Combined phylogenetic analysis of the subclass Marchantiidae (Marchantiophyta): towards a robustly diagnosed classification

Abstract

The most extensive combined phylogenetic analyses of the subclass Marchantiidae yet undertaken was conducted on the basis of morphological and molecular data. The morphological data comprised 126 characters and 56 species. Taxonomic sampling included 35 ingroup species with all genera and orders of Marchantiidae sampled, and 21 outgroup species with two genera of Blasiidae (Marchantiopsida), 15 species of Jungermanniopsida (the three subclasses represented) and the three genera of Haplomitriopsida. Takakia ceratophylla (Bryophyta) was employed to root the trees. Character sampling involved 92 gametophytic and 34 sporophytic traits, supplemented with ten continuous characters. Molecular data included 11 molecular markers: one nuclear ribosomal (26S), three mitochondrial genes (nad1, nad5, rps3) and seven chloroplast regions (atpB, psbT‐psbH, rbcL, ITS, rpoC1, rps4, psbA). Searches were performed under extended implied weighting, weighting the character blocks against the average homoplasy. Clade stability was assessed across three additional weighting schemes (implied weighting corrected for missing entries, standard implied weighting and equal weighting) in three datasets (molecular, morphological and combined). The contribution from different biological phases regarding node recovery and diagnosis was evaluated. Our results agree with many of the previous studies but cast doubt on some relationships, mainly at the family and interfamily level. The combined analyses underlined the fact that, by combining data, taxonomic enhancements could be achieved regarding taxon delimitation and quality of diagnosis. Support values for many clades of previous molecular studies were improved by the addition of morphological data. The long‐held assumption that morphology may render spurious or low‐quality results in this taxonomic group is challenged. The morphological trends previously proposed are re‐evaluated in light of the new phylogenetic scheme.

Wanted dead or alive (probably dead): Stem group Polytrichaceae

“…Continuous characters provide useful information and complement the phylogenetic signal of the discrete characters, improving resolution. These results suggest that studies using a total evidence approach, which incorporate both molecular and morphological data (including continuous characters), may be particularly useful for resolving phylogenetic relationships within polytrichaceous mosses, similar to the level of resolution obtained by Flores et al (2017a) with the marchantiidean liverworts.…”

Reassessing the role of morphology in bryophyte phylogenetics: Combined data improves phylogenetic inference despite character conflict

“…Nevertheless, empirical studies conducted on a broad range of taxa have suggested that morphology may still contribute to inferring phylogenetic patterns at a variety of taxonomic levels regardless of their homoplasy (Flores et al, 2017a;Gatesy and Arctander, 2000;Lee, 2009;Schneider et al, 2009;Wahlberg et al, 2005). In their analysis of vascular plants, Bremer et al (1999) showed that morphological data alone generally recover few clades with significant support values (>75).…”

“…Indeed, support values are higher in large data sets that result from the combination of molecular and morphological data (Bremer et al, 1999(Bremer et al, , 2001. In a recent study on complex thalloid liverworts, Flores et al (2017a) showed that both robustness of phylogenetic analyses and diagnoses could be improved by supplementing sequence-level data with large numbers of morphological characters. Along with the enhanced robustness and amended diagnoses, Flores et al (2017a) indicated that down-weighting morphological characters in such large matrices could increase the congruence between data types.…”

Rooting morphologically divergent taxa – slow-evolving sequence data might help

“…In this study, we revisit the phylogeny of a highly divergent group of mosses, class Polytrichopsida. We used a total evidence approach, following the example of Flores & al. (2017) wherein we supplemented the morphological matrix by adding sequence data into the analyses.…”

“…Discussions of strengths and weaknesses of different optimality criteria in phylogenetic analysis abound in the recent literature, and are beyond scope of this study. Nevertheless, we refer the reader to Flores & al. (2017), and particularly to Goloboff & al.…”