Diaphoretickes

Herbarium specimen of Gastridium articulatum, from University of California, Berkeley.

Belongs within: Eukaryota.
Contains: Vendophyceae, Ischyrospongia, Haptista, Corbihelia, Sar, Cryptista, Conferva, Rhodophyta, Glaucophyta, Chlorophyta, Streptophyta.

The Diaphoretickes are a clade of eukaryotes supported by molecular phylogenies that might be described as comprising the major algal lineages and related taxa. Cavalier-Smith et al. (2015) defined an equivalent clade under the name Corticata as including all descendents of the common ancestor of Arabidopsis and Paramecium. Many members of this clade are photosynthetic; members of the subclade Archaeplastida possess chloroplasts with chlorophyll a as the primary pigment that is believed to have arisen through a single primary endosymbiosis with a cyanobacterium. Other photosynthetic members of Diaphoretickes usually have a chlorophyll c-containing chloroplasts that arose through secondary endosymbiosis with another photosynthetic eukaryote, leading to their association at times (e.g. Cavalier-Smith et al. 2015) within a major taxon named Chromista. Debate continues, however, as to whether there was a single such event near the base of a monophyletic chromist clade (followed by multiple chloroplast losses) or whether the various photosynthetic ‘chromist’ lineages acquired their chloroplasts independently.

Fossil macroscopic algae have also been assumed herein to belong within the Corticata, though the true relations of groups such as Vendophyceae and Chuariaphyceae to modern multicellular algae remain uncertain.

Crossing the algal divide
Published 6 May 2009
Glaucocystis, a member of the primary chloroplast-carrying glaucophytes. Photo by Jason Oyadomari.

It has become pretty much universally acknowledged that at least two of the organelles found in eukaryotic cells, mitochondria and chloroplasts, are derived from endosymbiotic bacteria that progressively gave up more and more of their vital functions to their host cells until they became inextricably linked to them. Mitochondria are probably derived from Alphaproteobacteria (Gray et al. 2004), while chloroplasts are certainly derived from Cyanobacteria. Endosymbiotic origins have been suggested for other organelles, most notably the eukaryotic flagellum, but have not reached the same level of acceptance. While a number of eukaryotes lacking mitochondria are found in the world today, the weight of current evidence suggests that most if not all are descended from mitochondria-carrying ancestors, and the origin of the mitochondrion pre-dates the known eukaryote crown group. The origin of the chloroplast, however, is not quite so simple.

Cryptomonas, another unicellular alga from a different group, the cryptomonads. Photo from here.

The chloroplast was undoubtedly a later innovation than the mitochondrion. As I’ve alluded to elsewhere, the basalmost division in eukaryotes currently seems to be between unikonts (including animals, fungi and amoebozoans) on one side and bikonts (plants and most other protists) on the other. All eukaryotes with chloroplasts are bikonts (with the exception of sequestered chloroplasts in some marine molluscs and flatworms), so chloroplasts at least post-date this division. Unfortunately, bikonts are a much more disparate bunch than unikonts, and our understanding of how the various major groups of bikonts are related to each other is correspondingly less. Among the bikonts, chloroplasts or clear chloroplast derivatives are found in twelve well-supported monophyletic groups (as a cautious maximum). However, different groups have chloroplasts with different physiologies and ultrastructures, indicating different modes of origin. Some groups have what are called primary chloroplasts, derived directly from endosymbiotic cyanobacteria. Primary chloroplasts have two membranes separating the host cell and chloroplast cytoplasm, corresponding to the two cell membranes of a free-living cyanobacterium. Most cyanobacteria contain a single type of chlorophyll, chlorophyll a, and so do the primary chloroplasts of glaucophytes* (a small group of unicellular algae), rhodophytes (red algae) and the shelled amoeboid Paulinella. The fourth group of eukaryotes with primary chloroplasts, Viridiplantae (green algae and land plants), differ in having two types of chlorophyll, both the original a and an additional form called chlorophyll b**. Glaucophyte, rhodophyte and viridiplantaean chloroplasts share a number of genetic signatures absent from cyanobacteria, suggesting that their chloroplasts are derived from a single endosymbiotic event (Kim & Graham 2008). The chloroplast of Paulinella, on the other hand, is more similar to a cyanobacterium, and Paulinella has clear and close non-photosynthetic relatives among the group of unicellular protists known as Cercozoa. Paulinella is therefore believed to have acquired its chloroplast recently and completely independently of the other groups.

*As an intriguing aside, it was long debated whether it was more appropriate to regard the photosynthetic enclusions in glaucophytes as “chloroplasts” or “endosymbiotic cyanobacteria”, and a number of glaucophyte chloroplasts were given names as taxa in their own right.

*Just to confuse matters, there are also three species of cyanobacteria that possess chlorophyll b. Current indications are that these species are not closely related to Viridiplantae chloroplasts—nor, indeed, are they closely related to each other. The odd scattered distribution of chlorophyll b remains as yet completely unexplained.

Diagram of the origin of secondary chloroplasts in chlorarachniophytes through the engulfment of one eukaryote by another. From ToLWeb.

The remaining groups of photosynthetic eukaryotes, in contrast, have what are called secondary chloroplasts (or, in a few cases, tertiary or even quaternary chloroplasts). Secondary chloroplasts have three or four membranes surrounding them, and are not derived directly from a cyanobacterium, but from a eukaryotic alga containing a primary chloroplast. In those secondary chloroplasts with four membranes, then, the membranes represent the two membranes of the primary chloroplast, the outer cell membrane of the endosymbiotic eukaryotic alga, and the membrane surrounding the vacuole in which the secondary host contained its endosymbiont. Clear support for this complicated origin can be seen in the two secondary-chloroplast groups, the amoeboid chlorarachniophytes and the flagellate crytomonads, where a small dark mass sits wedged between the second and third membranes. This mass contains DNA, and is nothing less than the degraded remnants of the endosymbiotic alga’s original nucleus.

Coccolithophores, shelled algae of the Haptophyta. Image from here.

Two groups of secondary-chloroplast algae, the chlorarachniophytes and the euglenoids (Euglena is probably about the most commonly-illustrated flagellate in any textbook), possess chlorophylls a and b, indicating an ancestor among the Viridiplantae for their chloroplasts. For the remaining groups, phylogenetic analyses indicate a rhodophyte origin for their chloroplasts. The recently discovered Chromera only has chlorophyll a, like a rhodophyte, while Chromera‘s relatives in the parasitic Coccidiomorpha (a subgroup of the Sporozoa) possess chlorophyll-less chloroplast derivatives. The remaining four groups—cryptomonads, haptophytes (coccolithophores), ochrophytes (which include brown and golden algae and diatoms) and dinoflagellates—possess two types of chlorophyll, a and a form called chlorophyll c that is unique to these taxa.

The big question hovering over eukaryote phylogenetics is how many times these secondary endosymbioses occurred. One of the most prolific authors in this field has been the British researcher Tom Cavalier-Smith. Cavalier-Smith’s writings can induce feelings of great admiration or extreme loathing (sometimes both over the course of a single page)*, but one certainly can’t go very far without coming up against them. A lot of Cavalier-Smith’s views (some of them since adjusted) were summarised in what was published in 2002 as two papers (Cavalier-Smith 2002a, 2002b) but should really be read as one single gigantic über-paper on the origins of life, the universe and everything (well, not the universe, but you get the idea). Using a combination of molecular and morphological interpretations, Cavalier-Smith divided the bikonts into five major clades, all but one including both photosynthetic and non-photosynthetic major subgroups—Excavata (including euglenoids, among others), Rhizaria (to which belong chlorarachniophytes and Paulinella, as well as foraminifera and radiolarians), Plantae (the remaining primary-chloroplast organisms), Alveolata (dinoflagellates, sporozoans and ciliates) and Chromista (cryptomonads, haptophytes and heterokonts—the last includes the ochrophytes). He further proposed that the Alveolata and Chromista together formed a clade called chromalveolates, uniting all the chlorophyll c-containing organisms. Supposedly, the rhodophyte endosymbiosis giving rise to the chromalveolate chloroplast happened just once, and the non-photosynthetic chromalveolates are derived from ancestors that lost their chloroplasts.

*At least in the late 1990s and the early 2000s, a rough indication of the amount of ire that Cavalier-Smith’s publications generated in some circles could be gained by scanning the works of other protistologists and noting the lengths some of them went to not to cite Cavalier-Smith.

Paulinella. This genus is the only eukaryote lineage to have acquired its chloroplasts separately from the archaeplastid lineage. Photo from here.

A major factor in Cavalier-Smith’s proposals has been the idea that chloroplast acquisition is far more difficult than chloroplast loss, because gaining a working chloroplast requires not only the endosymbiont but the evolution of appropriate molecular channels for transporting metabolites between the endosymbiont and the host cell, so the phylogeny that minimises the number of chloroplast acquisitions is most likely to be true (as an extreme example, in 1999 he also suggested that Excavata and Rhizaria formed a clade derived from a single green algal endosymbiosis, which the resulting chloroplast lost in all members of both clades except chlorarachniophytes and euglenoids. Because chlorarachniophytes and euglenoids are both nested reasonably deeply within their respective clades, necessitating a fairly large number of chloroplast losses in this scenario, nobody except for Cavalier-Smith himself seems to have given it a huge amount of credence). Other researchers, on the other hand, hold the opposite view—that chloroplasts perform such a significant role in their host cells that losing them would be a Very Bad Thing—and point to the fact that many photosynthetic groups have clear closest relatives among non-photosynthetic groups. Unfortunately, most phylogenetic analyses in this field have lacked strong resolution or support, probably simply due to the incredibly long time since the lineages diverged.

So where do things stand now? In the last couple of years, analyses of sometimes quite huge amounts of data have been released. Of Cavalier-Smith’s (2002b) five groups, the Rhizaria and Alveolata have continued to receive support from almost all angles. The Excavata continue to cause a bit of hemming and hawing (though Hampl et al., 2009, recently presented the first molecular analysis to support excavate monophyly), but with only one photosynthetic subgroup they’re not really relevant to the current discussion anyway. The monophyly of the Plantae (renamed Archaeplastida in the eukaryote classification of Adl et al., 2005, to avoid the confusion of the many different uses of the name “Plantae”) is at a bit of a draw—Patron et al. (2007) and Burki et al. (2008), for instance, found it as monophyletic, but Kim & Graham (2008) and Hampl et al. (2009) did not. None of the recent analyses, however, have found a monophyletic Chromista. The cryptomonads and haptophytes look to form a clade that may be close to (Patron et al. 2007; Burki et al. 2008) or even within (Kim & Graham 2008; Hampl et al. 2009) the archaeplastids. The heterokonts seem to form a clade (with a certain degree of irony) with the alveolates—which brings up the possibility that, depending on how you choose to use the names, “chromalveolates” may be monophyletic even if “chromists” are not. A surprising result of a number of recent analyses (including most of the ones cited above) is that this reduced chromalveolate clade may be sister to the Rhizaria.

As shown in the figure above from Bodył et al (2009) summarising all this, this implies a number more chloroplast origins than Cavalier-Smith’s model. Does this vindicate those who hold that chloroplast acquisition is easier than chloroplast loss? Well, as often happens in biology, there is a third possibility. As well as chloroplast gain and chloroplast loss, there is also chloroplast replacement. Dinoflagellates, the one group of eukaryotes that never manage to do anything sensibly, include some members with secondary rhodophyte-derived chloroplasts, and others with tertiary chloroplasts that seem to be derived from haptophytes. It seems that these serial hosts have shucked out their original secondary chloroplasts in favour of a new endosymbiont. Chloroplast replacement sidesteps some of the theoretical difficulties of acquiring a chloroplast entirely de novo, because the host already possesses the biochemical pathways to communicate with its new chloroplast. If the cryptomonad-haptophyte clade is nested within archaeplastids, as indicated by some phylogenies, this may represent a case of chloroplast replacement rather than chloroplast gain.

Systematics of Diaphoretickes

Characters (from Cavalier-Smith et al. 2015, as Corticata): Eukaryotes ancestrally with ventral feeding groove and cytoskeleton comprising single dorsal centriolar microtubular root and dorsal fan, posterior split right root with I fibre and left root with C fibre, and intermediate single root; cortical alveoli present; ciliary hairs often not associated with latticed paraxonemal rod.

<==Diaphoretickes (see below for synonymy)LE18
    |--+--HaptistaLE18
    |  `--+--CorbiheliaLE18
    |     `--SarLE18
    `--+--CryptistaLE18
       `--Archaeplastida [Arthromorpha, Phyllomorpha, Plantae]LE18
            |  i. s.: ConfervaceaeG64
            |           |--ConfervaC94
            |           |--Vagabundia fracta [=Cladophora fracta]G64
            |           |--Cytophora littoreaG64
            |           `--HormotrichiumG64
            |                |--H. bangoides [=Conferva bangoides]G64
            |                |--H. carmichaelii [=Lyngbya carmichaelii]G64
            |                |--H. collabens [=Conferva collabens]G64
            |                |--H. cutleriae [=Lyngbya cutleriae]G64
            |                |--H. speciosum [=Lyngbya speciosa]G64
            |                |--H. wormskioldiiG64
            |                `--H. youngianumG64
            |--RhodophytaLE18
            `--+--GlaucophytaLE18
               `--Viridiplantae (see below for synonymy)C-SCL15
                    |  i. s.: Scotiellopsis oocystiformisOV01
                    |         Pterosphaera Jörgensen 1900FT93
                    |         Pterospermopsis [Pteromorphitae]EB93
                    |--ChlorophytaC-SCL15
                    `--StreptophytaLE18
Diaphoretickes incertae sedis:
  VendophyceaeG03
  Bitelaria Istchenko & Istchenko 1979G03
  Himanthaliopsis Zalessky 1915G03
  Sarcinophycus Xiao & Knoll 2000X04
    |--*S. radiatus Xiao & Knoll 2000X04
    `--S. papilloformis Xiao 2004X04
  GastridiumRV01
    |--G. articulatumRV01
    |--G. obtusumRV01
    |--G. pinnatifidumRV01
    |--G. repensRV01
    `--G. tenuissimumRV01
  ‘Archidesmus’ loganensis Peach 1899WA04
  Kyrtuthrix maculansK98
  Ahnfeltiopsis flabelliformisKY97
  Buthotrephis Hall 1847S00, H75 [=Bythotrephis (l. c.)H75]
    `--B. rebskeiS00
  Koninckopora Lee 1912 [incl. Coeloceratoides Derville 1931]T64
    `--*Coeloceratoides’ fragilis Derville 1931T64
  Eyrea Cookson & Eisenack 1971E77
    `--E. nebulaE77
  Delesserites Sternberg 1833 [incl. Delesserella Ruedemann 1926, Delessertites Bronn 1853]H75
    |--*D. lamourouxii (Brongniart 1823) [=Fucoides lamourouxii]H75
    `--D. salicifolia Ruedemann 1925H75
  ‘Zonarites’ digitatus Sternberg 1833H75
  Aataenia Gnilovskaya 1976G79
    `--*A. reticularis Gnilovskaya 1976G79
  Lanceoforma Walter, Oehler & Oehler 1976G79
    `--*L. striata Walter, Oehler & Oehler 1976G79
  Proterotainia Walter, Oehler & Oehler 1976G79
    `--*P. montana Walter, Oehler & Oehler 1976G79
  Archaelagena Howchin 1888 [=Archealagena (l. c.)]LT64
    `--*A. howchiniana (Brady 1876) [=Lagena howchiniana]LT64
  Cellulina Zborzewski 1834LT64
  Coelotrochium Schlüter 1879LT64
  TestamoebiformiaLT64
    |--Cysteodictyina Carter 1880LT64
    |    `--*C. compressa Carter 1880LT64
    `--Holocladina Carter 1880LT64
         `--*H. pustulifera Carter 1880LT64
  Goniolina d’Orbigny 1850LT64
    `--*G. hexagona d’Orbigny 1850LT64
  Pseudogypsina Trauth 1918LT64
    `--*P. multiformis Trauth 1918LT64
  Siphonema Bornemann 1886LT64
  ChuariaphyceaeH98
    |--Beltina Walcott 1899 [Beltinaceae]HR94
    |    `--*B. danai Walcott 1899HR94
    `--Chuaria Walcott 1899H98 (see below for synonymy)
         |--*C. circularis Walcott 1899H98
         |--*Krishnania’ acuminata Sahni & Shrivastava 1954H62
         |--*Protobolella’ jonesi Chapman 1935M65
         |--*Fermoria’ minima Chapman 1935 [=*Protobolella minima]H75
         |--C. pendjariensisH98
         `--C. wimaniH75
  IschyrospongiaM13
  Munieria baconicaE56
  Macroporella preromangicaFP12
  Polyedriella helveticaR87
  Sinocylindra yunnanensisHCH18
  Ambiguaspora parvula Volkova 1976EB93
  Ancoracysta Janouskovec et al. 2017AB19
  Adlerocystis Feldm.-Muhs. & Havivi 1963KC01
  Trinitaria confervoides Bory de Saint-Vincent 1828 [incl. Sporochnus medius]BS-V28
  Guttoporella densaNW04
  Crinitella radiataNW04
  PalmatoporellaNW04
    |--P. lataNW04
    `--P. stenaNW04
  Inocaulis Hall 1852M14, B70 [Inocaulidae]
    |--*I. plumulosa Hall 1852B70
    |--‘Acanthograptus’ antiquus Quilty 1971R93
    `--I. multiramous Ruedemann 1947NS93
  Boucekocaulis Obut 1960M14
  Calyptograpsus Spencer 1878M14 [=CalyptograptusB70]
    `--*C. cyathiformis Spencer 1878B70
  Crinocaulis Obut 1960M14
    `--*C. flosculus Obut 1960B70
  Estoniocaulis Obut & Rytsk 1958M14
    `--*E. jaervensis (Rosenstein in Obut & Rytsk 1958) [=Inocaulis jaervensis]B70
  Leveillites Foerste 1923M14
    `--*L. hartnageli Foerste 1923B70
  Palmatophycus Bouček 1941M14
    `--*P. kettneri Bouček 1957B70
  Rhadinograptus Obut 1960M14
    `--*R. jurgensonae Obut 1960B70
  Thallograptus Ruedemann 1925M14
    |--*T. succulentus (Ruedemann 1904) [=Dendrograptus succulentus]B70
    `--T. cervicornisB70
Trace fossils: Delesserites foliosus Ludwig 1869H75
               Delesserites gracilisH75
               Delesserites sinuosusH75

Chuaria Walcott 1899H98 [incl. Fermoria Chapman 1935G79, Krishnania Sahni & Shrivastava 1954G79, Protobolella Chapman 1935G79, Vindhyanella Sahni 1936G79; Chuariaceae, Chuariales, Chuariidae]

Diaphoretickes [Biliphyta, Callomorpha, Chromalveolata, Chromista, Chromobiota, Chromophycophyta, Chromophyta, Corticata, Cystosporae, Dumontiae, Encoelii, Hacrobia, Lecaniellaceae, Macrosporae, Metaphyta, Ramicristea, Ramicristia, Zygosporae]LE18

Viridiplantae [Chlorobionta, Chlorobiota, Chlorophycophyta, Chlorophytina, Chloroplastida, Euchlorophyceae, Euchlorophyta, Prasinomonadida, Prasinophyceae, Prasinophyta]C-SCL15

*Type species of generic name indicated

References

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