Gray areas — tree of life

Taxa that are more black-and-white

• cellular life 🌿
  • prokaryotes 🌿
    • bacteria 🌿
    • archaea 🌿
      • eukaryotes 🌿
        • plants 🌿
        • animals 🌿   🌿 (over 98% of animal species are within the clade Bilateria   🌿)
        • fungi 🌿
• non-cellular life
  • viruses 🌿   🌿

Taxa that are more gray

Or, at least they're less well-known.

• cellular life
  • slime molds ^† they're sometimes considered fungal-like 🌿
  • pseudofungi ^† eukaryotes unrelated to fungi, but which have functional similarities (they have hyphae, and absorb externally-digested nutrients)
  • microfauna ^† microscopic organisms that have animal-like qualities
• subviral agents (which are non-cellular) [2]   [3]   [4] 🌿
  • prions discovered 1967 or 1982
  • viroids 🌿   🌿 discovered 1971
    • virusoids discovered 1980s
    • ambivirus discovered 2021
    • TODO: viroid-like elements
  • viriforms
    • gene transfer agents and transduction discovered 1974
  • ? nanobes ?
  • obelisks discovered 2024
  • coinfection
    • satellite viruses, satellite nucleic acids, and satellite-like nucleic acids   [2]   [3]   [4]
      • helper virus
      • helper dependent virus
      • defective interfering particle (DIP) discovered 1960s
      • virophage (and Category:Virophages) discovered 2008
      • satellite RNA discovered 1986
      • Alphasatellitidae
      • Hepatitis D is one of the more widely-known satellite viruses, and it needs hepatitis B as the helper virus. that it required a coinfection was discovered in 2009
  • horizontal gene transfer § Viruses in viruses
    • coinfection of bacteriphages, allowing a kind of "sex" to occur between to viruses
    • reassortment
    • antigenic shift
    • phenotype mixing
    • homologous recombination § Viruses
    • chimera

Multicellular protists

• brown algae
• red algae
• green algae — Depending on how you define 'plant', green algae are sometimes lumped in with land plants, and other times considered to be a disconnected eukaryote. However, recent evidence shows that land plants evolved from green algae. [1] [2] [3] [4]

Other information to explore: [1] [2] [3]

Animal-like protists

• naked and testate amoebae
• flagellates ^†
• ciliates ^†

Fungi-like protists

• the oomycetes, labyrinthulomycetes, and hyphochytrids, in Stramenopiles
• the myxomycetes, in Amoebozoa
• the phytomyxeans, in Rhizaria
• the perkinsozoans, in Alveolata

Prokaryote taxonomy

• https://www.khanacademy.org/science/biology/bacteria-archaea/prokaryote-metabolism-ecology/a/prokaryote-classification-and-diversity

Taxonomic characteristics:

• https://www.slideshare.net/slideshow/taxonomy-of-prokaryotes/249489731#11
• https://bio.libretexts.org/Courses/Manchester_Community_College_(MCC)/Remix_of_Openstax%3AMicrobiology_by_Parker_Schneegurt_et_al/04%3A_Prokaryotic_Diversity/4.03%3A_Prokaryote_Examples

Virus taxonomy

• classification by the ICTV (International Committee on Taxonomy of Viruses)   [2]
• Baltimore classification — Classified by their routes of transferring genetic information from the genome to messenger RNA (mRNA).   [2]
• Based on what the virus can infect — bacteria, archaea, animals, plants, and fungi
  • humans, algae, pests
• https://en.wikipedia.org/wiki/Virosphere — Several classifications mentioned.
• Virus morphology and classification | City University of New York

Other lists like this one

• https://en.wikipedia.org/wiki/Replicon_(genetics)#Non-cellular_entities
• https://en.wikipedia.org/wiki/Subviral_agents

see also

• https://en.wikipedia.org/wiki/Viral_metagenomics
• https://en.wikipedia.org/wiki/Two-domain_system 🌿 — A current debate that challenges acceptance of the three-domain system.
• https://en.wikipedia.org/wiki/Protist_classification

† Polyphyletic

TODO: look into these

• Provirus
  • Endogenous retrovirus — Weird.
    • Lysogenic cycle
  • Endogenous viral element
• Retrotransposon
• Replicon