Paper published on Pokémon Phylogenetics... with Prof. Oak as co-author!

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    Default Paper published on Pokémon Phylogenetics... with Prof. Oak as co-author!

    This was the product of months of data collecting and 16million generations of simulated Pokémon evolution.

    The results are surprisingly realistic! Pokémon life seems to have begun in the water, with terrestriality evolving later. The psychic pokemon evolved from the birds. The missing link between the grass types and the normal types is Venusaur. Nidoking and Nidoqueen are sister groups and should probably be lumped into the same species. Etc, etc.

    The best part: The paper was PUBLISHED in a peer reviewed [humor] journal! And PROFESSOR OAK IS THE CO-AUTHOR! Published in the Annals of Improbable Research, vol 18, nov 4, p15-17. "A Phylogeny and Evolutionary History of the Pokémon." by Matan Shelomi, Andrew Richards, Ivana Li, Yukinari Okido.

    Improbable Research

    See the tree below:
    http://i.imgur.com/e8eFs.jpg
    Last edited by PokéProf; 1st October 2012 at 12:33 PM. Reason: adding a spoiler around that huge picture

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    Default Re: Paper published on Pokémon Phylogenetics... with Prof. Oak as co-author!

    I find that the most interesting part is how the Pokemon mentioned are all fully-evolved, so there aren't any of those base ones that have multiple evolutions. Some of the branching is very strange also, like how Crobat is closely related to insects, and how Forretress is related to the minerals when it is more of an insect-based Pokemon. Perhaps the strangest has to be Smeargle and Ditto's relationship. One of the theories that is brought up in the forum is how Ditto and Mew are more closely related, so seeing Ditto and Smeargle in the same branch is very surprising.

    I don't understand what phylogeny is, so I may not be right with what I am going to say. When I think of a tree of related Pokemon, I would think of the Egg Groups and see if the Egg Group's Pokemon are grouped together. Some are just about right, like the plant-related Pokemon, but some are quite scattered, like the Amorphous ones, since this one is a bit scattered (Gardevoir, Magcargo, Jellicent). The Legendaries are rather flexible, so I don't have much of a say here. It looks like the grouping is based more on type than on species. I understand it's for humour, so I probably should think about it too much.

    Thanks for reading.
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    Default Re: Paper published on Pokémon Phylogenetics... with Prof. Oak as co-author!

    I can't pull up the bigger version in the link.

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    Default Re: Paper published on Pokémon Phylogenetics... with Prof. Oak as co-author!

    Quote Originally Posted by pokepimp View Post
    I can't pull up the bigger version in the link.
    He got the link wrong. It's http://i.imgur.com/e8eFs.jpg

    Anyway, I also think that a lot of it is a bit odd. First off, why are most of the nodes binary? Almost all of them only have 2 branches. Maybe I'm reading it wrong (I have no idea how to read phylogenic trees), but it appears that each parent node represenents an unknown extinct Pokémon that evolved into its children nodes
    But then there's some major problems with it:
    - All of the "fossil" Pokémon and "living fossil" should be at least a little further up the tree (especially Aerodactly who should be way further up)
    - Unown should be a lot further up the tree
    - "Alien" Pokémon (Clefairy, Deoxys) shouldn't even be on the tree as they didn't descend from anything on this planet
    - A lot of the Legendary Pokémon shouldn't be on the tree either, if the legends are taken to be true. If not, I guess they're fine, except for the fact that most do seem out of place
    - This tree is too concerned with the actual typing. The three birds should clearly be closely related. Same for the three beasts. Even more-so for the beasts if the theory is true that they had a different form before being revived by Ho-Oh, because for all we Entei wasn't always a Fire-type, Suicune wasn't always a Water-type, and Raikou wasn't always an Electric-type.
    - Mew and Mewtwo are wrong. I assume that this tree is thinking that the "Mew fossil" that Mewtwo was cloned from wasn't actually a Mew fossil but was instead the fossil of an extinct descendant of Mew. This could make sense, but I've always been under the impression that Mew was a "living fossil" (completely unchanged from the beginning). Especially if the theory is true that nearly all Pokémon descended from him, which would place him higher up on the tree (not to mention he'd be a parent node)
    - Many of the placements seem really odd or arbitrary just based on type alone. Example - why are Articuno and Delibird descended from a mammal? That doesn't reflect real-world evolution theory and isn't even consistent with how it's been done elsewhere on this tree
    Last edited by Xenidal; 12th September 2012 at 08:56 AM.
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    Default Re: Paper published on Pokémon Phylogenetics... with Prof. Oak as co-author!

    They seem to be based solely on body-type and typing. As if, "Zapdos is the precursor of electric birds and Articuno is the precursor of Ice birds!" And putting them in entirely different branches when they should be basically the same species.

    Then there's some ordering that simply makes no sense either from disregarding entirely the pokémon's concept (Not just legendary pokémon, that shouldn't even be there. It lumps pokémon that clearly are related far from within each other simply out of typing and body type), or even from a biological standpoint (what the hell is Volcarona doing NOT with the lepidoptera while CROBAT is?!)

    [/overexposition]

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    Default Re: Paper published on Pokémon Phylogenetics... with Prof. Oak as co-author!

    Thanks for all your comments!

    All phylogenetic trees, including those in real science, are hypotheses and not necessarily correct. Crobat's presence among the bug pokemon is obviously wrong, but the reason it occurred is called "long branch attraction," a common error in such trees.

    Remember, this tree wasn't done manually. It was all done with a computer that was fed data on pokémon attacks, and this tree was one of the best responses from the many possible trees the computer created. It is a tree based solely on the data, so the fact that the tree resembles real-life evolution and cites pokémon lore as closely as it did is pretty incredible, but of course it won't reflect the pokémon canon 100% accurately anymore than, say, real evolutionary trees reflect creation myths (in the Pokémon world, Arceus-Creationists are threatened by Evolution Science and a

    Xenidal is right: each parent node represents an unknown, probably extinct ancestor of the current, extant pokemon. That's how evolution works: it's a tree not a ladder. For example, humans didn't evolve from the apes, but a common ancestor split into apes and humans.
    You're right that Alien pokémon shouldn't be on the tree… except their ability to breed with other pokémon suggests they aren't so much aliens as they are extraterrestrial cousins. Maybe Pokémon life started in space? Or maybe the tree counters their extraterrestrial origin.
    The tree used attacks (which are often type-based) to form, and this works surprisngly well! The dog pokemon are mostly together, the cat pokemon mostly together, etc. Frankly, I'm amazed the tree works as well as it does!
    Why should the original legendary birds be together? Most legendaries came out as closely related (as expected), except the Articuno/Zapdos/Moltres trio. If we trust the tree, then this suggests the legendariness of those birds was based on their similarities (huge elemental birds) and not on any actual relatedness between them.
    Why are Mew and Mewtwo wrong? Remember, Mewtwo is a genetically engineered creature. Who knows what they did to his genome? That he came up as close to Mew as he did impresses me on the strength of this tree, and the finding that Mr. Mime (the most humanlike pokemon) is also the most "advanced" Pokémon on the tree is nice too.
    Why are ditto and smeargle so close together? Because both have only one move unique to them. The computer used Ditto as an "outgroup," meaning the tree initially assumes he's the origin of all life due to his, well, ability to turn into all life. It makes sense that Ditto's put near Smeargle on the tree, but their lack of attacks means the computer had little data to work with so their placement on the tree is likely the least trustworthy. The strength of a tree is measurable in "bootstrap values" which I did not include on this tree (it would take days to calculate that!), but I imagine some nodes on the tree have high values and some low.

    Here's another fun result from the tree: The Kangaskhan/Cubone relatedness hypothesis has been disproved.

    Thanks for your comments! Let me know if you have more questions.
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    Default Re: Paper published on Pokémon Phylogenetics... with Prof. Oak as co-author!

    Another problem is that some Pokemon on the tree such as Golurk and Muk are known to be man-made, and couldn't possibly be descended from anything. Do you have a list of the characters that were used to define the clades? It would appear that typing is usually an ancestral character in this tree, which is something I would consider to be highly unlikely.
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    Default A Rebuttal of the UC Davis Pokemon Family Tree

    Hello everyone, recently I constructed sort of a pseudo-essay in response to the UC Davis Pokemon Family Tree which can be seen here: http://i.imgur.com/e8eFs.jpg

    To me, the family tree seemed flawed so I tested their hypothesis of the Pokemon Family Tree by analyzing the Moths and Butterflies and focusing on their unique and shared characteristics. This was done for the fun of it and I would like to hear what you guys think of it and to the UC Davis Family Tree in general. Thanks for your time!

    https://dl-web.dropbox.com/get/Public/A%20Rebuttal%20of%20the%20UC%20Davis%20Pokemon%20Family%20Tree%20Using%20the%20Butterflies%20and%20M oths.pdf?w=49984978
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    Default Re: A Rebuttal of the UC Davis Pokemon Family Tree

    Quote Originally Posted by LibraSnakes13 View Post
    Hello everyone, recently I constructed sort of a pseudo-essay in response to the UC Davis Pokemon Family Tree which can be seen here: http://i.imgur.com/e8eFs.jpg

    To me, the family tree seemed flawed so I tested their hypothesis of the Pokemon Family Tree by analyzing the Moths and Butterflies and focusing on their unique and shared characteristics. This was done for the fun of it and I would like to hear what you guys think of it and to the UC Davis Family Tree in general. Thanks for your time!

    https://dl-web.dropbox.com/get/Public/A%20Rebuttal%20of%20the%20UC%20Davis%20Pokemon%20Family%20Tree%20Using%20the%20Butterflies%20and%20M oths.pdf?w=49984978
    Sorry, it returns a 403 error.


    Pokémon evolution (say, "evolution" in the real-life sense) is something interesting I've thinking for a while. As other people said, looks like this tree was generated considering types first, which is wrong (for example, clearly Woobat and Zubat are much closer; both are bats. Also, where go Eeveelutions?).

    I think a first approach to make a better tree, could be Egg groups. Clearly if two Pokémon can breed, they must be (although distantly) related. It gets a bit complicated with Pokémon belonging to more than a group, however.


    As for the Legendaries' case, I've always assume that they belonging to no group doesn't mean they aren't able to breed, but it has been impossible to breed them at a man-made environment. That's something that happens even in real life; some species don't breed at all if not in the wild.
    Last edited by Ziggy Stardust; 1st January 2013 at 10:43 AM.

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    Default Re: Paper published on Pokémon Phylogenetics... with Prof. Oak as co-author!

    Ah, that's a bit embarrassing, it worked when I tried it, I believe this link will work though...

    A Rebuttal of the UC Davis Family Pokmeon Tree

    Egg groups are actually something that I addressed in the paper. The fact that many pokemon can breed and interbreed with it each means that it can highly confuse any potential family trees. Egg groups would point towards a world that was more God created (which it is for the most part) than a step-by-step evolving process where species change over time. Legendaries are also tricky to comprehend but maybe for this scenario they're just really powerful pokemon that live, breed and die just like any other pokemon.
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    I REFUSE TO ACCEPT THAT RAMPARDOS AND A DUNSPARCE ARE THAT CLOSELY RELATED

    Looks like a reasonably well made tree of evolution.

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    Default Re: Paper published on Pokémon Phylogenetics... with Prof. Oak as co-author!

    Hi Everyone,

    To reiterate, types were NOT the basis of this tree. Attacks were, although i also included type, egg group, and body group data as well. That the results break up into types suggests that the Pokémon evolved along those lines and that types are monophyletic groups… assuming Pokémon evolved and are not just fictional creatures invented by Nintendo.

    Also, NO manual manipulation of the tree was performed. The tree is the result of 16million computer simulations, and that's it. I could have manipulated the tree to get rid of some glaring oddities, but that would be subjective and not the kind of quantitative science done by molecular biologists today. I've made no claims that this phylogeny represents reality as, again, Pokémon are not real.

    The full text of the article has been pasted here. It should clarify everything, and is a fun read if I do say so myself. A Phylogeny and Evolutionary History of the Pokémon - Neatorama

    @LibraSnakes, as much as I love rebuttals, I notice you picked the one part of the tree I am least pleased with. I have mentioned above that Crobat in the bug groups is an error caused by long-branch attraction. As for how Dustox and Beautifly were not placed as sister groups, this always bothered me about my tree. Other male/female pokémon in the tree, however, were always placed as sister groups. I suspect if you ran your analysis method on another branch of the tree, you would probably reach conclusions similar/identical to mine.

    In the real world, trees made with genetic data include a statistic called a bootstrap value, which shows, for each node of the tree, how much statistical support the node has (from 0-100, with 100 being a strongly supported relationship, and anything below 50 being unreliable). Our tree didn't include these because, well, it would have taken days to run the program and the computers were needed for real science. If we had, the bug part of the tree could show low bootstrapping values.

    I would be interested in seeing how the tree looks when one factors levels of attacks into it, or if egg group is weighted heavily, etc. If any of you are in the biological sciences, I look forward to seeing what you can do with the ample data on bulbapedia and serebii.net!
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    Default Re: Paper published on Pokémon Phylogenetics... with Prof. Oak as co-author!

    " Conservationists have highlighted the importance of documenting extant Pokémon, many of which are known only from single specimens and all of which are threatened by the Pokémon fighting rings that are growing rapidly in popularity, particularly among urban youth."
    Oh my god, this is the most hilarious way I've heard pokemon training described in the history of history.
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    Default Re: Paper published on Pokémon Phylogenetics... with Prof. Oak as co-author!

    Why is Toxicroak a relative of Honchkrow rather than Seismitoad? Why is Volcarona more closely related to Beedrill and Ledian than to Mothim, Beautifly, Dustox, and Butterfree? Why are manmade Pokemon like Spiritomb, Golurk, Garbodor, etc. on there? This looks logical, but there are a few errors...

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    Default Re: Paper published on Pokémon Phylogenetics... with Prof. Oak as co-author!

    While I disagree with many many many things in that chart, I'm SO Glad it exists, shows that people can still work hard for Pokémon, even if the result was cheese.

    Also, would like to point out that Prof. Oak wouldn't be the best help in the matter, how about Prof. Elm and Rowan? Surely their lines of works have more to do with this.

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