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User:Arkuat/Taxonomy

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Please browse the many articles that our Wikipedia has about the various taxa of living organisms!

The sorting order of these lists tries to follow the principle of most-familiar-first. Whenever a list of obscure taxa needs to be sorted, we try to follow the principle of listing the taxa in order of first published description. This last principle can be tricky too, and since we don't have access to all the relevant information about dates of first public description, many of the sublists in this outline are in semirandom order.

The names of phyla and divisions (equivalent taxonomical levels reflecting differences of nomenclature between zoologists and botanists) are in bold text.

I am planning to do a big update soon, but first I want to say here: what with horizontal gene transfer and all, prokaryote "taxonomy" is in even worse shape than when I looked at it 20 years ago, and it was in much worse shape then than I figured out at the time. For example, many taxa in common use make no sense whatsoever (for example, E. coli should be at least a family, possibly an order, definitely not a species) but there is strong pressure not to change any names commonly used in medicine (and there are a lot of those), whether they make any taxonomic sense at all. This goes for Eubacteria, especially the medical terminology aspect, but also to Archaea. After all, any asexually-reproducing species that engages in horizontal gene transfer with like organisms of various different species can hardly be shoe-horned into the Linnaean scheme. So all the parts of this document that refer to prokaryote taxa are going away, and where I mention "taxa of living organisms" up there, I'm going to have to change that to the considerably less glamorous-sounding "eukaryotes." For prokaryote taxonomy, whatever that is, you'll have to consult a real expert: I'm just an amateur.

For the record, I do not subscribe to the notion that Eukaryota are a subtaxon of Archaea. You can't have eukaryotes without mitochondria (except for extreme parasitic forms which lost them), mitochondria have their own little genome, and mitochondria are not Archaea; they're descended from a common ancestor shared with alphaproteobacteria.

A preview of the coming changes

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There are no more Animal, Plant, Fungi, and Protist kingdoms: now there are only Diaphoretickes, Amorphea, and various protistan taxa formerly thought of as excavata (namely Discoba, Neolouka, & Metamonada), along with non-excavate Hemimastigophora, another protist.

The other protists are scattered among the Diaphoretickes and Amorphea, along with Obazoa in Amorphea and Embryophyta in Diaphoretickes.

Embryophyta includes all the land plants, but not (for instance) kelp: kelp is among the Stramenopiles AKA heterokonts, which is a subtaxon of a subtaxon of Diaphoretickes, sort of as if Phaeophyta (which includes kelp) were Embryophyta's first cousin once removed. And then there are red and green algae, which are each a whole different thing. Brown, green, and red have three different ancestors, each of which independently acquired chloroplasts by absorbing but failing to digest three different photosynthesizing eukaryotic species: endosymbiosis, like the earlier acquisition of mitochondria. So the last common ancestor of all three types of algae was decidedly not photosynthetic, so they're like three different kingdoms of algae or something.

The best replacements for the animal and fungus kingdoms are probably the two halves of the Opisthokont subtaxon Obazoa, namely Holozoa and Holomycota respectively.

I'm probably not going to delete the the prokaryote (Bacteria and Archea) sections entirely, but they'll be prefaced by similar language to that now prefacing the viruses section, except for prokaryotes it will be complaining about horizontal gene transfer instead of complaining about lack of an independent metabolism.

Domain Eucarya

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The eukaryote regna are sorted this way to reflect the idea that animals and fungi are closely related to the opisthokont group of protists, and the plants are related to another group of protists. Protists are the paraphyletic subtaxon of eukaryotes. So yes, plants are much more familiar than protists and were discovered earlier.

Regnum Animalia

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Deuterostomes
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Ecdysozoans
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Lophotrochozoans
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Platyzoans
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Other bilaterian phyla
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Non-bilaterian animal phyla
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Regnum Fungi

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Regnum Protista

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(Soon to be many regna. See also: eukaryote.)

bikonts:

and unikonts:

Regnum Plantae

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Domain Bacteria

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Domain Archaea

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as with domain Bacteria, phyla/divisions are gradually morphing into kingdoms

Viruses (not alive, i. e. ametabolic, but evolving anyway)

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See also

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