User:Jtwsaddress42/Clade

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Clades

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Clades Sitemap
Biosphere Components
 Earth/Moon 
 

 Moon 

 
 
 Stationary 
 
 

 Core 

 Metallic 
 

 Mesosphere 

 
 

 Lithosphere 

 Ionic 
 Geosphere 
 

 Cryosphere 

 Ice 
 Phase 
 Mobile 
 

 Liposphere 

 Nonpolar 
 

 Hydrosphere 

 Polar 
 

 Atmosphere 

 Gases 
 Phase 
 Earth 
Biosphere
 System 
Gracilicutes to Proteobacteria
 
 Lipooligosaccharide[c] 

 Spirochaetae  

 
 RNA polβ BBM1 insert
 Shingolipids/Sulfonolipids 

 Sphingobacteria  

 
 Type III Secretion 
 Murein Loss/Reduction 

 Planctobacteria  

 
 
 
 

 Proteobacteria  

 
 
 Endosymbiosis[b] 

Mitochondria  

 0.9 GYA 
 
 
 
 
& alanyl‑tRNA synthase 4‑aa insert 
Endosymbiotic Eukaryotic Organelle
Gracilicutes[d] 
Iron-Sulfur World
 CS2,COS,CO2 
 FeS/H2S ⇒ FeS2 + 2 H+ + 2 e‑ 
 FeS/H2S ⇒ FeS2 + H2O 

 Fe-S Clusters 

 Exergonic 
 R‑COSH + CO2 ⇒ R‑CO‑COSH 
 Thiols,Thials,Thiones 

 Thioacetal 
 Chemistry 

 Carbonyl [H] Rxns 
 α‑Ketoacids 
 

 Chemoautotrophic 
 RCC Core 

 
 

 Iron-Sulfur World 

 
 Autocatalytic Cycle 
 Thiocarboxylates 
 & Carbon Fixation 
 Chemoautotrophic 
 Ignition 

4.56 - 3.9 GYA 
LUCA to Neomura
 
 

 Chlorobacteria - (Glidobacteria - Eobacteria)

 
 OM β-barrel insertion (Omp85)[n] 
 

 Hadobacteria   - (Glidobacteria - Eobacteria) 

 
 Lipopolysaccharides[m] 
 

 Cyanobacteria   - (Glidobacteria - Glycobacteria)

 
 Flagella 
 

 Gracilicutes[e]   - (Glycobacteria)

 
 Endospores[l] 
 

 Eurybacteria   - (Glycobacteria)

 
 OM Loss[k] 
 

 Endobacteria[f]  

 
 Exospores[j] 
 

 Actinobacteria  

 
 Cell Wall Loss[i] 
 Isoprenopid Ether Lipids[g] 

 Archaebacteria 

 
 Phagocytosis[h] 

 Eukaryota 

 
 Neomura 
 0.9 GYA 
 
 ~2.0 GYA 
 
 
 2.8 GYA 
 
Negibacteria
Posibacteria
Neomura
LUCA[o]  
3.5 GYA 
Neomura to Podiata
 Loss of Cell Wall 
 Isoprenopid Ether Lipids[y] 

 Archaebacteria  

 
 Phagocytosis[z] 
 Cytopharynx & Ciliary Paraxonemal Rods 

 Euglenozoa  

 
 Ventral Feeding Groove 
 Eruptive Psuedopodia[x] 

 Percolozoa[p]  

 
 Dorsal Ciliary Vane 
 

 Eolouka[q]  

 
 Ventral Ciliary Vane[w] 
 Myosin Domain Fusions 
 
 

 Neolouka[r]  

 
 Anaerobes[t] 

 Metamonada[s]  

 
 
 Ciliary Gliding[u] 

Podiata 

 Podiates 
 Scotokaryotes 
 Cortical Alveoli 
 Chloroplast Endosymbiont 

 Plantae[v]  

 
 Plantae Endosymbiont 
 

 Hacrobia  

 
 

 SAR supergroup  

 
 Chromista 
 Corticates 
 Neokaryotes 
 Orthokaryotes 
 Eokaryotes 
 Protokaryotes 
Archaebacteria
Eozoa[aa]
Neozoa[ab]
Corticata
Neomura[ac] 

 0.9 GYA 
Opisthokonta to Metazoa

Cavalier-Smith describes the Opisthokonts as being comprised of Choanozoa, Metazoa, and Fungi.[2] In this diagram Cavalier-Smith's Fungi equates to Holomycota and Fungi is used more restrictively. Cavalier-Smith's Choanozoa equates to all Holozoans except Animals (Metozoa). Here Choanozoa is used in a more conventional and restrictive manner.

 Loss of Anterior Cilium 
 Tapering Psuedopods[af] 
 

 Cristidiscoidea  

 
 
 
 

 Rozellidea  

 
 

 Microsporidia  

 
 
 Cell Walls & Branching Hyphae 

 Fungi  

 
 
Holomycota
 Holomycota 
 Ubiquitin S‑30 Fusion 
 Cell Walls Replace Psuedopods 

 Ichthyosporea  

 
 
 

 Pluriformea  

 
 CAMs & Filose Tentacles[ae] 
 

 Filosporidia  

 
 Collar Filter 
 

 Choanoflagellatea  

 
 Epithelia & Mesenchyme[ad] 

Animalia  

 Metazoa 
 665 MYA 
 Choanozoa 
 Filozoa 
 
Holozoa
 Holozoa 
Opisthokonta[ag] 
Phosphoester World
 Phosphate Invasion 
 
 Peptides 

 Proto-Kinase Rxns 

 
 Carbohydrates 

 Proto-Neoglucogenesis 

 
 Phosphorylation 
 Rxns 
 
 
 

 Aminoglycan Pathways 

 
 

 Nucleoside Pathways 

 
 
  
 
 

 Nucleotide Coenzymes 

 
 

 Energy Carriers 

 
 
 
 

 Nucleic Acid Chemistry 

 
 

 Phosphoester World 

  
 Polymerization 
 Rxns 
 Bioenergetic 
 Transfer 
 Phosphoanhydride 
 Takeover 
 Thioester World 

Podiata to Opisthokonta
 Ciliary Gliding 
 

 Planomonadida[ah] 

 
 Psuedopods[al] 
 
 

 Mantamonas 

 
 

 Diphylledia  

 
 CRuMs 
 Catenins[aj] 
 Broad Psuedopods 

 Amoebozoa  

 
 Narrow Psuedopods[ai] 
 

 Breviatea  

 
 
 

 Apusomonadida  

 
 Anterior Cilium Lost 

Opisthokonta 

 
 
 Obazoa 
 Unikonts[ak] 
 
Varisulca[am]
Amoebozoa
Obazoa

Podiata 
Solar System
 
 
 
 
 
 
 
 
 
 
 

 Sun 

 
 
 

 Atomic Species 

 
 

 Molecular Species 

 
 

 Circumstellar Dust 

 
 Plasma Condensation Zone 
 
 
 
 
 

 Mercury 

 
 

 Venus 

 
 
 

 Earth 

 Habitable Zone 
 
 
 

 Mars 

 
 Terrestrial Systems 
 
 

 Asteroid Belt 

 
 
 
 
 
 

 Jupiter 

 
 

 Saturn 

 
 
 

 Uranus 

 
 
 

 Neptune 

 
 Jovian Systems 
 
 

 Kuiper Belt 

 
 
 
 

 Termination Shock 

 
 
 

 Helioplause 

 
 Heliosphere 
 

 Bow Shock 

 
 
 

 Oort Cloud 

 
 Solar System 
Sun Structure
 
 
 
 
 
 
 
 

 Core 

 
 

 Radiative Zone 

 
 
 

 Convection Zone 

 
 
 

 Photosphere 

 
 
 

 Chromosphere 

 
 
 

 Transition Zone 

 
 
 

 Corona 

 
 
 Sun 
Surface Metabolist to LUCA
 
 

 Lipid World 

 
 
 
 

 Lipid-protected NA Epoch 

 
 
 
 

 Lipid-anchored RNA World 

 
 
  
 
 

 Lipid-anchored Lipo-Ribo-Protein Epoch 

 
 
 
 

 Lipid-anchored Proteo-Ribosomal Epoch 

 
 
 
 

 Lipid-anchored Virion Epoch 

 
 
 
 

 Lipid-anchored Enzyme Epoch 

 
 
 
 

 Water-Soluble Virionic/Enzymatic Ecology 

 
 
 
 

 Cytoplasmic Cellularity 

 
 
 

 Viral-Virovore Ecology 

 
 
 
 

 Genomic Cellularity 

 
 
 
 

 Rampant HGT Epoch 

 
 

 
 

 HGT Refractory Period 

 
 
 

 Darwinian Threshold 

 
 
 
 

 Cellular Biosphere 

 
 

 LUCA 

 
 Natural 
 Selection 
 VGT 
 Amino‑Acyl tRNA 
 Synthase 
 Selection 
 RNA/DNA 
 Polymerases 
 Ribonucleotide 
 Reductase 
 Virovory 
 Obcell 
 Fusion 
 Proteolytic 
 Enzymes 
 Enzymatic 
 Takeover 
 Capsid 
 Encoding 
 Ribosomal 
 Encoding 
 Peptidyl 
 Transferase 
 
 Obcell 
 
 Lipid 
 Bilayer 

Surface Metabolist 
Thioester World


 Nitrogen Invasion 
 Branch Pathways 
 
 FeS/H2S ⇒ FeS2 
 

 αKG ⇒ Glu (Acidic)

 
 

 OXO ⇒ Asp (Acidic)

 
 

 PYR ⇒ Ala (Neutral Non-polar)

 
 Reductive Amination 
 FeS/H2S ⇒ FeS2 
 

 Glu + Glu ⇔ αKG + Gln (Neutral Polar)

 
 

 Glu + Asp ⇔ αKG + Asn (Neutral Polar)

 
 Synthase Rxns 
 

 α-Ketoacids ⇔ α-Amino Acids

 Transanimase Rxns 
 AA Synthesis 
 
 

 Non-coded Polypeptides 

 Condensation Rxns 
 
 

 Biotin 

 
 

 Pyridoxal 

 
 

 Pantetheine 

 
 

 Proto-Thiamine 

 
 Proto‑Coenzymes 
 

 Thioester World 

 
 
 Chemoautotrophic 
 RCC Core 
 Iron-Sulfur World 

Notes & Commentary

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Notes & Commentary
  1. ↑ Subject to major change, revision ,and/or retraction at any moment.
  2. ↑ Proteobacteria phagocytosed by Protoeukaryotic Neomuran. Also: Murein/LPS/Lipoprotein Loss
  3. ↑ Also: endoflagella L-ring lost;
  4. ↑ Glycobacteria possessing flagella excluding Eurybacteria. Also: 4 Protein Insertions
  5. ↑ 4 Protein Insertions
  6. ↑ a.k.a Firmicutes
  7. ↑ Also: Reverse DNA gyrase; 2 genes split; novel stabler flagella; copious gene losses
  8. ↑ Also: Endomembranes; Endoskeleton; Mitochondria; 26S proteasomes; tricorn & TET peptidases lost
  9. ↑ Also: Cholesterol; 20S proteasomes; new ring ATPase; murein lost; Lipoproteins & ClpP lost; N-linked glycoproteins replace lipoproteins; core hisones replace DNA gyrase
  10. ↑ also: Phosphotidylinositol
  11. ↑ Also: Sortase lipoprotein secretion
  12. ↑ Also: Hsp70 & 90 deletions; MFIcc to MFIc operon; glycerol-1-P dehydrogenase
  13. ↑ Also: Hopanoids; TolC; TonB; Group I Nif
  14. ↑ Also: Photosystem Duplication; HsIVU ring protease; Cytochrome b; Type II Secretion
  15. ↑ "The last ancestor of all life was a eubacterium with acyl-ester membrane lipids, large genome, murein peptidoglycan walls, and fully developed eubacterial molecular biology and cell division. It was a non-flagellate negibacterium with two membranes, probably a photosynthetic green non-sulphur bacterium with relatively primitive secretory machinery..."[1] - Other key features: Peptidoglycan; Gliding; Lipoprotein; CLpP; Ion Proteases; Cytochrome c; group II Nif Nitrogen Fixation;
  16. ↑ alternative taxonomy membership: Excavata
  17. ↑ alternative taxonomy membership: Excavata - Loukozoa
  18. ↑ alternative taxonomy membership: Excavata - Loukozoa
  19. ↑ alternative taxonomy membership: Excavata - Loukozoa
  20. ↑ Also: 4 Cilia/Centrosome, loss of Mitochondria
  21. ↑ Dorsal Pellicle
  22. ↑ a.k.a. Archaeplastida
  23. ↑ Also: Novel cytochrome c biogenesis
  24. ↑ Also: 4 cilia/centrioles
  25. ↑ Also: Reverse DNA gyrase; 2 genes split; novel stabler flagella; copious gene losses
  26. ↑ Also: Endomembranes; Endoskeleton; Mitochondria; 26S proteasomes; tricorn & TET peptidases lost
  27. ↑ Ancestral aerobic, bicilate, phagotrophic Eukaryotes
  28. ↑ a.k.a. Scotokaryotes
  29. ↑ Also: Cholesterol; 20S proteasomes; new ring ATPase; murein lost; Lipoproteins & ClpP lost; N-linked glycoproteins replace lipoproteins; core hisones replace DNA gyrase
  30. ↑ Also: Extracellular Matrix, Oogamy
  31. ↑ Unbranched Non-tapering. Also: Cadherins
  32. ↑ Sometimes Branched.
  33. ↑ Loss of anterior cilium
  34. ↑ a.k.a. Ancyromonadida
  35. ↑ Also: Integrins
  36. ↑ The primordial role of the Catenins is tethering other proteins to actin I suspect.
  37. ↑ a.k.a. Sarcomastigo, Amorphea
  38. ↑ Also: Myosin II
  39. ↑ Varisulca lacks molecular phylogenetic support and appear to be strongly non-monophyletic. Planomonadida are not inferred to be the sister group to CRuMs and lacks wide acceptance as such.

Citations

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List of Citations
  1. ↑ Cavalier-Smith 2006.
  2. ↑ Shalchian-Tabrizi et al. 2007.

Sources & References

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Sources and References go here

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