Molecular phylogenetics of tribe Epidendreae with emphasis on subtribe Laeliinae (Orchidaceae)

In this project, the phylogenetic relationships of tribe Epidendreae, especially
subtribe Laeliinae were assessed by using DNA sequence data. At the tribal level, I
used data from three DNA regions, namely internal transcribed spacers of nuclear
ribosomal DNA (ITS), and plastid matK (gene and spacers) and trnL-F (intron, exon
and spacer). After individual and combined phylogenetic analysis using parsimony, it
was possible to delimit Epidendreae as an exclusively Neotropical tribe (composed
of subtribes Laeliinae, Pleurothallidinae, Ponerinae, Bletiinae and Chysinae). It is
still unclear whether Coeliinae and Calypsoeae should be also included in
Epidendreae. All Old World subtribes placed in Epidendreae in Dressler’s (1993)
system belong to different tribes of subfamily Epidendroideae. The revised subtribe
Bletiinae is composed only of Bletia, Hexalectris and Basiphyllaea. All Old World
genera previously placed in Bletiinae belong also to Old World groups. Arpophyllum
(previously Arpophyllinae) and Meiracyllium (previously Meiracyllinae) should be
included in Laeliinae. Neocogniauxia and Dilomilis belong to a clade sister to
Pleurothallidinae. Ponera, Isochilus and Helleriella (previously in the Scaphyglottis
alliance within Laeliinae) belong to a recircumscribed version of Ponerinae, which is
sister to Bletiinae. Two other datasets were collected to investigate in more detail
phylogenetic relationships within Laeliinae. The first dataset used 295 ITS sequences
to assess generic delimitation and species phylogenies. Because the levels of
variation were low, there was little resolution along the spine of the tree, and few
generic groups achieved strong internal support. However, most species groups
obtained were coincident with previous taxonomic groups at the infrageneric level,
but several genera were found to be polyphyletic, including Cattleya, Laelia,
Encyclia, and Schomburgkia. A second analysis of Laeliinae used the same three
gene regions as in the Epidendreae study. This analysis found increased support for
generic groups, confirmed polyphyly of several genera, and clarified unusual
relationships in the ITS study. It also confirmed the suspicion that some ITS
sequences were paralogous copies, although the underlying cause of the paralogy
remains uncertain. Comparison of the three studies emphasise the importance of both
taxon and character sampling in phylogenetic reconstruction.