Nuclear sequence data are needed for plant systematics studies in order to supplement data from the chloroplast genome and from morphology. We cloned and sequenced a partial sequence of LEAFY, from the 3′ end of the second intron to the 3′ end of the third exon, for 44 species from the three Leguminosae subfamilies, but with greater taxon sampling in the basal subfamily Caesalpinioideae. Only one copy of LEAFY was amplified in most of the Leguminosae studied, but in members of tribe Detarieae, our phylogenetic analyses suggest that two copies are present, one of which may be a pseudogene. Sampled species of Brownea Jacq. and Browneopsis Huber (Detarieae) possess a large, unique insertion, which seems to be a useful taxonomic marker for this bigeneric group. The rate of substitution in the coding sequences of LEAFY gives a phylogenetic signal at a broad spectrum of phylogenetic levels, from the intergeneric level to the family level. The second intron is highly variable, and for the copy that seems to be under relaxed selective constraint, the sequences cannot be compared between species of different tribes or subfamilies. The phylogenetic analysis of LEAFY sequences results in topologies that, overall, are consistent with past taxonomy and chloroplast sequence analyses. However, incongruence between the chloroplast trnL intron and one of the copies of LEAFY is found in the tribe Detarieae. This incongruence remains poorly explained, but may result from hidden paralogy or lineage sorting of divergent alleles. This study provides an example of the unexpected complexity that can arise when evaluating the phylogenetic utility of a low-copy nuclear gene.
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