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The science and practice of organizing and classifying Pokémon into a coherent ordering that does not directly contradict the already well-established taxonomy of all other life forms is a daunting task that has troubled Pokémon biologists for some time due to several main factors: the general differences between Pokémon and other life forms at the cellular level; contrary to that, the similarities in body structure of many Pokémon and similar animals; the dilemma of whether to count Pokémon as more closely related by Elemental type or by body structure; and the lack of any sort of clear pattern of common decent amongst Pokémon, contrary to most other categories of life.

The first and foremost point that must be addressed in Pokémon Biology is their inherent cellular energy signature.  This is the reason why Pokémon's cell structure can be easily destabilized and compressed into energy for storing inside a Poké ball.  It is also the reason why Pokémon evolve—rather than undergoing a gradual process of maturity like ordinary plants and animals, their energy signature changes at once from a stimulus, be it an increase in strength, radiation from an Elemental Stone, or a certain emotional state.  This fluctuation triggers the genome for their evolved form and starts a sudden change in body structure.  (It is, of course, important to recognize Pokémon evolution as a metamorphosis completely unrelated to the principle of evolutionary descent.  Also of note is the fact that this process is separate from sexual maturity, as the vast majority of Pokémon do not need to reach a higher evolutionary level in order to reproduce.)

A family is a self-contained evolutionary line of Pokémon.  Each individual Pokémon has a unique energy signature, much like each life form has a unique genetic code—similarities that determine how closely related a Pokémon is to others are determined by species, element, and type.

Upper Classification Split

There is relatively little debate that Pokémon fit into the Domain of Eukarya.  The fact that their cell structure is distinctly different from other life forms was originally a cause for concern, but it is agreed upon that this difference is generally on the same level as the cell difference between plants and animals.  This, however, requires that Pokémon be placed in a separate Kingdom of Pokémonia.

The trouble is that Pokémon share many of the classifying characteristics and body structures of Animals and Plants, requiring a split in the traditional taxonomic setup.  Pokémon can be sorted into Sub-kingdoms of Animalia, Plantae, and Umbrae (gaseous or spirit-like Pokémon, or those with amorphous bodies ).  It is important to note that even Pokémon that may be sorted into a Sub-kingdom other than Animalia generally have many similarities with animals, often being heterotrophs to a certain degree alongside photosynthesis or other feeding methods, and by being motile.

Energy signature classification is fairly simple, being based solely on the Pokémon's Elemental Type, and further categorized into subtypes within each Element (for Elements that have subtypes).

The Elemental Conundrum

For the longest time, the only concrete method of organizing Pokémon taxonomically was by Element, as ever since technology allowed for easy harnessing of Pokémon energy, it has been quite simple to analyze the variations in different Pokémon's energy signatures.  Even before this breakthrough, Pokémon Elemental types are easily observed.  There is a definite relationship between Pokémon of the same Element, but how does this compare with similarities in body structure, and what really is the "right" way to categorize Pokémon relations?

It has long been accepted that different body structures in Pokémon arose separately from different Elements, as there is little correlation between the two.  For example, a Pokémon that resembles an animal in the reptile family may have any number of different Elements, but a Pokémon that is similar to a mammal could have them just the same.  It is now theorized that somewhere very early in Pokémon development, the creatures' cell structure deviated towards being energy based and capable of being destabilized.  This would be considered a "neutral" element that does not exist today.  After Pokémon had already diversified in body form, the neutral energy structure reached a level that made it highly susceptible to outside influence, either from environmental factors or from the rich energy in the earth throughout certain regions that Pokémon first inhabited.  These energies within the earth are now thought to be the origin of Elemental Stones.  A combination of environmental pressures and reactions with outside energies caused Pokémon to pick up elemental traits.  Depending on the particular area or situation, a wide variety of Pokémon could develop the same Element despite not being closely related.  This is the reason why Pokémon whose DNA is rather dissimilar may in fact have very similar energy signatures.

The Normal type is the closest modern link to the neutral element (but it itself is clearly not neutral, as Normal-type Pokémon are often capable of learning a wide range of elemental moves).  Eevee is the only living Pokémon to be very close to a neutral element (as evidenced by its highly reactive energy signature.)

It has recently been proposed that Elements be incorporated into the newly categorized Breeding Group system, as it is a more specific trait (as such, it is located near the bottom of a complete taxonomic ordering, just above family-species.)

Differences from Traditional Classification

While other life forms are sorted by their degree of relation to other species, it is largely impossible to do that with Pokémon due mainly to the unique fact that Pokémon can breed with other species within a wide range known as a breeding group.  This is clearly the most distinct and definite observable pattern of relationships amongst Pokémon species, as it forms a rough guideline for patterns of body type, as well as the obvious reproductive compatibility that links Pokémon of similar physical structure.

Pokémon biologists must remember that Pokémon can be capable of breeding within two breeding groups, either by being close to the "branch" of two groups, or by having developmentally converged towards a second group.  There are many branches in Pokémon development that join back together—this is a very major difference from animals.  For example, Wailmer, despite being mammalian (and in the ground group), can breed with other water-group Pokémon of similar body structure to it, even though they are fish.

Notes:

The indeterminate group is mostly comprised of umbra Pokémon, but there are a few animalian Pokémon such as the Slugma and Ralts lines.  They are the closest link between the two sub-kingdoms.  Even when umbra Pokémon diverged from the animalian line, they retained the ability to breed with those in their group.

Baby Pokémon and Pokémon incapable of breeding should be classified according to the other species in their family, if any.

Scientists have concluded that Unown reproduce in a method vastly different from other Pokémon, and cannot and/or will not do so when captured.  No details on the true method have been observed, however, so no efforts to duplicate this effect can been made, by either trainers or researchers.  The Pokémon is essentially non-breedable, but until further notice, shall be classified as Indeterminate due to some DNA similarities.

The only other Pokémon that have no recorded breeding capabilities are Legendary Pokémon.  For the Legendaries who are presumed non-unique, it is believed that they only reproduce with others of their own species, (though even this is enigmatic, as the sex of most Legendaries is impossible to determine.  Even chromosomal analysis on DNA samples yields no conclusive evidence.)

For Legendaries that are, in fact, believed to be one-of-a-kind, some manner of asexual reproduction or rebirth may take place.  All Legendaries exhibit a unique fluctuation in energy structure that developed long before most Elemental-type distinctions had been made.  For this reason, all Legendaries, unique or not, are placed into the group Aethereus.


Ground – Terramammus
Monster – Belluae
Dragon – Anguis
Flying – Volatus
Fairy – Tenerrimus
Humanshape – Hominiformes
Bug – Bestiolae
Water1 – Aquatilis
Water2 – Piscis
Water3 – Sineosseus
Plant – Herbae
Mineral – Minerales
Indeterminate – Amorphes
Nonbreeding – Aethereus


Elemental Connections

Again, it must be stressed that for the majority of Pokémon, there is little to no connection between body type and energy signature.  The two factors are almost universally agreed to have arisen separately.  However, there are certain exceptions where body type did in fact influence what Element a Pokémon gained, which shall be addressed here.

Dragon
There is a high correlation between Pokémon in the Dragon breeding group and Pokémon that are Dragon-type.  As Pokémon with a draconian body structure began to branch out, the Dragon-type energy structure became linked to it.

Bug
There is a high correlation between Pokémon in the Bug breeding group and Pokémon that are Bug-type.  Similarly to dragons, the bug element arose in Pokémon whose bodies were structured most similarly to animal arthropods and insects.

Flying
All Pokémon in the flying breeding group are Flying-types.  The Flying element obviously arose through flight, even in the cases of flightless Pokémon closely related to other flying Pokémon (like Doduo.)  This is why even Pokémon not remotely related to flying-group Pokémon (like Charizard) still exhibit the Element.  Not all flight-capable Pokémon would develop the Element, however, if another influence was stronger (such as with Flygon.)

Water
Almost all Water-type Pokémon are related to one of the three water breeding groups.  It is clear that an aquatic lifestyle influenced the development of the Water Element.

Grass
All plant-division Grass-types are in the plant breeding group.  This split in the way Grass types are sorted is much higher in the taxonomic order than Elemental sub-types, and should be regarded as more significant.  Animalian Grass-type Pokémon might have gained their element through specific regional/environmental pressures, coupled with certain types of energy-based plant-life in the Pokémon regions, allowing their bodies to symbiotically grow vegetation with the same energy type that the plant-division Grass-types developed.  This is one of the only examples of convergent evolution within an Element or breeding group.  The influence of the plant growth would allow animalian Grass-types to breed with plant-division ones.


There are several more minor connections, such as a slight correlation between Ghost-types and the indeterminate breeding group, for example.  However, it must be noted this factor does not oppose what is already known about Pokémon development.  It simply means that Pokémon with those body types were more predisposed to develop certain elemental traits (for example, the Flying Element obviously had a tendency to develop in Pokémon capable of flight, but could still develop in other similar Pokémon just as well).  It does not mean that their Elements developed any differently than other Pokémon's.


A Complete Example

Presented here is a diagram of a relatively simple animalian Pokémon's full taxonomic classification.

Lucario:

Kingdom – Pokémonia
----- Sub-kingdom – Animalia
Group – Terramammus
----- Sub-group – Hominiformes
Element – Combatamechana
----- Sub-type – Adamasinteri
Family – Etherus
Species – Sentire


Some important notes to keep in mind:

Lucario's Elemental sub-type is presented because Steel-types are very clearly classified into two groups: internal and external (depending on whether they exhibit a metallic hide/appendages, or a metallic skeleton).  Not all types have such distinctions.  And in the case of some types (such as Electric), there are several overlapping subdivisions.  For this reason, Pokémon biologists need not specify sub-type distinctions in their scientific papers if they do not wish to.  Such a task is best left to type experts.

Pokémon within the same evolutionary family obviously share the same family name, but some closely related Pokémon lines will share the same family name.  There is some dispute amongst Pokémon biologists over whether the family name should be restricted to evolutionary families, and a new taxonomic level be used to sort closely related Pokémon families.  However, the aforementioned problem of breeding groups makes it difficult to determine how closely related two lines of Pokémon are, since Pokémon cannot be sorted into clades like animals can.

Use of either a Pokémon's binomial or trinomial name in scientific use has come down to personal preference.  The individual Element names have already been categorized and are generally well-known.  Many Pokémon have not been sorted into family-species, however.  Pokémon biologists are encouraged to do so when researching a particular specimen.
This took me way longer that it should have.

So, after months of being delayed by projects, work, surgery and other things, I've finally finished a complete report on everything relating to Pokemon taxonomy. However, its current state is far from static. I can and will make many changes to it, and I encourage all my fellow Pokemon biologists to make suggestions.

One of my biggest concerns was canon. Even though Pokemon do not exist, for the Pokemon Professors group to study them in a legitimately scientific way, it makes sense to go amount things in a standardized way. The problem is, by default, having a large group of people all working towards one goal makes it near impossible to have one set of rules on how things should be. Different people are going to have different opinions and are going to write their papers and draw their illustrations in line with their own theories. My goal in this paper was to be detailed while still having a broad enough scope to be compliant with many different theories. For example, I support the view that Legendaries are unique, but I deliberately compromised on that issue in this paper.

Since many of the reports on individual Pokemon utilized the Elemental name as part of the full scientific name, I incorporated that existing system into this.

Coming up with the breeding group names was challenging, I will admit. I still want better names for some of them, especially Bug and Water 3.

I'm gonna dust off my report on Electric-types and submit that soon, and then hopefully get to work writing some reports on Legendary Pokémon, which I'm particularly excited to do.

Also, I must ask...if writing a report on a Pokémon that has already been written about, or rather, already has a scientific name, do we have to use that name? I ask because I only just recently saw that all of the Kanto Pokemon already had names submitted to the group. Most of the Pokés I want to write about are 4th-gen, so it doesn't matter too much, but I was wondering.

I'm more than willing to go through the Pokédex and come up with genus-species names (well, for everything 2nd-gen and onward), but I'm not sure if this would be helpful if people want to come up with their own names when doing reports.


(And this is random, but for the life of me, I cannot figure out which deviantArt category to put this into. The only "academic paper" category is under non-fiction. x.X
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:iconheraldofopera:
HeraldOfOpera Featured By Owner Jan 8, 2017
One minor error: Doduo can, in fact, fly, because it can learn the move Fly via HM. Nobody's quite sure how that works.
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:iconfusroderp:
FusRoDerp Featured By Owner Edited Mar 28, 2016  Hobbyist General Artist
Families normally end in the suffix -idae, and there is also a genus after families. I know taxonomy from my studies on spiders, but good work overall.

For example, the Daring Jumping Spider

Domain Eukaryota
Kingdom Animalia
Phylum Arthropoda
Subphylum Chelicerata <Has Chelicerae: Arachnids, Sea Spiders, and Horseshoe Crabs>
Class Arachnida
Order Aranae
Suborder Opisthothelae <Non segmented abdomen>
Infraorder Araneomorphae or Labidognatha <True Spiders>
Family Salticidae <Jumping Spiders>
Genus Phidippus <Jumpers with Iridescent Green Chelicerae>
Species P. audax

Again, good work.
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:iconreptillicus:
Reptillicus Featured By Owner Oct 22, 2013
my god your a poke- genius
Reply
:iconstarwolf66:
starwolf66 Featured By Owner Aug 2, 2012
my brain is hurting from the sheer amount of lines in this!I lose my place sometimes!
Natsu Dragneel:*brain broke after first paragraph*
Allen Walker:*attempted to read this,brain broke after 7th paragraph*
Laharl:*didn't bother to read it after the title*
Me:...........believe me I'm a bookworm and losing my place happens often.
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:iconhs666:
hs666 Featured By Owner May 18, 2012  Hobbyist General Artist
thank you college biology for helping me understand the big words, now... back to being stupid [link]
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:iconchammy3760:
chammy3760 Featured By Owner Oct 10, 2011  Student General Artist
Okay, in my fanfic I've written myself into a bit of a corner, and I'm trying to find a way out of it that isn't completely devastating to my characters. Long story.
Anyways, I plan on saying that an Arcanine was captured while in the process of evolving. The poke ball encoded her energy pattern while it was halfway between growlithe and arcanine, and she was never exposed to fire stone radiation after being captured. As a result, she's stuck halfway-evolved, but a fire stone now should allow the transformation to finish.

This would be the easiest solution to work into my story as I've already depicted this Arcanine as being abnormally small and lacking the tufts of fur that most Arcanine have on their legs. I just want to know if it sounds feasible to you.
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:iconchibi-pika:
Chibi-Pika Featured By Owner Oct 13, 2011  Student General Artist
Oof, sorry about the delayed response. That's actually a really cool idea, and one that I never would have thought of. I can easily see a Pokemon having its energy compressed while in the midst of evolution being stuck halfway. And yeah, in that case, being exposed to another Fire Stone and reinitiating the transformation would make sense as the way to make the full transition to Arcanine (since she's still part Growlithe, she could still react with a stone.)
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:iconchammy3760:
chammy3760 Featured By Owner Oct 14, 2011  Student General Artist
well, after careful consideration and a bit of counsel from another fanfic writer I decided that introducing this now would be overcomplicating things way more than necessary, but I may use the idea at some other point. Thanks for your input :D
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:icontotaldramafan16:
TotalDramaFan16 Featured By Owner Sep 5, 2011  Hobbyist
I cant believe I read all of this
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:iconsoldierofdawn:
SoldierOfDawn Featured By Owner Jul 27, 2011  Hobbyist Writer
It's as if it were written by Professor Oak himself.
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:iconrosutu:
rosutu Featured By Owner Apr 27, 2011
This...is...glorious.

The grounding in scientific principles (to a degree of "scientific"), the inclusion of both elemental types and egg groups as means of classification, the incredibly simple explanation for Pokemon evolution...

This just puts all of my pieces to shame. Fantastic.
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:iconchibi-pika:
Chibi-Pika Featured By Owner Apr 27, 2011  Student General Artist
Thank you very much. =) It was very interesting to write, sort of like a culmination of all my theories.
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:iconshinwa-tsuki:
Shinwa-Tsuki Featured By Owner Apr 1, 2011
Very nice!

Er, what do you mean with the Water 1, Water 2, and Water 3 - in the main body of text, I don't understand that.

I do know, that I will end up using this to help.
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:iconchibi-pika:
Chibi-Pika Featured By Owner Apr 5, 2011  Student General Artist
Ah, those are the actual names of the in-game breeding groups. Water 1 are Pokemon with an amphibious nature. Water 2 are fish. And Water 3 are shellfish/invertebrates.
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:iconshinwa-tsuki:
Shinwa-Tsuki Featured By Owner Apr 5, 2011
Ah, okay.
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:iconmadgenius2013:
madgenius2013 Featured By Owner Mar 21, 2011  Hobbyist General Artist
So, what would Mew's taxonomy be?

By the way, this is great!
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:iconrayhak:
Rayhak Featured By Owner Feb 22, 2011  Hobbyist Digital Artist
You're a genious ChibiPika!
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:iconwolfenphoenix:
wolfenphoenix Featured By Owner Dec 26, 2010
Very well done! Taking something like pokemon, and applying realism and/or science to it is always fascinating. *can't press the favourite button enough*
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:icontitanwarrior17:
TitanWarrior17 Featured By Owner Nov 5, 2010  Student General Artist
My God this is Brilliant!!
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:iconmegalemon:
Megalemon Featured By Owner Sep 24, 2010  Hobbyist Digital Artist
I would just like to very maturely say...

That. Was. The. Shit.

...Er, so to speak.

Of any piece of science-fictional writing (especially taxonomy) that I've read, THIS. This was the absolute "bee's knees". I can safely say this is the default behind Pokemon science for me, because you made sense of every concept about Pokemon that I could not grasp nor understand.

Ah, nevermind me. I know you've heard all this before. I just had to express my thoughts on this somehow.
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:iconcarl-linnaeus:
Carl-Linnaeus Featured By Owner Sep 18, 2010   Photographer
This is quite relevant to my interests.
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:iconchibi-pika:
Chibi-Pika Featured By Owner Sep 18, 2010  Student General Artist
Why thank you, it's an honor to have the father of taxonomy post on my studies. ;)
Reply
:iconcarl-linnaeus:
Carl-Linnaeus Featured By Owner Sep 21, 2010   Photographer
But of course. I found them rather fascinating.
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:iconarcel-windwing:
Arcel-Windwing Featured By Owner Sep 6, 2010
... thank you so much for writing this! I myself was always curious about pokemon Taxonomy and finding connections between them all. Though mine was more in the physical simularities, this is still so amazing!

Big Fave for me so I can finish reading it soon.
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:iconderfisch95:
derFisch95 Featured By Owner Sep 4, 2010  Hobbyist General Artist
Wow, if there was anything that needed such areport, it was Pokémon. :XD:
No, really. It's nice to see someone act all professionally about such an underappreciated topic.
Reply
:iconparadoxincarnate:
ParadoxIncarnate Featured By Owner Aug 30, 2010
Epic.

I love the idea of applying the scientific method to almost everything, and you did it FANTASTICALLY.
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:iconhawktakesflight:
hawktakesflight Featured By Owner Aug 21, 2010
This is a remarkable job. There are so many problem inherent in classifying Pokemon as such, but you managed to provide a workable solution, and to top it all, presented it in an interesting and clear manner.

Once again, a very well done piece of work.

hawk
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:iconsoopaninja:
SoopaNinja Featured By Owner Aug 18, 2010  Hobbyist General Artist
So are yo a pokemon professor, or do you just play one on TV?
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:iconchibi-pika:
Chibi-Pika Featured By Owner Aug 18, 2010  Student General Artist
Heh, well I play one on the internet. =P
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:iconboltfraction:
BoltFraction Featured By Owner Aug 17, 2010  Hobbyist Digital Artist
Bravo. You tackled a very daunting topic in the realm of Pokemon biology.

As much as I'd love to really pick through the details of the article myself, I admit I'm not very familar with Pokemon breeding in general. (Having not played the games up to where that mechanic was introduced.) Regardless, your article was coherent, very well written and explained, and easy to comprehend, even to someone with no experience in the subject.

Again, a job very well done.

Ah, if only all reports on taxonomic issues were so interesting to read!

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