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- Analyses of charophyte chloroplast genomes help characterize theancestral chloroplastgenomeof land plantsPublication . Civáň, Peter; Foster, P. G.; Embley, T. M.; Séneca, A.; Cox, C. J.Despitethesignificanceoftherelationshipsbetweenembryophytesandtheircharophytealgalancestorsindecipheringtheoriginand evolutionary success of land plants, few chloroplast genomes of the charophyte algae have been reconstructed to date. Here, we present new data for three chloroplast genomes of the freshwater charophytes Klebsormidium flaccidum (Klebsormidiophyceae), Mesotaenium endlicherianum (Zygnematophyceae), and Roya anglica (Zygnematophyceae).
- The chloroplast land plant phylogeny: analyses employing better-fitting tree- and site-heterogeneous composition modelsPublication . Sousa, Filipe; Civáň, Peter; Foster, Peter G.; Cox, Cymon J.The colonization of land by descendants of charophyte green algae marked a turning point in Earth history that enabled the development of the diverse terrestrial ecosystems we see today. Early land plants diversified into three gametophyte-dominant lineages, namely the hornworts, liverworts, and mosses, collectively known as bryophytes, and a sporophyte-dominant lineage, the vascular plants, or tracheophytes. In recent decades, the prevailing view of evolutionary relationships among these four lineages has been that the tracheophytes were derived from a bryophyte ancestor. However, recent phylogenetic evidence has suggested that bryophytes are monophyletic, and thus that the first split among land plants gave rise to the lineages that today we recognize as the bryophytes and tracheophytes. We present a phylogenetic analysis of chloroplast protein-coding data that also supports the monophyly of bryophytes. This newly compiled data set consists of 83 chloroplast genes sampled across 30 taxa that include chlorophytes and charophytes, including four members of the Zygnematophyceae, and land plants, that were sampled following a balanced representation of the main bryophyte and tracheophyte lineages. Analyses of non-synonymous site nucleotide data and amino acid translation data result in congruent phylogenetic trees showing the monophyly of bryophytes, with the Zygnematophyceae as the charophyte group most closely related to land plants. Analyses showing that bryophytes and tracheophytes evolved separately from a common terrestrial ancestor have profound implications for the way we understand the evolution of plant life cycles on land and how we interpret the early land plant fossil record.
- Land plant molecular Phylogenetics: a review with comments on evaluating incongruence among PhylogeniesPublication . Cox, Cymon J.Land plants evolved from freshwater charophyte algal ancestors during a single transition to the terrestrial environment. The six major lineages of land plants are divided into two groups, the bryophytes (liverworts, mosses, and hornworts) and the tracheophytes (lycophytes, ferns, and seed plants), but while the tracheophytes are thought to be monophyletic, the bryophytes have typically been considered as the direct ancestors of tracheophytes and therefore an artificial, nonmonophyletic, group. Here the molecular phylogenetic evidence for relationships is reviewed and evaluated especially in-light of large genome-level studies that have been completed in the last few years. Consideration is given to how to evaluate competing hypotheses with respect to the underlying evolutionary assumptions of the models used to analyse the molecular data, and the degrees of support for particular hypotheses. It is concluded that currently the two most-favourable hypotheses are that the bryophytes are a monophyletic group, or that a lineage consisting of liverworts and mosses branched first among land plants with the hornworts the most-closely related lineage to tracheophytes. Although hitherto rarely considered, the possible monophyly of bryophytes has important implications for the morphological reconstruction of the last common ancestor of all land plants. Indeed, it might suggest that the ancestor of land plants was vascularised and had alternating generations that were more isomorphic than is found in extant taxa. The evolution of the bryophytes might then have proceeded through elaboration of the gametophyte and reduction of the sporophyte, while the opposite being true of the tracheophyte lineage.
- The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution modelsPublication . Sousa, Filipe; Civáň, Peter; Brazão, João; Foster, Peter G.; Cox, Cymon J.Congruence among analyses of plant genomic data partitions (nuclear, chloroplast and mitochondrial) is a strong indicator of accuracy in plant molecular phylogenetics. Recent analyses of both nuclear and chloroplast genome data of land plants (embryophytes) have, controversially, been shown to support monophyly of both bryophytes (mosses, liverworts, and hornworts) and tracheophytes (lycopods, ferns, and seed plants), with mosses and liverworts forming the clade Setaphyta. However, relationships inferred from mitochondria are incongruent with these results, and typically indicate paraphyly of bryophytes with liverworts alone resolved as the earliest-branching land plant group. Here, we reconstruct the mitochondrial land plant phylogeny from a newly compiled data set. When among-lineage composition heterogeneity is accounted for in analyses of codon-degenerate nucleotide and amino acid data, the clade Setaphyta is recovered with high support, and hornworts are supported as the earliest-branching lineage of land plants. These new mitochondrial analyses demonstrate partial congruence with current hypotheses based on nuclear and chloroplast genome data, and provide further incentive for revision of how plants arose on land.
- Extant diversity of bryophytes emerged from successive post-Mesozoic diversification burstsPublication . Laenen, B.; Shaw, B.; Schneider, H.; Goffinet, B.; Paradis, E.; Desamore, A.; Heinrichs, J.; Villarreal, J. C.; Gradstein, S. R.; McDaniel, S. F.; Long, D. G.; Forrest, L. L.; Hollingsworth, M. L.; Crandall-Stotler, B.; Davis, E. C.; Engel, J.; Von Konrat, M.; Cooper, E. D.; Patino, J.; Cox, C. J.; Vanderpoorten, A.; Shaw, A. J.Unraveling the macroevolutionary history of bryophytes, which arose soon after the origin of land plants but exhibit substantially lower species richness than the more recently derived angiosperms, has been challenged by the scarce fossil record. Here we demonstrate that overall estimates of net species diversification are approximately half those reported in ferns and similar to 30% those described for angiosperms. Nevertheless, statistical rate analyses on time-calibrated large-scale phylogenies reveal that mosses and liverworts underwent bursts of diversification since the mid-Mesozoic. The diversification rates further increase in specific lineages towards the Cenozoic to reach, in the most recently derived lineages, values that are comparable to those reported in angiosperms. This suggests that low diversification rates do not fully account for current patterns of bryophyte species richness, and we hypothesize that, as in gymnosperms, the low extant bryophyte species richness also results from massive extinctions.