Monophyly of Archaeplastida supergroup and relationships among its lineages in the light of phylogenetic and phylogenomic studies. Are we close to a consensus?

Abstract

One of the key evolutionary events on the scale of the biosphere was an endosymbiosis between a heterotrophic eukaryote and a cyanobacterium, resulting in a primary plastid. Such an organelle is characteristic of three eukaryotic lineages, glaucophytes, red algae and green plants. The three groups are usually united under the common name Archaeplastida or Plantae in modern taxonomic classifications, which indicates they are considered monophyletic. The methods generally used to verify this monophyly are phylogenetic analyses. In this article we review up-to-date results of such analyses and discussed their inconsistencies. Although phylogenies of plastid genes suggest a single primary endosymbiosis, which is assumed to mean a common origin of the Archaeplastida, different phylogenetic trees based on nuclear markers show monophyly, paraphyly, polyphyly or unresolved topologies of Archaeplastida hosts. The difficulties in reconstructing host cell relationships could result from stochastic and systematic biases in data sets, including different substitution rates and patterns, gene paralogy and horizontal/endosymbiotic gene transfer into eukaryotic lineages, which attract Archaeplastida in phylogenetic trees. Based on results to date, it is neither possible to confirm nor refute alternative evolutionary scenarios to a single primary endosymbiosis. Nevertheless, if trees supporting monophyly are considered, relationships inferred among Archaeplastida lineages can be discussed. Phylogenetic analyses based on nuclear genes clearly show the earlier divergence of glaucophytes from red algae and green plants. Plastid genes suggest a more complicated history, but at least some studies are congruent with this concept. Additional research involving more representatives of glaucophytes and many understudied lineages of Eukaryota can improve inferring phylogenetic relationships related to the Archaeplastida. In addition, alternative approaches not directly dependent on phylogenetic methods should be developed.

Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life

“…Two lineages may need to be added: Microhelida, suggested to be related to Centrohelida, but with molecular phylogenetic evidence being inconclusive (121), and rappemonads, identified as a possible new deep lineage of algae in environmental surveys of plastid gene sequences, but possibly just representing a new class of haptophytes (122). Some of these lineages may be related to the SAR clade, whereas others may be related to, or even interrupt, the monophyly of the supergroup Archaeplastida (117,119,123) Second, a growing number of minor, but evolutionarily significant, lineages of flagellates, amoebae, or amoeboflagellates, referred to as microkingdoms, cannot be readily fitted into any of the supergroups (124). In addition to those mentioned (the different Hacrobia), the microkingdoms include Apusomonadida and Breviatea (recently united with Opisthokonta as a new major eukaryotic grouping dubbed Obazoa) (125), Ancyromonadida (=Planomonadida), Mantamonadida, Rigifilida, and Collodictyonida (=Diphyllatea).…”

Cymbomonas tetramitiformis - a peculiar prasinophyte with a taste for bacteria sheds light on plastid evolution

“…Before the transformation, however, the cyanobacteria were hunted and phagocytized by their prospective eukaryotic host. This initially hostile interaction triggered the evolution of Archaeplastida (Plantae), a supergroup of eukaryotes that comprises three photosynthetic lineages: glaucophytes (Glaucophyta), red algae (Rhodophyta), and green algae & higher plants (Viridiplantae) (De Clerck et al 2012; Löffelhardt 2014; Mackiewicz and Gagat 2014). …”

The Glaucophyta: the blue-green plants in a nutshell

“…Given the putative ancestral nature of both the PGW and the CLBs, glaucophytes have been considered as the "earliest diverging" lineage within the Archaeplastida, and colloquially called "living fossils" [61,62]. However, recent comparative genomics and phylogenetic studies have not conclusively resolved the branching position of the group, and the early branching history of the Archaeplastida lineages is still uncertain [8,10,18,19,63]. The euglyphid amoeba Paulinella chromatophora Lauterborn 1895 [64], a member of the Rhizaria supergroup, also harbors photosynthetic organelles with PGWs, carboxysomes and concentric thylakoids that visually resemble the glaucophyte plastids [65], but molecular phylogenetic analyses have unambiguously demonstrated the independent origin of the cyanobacterial-derived organelles of glaucophytes and P. chromatophora [66].…”

“…However, these prominent hypotheses still require conclusive answers to better understand the origin and diversification of the major groups of photosynthetic eukaryotes [19,26,27]. A major restriction when testing current working hypotheses regarding the evolution of the Archaeplastida has been the relative scarcity of information from Glaucophyta [16,30].…”