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Background  The genus  Pyrus  belongs to the tribe Pyreae (the former subfamily Maloideae) of the family Rosaceae, and includes one of the most important commercial fruit crops, pear. The phylogeny of  Pyrus  has not been definitively reconstructed. In our previous efforts, the internal transcribed spacer region (ITS) revealed a poorly resolved phylogeny due to non-concerted evolution of nrDNA arrays. Therefore, introns of low copy nuclear genes (LCNG) are explored here for improved resolution. However, paralogs and lineage sorting are still two challenges for applying LCNGs in phylogenetic studies, and at least two independent nuclear loci should be compared. In this work the second intron of  LEAFY  and the alcohol dehydrogenase gene ( Adh ) were selected to investigate their molecular evolution and phylogenetic utility.    Results  DNA sequence analyses revealed a complex ortholog and paralog structure of  Adh  genes in  Pyrus  and  Malus , the pears and apples. Comparisons between sequences from RT-PCR and genomic PCR indicate that some  Adh  homologs are putatively nonfunctional. A partial region of  Adh1  was sequenced for 18  Pyrus  species and three subparalogs representing  Adh1-1  were identified. These led to poorly resolved phylogenies due to low sequence divergence and the inclusion of putative recombinants. For the second intron of  LEAFY , multiple inparalogs were discovered for both  LFY1int2  and  LFY2int2 .  LFY1int2  is inadequate for phylogenetic analysis due to lineage sorting of two inparalogs.  LFY2int2-N , however, showed a relatively high sequence divergence and led to the best-resolved phylogeny. This study documents the coexistence of outparalogs and inparalogs, and lineage sorting of these paralogs and orthologous copies. It reveals putative recombinants that can lead to incorrect phylogenetic inferences, and presents an improved phylogenetic resolution of  Pyrus  using  LFY2int2-N .    Conclusions  Our study represents the first phylogenetic analyses based on LCNGs in  Pyrus . Ancient and recent duplications lead to a complex structure of  Adh  outparalogs and inparalogs in  Pyrus  and  Malus , resulting in neofunctionalization, nonfunctionalization and possible subfunctionalization. Among all investigated orthologs,  LFY2int2-N  is the best nuclear marker for phylogenetic reconstruction of  Pyrus  due to suitable sequence divergence and the absence of lineage sorting.

Molecular evolution of Adh and LEAFY and the phylogenetic utility of their introns in Pyrus (Rosaceae)