Choanoflagellates are a group of free-living unicellular and colonial flagellate eukaryotes considered to be the closest living relatives of animals. The name refers to the characteristic funnel-shaped "collar" of interconnected microvilli and the presence of a flagellum. Choanoflagellates are found globally in aquatic environments, and they are of particular interest to evolutionary biologists studying the origins of multicellularity in animals.
The flagellum of choanoflagellates is surrounded by microvilli at its base. Movement of the flagellum creates water currents that can propel free-swimming choanoflagellates through the water column and trap bacteria and detritus against the microvilli, where these foodstuffs are engulfed. This feeding plays an ecological role in the carbon cycle by linking different trophic levels.
Choanoflagellates bear morphological similarities to the choanocyte, a type of cell in sponges. As the closest living relatives of animals, choanoflagellates serve as a useful model for reconstructions of the last unicellular ancestor of animals. According to a 2021 study, crown group craspedids (and perhaps crown group choanoflagellates if Acanthoecida arose within Craspedida) appeared 422.78 million years ago, although a previous study from 2017 recovered the divergence of the crown group choanoflagellates (craspedids) at 786.62 million years.
Etymology Choanoflagellate is a hybrid word from Greek meaning "funnel" (due to the shape of the collar) and the Latin word (whence English flagellum).Merriam-Webster. (n.d.). Choanoflagellata. In Merriam-Webster.com dictionary. Retrieved September 17, 2025, from https://www.merriam-webster.com/dictionary/Choanoflagellata
Appearance
Each choanoflagellate has a single flagellum, surrounded by a ring of actin-filled protrusions called microvilli, forming a cylindrical or conical "collar" ( in Greek). Movement of the flagellum draws water through the collar, and bacteria and detritus are captured by the microvilli and ingested. Water currents generated by the flagellum also push free-swimming cells along, as in animal sperm. In contrast, most other flagellates are pulled by their flagella.Klindt, G. S., & Friedrich, B. M. (2015). Flagellar swimmers oscillate between pusher- and puller-type swimming. Physical Review E, 92(6), 063019. https://doi.org/10.1103/PhysRevE.92.063019
In addition to the single apical flagellum surrounded by actin-filled microvilli that characterizes choanoflagellates, the internal organization of organelles in the cytoplasm is constant. A flagellar basal body sits at the base of the apical flagellum, and a second, non-flagellar basal body rests at a right angle to the flagellar base. The nucleus occupies an apical-to-central position in the cell, and food vacuoles are positioned in the basal region of the cytoplasm. Additionally, the cell body of many choanoflagellates is surrounded by a distinguishing extracellular matrix or periplast. These cell coverings vary greatly in structure and composition and are used by taxonomists for classification purposes. Many choanoflagellates build complex basket-shaped "houses", called lorica, from several silica strips cemented together. The functional significance of the periplast is unknown, but in sessile organisms, it is thought to aid attachment to the substrate. In planktonic organisms, there is speculation that the periplast increases drag, thereby counteracting the force generated by the flagellum and increasing feeding efficiency.
Choanoflagellates are either free-swimming in the water column or sessile, adhering to the substrate directly or through either the periplast or a thin pedicel. Although choanoflagellates are thought to be strictly free-living and heterotrophic, several choanoflagellate relatives, such as members of Ichthyosporea or Mesomycetozoa, follow a parasitic or pathogenic lifestyle. The life histories of choanoflagellates are poorly understood. Many species are thought to be solitary; however, coloniality seems to have arisen independently several times within the group, and colonial species still retain a solitary stage.
Ecology
Over 125 extant species of choanoflagellates are known, distributed globally in marine, brackish and freshwater environments from the Arctic to the tropics, occupying both pelagic and benthic zones. Although most sampling of choanoflagellates has occurred between , they have been recovered from as deep as in open water and under Antarctic ice sheets.
Many species are hypothesized to be cosmopolitan on a global scale [e.g., Diaphanoeca grandis has been reported from North America, Europe and Australia (OBIS)], while other species are reported to have restricted regional distributions. Co-distributed choanoflagellate species can occupy quite different microenvironments, but in general, the factors that influence the distribution and dispersion of choanoflagellates remain to be elucidated.
A number of species, such as those in the genus Proterospongia, form simple colonies, planktonic clumps that resemble a miniature cluster of grapes in which each cell in the colony is flagellated or clusters of cells on a single stalk. A colonial species from Mono Lake, Barroeca monosierra, forms spheres filled with a branched network of an extracellular matrix where a microbiome of different species of symbiotic bacteria live. In October 2019, scientists found a new band behaviour of choanoflagellates: they apparently can coordinate to respond to light. Studies on the colonial species Salpingoeca rosetta have shown that the individual cells use electrical signals to coordinate their movements and synchronize flagellar beating within the colony, using the same type of voltage-gated calcium channels as those found in animal neurons and muscles.Electrical signaling and coordinated behavior in the closest relative of animals
The choanoflagellates feed on bacteria and link otherwise inaccessible forms of carbon to organisms higher in the trophic chain. Even today, they are important in the carbon cycle and microbial food web. There is some evidence that choanoflagellates feast on viruses as well.
Life cycle
Choanoflagellates grow vegetatively, with multiple species undergoing longitudinal fission; however, the reproductive life cycle of choanoflagellates remains to be elucidated. A paper released in August 2017 showed that environmental changes, including the presence of certain bacteria, trigger the swarming and subsequent sexual reproduction of choanoflagellates. The ploidy level is unknown;Claus Nielsen. Animal Evolution: Interrelationships of the Living Phyla. 3rd ed. Claus Nielsen. Oxford, UK: Oxford University Press, 2012, p. 14. however, the discovery of both retrotransposons and key genes involved in meiosis previously suggested that they used sexual reproduction as part of their life cycle. Some choanoflagellates can undergo encystment, which involves the retraction of the flagellum and collar and encasement in an electron dense fibrillar wall. On transfer to fresh media, excystment occurs; though it remains to be directly observed.
Evidence for sexual reproduction has been reported in the choanoflagellate species Salpingoeca rosetta. Evidence has also been reported for the presence of conserved meiotic genes in the choanoflagellates Monosiga brevicollis and Monosiga ovata.
Silicon biomineralization The Acanthoecid choanoflagellates produce an extracellular basket structure known as a lorica. The lorica is composed of individual costal strips, made of a silica-protein biocomposite. Each costal strip is formed within the choanoflagellate cell and is then secreted to the cell surface. In nudiform choanoflagellates, lorica assembly takes place using a number of tentacles once sufficient costal strips have been produced to comprise a full lorica. In tectiform choanoflagellates, costal strips are accumulated in a set arrangement below the collar. During cell division, the new cell takes these costal strips as part of cytokinesis and assembles its own lorica using only these previously produced strips.
Choanoflagellate biosilicification requires the concentration of silicic acid within the cell. This is carried out by silicon transporter (SiT) proteins. Analysis of choanoflagellate SiTs shows that they are similar to the SiT-type silicon transporters of diatoms and other silica-forming stramenopiles. The SiT gene family shows little or no homology to any other genes, even to genes in non-siliceous choanoflagellates or stramenopiles. This suggests that the SiT gene family evolved via a lateral gene transfer event between Acanthoecids and Stramenopiles. This is a remarkable case of horizontal gene transfer between two distantly related eukaryotic groups, and has provided clues to the biochemistry and silicon-protein interactions of the unique SiT gene family.
Classification
Relationship to metazoans Félix Dujardin, a French biologist interested in protozoan evolution, recorded the morphological similarities of choanoflagellates and sponge choanocytes and proposed the possibility of a close relationship as early as 1841. Over the 1990s and the 2000s, this hypothesized relationship between choanoflagellates and animals has been upheld by independent analyses of multiple unlinked genetic sequences: 18S rDNA, nuclear protein-coding genes, and mitochondrial genomes (Steenkamp, et al., 2006; Burger, et al., 2003; Wainright, et al., 1993). Importantly, comparisons of mitochondrial genome sequences from a choanoflagellate and three sponges confirm the placement of choanoflagellates as an outgroup to Metazoa (animals, also known as Animalia) and negate the possibility that choanoflagellates evolved from metazoans (Lavrov, et al., 2005). Finally, a 2001 study of genes expressed in choanoflagellates has revealed that choanoflagellates synthesize homologues of metazoan cell signaling and adhesion genes. Genome sequencing shows that, among living organisms, the choanoflagellates are most closely related to animals.
Because choanoflagellates and metazoans are closely related, comparisons between the two groups promise to provide insights into the biology of their last common ancestor and the earliest events in metazoan evolution. The choanocytes (also known as "collared cells") of sponges (considered among the most basal metazoa) have the same basic structure as choanoflagellates. Collared cells are found in other animal groups, such as ribbon worms, suggesting this was the morphology of their last common ancestor. The last common ancestor of animals and choanoflagellates was unicellular, perhaps forming simple colonies; in contrast, the last common ancestor of all eumetazoan animals was a multicellular organism, with differentiated tissues, a definite "body plan", and embryonic development (including gastrulation). The timing of the splitting of these lineages is difficult to constrain, but was probably in the late Precambrian, >.
External relationships of Choanoflagellatea.
Phylogenetic relationships The choanoflagellates were included in Chrysophyceae until Hibberd, 1975.Reviers, B. de. (2006). Biologia e Filogenia das Algas. Editora Artmed, Porto Alegre, p. 156. Recent molecular phylogenetic reconstruction of the internal relationships of choanoflagellates allows the polarization of character evolution within the clade. Large fragments of the nuclear SSU and LSU ribosomal RNA, alpha tubulin, and heat-shock protein 90 coding genes were used to resolve the internal relationships and character polarity within choanoflagellates. Each of the four genes showed similar results independently and analysis of the combined data set (concatenated) along with sequences from other closely related species (animals and fungi) demonstrate that choanoflagellates are strongly supported as monophyletic and confirm their position as the closest known unicellular living relative of animals.