A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses

Pirie, Michael D.; Humphreys, Aelys M.; Galley, Chloé; Barker, Nigel P.; Verboom, G. Anthony; Orlovich, David A.; Draffin, Suzy Jane; Lloyd, Kelvin M.; Baeza, Carlos M.; Negritto, María A; Ruíz, Eduardo; Sanchez, J. Hugo Cota; Reimer, Elizabeth; Linder, H. Peter

doi:10.1016/j.ympev.2008.05.030

Cited by 66 publications

(98 citation statements)

References 48 publications

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“…We sampled globally, expanding on the existing datasets of Barker et al (2000Barker et al ( , 2003Barker et al ( , 2007, Verboom et al (2006) and Pirie et al (2008). Main obstacles to achieving complete taxon sampling were geographical inaccessibility and rarity or possible extinction of species.…”

Section: Taxon Samplingmentioning

confidence: 99%

“…Zotov, Danthonia alpina Vest, Lamprothyrsus peruvianus Hitchc., and Pseudopentameris macrantha (Schrad.) Conert) were chosen to represent the most closely related clades found in the analyses of Pirie et al (2008). Plant material was collected in the field during the austral summer of [2005][2006] and dried in silica gel.…”

Section: Taxon Samplingmentioning

confidence: 99%

“…We filled in the gaps in the datasets used by Verboom et al (2006) and Pirie et al (2008) for the non-coding regions atpB-rbcL, the rpl16 intron, trnL-trnF and protein coding regions ndhF, matK and rbcL of chloroplast DNA (cpDNA) and ITS of nuclear ribosomal DNA (nrDNA) (Appendix A). With the aim to improve resolution within the Rytidosperma clade we sampled two further non-coding cpDNA regions: trnT-trnL, which has been shown to be useful at the species level in the Danthonioideae and trnD-psbM-ycf6-trnC, which has been recommended for use at the species level based on trials on diverse plant groups (Shaw et al, 2005) (Appendix A).…”

Section: Molecular Marker Selectionmentioning

confidence: 99%

“…There is an increasing trend toward the use of nucleotide sequence data in taxonomic studies at the generic rank . Danthonioideae is no exception: a string of recent molecular phylogenetic studies have addressed generic delimitation of certain groups (Cortaderia: Barker et al, 2003; African members of the Rytidosperma clade: Verboom et al, 2006; Pentaschistis and allies: Galley and Linder, 2007) or have assessed generic limits in the subfamily as a whole (Pirie et al, 2008). However, none of these studies has provided resolution of the Rytidosperma clade that is informative enough to serve as a guideline for a generic classification.…”

Section: Introductionmentioning

confidence: 99%

“…However, none of these studies has provided resolution of the Rytidosperma clade that is informative enough to serve as a guideline for a generic classification. To complicate matters further, several studies in the Danthonioideae have revealed well supported conflict between nuclear and plastid (chloroplast) gene trees Pirie et al, 2008Pirie et al, , 2009), which has been attributed to ancient hybridisation events (Pirie et al, 2009). Here we increase both taxon and character sampling of the Australasian and South American members of the Rytidosperma s.l.…”

Section: Introductionmentioning

confidence: 99%

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A plastid tree can bring order to the chaotic generic taxonomy of Rytidosperma Steud. s.l. (Poaceae)

Humphreys¹,

Pirie²,

Linder³

2010

Molecular Phylogenetics and Evolution

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Rytidosperma s.l., wallaby grasses and allies, is in dire need of a single, unanimously accepted generic taxonomy. Motivated by the desire to establish a generic classification that complies with phylogeny, we investigated how much phylogenetic signal is contained within a plastid (cpDNA) tree, given that the nrDNA tree (ITS) was uninformative and that a phylogenetic hypothesis based on a single genome may not be reliable. We find that the plastid tree is significantly different from a morphological cladogram and show that this is the result of homoplasy in the morphological dataset. Treated individually, several morphological characters fit the plastid tree very well. Similarly, we find a good fit of the plastid tree with ecological and distribution characters and with biogeographical patterns in the Southern Hemisphere. We conclude that a significant level of the species phylogeny is resolved by the plastid tree and are confident it can form a sound basis for a reconsideration of generic limits. None of the currently recognised seven genera in the Rytidosperma clade is monophyletic. Therefore, we propose combining the segregate genera in Australasia within a broadly construed Rytidosperma, including all the species from Australia, New Guinea, New Zealand and South America.

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Section: Taxon Samplingmentioning

confidence: 99%

Section: Taxon Samplingmentioning

confidence: 99%

Section: Molecular Marker Selectionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

A plastid tree can bring order to the chaotic generic taxonomy of Rytidosperma Steud. s.l. (Poaceae)

Humphreys¹,

Pirie²,

Linder³

2010

Molecular Phylogenetics and Evolution

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Phylogenetic lineages and the role of hybridization as driving force of evolution in grass supertribe Poodae

Tkach

Schneider

Döring

et al. 2020

TAXON

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To investigate the evolutionary diversification and morphological evolution of grass supertribe Poodae (subfam. Pooideae, Poaceae) we conducted a comprehensive molecular phylogenetic analysis including representatives from most of its accepted genera. We focused on generating a DNA sequence dataset of plastid matK gene-3′trnK exon and trnL-trnF regions and nuclear ribosomal (nr) ITS1-5.8S gene-ITS2 and ETS that was taxonomically overlapping as completely as possible (altogether 257 species). The idea was to infer whether phylogenetic trees or certain clades based on plastid and nrDNA data correspond with each other or discord, revealing signatures of past hybridization. The datasets were analysed separately, in combination, by excluding taxa with discordant placements in the individual gene trees and with duplication of these taxa in a way that each duplicate has only one data partition (plastid or nrDNA). We used maximum likelihood, maximum parsimony and Bayesian approaches. Instances of severe conflicts between the phylogenetic trees derived from both datasets, some of which have been noted earlier, point to hybrid origin of several lineages such as the ABCV clade encompassing several subtribes and subordinate clades,

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Widely acclaimed but poorly named: Phylogeny and systematics of the African daisy genus Dimorphotheca (Asteraceae, Calenduleae)

Parker,

Verboom,

Ellis

et al. 2024

TAXON

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Phylogenetic relationships in the South African daisy genus Dimorphotheca have long been uncertain, with the taxonomy of the genus relying on a few morphological traits, most prominently capitulum sexual system (e.g., cypsela type) and ray colour, which may not be evolutionarily conserved. Here we present the first well‐sampled molecular phylogeny of Dimorphotheca, based on nuclear ribosomal (ITS, ETS) and plastid trnL‐trnF region DNA sequences from multiple accessions per species. Although the relationships suggested by these markers are broadly congruent, we do find some instances of incongruence which we resolve using a combined decomposition and deletion approach. Using our best estimate of phylogenetic relationships, we reconstruct the evolution of capitulum fertility and ray colour to assess the evolutionary conservatism of these traits and their taxonomic utility. We find support for the monophyly of Dimorphotheca, excluding the recently segregated Osteospermum polypterum, and our data thus support the modern, enlarged circumscription of the genus incorporating the former genus Castalis and Osteospermum sect. Acanthotheca and O. sect. Blaxium. Major subclades within Dimorphotheca are largely cohesive in terms of geographic distribution and morphological traits such as growth form and cypsela structure. While many species are resolved as monophyletic, the polyphyly of a few species suggests a need for taxonomic re‐evaluation. On the basis of both morphological and molecular data, we describe one new species, and elevate one variety to species level. A full taxonomic key to the enlarged genus is presented for the first time. Ancestral reconstructions show that capitulum sexual system and ray lamina colour are not evolutionarily conserved and that neither can therefore be used to delimit major lineages within Dimorphotheca. While our findings resolve some taxonomic problems, they also highlight the need for further species‐level taxonomic work on Dimorphotheca.

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A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses

Cited by 66 publications

References 48 publications

A plastid tree can bring order to the chaotic generic taxonomy of Rytidosperma Steud. s.l. (Poaceae)

A plastid tree can bring order to the chaotic generic taxonomy of Rytidosperma Steud. s.l. (Poaceae)

Phylogenetic lineages and the role of hybridization as driving force of evolution in grass supertribe Poodae

Widely acclaimed but poorly named: Phylogeny and systematics of the African daisy genus Dimorphotheca (Asteraceae, Calenduleae)

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