Chloroplast DNA evolution and phylogenetic relationships in Lycopersicon

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Abstract
Chloroplast DNA was purified from 12 accessions that represent most of the species diversity in the genus Lycopersicon (family Solanaceae) and from 3 closely related species in the genus Solanum. Fragment patterns produced by digestion of these DNA with 25 different restriction endonucleases were analyzed by agarose gel electrophoresis. In all 15 DNAs, a total of only 39 restriction site mutations were detected among 484 restriction sites surveyed, representing 2800 base pairs of sequence information. This low rate of base sequence change is paralleled by an extremely low rate of convergent change in restriction sites; only 1 of the 39 mutations apparently occurred independently in 2 different lineages. Parsimony analysis of shared mutations allowed the construction of a maternal phylogeny for the 15 accessions. This phylogeny is generally consistent with relationships based on morphology and crossability but provides more detailed resolution at several places. All accessions within Lycopersicon form a coherent group, with 2 of the 3 spp. of Solanum as outside reference points. Chloroplast DNA analysis places S. pennellii firmly within Lycopersion, confirming recent studies that have removed it from Solanum. Red-orange fruit color is a monophyletic trait in 3 spp. of Lycopersicon, including the cultivated tomato, L. esculentum. Analysis of 6 accessions within L. peruvianum reveals a limited amount of intraspecific polymorphism which, however, encompasses all the variations observed in L. chilense and L. chmielewskii. These latter 2 accessions may be relegated to positions within the L. peruvianum complex.