Carlos Leopardi

A phylogeny of Bromeliaceae (Poales, Monocotyledoneae) derived from an evaluation of nine supertree methods

There are 26 phylogenetic studies for Bromeliaceae based on different sources of evidence. Despite this broad phylogenetic coverage of Bromeliaceae, however, the available phylogenetic data display a scattered sampling, with little overlap among different types of evidence. The aim of this study is to integrate the available phylogenetic information of the Bromeliaceae in one hypothesis using a supertree. To test which of them integrates best the information for Bromeliaceae, nine supertree methods were employed: Avcon, MSS, MinFlip, MMC, MRP, PhySIC_IST, Robinson–Foulds Supertree, Sfit, and SuperFine. Supertrees were compared with a reference tree, generated from the maximum likelihood (ML) analysis of a supermatrix integrated by 120 taxa of Bromeliaceae and seven cpDNA regions. In order to select which method best reconstructs the most robust phylogeny, two different sets of source trees were used: (i) those generated from the analysis of each individual DNA regions; and (ii) four selected phylogenies (from the 26 published works). We used the consensus fork index, normalized partition metric, patristic distance coefficient, and the Shimodaira–Hasegawa test to compare supertrees with the reference tree. The best performing methods were used to construct a supertree using all phylogenies of Bromeliaceae. The SuperFine method generated the best supertree. The lack of overlapping among phylogenies was the major limiting factor for the integration of the phylogenetic information of Bromeliaceae. Nonetheless, supertree methods helped in the identification of poorly sampled groups, as well as to explore levels of agreement among published phylogenetic studies for Bromeliaceae.

A Combined Evidence Phylogenetic Re-Circumscription and a Taxonomic Revision of Lophiarella (Orchidaceae: Oncidiinae)

Abstract We demonstrate, through separate and combined phylogenetic analyses of morphological characters, nucleotide sequences, and coded gaps of two DNA regions (plastid rpl32-trnL and nrDNA-ITS) using parsimony and Bayesian inference, that Lophiarella (Orchidaceae), as originally circumscribed, is polyphyletic. We re-circumscribe the genus to exclude one of the two species included in the original description and include two others, which requires two new combinations: Lophiarella splendida and Lophiarella flavovirens. As newly circumscribed, Lophiarella is strongly supported as a monophyletic assemblage within the Trichocentrum-clade, where it is sister to the (Cohniella, (Trichocentrum, Lophiaris)) clade. Lophiarella is easily diagnosable within the Trichocentrum-clade, among other characters, by the conduplicate yet rigidly fleshy-coriaceous leaves and the rigidly erect inflorescences with peduncles coated with a conspicuous, waxy film. In the context of a phylogenetic analysis, we discuss the evolution of several taxonomically, ecologically and biogeographically relevant characters, such as rostellum shape, vegetative architecture, labellum, and column structure. We also present a key to the genera of the Trichocentrum-clade and a taxonomic revision of the species of Lophiarella with keys, descriptions, nomenclature, iconography, discussion of affinities, ecological and biogeographical information, a distribution map, and full exsiccata citations.