Defying death: incorporating fossils into the phylogeny of the complex thalloid liverworts (Marchantiidae, Marchantiophyta) confirms high order clades but reveals discrepancies in family‐level relationships

Flores, Jorge R.; Bippus, Alexander C.; Suárez, Guillermo M.; Hyvönen, Jaakko

doi:10.1111/cla.12442

Cited by 14 publications

(44 citation statements)

References 88 publications

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“…Aspects such as forms of statistical likelihood used as an optimality criteria in model-based analyses, how sequence alignment is performed, modelling of compositional heterogeneity and substitutional saturation of synonymous sites in protein coding regions (e.g., De Sousa et al 2018) all have the potential to greatly affect results. Equally important is the incorporation of fossils in analyses as recently pointed out for example by Lehtonen et al (2020) and Flores et al (2021), showing how even poorly known fossils can enhance the accuracy of phylogenetic analyses.…”

Section: Future Workmentioning

confidence: 99%

The diversity of the Polytrichopsida—a review

Bell

Kariyawasam

Flores

et al. 2021

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The class Polytrichopsida are a phylogenetically isolated moss lineage of around 200 species. The nematodontous peristome found in most species has a fundamentally different structure from the arthrodontous peristome of the Bryopsida and may be independently evolved from an ancestral type of spore dehiscence apparatus. Within the class generic circumscriptions and relationships are now fairly confidently resolved and more or less congruent with the most developed pre-molecular taxonomy. Drawing on previously published datasets, we conducted a phylogenetic analysis of a novel matrix of terminals representing diversity across the Polytrichopsida. The class comprises 17 extant genera and two known only from fossils. Most of these are numerically small, the most notable exception being Pogonatum with over 50 species. Considering current phylogenetic hypotheses in the light of morphology and global distributions, Alophosia, Bartramiopsis and Lyellia, the earliest diverging lineages according to recent phylogenetic analyses, appear to be relicts, with scattered and disjunct distributions. All of these genera lack peristomes, while all later originating lineages have nematodontous peristomes developed from bundles of “u-shaped” whole cells. The genus Dawsonia, sister to all other peristomate taxa, differs in its unique peristome composed of long, bristle-like teeth arranged in concentric layers. Many members of some traditional genera found to be polyphyletic in recent studies are part of a southern hemisphere grade and only distantly related to the superficially similar northern hemisphere species with which they were historically classified. A large apical clade including eight genera accounts for the majority of the diversity, these being most speciose in northern temperate regions or the Asian tropics. Many of the Polytrichopsida are relatively large plants with well-developed vasculature and a “pseudo-mesophyll” capable of supporting relatively high rates of photosynthesis in moist, well-illuminated environments. With ten described species, Cenozoic fossils of Polytrichopsida are fairly numerous compared with other mosses. Records of fossils from older sediments have been rare, but recently several well-preserved fossils of Polytrichopsida have been found, most of which still await detailed description.

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Section: Future Workmentioning

confidence: 99%

The diversity of the Polytrichopsida—a review

Bell

Kariyawasam

Flores

et al. 2021

BDE

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“…Carr from Marchantiales to Sphaerocarpales (Forrest et al, 2015); and (3) treatment of Bucegia Radian and Preissia Corda as synonyms of Marchantia L. and transfer of Exormothecaceae to Corsiniaceae (Long et al, 2016). In recent comprehensive analyses of the Marchantiopsida based on 11 genes, 128 morphological characters and four Marchantiopsida fossils, Flores et al (2018Flores et al ( , 2021 proposed the reduction of Lunulariales and introduction of several broadly defined families, including Corsiniaceae, Monocleaceae, Ricciaceae and Targioniaceae. Although molecular analyses based on genetic markers have successfully delimited subclasses and orders within Marchantiopsida (Flores et al, 2018(Flores et al, , 2021Villarreal et al, 2016), most deep nodes within Marchantiales remain ambiguous or, at best, have low support values.…”

Section: Introductionmentioning

confidence: 99%

New insights into the phylogeny of the complex thalloid liverworts (Marchantiopsida) based on chloroplast genomes

et al. 2022

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Marchantiopsida (complex thalloid liverworts) are one of the earliest lineages of embryophytes (land plants), and well‐known for their air pores and chambers, pegged rhizoids, and absence of organellular RNA editing sites. Despite their importance to an understanding of early embryophyte evolution, many key nodes within this class remain poorly resolved, owing to the paucity of genetic loci previously available for phylogenetic analyses. Here, we sequenced 54 plastomes, representing 28 genera, nearly all families, and all orders of Marchantiopsida. Based on these plastomes, we present a hypothesis of deep relationships within the class, and make the first investigations of gene contents and synteny. Overall, the Marchantiopsida plastomes were well‐conserved, with the exception of the genus Cyathodium that has plastomes with higher GC content, fewer single sequence repeats (SSRs), and more structural variations, implying that this genus might possess RNA editing sites. Abundant repetitive elements and six highly divergent regions were identified as suitable for future infrafamilial taxonomic studies. The phylogenetic topology of Sphaerocarpales, Neohodgsoniales and Blasiales within Marchantiopsida was essentially congruent with previous studies but generally we obtained higher support values. Based on molecular evidence and previous morphological studies, we include Lunulariales in Marchantiales and suggest the retention of narrowed delimitation of monotypic families. The phylogenetic relationships within Marchantiales were better resolved, and 13 monophyletic families were recovered. Our analyses confirmed that the loss of intron 2 of ycf3 is a synapomorphy of Marchantiidae. Finally, we propose a new genus, Asterellopsis (Aytoniaceae), and present an updated classification of Marchantiopsida. The highly supported phylogenetic backbone provided here establishes a framework for future comparative and evolutionary studies of the complex thalloid liverworts.

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“…Although standard implied weighting has been employed to analyze paleontological data (e.g., Gernandt et al 2016), down-weighting characters against their homoplasy while extrapolating such homoplasy to missing entries has less frequently been assessed regarding taxon instability (e.g., Flores et al 2020). Overall, the evaluations carried out here suggest that analyzing the data under extended implied weighting—especially taking into account the number of missing entries—is a desirable strategy to improve the stability of taxa across optimal trees and their potential impact on branch support.…”

Section: Discussionmentioning

confidence: 99%

Exploring the impact of unstable terminals on branch support values in paleontological data

2021

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Recent studies have acknowledged the many benefits of including fossils in phylogenetic inference (e.g., reducing long-branch attraction). However, unstable taxa are known to be problematic, as they can reduce either the resolution of the strict consensus or branch support. In this study, we evaluate whether unstable taxa that reduce consensus resolution affect support values, and the extent of such impact, under equal and extended implied weighting. Two sets of analyses were conducted across 30 morphological datasets to evaluate complementary aspects. The first focused on the analytical conditions incrementing the terminal instability, while the second assessed whether pruning wildcards improves support. Changes in support were compared with the “number of nodes collapsed by unstable terminals,” their “distance to the root,” the “proportion of missing data in a dataset,” and the “proportion of sampled characters.” Our results indicate that the proportion of missing entries distributed among closely related taxa (for a given character) might be as detrimental for stability as those distributed among characters (for a given terminal). Unstable terminals that (1) collapse few nodes or (2) are closely located to the root node have more influence on the estimated support values. Weighting characters according to their extra steps while assuming that missing entries contribute to their homoplasy reduced the instability of wildcards. Our results suggest that increasing character sampling and using extended implied weighting decreases the impact of wildcard terminals. This study provides insights for designing future research dealing with unstable terminals, a typical problem of paleontological data.

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Defying death: incorporating fossils into the phylogeny of the complex thalloid liverworts (Marchantiidae, Marchantiophyta) confirms high order clades but reveals discrepancies in family‐level relationships

Cited by 14 publications

References 88 publications

The diversity of the Polytrichopsida—a review

The diversity of the Polytrichopsida—a review

New insights into the phylogeny of the complex thalloid liverworts (Marchantiopsida) based on chloroplast genomes

Exploring the impact of unstable terminals on branch support values in paleontological data

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