| Summary: | <p>Abstract</p> <p>Background</p> <p>The rapidly increasing number of available plant genomes opens up almost unlimited prospects for biology in general and molecular phylogenetics in particular. A recent study took advantage of this data and identified a set of nuclear genes that occur in single copy in multiple sequenced angiosperms. The present study is the first to apply genomic sequence of one of these low copy genes, <it>agt1</it>, as a phylogenetic marker for species-level phylogenetics. Its utility is compared to the performance of several coding and non-coding chloroplast loci that have been suggested as most applicable for this taxonomic level. As a model group, we chose <it>Tildenia</it>, a subgenus of <it>Peperomia </it>(Piperaceae), one of the largest plant genera. Relationships are particularly difficult to resolve within these species rich groups due to low levels of polymorphisms and fast or recent radiation. Therefore, <it>Tildenia </it>is a perfect test case for applying new phylogenetic tools.</p> <p>Results</p> <p>We show that the nuclear marker <it>agt1</it>, and in particular the <it>agt1 </it>introns, provide a significantly increased phylogenetic signal compared to chloroplast markers commonly used for low level phylogenetics. 25% of aligned characters from <it>agt1 </it>intron sequence are parsimony informative. In comparison, the introns and spacer of several common chloroplast markers (<it>trnK </it>intron, <it>trnK</it>-<it>psbA </it>spacer, <it>ndhF</it>-<it>rpl32 </it>spacer, <it>rpl32</it>-<it>trnL </it>spacer, <it>psbA</it>-<it>trnH </it>spacer) provide less than 10% parsimony informative characters. The <it>agt1 </it>dataset provides a deeper resolution than the chloroplast markers in <it>Tildenia</it>.</p> <p>Conclusions</p> <p>Single (or very low) copy nuclear genes are of immense value in plant phylogenetics. Compared to other nuclear genes that are members of gene families of all sizes, lab effort, such as cloning, can be kept to a minimum. They also provide regions with different phylogenetic content deriving from coding and non-coding parts of different length. Thus, they can be applied to a wide range of taxonomic levels from family down to population level. As more plant genomes are sequenced, we will obtain increasingly precise information about which genes return to single copy most rapidly following gene duplication and may be most useful across a wide range of plant groups.</p>
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