Species-level phylogenetics of large genera: Prospects of studying coevolution and polyploidy

The problems facing workers trying to produce phylogenetic hypotheses of large genera are usually surmountable if the group in question is well studied previously. The major problems faced in plants are caused by hybridisation between species and low levels of variability in the standard phylogenetic markers. Many researchers use plastid DNA and the internal transcribed spacers of nuclear ribosomal DNA (nrDNA), neither of which alone is suitable for the detection of hybrids, the former because it is inherited through the maternal lineage and the latter because it is subject to concerted evolution via gene conversion. Sequencing low copy, protein coding, regions is a good alternative, but these are often neither easily amplified nor suitable for other reasons. Low levels of variability in the standard markers can alternatively be dealt with by using markers such as amplified fragment length polymorphisms (AFLPs). Some prospects, problems and solutions will be discussed and exemplified with work on figs (Ficus, Moraceae) and tobacco (Nicotiana, Solanaceae).