Phylogenetic Relationships of the Pseudobulbous <i>Tillandsia</i> species (Bromeliaceae) Inferred from Cladistic Analyses of ITS 2, 5.8S Ribosomal RNA Gene, and ETS Sequences

Chew, Tania; Luna, Efraín De; González, Dolores

doi:10.1600/036364410790862632

Cited by 26 publications

(22 citation statements)

References 58 publications

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“…Four subtribes are currently recognized: Schreberinae, Ligustrinae, Fraxininae and Oleinae (Wallander & Albert, 2000). The phylogenetic relationships within each subtribe are complex, with some of the recognized genera being polyphyletic (Besnard, Rubio de Casas, Christin, & Vargas, 2009;Guo et al, 2011;Hong-Wa & Besnard, 2013;Yuan, Zhang, Han, Dong, & Shang, 2010;Zedane et al, 2016) or paraphyletic (Li, Alexander, & Zhang, 2002). Furthermore, extensive incongruence between the plastid DNA (cpDNA) and nrDNA phylogeny has been reported, suggesting hybridization and/or incomplete lineage sorting within several genera (Besnard et al, 2009;Hinsinger et al, 2013;Hong-Wa & Besnard, 2013), although heterogeneous evolutionary rates might also account for biased inferences based on nrDNA (Zedane et al, 2016).…”

Section: The Oleeae Tribe As a Study Systemmentioning

confidence: 99%

Phylogenomics using low‐depth whole genome sequencing: A case study with the olive tribe

Olofsson

Cantera

Paer

et al. 2019

Molecular Ecology Resources

105

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Species trees have traditionally been inferred from a few selected markers, and genome‐wide investigations remain largely restricted to model organisms or small groups of species for which sampling of fresh material is available, leaving out most of the existing and historical species diversity. The genomes of an increasing number of species, including specimens extracted from natural history collections, are being sequenced at low depth. While these data sets are widely used to analyse organelle genomes, the nuclear fraction is generally ignored. Here we evaluate different reference‐based methods to infer phylogenies of large taxonomic groups from such data sets. Using the example of the Oleeae tribe, a worldwide‐distributed group, we build phylogenies based on single nucleotide polymorphisms (SNPs) obtained using two reference genomes (the olive and ash trees). The inferred phylogenies are overall congruent, yet present differences that might reflect the effect of distance to the reference on the amount of missing data. To limit this issue, genome complexity was reduced by using pairs of orthologous coding sequences as the reference, thus allowing us to combine SNPs obtained using two distinct references. Concatenated and coalescence trees based on these combined SNPs suggest events of incomplete lineage sorting and/or hybridization during the diversification of this large phylogenetic group. Our results show that genome‐wide phylogenetic trees can be inferred from low‐depth sequence data sets for eukaryote groups with complex genomes, and histories of reticulate evolution. This opens new avenues for large‐scale phylogenomics and biogeographical analyses covering both the extant and the historical diversity stored in museum collections.

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Section: The Oleeae Tribe As a Study Systemmentioning

confidence: 99%

Phylogenomics using low‐depth whole genome sequencing: A case study with the olive tribe

Olofsson

Cantera

Paer

et al. 2019

Molecular Ecology Resources

105

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“…Tillandsia has been studied by several specialists in the family (e.g. Gardner, , ; Grant, ; Espejo‐Serna, ; Chew et al., ). Thus, the relationships of many species have been clarified, but there are still incongruences between studies employing classical taxonomy and phylogenetic studies.…”

Section: Discussionmentioning

confidence: 99%

“…Phylogenetic analyses in Tillandsioideae have focused on overall relationships within the subfamily (Terry et al., ; Horres et al., ; Crayn et al., ; Barfuss et al., , ) or within individual genera (Chew et al., ; Gomes‐da‐Silva et al., ; Versieux et al., ; Costa et al., ). Based on molecular data, the subfamily has been divided into four lineages, treated as tribes: Catopsideae, Glomeropitcairnieae, Vrieseeae and Tillandsieae (Barfuss et al., , ); two new subtribes, Cipuropsidinae and Vrieseinae, have been described within the tribe Vrieseea (Barfuss et al., ).…”

Section: Introductionmentioning

confidence: 99%

What actually is Vriesea? A total evidence approach in a polyphyletic genus of Tillandsioideae (Bromeliaceae, Poales)

Gomes‐da‐Silva

Souza-Chies

2017

Cladistics

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The taxonomic delimitation of Vriesea is challenging because several diagnostic traits of the genus are shared with other genera in Tillandsioideae. The genus has no unique morphological features that distinguish it from other taxa. Earlier phylogenetic studies suggested a polyphyletic status of this genus, but taxon sampling was limited, and tests of congruence for morphological characters have not yet been performed. Here we used a total evidence approach and a more comprehensive Brazilian taxon sampling to help circumscribe Vriesea s.s. (the lineage that contains the type species). We concatenated morphological and molecular datasets for the first time to reconstruct phylogenetic hypotheses. We used 99 morphological characters and ~4 kb of plastid data (psbA‐trnH, trnK5′‐rps16, matK, trnL‐trnF) for 172 terminals, including nine genera of Tillandsioideae. We analysed datasets by parsimony analyses, with several weighting schemes considered for character‐state changes (equal weights and an implied weighting scheme that we used as a sensitivity analysis). The concatenated data resulted in a well‐resolved phylogenetic inference that provided strong evidence that the genus is not monophyletic as traditionally circumscribed. Given the congruence between morphological, molecular and geographical sources of data, we separated Vriesea into distinct lineages, and proposed a new circumscription that includes only species of Vriesea s.s. found in the Chacoan and Parana subregions.

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“…The first studies were based on single markers and, until recent years, all bromeliad phylogenetic analyses were based on the plastid genome (see Table 1). Only in the last years, nuclear sequence markers, mainly the single copy nuclear gene PHYC, have been added to the phylogenetic analyses Chew, De Luna & Gonz alez, 2010;Jabaily & Sytsma, 2010;Sass & Specht, 2010;Versieux et al, 2012;Krapp et al, 2014;Louzada et al, 2014;Silvestro et al, 2014). Terry et al, 1997a;Horres et al, 2000Horres et al, , 2007Crayn et al, 2004;Schulte et al, 2005Schulte et al, , 2009Sousa et al, 2007;Jabaily & Sytsma, 2010;Sass & Specht, 2010;Krapp et al, 2014).…”

Section: Evolution and Phylogeneticsmentioning

confidence: 99%

Advances in and perspectives on evolution in Bromeliaceae

et al. 2016

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Phylogenetic Relationships of the Pseudobulbous Tillandsia species (Bromeliaceae) Inferred from Cladistic Analyses of ITS 2, 5.8S Ribosomal RNA Gene, and ETS Sequences

Cited by 26 publications

References 58 publications

Phylogenomics using low‐depth whole genome sequencing: A case study with the olive tribe

Phylogenomics using low‐depth whole genome sequencing: A case study with the olive tribe

What actually is Vriesea? A total evidence approach in a polyphyletic genus of Tillandsioideae (Bromeliaceae, Poales)

Advances in and perspectives on evolution in Bromeliaceae

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