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

Abstract

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.

Photosynthetic pathways in Bromeliaceae: phylogenetic and ecological significance of CAM and C3based on carbon isotope ratios for 1893 species

“…The last two lineages containing CAM species are Puya (now raised to the status of subfamily Puyoideae: Givnish et al, 2007Givnish et al, , 2011 and its sister group Bromelioideae. Phylogenetic relationships among the early-diverging lineages of both of these lineages are currently not well resolved, and so it cannot yet be inferred whether the last common ancestor of these two subfamilies was C 3 or CAM (Crayn et al, 2004;Schulte et al, 2009;Escobedo-Sarti et al, 2013;Givnish et al, 2014;Silvestro et al, 2014). In Puya (stem node, 10.7 Ma; crown node, 9.4 Ma), the earliest diverging lineages are found in the southern part of the present-day range of the genus in Chile, but the majority of the 220 species are Andean, and indeed the genus may have diversified in a northerly direction in the late Miocene and Pliocene, coincident with the final uplift of the Andes (Jabaily & Sytsma, 2010, 2013Schulte et al, 2010).…”

Morphoanatomy of the ovary and ovule in Bromeliaceae subfamily Tillandsioideae and its systematic relevance

“…The monophyly of Tillandsioideae has been verified with morphological and molecular data (Gilmartin & Brown, 1987;Terry & Brown, 1996;Horres et al, 2000;Crayn, Winter & Smith, 2004;Barfuss et al, 2005;Givnish et al, 2007Givnish et al, , 2011Escobedo-Sarti et al, 2013) and according to Luther (2014) (620 species), Vriesea Lindl. (266 species) and Werauhia J.R. Grant (87 species).…”

Think tank: water relations of Bromeliaceae in their evolutionary context

“…Informative analyses have been conducted to assess the impact of putative key innovations on net diversification rates, demonstrating links between the accumulation of species richness in specific lineages and characters such as epiphytism, crassulacean acid metabolism (CAM), impounding tanks, entangling seeds and occurrence in moist, fertile habitats in South American cordilleras (Givnish et al, 2014;Silvestro, Zizka & Schulte, 2014). and Greigia Regel (Schulte, Barfuss & Zizka, 2009;Givnish et al, 2011Givnish et al, , 2014Escobedo-Sarti et al, 2013). Quezada & Gianoli (2011) ostensibly recovered CAM as a driver of diversification in Bromeliaceae, but there were two fundamental problems with their analysis rendering this result highly questionable.…”

“…For example, the weight of evidence does not support a sister-group relationship between Puya Molina and a clade comprising Fascicularia Mez, Ochagavia Phil. and Greigia Regel (Schulte, Barfuss & Zizka, 2009;Givnish et al, 2011Givnish et al, , 2014Escobedo-Sarti et al, 2013). Second, the character coding fails to capture the complexity of variation in CAM within and between lineages.…”