A multi-locus analysis of phylogenetic relationships within grass subfamily Pooideae (Poaceae) inferred from sequences of nuclear single copy gene regions compared with plastid DNA

Hochbach, Anne; Schneider, Julia; Röser, Martin

doi:10.1016/j.ympev.2015.03.010

Cited by 35 publications

(55 citation statements)

References 72 publications

(181 reference statements)

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“…However, based on our data, but also previously published chloroplast data [26, 35, 90], the monophyly of Triticeae was either rejected or not supported. As morphology [23] and also phylogenies based on nuclear data place Psathyrostachys at the base of Triticeae close to Hordeum ([10]; own unpublished data), we see two possibilities to explain the chloroplast phylogeny.…”

Section: Discussioncontrasting

confidence: 47%

Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

et al. 2017

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BackgroundTriticeae, the tribe of wheat grasses, harbours the cereals barley, rye and wheat and their wild relatives. Although economically important, relationships within the tribe are still not understood. We analysed the phylogeny of chloroplast lineages among nearly all monogenomic Triticeae taxa and polyploid wheat species aiming at a deeper understanding of the tribe’s evolution. We used on- and off-target reads of a target-enrichment experiment followed by Illumina sequencing.ResultsThe read data was used to assemble the plastid locus ndhF for 194 individuals and the whole chloroplast genome for 183 individuals, representing 53 Triticeae species and 15 genera. We conducted Bayesian and multispecies coalescent analyses to infer relationships and estimate divergence times of the taxa. We present the most comprehensive dated Triticeae chloroplast phylogeny and review previous hypotheses in the framework of our results. Monophyly of Triticeae chloroplasts could not be confirmed, as either Bromus or Psathyrostachys captured a chloroplast from a lineage closely related to a Bromus-Triticeae ancestor. The most recent common ancestor of Triticeae occurred approximately between ten and 19 million years ago.ConclusionsThe comparison of the chloroplast phylogeny with available nuclear data in several cases revealed incongruences indicating past hybridizations. Recent events of chloroplast capture were detected as individuals grouped apart from con-specific accessions in otherwise monopyhletic groups.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0989-9) contains supplementary material, which is available to authorized users.

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Section: Discussioncontrasting

confidence: 47%

Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

et al. 2017

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“…Study of low-copy nuclear genes is also needed, as these are biparentally and independently inherited and can be used to characterize reticulation within lineages. Low-copy nuclear genes have been explored in taxa of Poeae chloroplast group 1 in a few studies (Essi et al 2008, Winterfeld et al 2012, Wölk and Röser 2014, 2017, Hochbach et al 2015, Minaya et al 2015, Wölk et al 2015). …”

Section: Discussionmentioning

confidence: 99%

“…Three of the four species of Gaudinia have previously been included in molecular studies ( G. fragilis , G. coarctata T. Durand & Schinz and G. hispanica ). Two studies included two species of Gaudinia (Soreng et al 2007, Schaefer et al 2011) where they formed a clade, whereas most included only one species (Soreng and Davis 2000, Quintanar et al 2007, Bouchenak-Khelladi et al 2008, Grass Phylogeny Working Group II 2012, Hochbach et al 2015, Wölk and Röser 2017). In all these phylogenetic studies, Gaudinia is resolved in Koeleriinae clade A.…”

Section: Discussionmentioning

confidence: 99%

“…In a previous ITS tree, S. intermedia was part of a lineage including species of Koeleriinae clade B (Saarela et al 2010). In a nuclear multi-gene study (Hochbach et al 2015), S. obtusata was closely related to Limnodea arkansana (Benth.) L.H.…”

Section: Discussionmentioning

confidence: 99%

“…In a study of the phylogenetics of Pooideae based on combined nuclear regions ( Topo6 , PhyB , Acc1 ), Sesleriinae is not monophyletic (Hochbach et al 2015). Instead, Mibora is sister to Aveninae s.l.…”

Section: Discussionmentioning

confidence: 99%

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Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1)

Saarela¹,

Bull²,

Paradis³

et al. 2017

138

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Circumscriptions of and relationships among many genera and suprageneric taxa of the diverse grass tribe Poeae remain controversial. In an attempt to clarify these, we conducted phylogenetic analyses of >2400 new DNA sequences from two nuclear ribosomal regions (ITS, including internal transcribed spacers 1 and 2 and the 5.8S gene, and the 3’-end of the external transcribed spacer (ETS)) and five plastid regions (matK, trnL–trnF, atpF–atpH, psbK–psbI, psbA–rps19–trnH), and of more than 1000 new and previously published ITS sequences, focused particularly on Poeae chloroplast group 1 and including broad and increased species sampling compared to previous studies. Deep branches in the combined plastid and combined ITS+ETS trees are generally well resolved, the trees are congruent in most aspects, branch support across the trees is stronger than in trees based on only ITS and fewer plastid regions, and there is evidence of conflict between data partitions in some taxa. In plastid trees, a strongly supported clade corresponds to Poeae chloroplast group 1 and includes Agrostidinae p.p., Anthoxanthinae, Aveninae s.str., Brizinae, Koeleriinae (sometimes included in Aveninae s.l.), Phalaridinae and Torreyochloinae. In the ITS+ETS tree, a supported clade includes these same tribes as well as Sesleriinae and Scolochloinae. Aveninae s.str. and Sesleriinae are sister taxa and form a clade with Koeleriinae in the ITS+ETS tree whereas Aveninae s.str. and Koeleriinae form a clade and Sesleriinae is part of Poeae chloroplast group 2 in the plastid tree. All species of Trisetum are part of Koeleriinae, but the genus is polyphyletic. Koeleriinae is divided into two major subclades: one comprises Avellinia, Gaudinia, Koeleria, Rostraria, Trisetaria and Trisetum subg. Trisetum, and the other Calamagrostis/Deyeuxia p.p. (multiple species from Mexico to South America), Peyritschia, Leptophyllochloa, Sphenopholis, Trisetopsis and Trisetum subg. Deschampsioidea. Graphephorum, Trisetum cernuum, T. irazuense and T. macbridei fall in different clades of Koeleriinae in plastid vs. nuclear ribosomal trees, and are likely of hybrid origin. ITS and matK trees identify a third lineage of Koeleriinae corresponding to Trisetum subsect. Sibirica, and affinities of Lagurus ovatus with respect to Aveninae s.str. and Koeleriinae are incongruent in nuclear ribosomal and plastid trees, supporting recognition of Lagurus in its own subtribe. A large clade comprises taxa of Agrostidinae, Brizinae and Calothecinae, but neither Agrostidinae nor Calothecinae are monophyletic as currently circumscribed and affinities of Brizinae differ in plastid and nuclear ribosomal trees. Within this clade, one newly identified lineage comprises Calamagrostis coarctata, Dichelachne, Echinopogon (Agrostidinae p.p.) and Relchela (Calothecinae p.p.), and another comprises Chascolytrum (Calothecinae p.p.) and Deyeuxia effusa (Agrostidinae p.p.). Within Agrostidinae p.p., the type species of Deyeuxia and Calamagrostis s.str. are closely related, supporting classification of Dey...

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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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A multi-locus analysis of phylogenetic relationships within grass subfamily Pooideae (Poaceae) inferred from sequences of nuclear single copy gene regions compared with plastid DNA

Cited by 35 publications

References 72 publications

Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1)

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

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