The ability to sequence DNA has lead to a refinement of orchid classification (and other groups). This has occurred in the same time frame as the shift in cladistic theories from phenetic to parsimony algorithms for phylogenetic analyses. Phenetic analysis groups organisms based on overall similarity while parsimony analysis forms groups based on shared evolved characteristics. While changes in classifications get much attention in journals, DNA analyses often confirm traditional classification schemes.
Traditional classification schemes were phenetic in nature with more weight given to sexual characters. This approach resulted in some classification schemes that inferred false evolutionary relationships. Current taxonomic thinking favors phylogenetic based classifications. However a phylogeny is not a classification and the application of rank levels (family, tribe, genus, etc.) to monophyletic groups is still subjective. Since a classification scheme is an end-user tool for plant identification, morphology-based application of ranks is preferred.
The following three examples of changes in orchid classification prompted by DNA analyses demonstrate the vulnerability of morphology-only based classification to convergent evolution. These examples involve homoplasy in floral morphology.
Laelia was a genus with disjunct populations in Mexico and Brazil. These populations are clearly members of the same subtribe and were placed in the same genus of the basis of pollinia number (8). An analysis of nrDNA sequences found that there are many other genera in the subtribe more closely related to the Brazilian laelias than to the Mexican laelias. Therefore the Brazilian laelias have been placed in a new genus Hadrolaelia. This was no surprise to horticulturalist that already knew that the two populations responded differently to culture.
In the genus Oncidium the pollinator is attracted by deception. The orchid flowers mimic Malpigiaceae flowers that grow sympatricly. An analysis of five DNA regions in the nuclear and plastid genomes show this genus as currently delimited is not monophyletic. The plastic floral form is pollinator driven convergent evolution. Reclassification of this large genus is ongoing based on a new understanding of mimicry and plasticity of flower morphology.
Species in the genus Vanilla have flowers that resemble the Epidendriod floral form but have soft mealy pollen instead of pollinia. The placement of this genus with the higher Epidendroideae was accepted until DNA provided new information. An analysis of rbcL sequences places Vanilla in a clade with other more primitive orchids that also have soft mealy pollen. This discovery has lead to the establishment of a new subfamily Vanilloideae.
These examples show that a taxonomist does not intuitively know which morphological characters are homoplasious. The use of molecular data helps remove some of the subjectivity of character state assignment. Holomorphology is a new approach that uses total evidence by combining characters from morphology, anatomy, chemistry, and DNA as the best estimate of evolution.