High intraindividual variation in internal transcibed spacer sequences in Aeschynanthus (Gesneriaceae): implications for phylogenetics

Aeschynanthus (Gesneriaceae) is a large genus of tropical epiphytes that is widely distributed from the Himalayas and China throughout South-East Asia to New Guinea and the Solomon Islands. Polymerase chain reaction (PCR) consensus sequences of the internal transcribed spacers (ITS) of Aeschynanthus nuclear ribosomal DNA showed sequence polymorphism that was difficult to interpret. Cloning individual sequences from the PCR product generated a phylogenetic tree of 23 Aeschynanthus species (two clones per species). The intraindividual clone pairs varied from 0 to 5.01%. We suggest that the high intraindividual sequence variation results from low molecular drive in the ITS of Aeschynanthus. However, this study shows that, despite the variation found within some individuals, it is still possible to use these data to reconstruct phylogenetic relationships of the species, suggesting that clone variation, although persistent, does not pre-date the divergence of Aeschynanthus species. The Aeschynanthus analysis revealed two major clades with different but overlapping geographic distributions and reflected classification based on morphology (particularly seed hair type).