The nuclear GBSSI gene is duplicated in all Rosaceae, and there is a second duplication in all members of subfamily Maloideae, including three genera with dry fruits that have not traditionally been included in the subfamily, Kageneckia, Lindleya, and Vauquelinia. We obtained sequence for about 1800 nucleotide sites, including seven complete exons and eight introns (only seven in two of the four copies of the gene) plus parts of the first and ninth exons at the 5' end of the gene. In a sample that includes all but two of the 32 genera in the family, we have sequences for all four copies of the gene for 14 genera, for three copies for 6 genera, for two copies for 9 genera, and for just one copy for Pseudocydonia. That we are readily able to align introns within each copy of the gene is compatible with the low sequence divergence in this gene (about 2 to 5% between Maloideae genera other than Kageneckia, Lindleya, and Vauquelinia) and in other molecular data. Analysis of GBSSI sequence data for our sample plus the sister group of Maloideae (Porteranthus) supports a sister-group relationship between Kageneckia, Lindleya, plus Vauquelinia and the remainder (core) of the Maloideae. We therefore use these three genera as outgroups for analyses of core Maloideae. The data give strong support for monophyly of core Maloideae and varying levels of support for several groups of two to three genera, namely Amelanchier, Malacomeles, plus Peraphyllum; Aria plus Chamaemespilus; Cotoneaster plus Malus; and Dichotomanthes plus Photinia. Short branch lengths characterize much of the most parsimonious trees, suggesting rapid diversification and frustrating our efforts to understand higher-level relationships in the subfamily.

Key words: exons, gene duplication, introns, Maloideae, Rosaceae, sequence divergence