Zea systematics: ribosomal ITS evidence

Ribosomal internal transcribed spacer (ITS) sequences were used to evaluatethe phylogenetics of Zea and Tripsacum. Maximum likelihood and polymorphismparsimony were used for phylogenetic reconstructions. Zea ITS nucleotidediversity was high compared to other plant species, but approximatelyequivalent to other maize loci. Coalescence of ITS alleles was rapidrelative to other nuclear loci; however, there was still much diversitywithin populations. Zea and Tripsacum form a clade clearly differentiatedfrom all other Poaceae. Four Zea ITS pseudogenes were identified byphylogenetic position and nucleotide composition. The phylogenetic positionof Z. mays ssp. huehuetenangensis was clearly established as basal to theother Z. mays. The ITS phylogeny disfavored a Z. luxurians and Z.diploperennis clade, which conflicted with some previous studies. Theintrogression of Z. mays alleles into Z. perennis and Z. diploperennis wasalso established. The ITS data indicated a near contemporary divergence ofdomesticated maize and its two closest wild relatives.