KINGDOM RHIZARIAE (Cavalier-Smith 2002)
| EUKARYOTA>CHROMALVEOLATA>RHIZARIAE |
KINGDOM RHIZARIAE LINKS
| Rhizaria (ri-ZA-ree-a) is derived from the Greek word for root (riza -ρίζα). The reference is to the fine, filose, and often branching pseudopodia in this group. |
| INTRODUCTION TO THE RHIZARIAE The rhizarians include an apparent eclectic mix of taxa which were defined by molecular means (e.g. Nikolaev et al. 2004) and seem to have filose rhizopods as a structural synapomorphy. A biochemical synapomorphy for many of the rhizarians includes one or two amino acid insertions between the monomer-monomer junction of polyubiquitin (Bass et al. 2005). The creation of this group brought together many of the sisterless taxa listed in Patterson (1999) and has been confirmed by several supergroup analyses (Nikolaev et al. 2004, Baldauf 2003a, and Keeling 2004). Monophyly of the rhizarians has been confirmed using genomic analyses (Burki et al. 2010, Sierra et al. 2013). Parfrey et al. (2006), Burki et al. (2007, 2008, 2009) and Hackett et al. (2007) provide convincing evidence that the Rhizariae are associated with the Chromalveolata in a group that Baldauf (2008) calls the RAS group (Rhizariae-Alveolatae-Stramenopilae group), and that Cavalier-Smith (2010) calls Chromista. Thus, the RAS/Chromista group effectively unites all of the chlorophyll a and c taxa together in one large group. |
| TABLE 1. The following table presents six characters and their states as they are distributed throughout the four phyla of the rhizarians. | ||||||
| PHYLA | PHOTOSYNTHESIS | PSEUDOPODIA | CELL COVERING | FLAGELLA | MINERALIZATION | POLYUBIQUITIN INSERTIONS |
| CERCOZOA | one group only; most are not | filopods or axopods | naked but with tests of silicaceous scales, organic test, etc. | most with 2 heterodynamic flagella | some with silicaceous internal skeleton and mineralized axopods; most do not | 2 |
| ENDOMYXA | no | reticulopods; many are plasmodial or intracellular parasites | naked; test, cyst or spore organic | poorly known; some with 2 heterodynamic flagella | no | 1 |
| FORAMINIFERA | some with symbionts | reticulopods- anastomosing web | naked | gametes with 2 heterodynamic flagella | calcium carbonate internal test that is perforated | 1 |
| RADIOLARIA | some with symbionts | axopods | naked | zoospores with 2 heterodynamic flagella | internal skeleton of strontium sulfate, silica, or organic material; a few without | 0 |
| Though membership in this kingdom has been established for many taxa, the determination of the particular groups of rhizarians has been a struggle. Much of the work on assembling the rhizarian tree used SSU rRNA (Cavalier-Smith and Chao 2003, Nikolaev et al. 2004), SSU rDNA (e.g. Chantangsi and Leander 2010, Groussin et al. 2011, Krabberod et al. 2011, Pawlowski and Burki 2009, Pawlowski and Holzmann 2002, Parfrey et al. 2010), certain proteins like actin (Groussin et al. 2011, Nikolaev et al. 2004) RBP1 (Groussin et al. 2011, Longet and Pawlowski 2007), and α-tubulin (Groussin et al. 2011). These studies supported the monophyly of the Rhizariae and also supported the monophyly of some of the groups within the kingdom. Nevertheless, relationships between the four groups of rhizarians still are quite problematic (see Table 1). SSU-based phylogenies have not satisfactorily resolved groups that, in this system, we refer to as Cercozoa. For example, Gromia, a large unicell with an organic test and retuculate filopods, has been placed in the Cercozoa, Endomyxa, and as a basal group of the Retaria (Foraminifera + Radiolaria, see Figure 1). Burki et al. (2002) suggest that Gromia is basal in the Cercozoa. To make matters more chaotic, Gromia was considered to be a primitive foraminiferan in older taxonomic systems (e.g. Grell 1973). Patterson (1999), which summarized the haphazard understanding of many eukayotic groups, separated the traditional radiolarian higher taxa into three groups: Phaeodaria, Polycystina, and Acantharia. Cavalier-Smith (2002) recognized that the Phaeodaria was more closely related to the cercozoans and subsumed into that group. He also recognized the association of the Foraminifera and Polycystina+Acantharia (Radiolaria, sensu stricto) and named that clade Retaria. The relationship of taxa within the retaria seems to hold in analyses with broad taxonomic sampling (e.g. Ishitani et al. 2011, Moreira et al. 2006, Takahashi et al. 2004, Yuasa et al. 2005, and Kunimoto et al. 2006). We use a modified version of the system created by Cavalier-Smith (2002), Cavalier-Smith and Chao (2003), and Bass et al. (2009). |
FIGURE 1. Two different topologies for the higher taxa of the radiolarians. Both topologies support the Retaria hypothesis. The left side of the cladogram follows Cavalier-Smith (2002), Cavalier-Smith and Chao (2003), and Bass et al. (2009) in which Endomyxa + Cercozoa is monophyletic while Sierra et al. (2013) suggest that the retarians, cercozoans, and endomyxans emerge as a set of nested clades. Click on the phyla below to read descriptions of the phyla and discussions of problems regarding monophyly within the respective taxa.
| PHYLA OF THE RHIZARIAE |
ENDOMYXA (Cavalier-Smith 2002)- CERCOZOA (Cavalier-Smith and Chao 2003)
FORAMINIFERA (d’Orbigny 1826)
RADIOLARIA (Müller 1858 em. Cavalier-Smith 1993)
| LITERATURE CITED Baldauf, S. L. 2003a. The deep roots of eukaryotes. Science. 300 (5626): 1701-1703. Baldauf, S. 2008. An overview of the phylogeny and diversity of eukaryotes. Journal of Systematics and Evolution. 46(3): 263-273. Bass, D., D. Moreira, P. Lopez-Garcia, S. Polet, E. E. Chao, S. von der Heyden, J. Pawlowski, and T. Cavalier-Smith. 2005. Polyubiquitin insertions and the phylogeny of Cercozoa and Rhizaria. Protist. 156:149-161. Bass, D., E. E.-Y. Chao, S. Nikolaev, A. Yabuki, K. Ishida, C. Berney, U. Pakzad, C. Wylezich, and T. Cavalier-Smith. 2009. Phylogeny of novel naked filose and reticulose Cercozoa: Granofilosea cl. n. and Proteomyxidea revised. Protist. 160: 75-109. Burki, F., C. Berney, and J. Pawlowski. 2002. Phylogenetic position of Gromia oviformis Dujardin inferred from nuclear-encoded small subunit ribosomal DNA. Protist. 153: 251-260. Burki, F., K. Shalchian-Tabrizi, M. Minge, A. Skaeveland, S. I. Nikolaev, K. S. Jakobsen, and J. Pawlowski. 2007. Phylogenomics reshuffles the eukaryotic supergroups. PLoS ONE. 8:790-795. Burki, F., K. Shalchian-Tabrizi, and J. Pawlowski. 2008. Phylogenomics reveals a new ‘megagroup’ including most photosynthetic eukaryotes. Biology Letters. 4: 366-369. Burki, F., Y. Inagaki, J. Brate, J. M. Archibald, P. J. Keeling, T. Cavalier-Smith, M. Sakaguchi, T. Hashimoto, A. Horak, S. Kumar, D. Klaveness, K. S. Jakobsen, J. Pawlowski, and K. Shalchian-Tabrizi. 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. Burki, F., A. Kudryavtsev, M. V. Matz, G. V. Aglyamova, S. Bulman, M. Fiers, P. J. Keeling, J. Pawlowski. 2010. Evolution of Rhizaria: new insights from phylogenomics analysis of uncultivated protists. BMC Evolutionary Biology. 10.377 http://www,biomedcentral.com/1471-2148/10/377 Cavalier-Smith, T. 2002. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. International Journal of Systematics and Evolutionary Microbiology. 52: 297-354. Cavalier-Smith, T. and E. E. Chao. 2003a. Phylogeny and classification of phylum Cercozoa (Protozoa). Protist. 154: 341-358. Chantangsi, C., M. Hoppenrath, B. S. Leander. 2010. Evolutionary relationships among marine cercozoans as inferred from combined SSU and LSU rDNA sequences and polyubiquitin insertions. Molecular Phylogenetics and Evolution. 57: 518-527. d’Orbigny, A. 1826. Tableau méthodique de la classe des Céphalopodes. Annales des Sciences Naturelles. 7: 245-314. Grell, K. G. 1973. Protozoology. Springer-Verlag. New York. Groussin, M., J. Pawlowski, and Z. Yang. 2011. Bayesian relaxed clock estimation of divergence times in foraminifera. Molecular Phylogenetics and Evolution. 61: 157-166. Hackett, J. D., H. S. Yoon, S. Li, A. Reyes-Prieto, S. E. Rummele, and D. Bhattacharya. 2007. Phylogenomic analysis supports the monoplyly of Cryptophytes and Haptophytes and the association of Rhizaria with Chromalveolates. Molecular Biology and Evolution. 24(8): 1702-1713. Hampl, V., L. Hug, J. W. Leigh, J. B. Dacks, B. F. Lang, A. G. B. Simpson, and A. J. Roger. 2009. Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”. Proceedings of the National Academy of Science. 106(10): 3859-3864. Ishitani, Y., S. A. Ishikawa, Y. Inagaki, M. Tsuchiya, K. Takahashi, and K. Takishita. 2011. Multigene phylogenetic analyses including diverse radiolarian species support the “Retaria” hypothesis – The sister relationship of Radiolaria and Foraminifera. Marine Micropaleontology. 81: 32-42. Keeling, P. J. 2004. The diversity and evolutionary history of plastids and their hosts. American Journal of Botany. 91(10): 1481-1493. Krabberod, A. K., J. Brate, J. K. Dolven, R. F. Ose, D. Klaveness, T. Kristensen, K. R. Bjorklund, K. Shalchian-Tabrizi. 2011. Radiolaria divided into Polycystina and Spasmaria in combined 18S and 28S rDNA phylogeny. PLoS ONE. 6(8): e23526. doi:10.1371/journal.pone.0023526 Kunimoto, Y., I. Sarashina, M. Iijima, K. Endo, K. Sashida. 2006. Molecular phylogeny of acantharian and polycystine radiolarians based on ribosomal DNA sequences, and some comparisons with data from the fossil record. European Journal of Protistology. 42: 143-153. Longet, D., and J. Pawlowski. 2007. Higher-level phylogeny of Foraminifera inferred from the RNA polymerase II (RPB1) gene. European Journal of Protistology. 43: 171-177. Moreira, D., S. Heyden, D. Bass, P. Lopez-Garcia, E. Chao, T. Cavalier-Smith. 2007. Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria, and Excavata. Molecular Phylogenetics and Evolution. 44: 255-266. Müller, J. 1858. Über die Thalassicollen, Polycystinen und Acanthometren des Mittelmeeres. Konigliche Preussische Akademie der Wissenschaften zu Berlin Abhandlungen. Jahre 1858: 1-62 . Nikolaev, S. I., A. P. Milnikov, C. Berney, J. Fahrni, J. Pawlowsli, V. V. Aleshin, and N. B. Petrov. 2004. Molecular phylogenetic analysis places Percolomonas cosmopolitus within Heterolobosea: evolutionary implications. Journal of Evolutionary Microbiology. 51(5): 575-581. Parfrey, L. W., E. Barbero, E. Lasser, M. Dunthorn, D. Bhattacharya, D. J. Patterson, and L.A. Katz. 2006. Evaluating support for the current classification of eukaryotic diversity. PLOS Genetics. 2:2062-2072. Parfrey, L. W., J. Grant, Y. I. Tekle, E. Lasek-Nesselquist, H. G. Morrison, M. L. Sogin, D. J. Patterson, and L. A. Katz. 2010. Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life. Systematic Biology. 59(5): 518-533. Patterson, D. J. 1999. The diversity of eukaryotes. American Naturalist. 154 (Suppl.): S96–S124. Pawlowski, J. and M. Holzmann. 2002. Molecular phylogeny of Foraminifera—a review: European Journal of Protistology. 38: 1–10. Pawlowski, J. and F. Burki. 2009. Untangling the phylogeny of amoeboid protists. Journal of Eukaryote Microbiology. 56(1): 16-25. Sierra, R., M. V. Matz, G. Aglyamova, L. Pillet, J. Decelle, F. Not, C. de Vargas, and J. Pawlowski. 2013. Deep relationships of Rhizaria revealed by phylogenetics: A farewell to Haeckel’s Radiolaria. Molecular Phylogenetics and Evolution. 67: 53-59. Takahashi, O., T. Yuasa, D. Honda, and S. Mayama. Molecular phylogeny of solitary shell-bearing Polycystinea (Radiolaria). Review de Micropaleontologie. 47: 111-118. Yuasa, T. O. Takahashi, D. Honda, S. Mayama. 2005. Phylogenetic analyses of the polycystine Radiolaria based on the 18S rDNA sequences of the Spumellarida and Nassellarida. European Journal of Protistology. 41: 287-298. |
| By Jack R. Holt. Last revised: 03/07/2014 |
