Basal angiosperm phylogeny inferred from duplicate phytochromes A and C

We have extended our studies of angiosperm phylogeny based on a pair of dup licated phytochrome (PHY) genes, PHYA and PHYC. Phylogenetic analyses of se quences from 52 species yield unrooted gene networks in which all of the el ements resolved in our previous analysis of 26 species appear. Amborella st ill emerges as the sister group of all other angiosperms. However, we canno t reject alternative rootings in which water lilies, either alone or in com bination with Amborella, are basal. Austrobaileya + Illicium diverges next from the remaining angiosperms. Eudicots and monocots form rather well-supp orted clades, as do Magnoliales, Laurales, Piperales, and winteroids, but r elationships among these major lineages remain uncertain, as do the positio ns of Chloranthaceae and Ceratophyllum. Magnoliales may be directly linked with Laurales and Piperales with winteroids, but support for these relation ships is not strong. Within eudicots, a basal split between ranunculids (Ra nunculales, Papaverales) and the rest of the eudicots is supported, though the position of Nelumbo is equivocal. These same relationships are obtained in combined analyses of PHYA and PHYC (species as terminals) when Ceratoph yllum is excluded. However, when Ceratophyllum is included, Austrobaileya Illicium and then Chloranthaceae diverge from the remaining angiosperms be fore Ceratophyllum + water lilies. Rooted species trees inferred from dupli cate gene networks by minimizing gene duplications and losses are highly co ngruent with the gene subtrees and with the results of recent analyses of o ther genes, even when Ceratophyllum is included. More attention must be pai d to the methods for obtaining rooted species trees from data sets that inc lude duplicate genes, especially if we are to fully implement the search fo r species trees that simultaneously minimize the multiple possible causes o f conflict among gene trees.