@Background Pony #8330  
Equestria was intelligently created by the artists at Hasbro and evolved over several successive writing teams.
 
 
@Frustration in Excelsis  
I’m really glad you made that comment. A single common ancestor is not an inherent implication of Darwinian evolution. The magic of Equestria seems to permit recombination events in macrobiology instead of reserving distant hybrid species for the realms of bacteria and viruses.

@Ghost Reviews  
Reality matters, that’s why philosophy and argumentation is very important, feelings don’t matter as much as the facts.

@Ghost Reviews  
It’s actually important to argue about beliefs, we need to try to figure which beliefs are false and which ones are true, because truth matters, truth is more important than anyone’s feelings.

Considering several of the chimeric creatures, including the literal chimera, separated into normal animals when fully drained of innate magic, some of the speculation in these comments might have been on the right track.

The center is Discord, out of the primordial Chaos all life formed.

deepest lore

@Frustration in Excelsis  
Chimeric creatures would have to include pegasi, which seem to be mammals but have six limbs, and possess both feathers and hair.

@Stotter
 
The real trick would be to place chimeric creatures like the chimera, or the manticores (where do vertebrates with arthropod bits fit in in the tree of life?). However, as @mathprofbrony touched on, it’s not really possible from this image alone to tell how evolution actually took place in the world of MLP.
 
One thing I want to say is that despite what seems to be a common misconception, the theory of evolution says nothing about how life originates: it is concerned entirely with what happens to preexisting life. Put simply it says that, assuming a population of organisms where vacation exists between individuals and that this variation is inheritable (so the traits of a creature depend on the traits of its parents), environmental pressures will cause the organisms best fit for surviving in their current environment to be more likely to live, to produce more young, and thus to alter the future makeup of the population. This describes how a preexisting tree of life develops, but does not say how it starts off – there are other theories for that.
 
What I’m trying to get that is that, even in a classical mythological world originating from a magical/divine creation event, evolution can still perfectly well occur. The fact that things do not originate as the did in our world does not, by itself, affect this.
 
So to actually address your comment: it’s possible that life in the pony world all branched off from a common ancestor. It’s also possible that they originate from hundreds or thousands of separate, simultaneous creation events which have since branched off and diversified. It’s possible it’s a hybrid of the two, with many small creations happening all the time. I’m tempted to go towards the third option – we’ve seen how even pre-alicorn Twilight can casually turn animals into plants or plant-animal hybrids and vice versa, and with centuries and more of wizards, alicorns and Discord running around throwing magic all over the place… I mean, just for example: think of how many creatures Discord causally remakes in his first two appearances, and imagine him doing this for centuries at a time. If even a few were common enough to create breeding populations…
 
What I mean to say is that it’s very likely, and worth considering, that a lot of the mythological and otherwise unusual beasties of the show’s world likely didn’t originate through natural means. Many may have been evolving naturally for a long time, but I bet you that once you go far back enough in the phylogenetic trees of manticores, chimeras, changelings, cockatrices, ursas and all the rest you might find that they originated in very odd ways.

I always wondered where certain mythological creatures would fit on a phylogenetic tree.  
Dragons for example, seem very placeable in the tree, but I’m only 100% sure they’re amniotes. Beyond that, you could end up with a kind of dragon down any of those paths.

This is clearly a phylogenetic tree and thus the concept must have some basis in Equestria. The presence of the formula suggests a notion of mutation rates or at least some steady measure of speciation; the jagged graph could be anything but in this context could well represent extinction/speciation events.
 
However, remember that part of the joke in this scene is that Fluttershy isn’t naturally a hard scientist or an experienced teacher. She’s familiar with this material but might be forgiven a minor mistake or two, such as missing a blue line connecting the blue group to the rest of the tree, or the central object to the other groups.
 
I think the best we can conclude from this brief flash on the screen, then, is that long-term, large-scale evolution is a recognized and measurable force in Equestrian ecology. Details of the creation of Equestria or how much “a wizard did it” affect the process are impossible to conclude with certainty from this context alone.

@Background Pony #D044  
Well, that’s not really evolution. It’s metamorphosis.

Why must there be arguements about evolution? Why can’t we just stop arguing and agree evolution in Pokemon and Digimon is awesome?

@Ninji  
>> I shut down arguments with logic
 
Accusing others of being “emotionally vulnerable people who have been abused and indoctrinated into turning off their brain” is not “logic” - it’s ad hominem. You will stop that, now. That’s not ok anywhere on the site.
 
@Ari Ardwolf  
You need to stop, too - it takes two to tango, and right now I am asking both of you to go somewhere else. Take it to PMs if you must.

@Ninji  
We’re trying to talk about a fyaying cartoon! We don’t need to apply what’s believed IRL in it to the extent you are. You’re literally attacking religion with no merit. Why do you think I talked to Derpy Hooves about this.

@Ninji  
Uhm … wow that is hard to parse, but it sure sounds like “come at me bro”, at which point I’m going to have to ask you to leave the bar and take it outside - preferably far enough away that the police won’t associate whatever you’re about to do next with our establishment.
 
The forums is far enough, if you want to keep going at it.

@Ari Ardwolf  
But I shut down arguments with logic, you shut arguments down with vague threats.

@Ninji  
It’s not wether you believe in a god nor not, I could care less. It’s the fact that you’re acting a Neigh-Say.

@Ari Ardwolf  
I will, can and would.
 
I’m interested about this god inspired personal attack. You can try to break yourself just to have a brief chance at being an inconvenience to me.

@Ninji  
Then go to the flipping forums and argue there. That’s what I was told to do. Please don’t trigger me, I will make your life torture, just ask anybody in the vore community I’m in

@Ari Ardwolf  
There ain’t going to be no big argument. It was a poke and a shove, creationist don’t actually have an argument, they just kinda tell you that they’re allowed to babble about whatever they want, which I true.. i guess.

@Ninji  
Ok, I’m bringing in the moderators. This is getting out of hand