The Tree of Beginning

The movie Pokémon: Lucario and the Mystery of Mew starts like most Pokémon movies do, with an introduction to what are Pokémon. However, this time, rather than random Pokémon in random squares in random space, the visuals are showing us something very interesting. We see something kinda like the phylogenetic tree of Pokémon - a visualization of speciation showing the relationships and relative timing of lifeforms. This tree starts with Mew, branches to show fossil Pokémon and other ancient Pokémon, and works its way up and up to the Legendary beasts and finally to Ho-oh.

In the unknown reaches of time, strange and wondrous creatures appeared on this planet. We call them Pokémon. Over the years, countless varieties of Pokémon developed. Researchers have identified hundreds of different types, but many more are yet to be discovered.
Mew shown as the last common ancestor Pokémon in the prologue of Pokémon: Lucario and the Mystery of Mew

Note that the Pokémon rain down at different speeds, and the tree branches grow up at different speeds, so any individual screenshot of this mess is going to be misleading. It isn't literally showing the branches and the relationships between the Pokémon, but more so a general sense of the relevant timing of the different Pokémon species emerging. Not every Pokémon that existed at the time is pictured, but there are some notable ones that we can think about.

Mew is known to be the common ancestor of all Pokémon, making it the very root of the Pokémon phylogenetic tree. This animation shows this by having Mew rain down the screen all by itself, and only then does the tree start to branch with more Pokémon raining down.

Animated gif of Mewtwo and Mew in the Season 1 opening

The visual here, with Mew traveling down toward the planet, seems to lend some support to the theory that Pokémon originally came from outer space. Mew could be an alien lifeform that arrived on the planet and then began the process of mutating and speciating to better suit its new environment.

Then we see Omanyte, Omastar, Kabuto, Kabutops, Aerodactyl, Lileep, Cradily, and Anorith. These were Pokémon that could be revived from fossils as of Generation III, so, of course, they would be at the beginning of the tree as ancient Pokémon. There is also Relicanth, which, while not revived from a fossil, is considered a "living fossil" which has been existing in its current form for millions of years.

Lileep and Cradily in the Tree of World's Origin
Ditto Carddass Illustration of a confused Ditto trying to simultaneously transform into Bulbasaur, Squirtle, and Charmander.

The next Pokémon is Ditto, an amoeba that is also kinda presented as being primordial and able to transform into anything. Ditto is the only Pokémon other than Mew which is able to learn Transform, a similarity which has spawned theories about their possible relationship. The theories will be discussed at a different point, but anyway, here is where Ditto was placed in this phylogenetic tree.

A little above we see Staryu and Starmie, which are based on starfish, which, in real life, have existed in some form since 450 million years ago. There is Yanma, which is based on a meganeura, an ancient kind of giant dragonfly. Nearby, there is Tropius, which is based on a dinosaur and a banana tree, both of which existed in the Cretaceous period. And there's Lunatone, which is based on the moon, and therefore old (Solrock is not there, though).

Tropius

Not shown in this visualization, but appearing in the movie itself, are more Pokémon at the base of the Tree of World's Origin. Together with the fossils and Yanma, we also see Ledian, Ledyba, Nidoran male and female, and Altaria. Ledian and Ledyba are based on ladybugs, which arose in the Cretaceous period. The Nidorans are like dinosaurian rabbits. Not sure about Altaria, but we can accept it as being ancient.

Slowking loses its hat and becomes confused
Slowking's timing relative to Slowpoke implies that ancient Slowking lost their "crowns", making them the more modern dull-witted Slowpoke

But going back to the phylogenetic tree in the opening, here is where a lot of more different Pokémon appear. We see Wooper and Quagsire, which are amphibians, and therefore belonging to a relatively ancient lineage. The same is true of Slowpoke and Slowbro, as alligators/hermit crabs/amphibians... whatever they are. Interesting that Slowking appears before them, implying that the modern form is less intelligent than its ancestor. We see Heracross, which is based on a stag beetle, and Shuckle, which is based on a barnacle. There is also Bellsprout, which is based on a pitcher plant, which seems like it would be older, but is actually a relatively recent group of plants. Whoops. There are also a few puzzling ones, such as Duskull... and Magnemite. We would have thought Magnemite evolved alongside human-made magnets, but we guess not. Maybe magnets were inspired by Magnemite.

A bit later we see Electrike and Manectric, which are simultaneously reptile-like and wolf-like. We see Farfetch'd and Psyduck, both of which are based on ducks, which form one of the older branches of birds. The first more evidently mammal-like Pokémon appear here: Sandshrew and Sandslash, which look somewhat reptilian, although in reality pangolins aren't actually that ancient.

Xatu

Next there is Roselia, representing the appearance of eudicots, the later branch of flowering plants. We see Pidgey, which can represent the more recent branch of birds. Now we start to see Pokémon that presumably interacted with ancient human culture. There are Natu and Xatu, which, in the Pokémon world, might have been the inspiration for totem poles. Similarly, there is Nosepass, a Moai come to life. There's also Mareep, representing the domestication of sheep - woolly sheep were bred by humans and do not exist in the wild.

The Legendary Birds

Next is where we see a few legendaries: Rayquaza, Articuno, and Moltres (but not Zapdos, and not Groudon or Kyogre). This is puzzling. It would seem like these would all be primordial deities, and therefore ancient, but it might not be the case. Or they might appear here due to the problem of the Ladder of Life seeing evolution as a progression from weak to strong, rather than just temporal relations.

After that, we see Entei, Suicune, and Raikou. It may seem weird to see more legendaries this late, but, actually, this does make chronological sense: the legendary beasts are some of the most recently-born lines of Pokémon, since they were brought to life by Ho-oh after the fall of the Brass Tower, which happened in human memory by the time of Pokémon Gold and Silver. In the games, you can talk with an old man next to the tower who says he was there when it happened. The recentness of these Pokémon stumbled even the anime writers, who made the core premise of the Raikou Special about how humans betrayed Raikou in ancient history. That can't be, if Raikou is about 60 years old.

Entei, Raikou, and Suicune in the Burned Tower
Ho-Oh

Last, and far away from everything else, there is Ho-Oh. Especially since we know Ho-oh's role in the emergence of the Legendary Beasts, implying that it should be chronologically before them, Ho-oh's position at the top might be less of an implication of Ho-Oh having evolved recently, and more of a reference to the mythical Simurgh, which is a bird said to roost on top of the biblical Tree of Life.

This sequence only shows a few Pokémon that existed at the time, between generations III and IV. It didn't show every Pokémon that existed, and it couldn't have shown other later-released Pokémon that we would have liked to see. Unlike the usual portrayal of the Tree of Life with humans at the top, we'd think recently-born Pokémon like Trubbish would be at the top, together with Grimer, Koffing, Voltorb, Porygon, and especially Mewtwo, which is conspicuously absent from this scene, since this movie didn't want you to be thinking about Mewtwo.

Arceus creating life
While Mew represents evolutionary theory in the Pokémon World, Arceus instead represents creationism.

We wonder what they would have done if Arceus had been released yet, to try to bridge the gap between these conflicting Pokémon cosmologies. The myths of Arceus, Dialga, Palkia, etc. imply that these Pokémon predated Mew - they were Pokémon that just sorta appeared in the cosmos and acted as creator deities, and are therefore not part of Pokémon phylogeny on the planet.

The Tree of Beginning

While this introduction of a Pokémon phylogenetic tree is very interesting and gives me a lot to ponder, it also appears as a literal location in the movie itself, which raises more questions than it answers. Depending on translation, it is called The Tree of World's Origin or the Tree of Beginning, and its role in the Pokémon World and its place in Pokémon cosmology, the reasons for it being a literal representation of the Tree of Life, the explanation for why it is simultaneously a giant organism and also a mountain made of rock and crystals, the part the Tree played in the great war a thousand years ago, the connection of the tree with the power of "wave" or aura, why the Tree sometimes needs to be healed through another creature's sacrifice, the Tree's stated symbiotic relationship with Mew and its implied ties with Ho-oh or the Legendary Golems or Bonsly or any of the other Pokémon that live around or within it, the vague implication that the area around the Tree allows for the bridging of time and space, the feeling that the Tree of Beginning is more like some sort of living diorama than a naturally occurring habitat, the Tree's nearness to Pewter City (a town with a museum full of Pokémon fossils) and Mt. Moon (the site believed by some to be where Pokémon first arrived on the planet), and any other ramifications of such a thing being in the Pokémon World are not adequately explored in the movie, unsatisfactorily leaving me alone with way too many questions that I need to fill-in with my own head-canons. But that's the subject of an article about the movie as a whole.