Morphology versus molecules in moss phylogeny: new insights (or controversies) from placental and vascular anatomy in Oedipodium griffithianum

Ligrone, Roberto; Duckett, Jeffrey G.

doi:10.1007/s00606-011-0496-1

Cited by 15 publications

(15 citation statements)

References 25 publications

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“…Furthermore, these species were grouped with T. pellucida, indicating Polytrichum as an apparent basal lineage; thus, the grouping characterizes the nematodontous mosses [8,36], supported by a pP of 1. This positioning is corroborated by other studies [37][38][39][40][41]. However, other authors have reported Tetraphidopsida as the basal group for Polytrichopsida [26].…”

Section: Phylogenetic Analysis: Chloroplast and Mitochondriasupporting

confidence: 81%

“…The other Polytrichaceae species included in the present analysis, Atrichum angustatum, was grouped with P. strictum to form a close clade. The topology of the tree not according to that proposed by Liu et al [38,43,44]. Atrichum angustatum, was grouped with P. strictum to form a close clade.…”

Section: Phylogenetic Analysis: Chloroplast and Mitochondriamentioning

confidence: 99%

“…Atrichum angustatum, was grouped with P. strictum to form a close clade. The topology of the tree not according to that proposed by Liu et al [38,43,44]. The presence (+) or absence (-) of each molecular character, absence of sequenced genome and molecular data disponible in GenBank (0) and pseudogene (Ψ) are shown.…”

Section: Phylogenetic Analysis: Chloroplast and Mitochondriamentioning

confidence: 99%

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Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

et al. 2018

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Abstract:In this study, the organelle genomes of Polytrichum juniperinum Hedw. and Polytrichum strictum Menzies ex Brid. (Polytrichaceae, Bryophyta) from Antarctica were sequenced and compared with the plastomes of the model moss species Physcomitrella patens Brid. The sizes of the cpDNA in P. juniperinum and P. strictum were estimated to be 55,168 and 20,183 bp, respectively; the sizes of the mtDNA were 88,021 and 58,896 bp, respectively. The genomes are very similar to each other, with the possible loss of petN in the cpDNA, which also showed some gene inversions when compared with the cpDNAs of P. patens Brid. In the mtDNA, it is possible that rps10 was lost. In contrast, Antarctic Polytrichaceae species have nad7 and orf187, without the occurrence of rearrangement events. Phylogenomic analyses of the plastid and mitochondria revealed that the majority-rule tree suggests some differences in the plastids ancestry, however, P. juniperinum and P. strictum were grouped in the same clade in chloroplast, but in mitochondria P. strictum was grouped with Atrichum angustatum (Brid.) Bruch & Schimp. This study helped us understand the evolution of plastomes and chondriosomes in the family Polytrichaceae, and suggest a hybridization event with relation to the mitochondrial data.

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Section: Phylogenetic Analysis: Chloroplast and Mitochondriasupporting

confidence: 81%

Section: Phylogenetic Analysis: Chloroplast and Mitochondriamentioning

confidence: 99%

Section: Phylogenetic Analysis: Chloroplast and Mitochondriamentioning

confidence: 99%

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Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

et al. 2018

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“…However, these relationships also remain somewhat controversial (Goffinet et al., ). For example, only one study has recovered Andreaeopsida–Andreaeobryopsida with strong support (Volkmar and Knoop, ), and Ligrone and Duckett () recently proposed a placement of Oedipodium within the peristomate moss clade based on morphology (although they did so without a formal phylogenetic analysis; note also that several lineages in the peristomate clade lack a well‐defined peristome, and may represent evolutionary reversals; Goffinet et al., ).…”

Section: Non‐peristomate Mossesmentioning

confidence: 99%

Patterns of clade support across the major lineages of moss phylogeny

Chang

Graham

2013

Cladistics

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Relationships among the major branches of moss phylogeny are understudied compared with other major land-plant groups. We addressed this by surveying 14-17 plastid genes from taxa representing the major lineages, using different phylogenetic methods (parsimony, likelihood) and codon-and gene-based data partitioning schemes (likelihood). Our phylogenetic inferences generally corroborated the best supported clades across multiple recent studies, with comparable or higher levels of clade support here. We resolved persistent ambiguities with strong to moderate support across analyses, including several early nodes in subclass Dicranidae, and relationships among other subclasses of peristomate mosses. In particular, we resolved a sister-group relationship between Bryidae and Dicranidae, between these subclasses and Timiidae, and between this entire clade and Funariidae. We consistently recovered Tetraphidopsida (a nematodontous class) as the sister group of arthrodontous mosses (Bryopsida), although with only weak support. Strongly conflicting arrangements at the base of moss phylogeny concerning Takakiopsida and Sphagnopsida, two non-peristomate moss lineages, were inferred in parsimony and likelihood analysis, but this depended on how base-frequency parameters were estimated and how data were partitioned in likelihood analysis. Relationships inferred for the remaining peristomate and non-peristomate moss clades, and their associated support values, were otherwise broadly congruent across analyses.

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“…In this case it would be most parsimonious to interpret Oedipodium as also primitively non-peristomate, even if it is sister to the Tetraphidopsida, Buxbaumia , and the arthrodontous mosses [9] rather than to all of the peristomate mosses [10]. Clearly, however, the nearly identical and highly regular development of the peristome-forming cell layers in Tetraphis , Buxbaumia and the arthrodontous mosses, and to a lesser extent the Polytrichopsida [16, 17], is likely to be homologous, even if it did not originally gave rise to what we would now call a peristome.…”

Section: Introductionmentioning

confidence: 99%

Organellar genomes of the four-toothed moss, Tetraphis pellucida

et al. 2014

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BackgroundMosses are the largest of the three extant clades of gametophyte-dominant land plants and remain poorly studied using comparative genomic methods. Major monophyletic moss lineages are characterised by different types of a spore dehiscence apparatus called the peristome, and the most important unsolved problem in higher-level moss systematics is the branching order of these peristomate clades. Organellar genome sequencing offers the potential to resolve this issue through the provision of both genomic structural characters and a greatly increased quantity of nucleotide substitution characters, as well as to elucidate organellar evolution in mosses. We publish and describe the chloroplast and mitochondrial genomes of Tetraphis pellucida, representative of the most phylogenetically intractable and morphologically isolated peristomate lineage.ResultsAssembly of reads from Illumina SBS and Pacific Biosciences RS sequencing reveals that the Tetraphis chloroplast genome comprises 127,489 bp and the mitochondrial genome 107,730 bp. Although genomic structures are similar to those of the small number of other known moss organellar genomes, the chloroplast lacks the petN gene (in common with Tortula ruralis) and the mitochondrion has only a non-functional pseudogenised remnant of nad7 (uniquely amongst known moss chondromes).ConclusionsStructural genomic features exist with the potential to be informative for phylogenetic relationships amongst the peristomate moss lineages, and thus organellar genome sequences are urgently required for exemplars from other clades. The unique genomic and morphological features of Tetraphis confirm its importance for resolving one of the major questions in land plant phylogeny and for understanding the evolution of the peristome, a likely key innovation underlying the diversity of mosses. The functional loss of nad7 from the chondrome is now shown to have occurred independently in all three bryophyte clades as well as in the early-diverging tracheophyte Huperzia squarrosa.

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Morphology versus molecules in moss phylogeny: new insights (or controversies) from placental and vascular anatomy in Oedipodium griffithianum

Cited by 15 publications

References 25 publications

Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

Patterns of clade support across the major lineages of moss phylogeny

Organellar genomes of the four-toothed moss, Tetraphis pellucida

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