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Attribution: User Jtwsaddress42 (discusscontribs) created this resource and is actively using it. Please coordinate future development with this user if possible.
Subject classification: this is a history resource.
Subject classification: this is a science resource.
Subject classification: this is a evolution resource
Subject classification: this is a biology resource.
Subject classification: this is a chemistry resource.
Subject classification: this is a physics resource.


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

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 

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

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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