Sequence Data from New Plastid and Nuclear COSII Regions Resolves Early Diverging Lineages in <I>Coffea</I> (Rubiaceae)

Abstract

Abstract— Resolving phylogenetic relationships within the economically important genus Coffea (Rubiaceae) has proven to be difficult due to low levels of plastid and nuclear ITS sequence divergence. The recent identification of a large number of conserved, single-copy, putatively orthologous genes (COSII) provides a unique opportunity to apply regions of the nuclear genome to phylogenetic studies of Euasterid species. We expand a previously published plastid data set of Coffea with the addition of three new plastid regions and a single COSII nuclear locus. Significant phylogenetic incongruence is identified between the plastid and nuclear COSII data sets, and a combined analysis is performed after removal of incongruent taxa. Phylogenetic results from plastid, nuclear, and combined plastid/nuclear data sets allow the novel identification of early diverging lineages in Coffea. Specifically, the data show that a group of predominately Lower-Guinea/Congolian Coffea species form a clade that is sister to the ...