Ribosomal internal transcribed spacer (ITS) sequences were used to eva
luate the phylogenetics of Zea and Tripsacum. Maximum likelihood and p
olymorphism parsimony were used for phylogenetic reconstructions. Zea
ITS nucleotide diversity was high compared to other plant species, but
approximately equivalent to other maize loci. Coalescence of TTS alle
les was rapid relative to other nuclear loci; however, there was still
much diversity within populations. Zea and Tripsacum form a clade cle
arly differentiated from all other Poaceae. Four Zea ITS pseudogenes w
ere identified by phylogenetic position and nucleotide composition. Th
e phylogenetic position of Z. mays ssp. huehuetenangensis was clearly
established as basal to the other Z. mays. The ITS phylogeny disfavore
d a Z. luxurians and Z. diploperennis clade, which conflicted with som
e previous studies. The introgression of Z. mays alleles into Z. peren
nis and Z. diploperennis was also established. The ITS data indicated
a near contemporary divergence of domesticated maize and its two close
st wild relatives.