Temporal range: Mesoproterozoic–Recent
|Indian paintbrush and wild huckleberry|
Adl et al., 2005
The Archaeplastida (or Plantae sensu lato) are a major group of eukaryotes, comprising the red and green algae and the land plants, together with a small group called the glaucophytes. The plastids (chloroplasts) of all of these organisms are surrounded by two membranes, suggesting they developed directly from endosymbiotic cyanobacteria. In all other groups, plastids are surrounded by three or four membranes, suggesting they were acquired secondarily from red or green algae.
Although many studies have suggested that the Archaeplastida form a monophyletic group, a 2009 paper argues that they are in fact paraphyletic. The enrichment of novel red algal genes in a recent study demonstrates a strong signal for Plantae (Archaeplastida) monophyly and an equally strong signal of gene sharing history between the red/green algae and other lineages. This study provides insight on how rich mesophilic red algal gene data is crucial for testing controversial issues in eukaryote evolution and for understanding the complex patterns of gene inheritance in protists.
The cells of the Archaeplastida typically lack centrioles and have mitochondria with flat cristae. There is usually a cell wall including cellulose, and food is stored in the form of starch. However, these characters are also shared with other eukaryotes.[which?] The main evidence the Archaeplastida form a monophyletic group comes from genetic studies, which indicate that their plastids probably had a single origin. This evidence is disputed. Photosynthetic organisms with plastids of different origin (like brown algae, for instance) do not belong to Archaeplastida.
The archaeplastidans fall into two main evolutionary lines. The red algae are pigmented with chlorophyll a and phycobiliproteins, like most cyanobacteria. The green algae and land plants – together known as Viridiplantae (Latin for "green plants") or Chloroplastida – are pigmented with chlorophylls a and b, but lack phycobiliproteins. The glaucophytes have typical cyanobacterial pigments, and are unusual in retaining a cell wall within their plastids (called cyanelles).
The consensus in 2005, when the group consisting of the glaucophytes, red and green algae and land plants was named 'Archaeoplastida', was that it was a clade, i.e. was monophyletic. Many studies published since this date have provided evidence which is in agreement. On the other hand, other studies have suggested that the group is paraphyletic. To date, the situation appears unresolved, but a strong signal for Plantae (Archaeplastida) monophyly has been demonstrated in a recent study (with an enrichment of red algal genes). The assumption made here is that Archaeplastida is a valid clade.
Various names have been given to the group. Some authors have simply referred to the group as plants or Plantae. However, the name Plantae is ambiguous, since it has also been applied to less inclusive clades, such as Viridiplantae and embryophytes. To distinguish, the larger group is sometimes known as Plantae sensu lato ("plants in the broad sense").
To avoid ambiguity, other names have been proposed. Primoplantae, which appeared in 2004, seems to be the first new name suggested for this group.
The name Archaeplastida was proposed in 2005 by a large international group of authors (Adl et al.) who aimed to produce a classification for the eukaryotes which took into account morphology, biochemistry and phylogenetics, and which had "some stability in the near term." They rejected the use of formal taxonomic ranks in favour of a hierarchical arrangement where the clade names do not signify rank. Thus the phylum name 'Glaucophyta' and the class name 'Rhodophyceae' appear at the same level in their classification. The divisions proposed for the Archaeplastida are shown below in both tabular and diagrammatic form.
- Glaucophyta Skuja, 1954 (Glaucocystophyta Kies & Kremer, 1986) – glaucophytes
- Glaucophytes are a small group of freshwater single-celled algae. Their chloroplasts, called cyanelles, have a peptidoglycan layer, making them more similar to cyanobacteria than those of the remaining Archaeplastida.
- Rhodophyceae Thuret, 1855, emend. Rabenhorst, 1863, emend. Adl et al., 2005 (Rhodophyta Wettstein 1901) – red algae
- Chloroplastida Adl et al., 2005 (Viridiplantae Cavalier-Smith 1981; Chlorobionta Jeffrey 1982, emend. Bremer 1985, emend. Lewis and McCourt 2004; Chlorobiota Kendrick and Crane 1997)
- Chloroplastida is the term chosen by Adl et al. for the group made up of the green algae and land plants (embryophytes). Except where lost secondarily, all have chloroplasts without a peptidoglycan layer and lack phycobiliproteins.
- Chlorophyta Pascher, 1914, emend. Lewis & McCourt, 2004 – green algae (part)
- Adl et al. employ a narrow definition of the Chlorophyta; other sources include the Chlorodendrales and Prasinophytae, which may themselves be combined.
- Chlorodendrales Fritsch, 1917 – green algae (part)
- Prasinophytae Cavalier-Smith, 1998, emend. Lewis & McCourt, 2004 – green algae (part)
- Mesostigma Lauterborn, 1894, emend. McCourt in Adl et al., 2005 (Mesostigmata Turmel, Otis, and Lemieux 2002)
- Charophyta Karol et al., 2001, emend. Lewis & McCourt, 2004 (Charophyceae Smith 1938, emend. Mattox and Stewart 1984) – green algae (part) and land plants
- Charophyta sensu lato, as used by Adl et al., is a monophyletic group which is made up of some green algae, including the stoneworts (Charophyta sensu stricto), as well as the land plants (embryophytes).
- Sub-divisions other than Streptophytina (below) were not given by Adl et al.
- Streptophytina Lewis & McCourt, 2004 – stoneworts and land plants
All archaeplastidans have plastids (chloroplasts) that carry out photosynthesis and are believed to be derived from captured cyanobacteria. In glaucophytes, perhaps the most primitive members of the group, the chloroplast is called a cyanelle and shares several features with cyanobacteria, including a peptidoglycan cell wall, that are not retained in other members of the group. The resemblance of cyanelles to cyanobacteria supports the endosymbiotic theory.
The cells of most archaeplastidans have walls, commonly but not always made of cellulose.
The Archaeplastida vary widely in the degree of their cell organization, from isolated cells to filaments to colonies to multi-celled organisms. The earliest were unicellular, and many groups remain so today. Multicellularity evolved separately in several groups, including red algae, ulvophyte green algae, and in the green algae that gave rise to stoneworts and land plants.
Because the ancestral archaeplastidan is hypothesized to have acquired its chloroplasts directly by engulfing cyanobacteria, the event is known as a primary endosymbiosis (as reflected in the name chosen for the group 'Archaeplastida' i.e. 'ancient plastid'). Evidence for primary endosymbosis includes the presence of a double membrane around the chloroplasts; one membrane belonged to the bacterium, and the other to the eukaryote that captured it. Over time, many genes from the chloroplast have been transferred to the nucleus of the host cell. The presence of such genes in the nuclei of eukaryotes without chloroplasts suggests this transfer happened early in the evolution of the group.
Other eukaryotes with chloroplasts appear to have gained them by engulfing a single-celled archaeplastidan with its own bacterially-derived chloroplasts. Because these events involve endosymbiosis of cells that have their own endosymbionts, the process is called secondary endosymbiosis. The chloroplasts of such eukaryotes are typically surrounded by more than two membranes, reflecting a history of multiple engulfment. The chloroplasts of euglenids and chlorarachniophytes appear to be captured green algae, whereas those of other photosynthetic eukaryotes, such as heterokont algae, cryptophytes, haptophytes, and dinoflagellates, appear to be captured red algae.
Fossil record 
Perhaps the most ancient remains of Archaeplastida are microfossils from the Roper group in northern Australia. The structure of these single-celled fossils resembles that of modern green algae. They date to the Mesoproterozoic Era, about 1500 to 1300 Ma (million years ago). These fossils are consistent with a molecular clock study that calculated that this clade diverged about 1500 Ma. The oldest fossil that can be assigned to a specific modern group is the red alga Bangiomorpha, from 1200 Ma.
- Ball S, Colleoni C, Cenci U, Raj JN, Tirtiaux C (January 2011). "The evolution of glycogen and starch metabolism in eukaryotes gives molecular clues to understand the establishment of plastid endosymbiosis". Journal of Experimental Botany 62 (6): 1775–1801. doi:10.1093/jxb/erq411. PMID 21220783.
- Vinogradov S. N.; Fernández, I.; Hoogewijs, D.; Arredondo-Peter, R. (October 2010). "Phylogenetic Relationships of 3/3 and 2/2 Hemoglobins in Archaeplastida Genomes to Bacterial and Other Eukaryote Hemoglobins". Molecular Plant 4 (1): 42–58. doi:10.1093/mp/ssq040. PMID 20952597.
- Nozaki, H.; Maruyama, S.; Matsuzaki, M.; Nakada, T.; Kato, S.; Misawa, K. (December 2009). "Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes". Molecular Phylogenetics and Evolution 53 (3): 872–80. doi:10.1016/j.ympev.2009.08.015. PMID 19698794.
- Chan, C. X.; Yang, E. C.; Banerjee, T.; Yoon, H. S.; Martone, P. T.; Estevez, J. M.; Bhattacharya, D. (2011). "Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes". Current Biology 21 (4): 328–333. doi:10.1016/j.cub.2011.01.037. PMID 21315598.
- Parfrey. L. W.; Barbero, E.; Lasser, E; et al. (December 2006). "Evaluating support for the current classification of eukaryotic diversity". PLoS Genetics 2 (12): e220. doi:10.1371/journal.pgen.0020220. PMC 1713255. PMID 17194223.
- Kim, E; Graham, L. E. (July 2008). "EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata". In Redfield, Rosemary Jeanne. PLoS ONE 3 (7): e2621. doi:10.1371/journal.pone.0002621. PMC 2440802. PMID 18612431.
- Adl, Sina M.; et al. (2005). "The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists". Journal of Eukaryotic Microbiology 52 (5): 399–451. doi:10.1111/j.1550-7408.2005.00053.x. PMID 16248873.
- Burki, Fabien; Kamran Shalchian-Tabrizi; Marianne Minge; Åsmund Skjæveland; Sergey I. Nikolaev; Kjetill S. Jakobsen; Jan Pawlowski (2007). "Phylogenomics Reshuffles the Eukaryotic Supergroups". In Butler, Geraldine. PLoS ONE 2 (8): e790. doi:10.1371/journal.pone.0000790. PMC 1949142. PMID 17726520.
- Burki, F.; Inagaki, Y.; Brate, J.; Archibald, J. M.; Keeling, P. J.; Cavalier-Smith, T., et al. (2009). "Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates". Genome Biology and Evolution 1: 231–238. doi:10.1093/gbe/evp022. PMC 2817417. PMID 20333193.
- Cavalier-Smith, Thomas (2009). "Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree". Biology Letters 6 (3): 342–345. doi:10.1098/rsbl.2009.0948. PMC 2880060. PMID 20031978.
- Rogozin, I. B.; Basu, M. K.; Csürös, M. & Koonin, E. V. (2009). "Analysis of Rare Genomic Changes Does Not Support the Unikont–Bikont Phylogeny and Suggests Cyanobacterial Symbiosis as the Point of Primary Radiation of Eukaryotes". Genome Biology and Evolution 1: 99–113. doi:10.1093/gbe/evp011. PMC 2817406. PMID 20333181.
- T. Cavalier-Smith (1981). "Eukaryote Kingdoms: Seven or Nine?". BioSystems 14 (3–4): 461–481. doi:10.1016/0303-2647(81)90050-2. PMID 7337818.
- Bhattacharya, Debashish; Yoon, Hwan Su; Hackett, Jeremiah (2003). "Photosynthetic eukaryotes unite: endosymbiosis connects the dots". BioEssays 26 (1): 50–60. doi:10.1002/bies.10376. PMID 14696040.
- Palmer, Jeffrey D.; Soltis, Douglas E.; Chase, Mark W. (2004). "The plant tree of life: an overview and some points of view". American Journal of Botany 91 (10): 1437–1445. doi:10.3732/ajb.91.10.1437. PMID 21652302.
- Simpson, A. G. B. (2004). "Highest-level taxa within Eukaryotes". First International Phylogenetic Nomenclature Meeting. Paris, July 6–9.
- Turmel, M.; Otis, C.; Lemieux, C. (2005). "The complete chloroplast DNA sequences of the charophycean green algae Staurastrum and Zygnema reveal that the chloroplast genome underwent extensive changes during the evolution of the Zygnematales". BMC Biology 3: 22. doi:10.1186/1741-7007-3-22. PMC 1277820. PMID 16236178.
- Andersson, Jan O.; Roger, Andrew J. (2002). "A cyanobacterial gene in non-photosynthetic protists – an early chloroplast acquisition in eukaryotes?". Current Biology 12 (2): 115–119. doi:10.1016/S0960-9822(01)00649-2. PMID 11818061.
- Javaux, Emmanuelle J.; Knoll, Andrew H.; Walter, Malcolm R. (2004). "TEM evidence for eukaryotic diversity in mid-Proterozoic oceans". Geobiology 2 (3): 121–132. doi:10.1111/j.1472-4677.2004.00027.x.
- Yoon, Hwan Su; Hackett, Jeremiah D.; Ciniglia, Claudia; Pinto, Gabriele; Bhattacharya, Debashish (2004). "A molecular timeline for the origin of photosynthetic eukaryotes". Molecular Biology and Evolution 21 (5): 809–818. doi:10.1093/molbev/msh075. PMID 14963099.
- Butterfield, Nicholas J. (2000). "Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes". Paleobiology 26 (3): 386–404. doi:10.1666/0094-8373(2000)026<0386:BPNGNS>2.0.CO;2.