade. Divergence estimates were assessed to determine potential factors that led to the rapid radiation of this lineage and its dominance of open habitats. This was accomplished via Next Generation Sequencing methods to provide complete plastome sequence for 12 species. Sanger Sequencing was performed on one species, Hakonechloa macra, to provide a reference. Phylogenomic analyses and divergence estimates were conducted on these plastomes in conjunction with six other previously banked plastomes. The results presented here support Panicoideae as the earliest diverging PACMAD lineage. The initial diversification of PACMAD subfamilies was estimated to occur 32.4 mya. Phylogenomic analyses of complete plastome sequences provide strong support for deep relationships of PACMAD grasses. The divergence estimate of 32.4 mya at the crown node of the PACMAD clade coincides with the Eocene-Oligocene Transition (EOT). Throughout the Eocene, prior to the EOT, was a period of global cooling and drying, which led to forest fragmentation and the expansion of open habitats now dominated by these grasses.