Phaeodarea

Phaeodarea
	"Phaeodaria" from Ernst Haeckel's Kunstformen der Natur, 1904
Scientific classification
Domain:	Eukaryota
Clade:	Diaphoretickes
Clade:	SAR
Phylum:	Cercozoa
Class:	Thecofilosea
Subclass:	Phaeodarea; Haeckel 1879
Orders
	Eodarida Phaeogymnocellida; Phaeocystida; ; Opaloconchida Phaeocalpida; Phaeoconchida; Phaeodendrida; Phaeogromida; Phaeosphaerida; ;
Synonyms
	Phaeodaria Haeckel 1879; Tripylea Hertwig 1879

Phaeodarea, or Phaeodaria, is a group of amoeboid cercozoan organisms. They are traditionally considered radiolarians,[1] but in molecular trees do not appear to be close relatives of the other groups, and are instead placed among the Cercozoa.[2] They are distinguished by the structure of their central capsule and by the presence of a phaeodium, an aggregate of waste particles within the cell.

The term "Radiozoa" has been used to refer to radiolaria when Phaeodarea is explicitly excluded.[3]

Phaeodarea produce hollow skeletons composed of amorphous silica and organic material, which rarely fossilize. The endoplasm is divided by a cape with three openings, of which one gives rise to feeding pseudopods, and the others let through bundles of microtubules that support the axopods. Unlike true radiolarians, there are no cross-bridges between them. They also lack symbiotic algae, generally living below the photic zone, and do not produce any strontium sulphate.

Taxonomy

Phylogeny

Through phylogenetic analyses it has been discovered that Phaeodarea is a monophyletic clade, but the historical orders and families comprising it aren't. Instead, the clade consists of 11 subclades defined by morphological and phylogenetic values that do not correspond with the traditional orders and families:[4]

	clade A

	clade B

clade C

	clade D

	clade E

clade F

	clade G

	clade H

Phaeoconchida

clade I

	clade J

	clade K

Despite this, the current taxonomy by Cavalier-Smith maintains the original classification of suborders[5] divided between two new orders:[6][7]

Eodarida, containing phaeodarea with no silica skeleton or with a skeleton made of simple radiating spicules. Contains two suborders: Phaeogymnocellina and Phaeocystina.
Opaloconchida, containing phaeodarea with a highly perforated, shell-like opaline silica skeleton. Contains the remaining five suborders: Phaeosphaeria, Phaeocalpia, Phaeogromia, Phaeoconchia and Phaeodendria.

Modern classification

The modern classification is the following, with the subclass containing a total of 2 orders, 7 suborders,[6][7] 16 families and 39 genera.[8]

Order Eodarida Cavalier-Smith 2012
- Suborder Phaeogymnocellina (=Phaeogymnocellida) Cachon & Cachon 1985
  - Family Phaeosphaeridae Cachon-Enjumet 1961 – Phaeopyla, Phaeodactylis, Phaeosphaera
  - Family Phaeodinidae Cachon-Enjumet 1961 – Phaeodina
  - Family Atlanticellidae Cachon-Enjumet 1961 – Gymnocelia, Halocelia, Lobocelia, Miracelia, Planktonetta
- Suborder Phaeocystina (=Phaeocystida) Haeckel 1887
  - Family Aulacanthidae Haeckel 1887 – Aulacantha
  - Family Astracanthidae Haeckel 1887 – Astracantha, Castanella, Castanissa
Order Opaloconchida Cavalier-Smith 2012
- Suborder Phaeosphaeria (=Phaeocystida) Haeckel 1887
  - Family Aulosphaeridae Haeckel 1887 – Aulosphaera, Aularia, Aulotractus
  - Family Cannosphaeridae Haeckel 1887 – Coelocantha
  - Family Sagosphaeridae Haeckel 1887 – Sagenoarium, Sagenoscena, Sagoscena
- Suborder Phaeocalpia (=Phaeocalpida) Haeckel 1887
  - Family Castanellidae Haecker 1906 – Castanea
  - Family Circoporidae Haeckel 1887 – Circoporus, Circospathis, Haeckeliana
  - Family Tuscaroridae Haeckel 1887 – Tuscarora, Tuscarilla, Tuscaretta
  - Family Porospathidae Borgert 1900 – Porospathis
  - Family Polypyramidae Reschetnjak 1966 – Polypyramis
- Suborder Phaeogromia (=Phaeogromida) Haeckel 1887
  - Family Challengeridae Murray 1886 – Challengeria, Challengeron
  - Family Medusettiidae Haeckel 1887 – Euphysetta, Gazelletta, Medusetta
  - Family Lirellidae Loeblich & Tappan 1961 – Borgertella, Lirella
- Suborder Phaeoconchia (=Phaeoconchida) Haeckel 1887
  - Family Concharidae Haeckel 1887 – Conchidium
- Suborder Phaeodendria (=Phaeodendrida) Haeckel 1887
  - Family Coelodendridae Haeckel 1887 – Coelodendrum, Coelographis

References

Polet S, Berney C, Fahrni J, Pawlowski J (March 2004). "Small-subunit ribosomal RNA gene sequences of Phaeodarea challenge the monophyly of Haeckel's Radiolaria". Protist. 155 (1): 53–63. doi:10.1078/1434461000164. PMID 15144058.
Nikolaev, Sergey I.; Cédric Berney; José F. Fahrni; Ignacio Bolivar; Stephane Polet; Alexander P. Mylnikov; Vladimir V. Aleshin; Nikolai B. Petrov; Jan Pawlowski (2004). "The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes". Proceedings of the National Academy of Sciences. 101 (21): 8066–8071. doi:10.1073/pnas.0308602101. ISSN 0027-8424. PMC 419558. PMID 15148395.
Moreira D, von der Heyden S, Bass D, López-García P, Chao E, Cavalier-Smith T (July 2007). "Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata". Mol. Phylogenet. Evol. 44 (1): 255–66. doi:10.1016/j.ympev.2006.11.001. PMID 17174576.
Nakamura Y, Imai I, Yamaguchi A, Tuji A, Not F, Suzuki N (July 2015). "Molecular Phylogeny of the Widely Distributed Marine Protists, Phaeodaria (Rhizaria, Cercozoa)". Protist. 166 (3): 363–373. doi:10.1016/j.protis.2015.05.004. PMID 26083083.
Calkins GN (1926). The biology of the Protozoa. Lea & Febiger, Philadelphia, New York.
Cavalier-Smith T, Chao EE (2012). "Oxnerella micra sp. n. (Oxnerellidae fam. n.), a Tiny Naked Centrohelid, and the Diversity and Evolution of Heliozoa". Protist. 163 (4): 574–601. doi:10.1016/j.protis.2011.12.005. ISSN 1434-4610. PMID 22317961.
Cavalier-Smith, Thomas; Chao, Ema E.; Lewis, Rhodri (April 2018). "Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria". Protoplasma. 255 (5): 1517–1574. doi:10.1007/s00709-018-1241-1. PMC 6133090. PMID 29666938.
Takahashi K, Anderson OR. "Class Phaeodaria". In Lee JJ, Leedale GF, Bradbury P (eds.). Illustrated Guide to the Protozoa (2nd ed.). Society of Protozoologists, Lawrence, Kansas. pp. 981–994.

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[pmid15144058-1] Polet S, Berney C, Fahrni J, Pawlowski J (March 2004). "Small-subunit ribosomal RNA gene sequences of Phaeodarea challenge the monophyly of Haeckel's Radiolaria". Protist. 155 (1): 53–63. doi:10.1078/1434461000164. PMID 15144058.

[Heliozoatwilight-2] Nikolaev, Sergey I.; Cédric Berney; José F. Fahrni; Ignacio Bolivar; Stephane Polet; Alexander P. Mylnikov; Vladimir V. Aleshin; Nikolai B. Petrov; Jan Pawlowski (2004). "The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes". Proceedings of the National Academy of Sciences. 101 (21): 8066–8071. doi:10.1073/pnas.0308602101. ISSN 0027-8424. PMC 419558. PMID 15148395.

[pmid17174576-3] Moreira D, von der Heyden S, Bass D, López-García P, Chao E, Cavalier-Smith T (July 2007). "Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata". Mol. Phylogenet. Evol. 44 (1): 255–66. doi:10.1016/j.ympev.2006.11.001. PMID 17174576.

[phaeodariaphylogeny-4] Nakamura Y, Imai I, Yamaguchi A, Tuji A, Not F, Suzuki N (July 2015). "Molecular Phylogeny of the Widely Distributed Marine Protists, Phaeodaria (Rhizaria, Cercozoa)". Protist. 166 (3): 363–373. doi:10.1016/j.protis.2015.05.004. PMID 26083083.

[BiologyofProtozoa1926-5] Calkins GN (1926). The biology of the Protozoa. Lea & Febiger, Philadelphia, New York.

[Oxnerella-6] Cavalier-Smith T, Chao EE (2012). "Oxnerella micra sp. n. (Oxnerellidae fam. n.), a Tiny Naked Centrohelid, and the Diversity and Evolution of Heliozoa". Protist. 163 (4): 574–601. doi:10.1016/j.protis.2011.12.005. ISSN 1434-4610. PMID 22317961.

[RhizariaPhylo2018-7] Cavalier-Smith, Thomas; Chao, Ema E.; Lewis, Rhodri (April 2018). "Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria". Protoplasma. 255 (5): 1517–1574. doi:10.1007/s00709-018-1241-1. PMC 6133090. PMID 29666938.

[class_phaeodaria-8] Takahashi K, Anderson OR. "Class Phaeodaria". In Lee JJ, Leedale GF, Bradbury P (eds.). Illustrated Guide to the Protozoa (2nd ed.). Society of Protozoologists, Lawrence, Kansas. pp. 981–994.