Eukaryota

• Metamonads

  (Based largely on what was and wasn't said at MBL 10-97.)
  C-S lumps Retortamonads+Oxymonads with Giardia&co., but Patterson suggests they are separate, potentially primitively amitochondriate. He also says that Jakobids are near relatives, though they clearly have mitos.
  As reported at IBC 1999, OGMP trees do not put Jakobids detectably deeper in mitochondriate euks than any other group.
  2-98 P. Keeling: Metamonads = Diplomonads + Retortamonds; these share tetrakont flagella/basal bodies. Jakobids may not belong here as SSU puts them at base of crown. Sogin&co. currently doing multigene diplo/retorta/Jakobid analysis (with tuf/gapdh/tubulin/cpn60?)
  • Oxymonads (no data yet on mito-origin genes)
    • Dinenympha (endosymbiont of termite hindgut -- see gbk AB007028)
  • Retortamonads & relatives (tetrakont flagellates that look essentially like 1/2 of a diplomonad; no data yet on mito-origin genes; SMBE 1998: Sogin showed SSU rRNA data that place retortamonads in basal multichotomy on tree-of-life with parabasalia, diplomonads, and microsporidia)
    • Chilomastix
    • Trimastix (sister to the retortamonads)
    • Carpediomonas (related to Chilomastix and the Jakobids?)
  • Diplomonads (Andrew Roger/Graham Clarke/Mitch Sogin have found mito-like hsp60 in Giardia, suggesting secondary loss of mito; note also that at 1998 SMBE Sogin indicated that Giardia genome contains spliceosome components, at least by BLAST...)
    • Giardia
    • Hexamita
  • Jakobids (=histionids?; related to the retortamonads? 1998 SMBE: Sogin's SSU rRNA puts Jakobids at base of euk crown)
    • Jakoba (only rpoBC in mtDNA so far: Gray MBL 10-97)
    • Reclinomonas (rpoABCD in mtDNA: Gray MBL 10-97; huge and gene-rich mtDNA: Lang 1997 Nature 387:493)
    • Malawimonas (no rpo in mtDNA: Gray MBL 10-97)

• Parabasalia

  (amitochondriate, but have hydrogenosome: C-S Evol of Cells 1991; hydrogenosome is probably a derived mito: Bui(1996)PNAS 93:9651; discoid cristae puts them in the Discicristata with Euglenozoa: C-S MBL 10-97 -- but note that Stechmann(2002)Science puts Parabasalia out of discicristata on branch with metamonda; tubulin trees are consistent with discicristata, and suggest a larger (discicristata+alveolate, maybe +plants) clade: P. Keeling, 2-98, and see Keeling and Doolittle 1996 MBE)
  • Trichomonadea
    • Trichomonas
    • Dientamoeba
  • Hypermastigotes
    • Barbulanympha, a roach hindgut endosymbiont (Peter Merrit 1996)

• Everything else

  This is essentially an expanded eukaryote "crown". The Crown is a tenuous concept, as taxa like Dictyostelium jump in and out of the crown, depending on the gene used, but there is still a consistent tendency of these taxa to form a more-or-less differentiated bush or radiation, so I am keeping the clade.
  Origin and radiation ~1 BYR: Knoll 1992, but of course, if the crown is not a natural grp and all euks are mito'd, then really this grp dates nearly to the origin of euks!
  Blair Hedges' land-invasion analysis (Science 2001) suggests A/F/P split about 1.6 BYA, fungal land invasion followed by diversification about 1.2 BYA, based on multi-protein clock analysis. This is much older than other estimates on most counts...
  All taxa "above" euglenozoa have spliceosomal introns (JML 11-11-94). Jeff in 1997 thinks this may not be meaningful, but C-S still uses it as a defining character: MBL 10-97.
  1. Euglenozoa (have snRNA-mediated trans-splicing and U-evens: JML 11-11-94; discoid cristae puts them in the Discicristata with Percolozoa/Heterolobosea: C-S MBL 10-97; tubulin trees are consistent with discicristata, and suggest a larger (discicristata+alveolate, maybe +plants) clade: P. Keeling, 2-98, and see Keeling and Doolittle 1996 MBE)
     • Euglenoids (secondary green plastid: JDP 10-13-94 Halifax notes)
       • Euglena
       • Astasia
       • Rhabdomonas
     • Kinetoplastids
       • Bodonids
       • Trypanosomatids
         • Leishmania
         • Trypanosoma
  2. Heterolobosea (have mito but not golgi) = Percolozoa? (discoid cristae puts them in the Discicristata with Euglenozoa: C-S MBL 10-97; tubulin trees are consistent with discicristata, and suggest a larger (discicristata+alveolate, maybe +plants) clade: P. Keeling, 2-98, and see Keeling and Doolittle 1996 MBE)(Gertraude Berger at IBC 1999 reports that OGMP data place Naegleria at base of euks, but this is on a VERY long branch.)
     • Naegleria (part of the Vahlkampfiidae?)
     • Psalteriomonas (for placement, see Corliss 1994; secondary red plastid...?:JDP 10-13-94; no mito, no peroxisomes, has hydrogenosomes. SSU rDNA puts it here: Weekers (1997) J. Euk. Microbio)
  3. Alveolata (this name from Corliss [from Cavalier-Smith] and Sogin; tubular mitochondrial christae (like stramenopiles), alveoli=compartments just inside cell membrane?)
     • Perkinsus (C-S MBL 10-97: should be in Dinozoa, but it is conventionally placed in Apicomplexa; Chuck Delwiche 1998 SMBE suggests that it is best put here, in a trichotomy)
     • Apicomplexa (=Sporozoa) (breakdown from Morrison&Ellis 1997 MBE 14:428)
       • Cryptosporidium
       • Coccidia
         • Eimeria
         • Toxoplasma
       • Hematozoa
         • Plasmodium (secondary red plastid? Chuck's tufA analysis says more likely green)
         • Piroplasms
           • Babesia
           • Theileria
     • Dinoflagellates (secondary plastid; I originally had this down as red, but I think I'll back off on that (IBC 1999). Beverly Green&C-S's Heterocapsa plastid genes group at least some dinos with apicomplexan plastids on LONG branch which goes either with greens or reds, depending on the analysis. Note also that she says fully 50% of dinos are non-plastidic!)(This list is REALLY rough...)
       • Peridinen-containing dinoflagellates (chlA+chlC+peridinen as carotenoid pigment; plastid genome consists of single-gene minicircles: Beverly Green 1999 IBC and July 1999 Nature)
         • Heterocapsa
       • Amphodinium
       • Gonyalux
     • Ciliates
       • Tetrahymena
       • Paramecium
       • Oxytricha
       • Euplotes
       • Stylonichia
       • Stentor
  4. Foraminifera
  5. Sarcodina (this may or may not be a natural group)
     • Rhizopoda
       • Entamoebidae (C-S now groups in Conosa with Mycetozoa: MBL 10-97)
         • Entamoeba (secondarily amitochondrial: Clark 1995)
         • Archamoebae (Formerly in the Archaezoa, but C-S now groups these with Entamoeba: MBL 10-97)
           • Pelomyxa
       • Lobose amoebae (Jeff suggests 10-97 that Acanthamoeba (and hence lobose amoebae?) belongs with the Mycetozoa)
         • Amoeba
         • Acanthamoeba
         • Hartmanella
     • Actinopoda (Corliss would break this into Heliozoa+Radiozoa)
  6. Mycetozoa (=Myxomycota=Myxomycetes) (Sandie Baldauf's EF-1a analyses make this a monophyletic grp and put it at the base of A+F, many proteins genes certainly put them in the crown, tubulin and actin put Dictyostelium and Physarum together; Jeff suggests 10-97 that Acanthamoeba (and hence lobose amoebae?) belongs here, too; C-S puts these with Entamoebids in the Conosa: MBL 10-97)
     • Plasmodial Slime Molds (=myxogastrids; amoeboflagellates, most forming large plasmodia with >10^4 synchronously dividing nuclei; e.g., Physarum)
     • Cellular Slime Molds (amoebae, forming macroscopic, motile, differentiated slug-like things under conditions of nutrient starvation; e.g., Dictyostelium)
     • Protostelid Slime Molds (mostly microscopic, showing a mixture of traits from the other two groups)
  7. Animals+Fungi+Choanoflagellates (C-S calls this opisthokonta, MBL 10-97)
     • Animals
     • Choanoflagellates (Inclusion here by Wainright 1993, FGMP mito prot trees, C-S MBL 10-97; note in this context that choanos have introns in their mtDNA, as do basal animal lineages and fungi; Sandie Baldauf 1998 SMBE indicated that EF-1a puts choanos closer to fungi than to animals)
     • Fungi
       • Microspora
         Precise affinity -- or even inclusion here -- uncertain, though concensus is virtually complete by summer 1999 that they are fungi. IBC 1999: Patrick Keeling puts them in the eumycota, but from what Will told me about his (hsp?70?) analyses, they could well be chytrids... Placement here, instead of at the base of the euk trunk, based on:
         presence of U2 (DiMaria 1996 NAR 24:515), U5 (unpub says Jeff), U6 (cited in C-S 1993 Microbio Rev but unpub?)
         tubulin phylogeny: Edlin 1996 MPE 5:359, Keeling&Doolittle 1996 MBE13:1297
         A+F signature insertion in EF-1a
         lack of Paramomycin binding site (like A+F): Katiyar 1995 Gene 152:27
         presence and phylogeny of fungal mito-type hsp70: Germot 1997 Mol Biochem Parasitology, 1998 MBE 95:683
         ...my memory is failing me...was it an aaRS?: Gogarten MBL 190-97
         • Vairimorpha
         • Glugea
       • Chytridiomycota (split from eumycota ~550 MYA: Berbee&Taylor 1993 Can J Bot)
         • Blastocladiella
         • Neocallimastix
       • Eumycota
         • Zygomycota
         • Ascomycetes+Basidiomycetes
           • Ascomycota
           • Basidiomycota
           • Schizosaccharomyces
  8. Chromista (this name from Corliss; essentially = Stramenopiles?; C-S calls this one of the big four Metakaryote groups, with A, F, P: MBL 10-97; tubular mitochondrial cristae (like alveolates), tripartite hairs on flagellum. This is one of the major monophyletic euk groups by OGMP multi-gene mtDNA analyses reported by Gertraude Berger at IBC 1999.)
     • Cercozoa (I may be mis-representing this taxon, as I am assembling it from recollections of talks and posters...;C-S puts Chlorarachnion host with Filose amoebae in Cercozoa: MBL 10-97; Tubulin puts Cercomonas sister to Chlorarachnion host, consistent with Cercozoa: P. Keeling lab meeting 2-12-98; Ishida&C-S poster at 1998 SMBE shows tetrachotomy of (numerous) Chlorarchniophytes/Cercomonas/Paulinella/Euglypha based on nuclear SSU rRNA)
       • Chlorarachniophytes (secondary green plastid plus NM; see Jeff and Chuck 1996 PNAS review)
       • Cercomonas
       • Filose amoebae (=testate amoebae?; are these really monophyletic?)
         • Paulinella
         • Euglypha
     • Cryptophytes (tubulins say that sister to Cryptophytes is Goniomonas: P.Keeling, 2-12-98)
       • Rhodomonas
       • Cryptomonas (now called Guillardia: Douglas MBL 10-97; Secondary green, or more likely, red plastid plus NM -- see Jeff and Chuck 1996 PNAS review)
     • Haptophytes (secondary red plastid)
     • Heterokonts
       • Chromophytes (secondary red plastid -- chlorophylls A&C)
         • Xanthophyceae
           • Vaucheria
         • Phaeophyceae
           • Costaria
           • Laminaria (Kelp)
         • Bacillariophyceae (Diatoms)
           • Skeletonema
           • Odontella
           • Coscinodiscus
           • Cyclotella
         • Chrysophyceae
           • Ochromonas
       • Labyrinthulomycetes (placement here by Battacharya&Medlin, C-S 1993 Microbio Rev.)
       • Blastocystis hominis (by Sogin&co: Silberman Nature 1996)
       • Oomycetes (placement here by Battacharya, C-S 1993 Microbio Rev.)
         • Achlya
         • Phytophthora
         • Lagenidium
  9. Plants (assuming a single primary endosymbiotic origin of plastids; for details see full page)
     • Rhodophyta (primary red plastids: JDP 10-13-94)(Plastids with Chlorophyll A and phycobilins)
     • Glaucocystophytes here?: Corliss 1994 -- Rhodophyta+Glaucocystophyta=Biliphyta (both have plastids with Chlorophyll A and phycobilins).
     • Viridiplantae (primary green plastids: JDP 10-13-94)(Plastids with Chlorophylls A&B)...accepting that Land Plants are derived Charophytes makes "Viridiplantae" = "Chlorophytes"...