Given that thestrals are very similar to Pegasi, but their numbers are quite small, the conclusion suggests itself that they can be artificial species. If they are artificial, where did they come from? Are they just converted pegasi? Or completely separate species?

For example, in my headcanon, batponies are divided into two "waves".
The first "wave" were pegasi tribe, which had been converted in times of severe war with the griffins, according to their contract with the Entity which later became known as the Nightmare Moon, long before the foundation of Equestria. In addition to normal pegasi magic they have so-called "Gifts of the Night" abilities of shadow magic unique to each batpony, are nocturnal, have echolocation ability and live longer then normal ponies. But they almost useless in the daytime, because the sunlight almost blinding to them. They also can't communicate with normal ponies without the help of special amulets, as their voices have too high of a frequency (in other words, without the special amulets they can produce only funny squeaks).
The second "wave" also comes from the group of pegasi. They were also converted according to the contract, but with different entity. Unlike the first "wave" they have no Gifts of the Night. What compensated by the lack of weaknesses of the first "wave", increased endurance, general resistance to magic and a certain tendency to become paladins of entity that changed them.

What ideas of the origin of the batponies you have?

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I like to think Luna created them, possibly around the time she became Nightmare Moon out of her desire for nocturnal ponies.

My headcannon is that they aren't related to bats at all; that's just a misconception due to their appearance. Their wings and slit eyes tell me that they may be the result of dragon and pony couplings.

My headcanon is that they are a seperate species from ponies altogether, with their own versions of the four tribes (thestrals, daywalkers, saberhorns, and baticorns) and they remained in the Ancient Lands even after the ponies left.

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well the semi-cannon reason faust gave is that they came from and like to live in high mountain caves. Biased on that I think bat ponies come from prehistorian pegasi who moved into said cave and over many generations evolved into bat ponies to adapt to their new environment. The Night vision and sensitive hearing are good for living in the darkness of deep caves, with the bat wings being better at catching and generating lift from thinner high altitude air.

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Personal headcanon is that they are another tribe of ponies. Nocturnal and even more isolated than the three main tribes were. Mainly did monster hunting as their contribution. Pegasus did weather, Earth pony did agriculture, Unicorns did the sun and moon, and bats controlled the monster population. The crystals were around too, sustaining the emotional spectrum.

When the wendigo's attacked, they retreated to their cave cities to wait out the blizzards, so were one of the last tribes to make it to Equestria, and even then they didn't fully integrate, starting their own colony near Equestria. Luna got along decently well with them, though Celestia didn't, and they sorta of joined Equestria after Discord's defeat. The Children of the Night fanon is involved, since she brokered an agreement with them to take in a large number of orphaned foals since their lands were less directly affected by Discord's 'games.' Night touched unicorns, earth ponies and even pegasus come from interbreeding since then.

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6281160. To: Seeking Dusk
Your idea actually would make more sense, i mean even changlings could be considered an off-shoot of ponies. The thestrals could be like the donkeys and mules and zebras, just another cousin equine species.

I wrote a story once where they were a small bottlenecked population of pre-unification pegasi (one of the groups looking for a new land), trapped in a small snowy area with a lot of magnetic ore that threw off their navigation (so they thought they were stuck so much so that they thought that was all there was in the world). Over time, they evolved darker coats for camouflage, better eyes for seeing differences in the snow, and leathery wings for silence (don't think about it too hard because it doesn't make sense). No echolocation or anything else bat-related, but lots of love for fruit.

My own headcanon is that the species is old. Older than many might think. They either existed or were created far prior to the NMM event. They were fiercely loyal to Luna, but once that happened, loyalties shifted. Some remained with the princess, siding with her in claiming Equestria for the Night. Others, seeing her obsession and rage slowly consumer her, fled back into their high mountain homes. Some tried to fight alongside Celestia, but they were immediately distrusted, and turned away.

Once the battle was over, and Luna was banished to the moon, the went into isolation. Some were just glad to no longer have a threat looming over them, and were more than happy to be thought of as a mere myth as the years went on, so as not to be disturbed. Others became fanatics, enraged by their ruler's "unlawful imprisonment" and actively worked in the shadows, looking into ancient tomes, trying to bring her back.

I'm trying to write a fanfic about what happened after Twilight and her friends saved Luna from herself. About the decision of whether to return to the world that had once shunned them. Some that want to just stay put and live like they always had, some that want to go out and see what they'd been missing. Some think it's a trap, and Celestia is only trying to lure them out so she can imprison or kill them. Others see it an omen. A return of their Goddess. When they see her so changed, so small, those few will stop at nothing to see her returned to her former "glory." Whether she likes it or not.

As for why they looks like they do? I've put FAR more research into this than is healthy XD

Ear Tufts: The main animal I can think of that has these are lynx. Snowy Canada ones and desert Caracals both have them. The main theory is that maybe the longer stiff hairs can more easily pick up sounds from prey under the snow or sand. The tufts are also always black, so maybe that high visibility aids in communication.

Slit Pupils: Common, but not universal for nocturnal animals. To my knowledge, there are no slit pupiled herbivores. Goats/sheep that have them, but horizontally. Horses have them as well, actually, they just aren't noticed as much.

Fangs: Yes, predatory teeth, but real horses often have sharp canines, used got fighting. They also sometimes have smaller "wolf teeth" that are sharp. They're kind of like our wisdom teeth. We don't really need them, and sometimes they need to be removed.

Bat Wings: These actually make far more sense from an evolutionary standpoint. They are mammals, after all, not birds. Something fascinating about bat wings is that elastic membrane. It catches the air differently than a bird, allowing for some interesting maneuvers, like when they flip upside down to roost. They're also better at recovering after being jostled by a gust of wind, or another member of their colony. They can quickly apply the brakes to catch prey, and then easily keep going. They can hover. Moving around in dense woods is a breeze (though smaller size might help with that).

Grey coloring-Well, nocturnal is one of the reasons, but there are plenty of night animals that aren't grey or black. Since the teeth might be a vestigial trait, I thought that perhaps color is too. The Dun, Pangare, and Leopard Spot patterns are all depicted in cave paintings. Primitive horses of today often have faint striping on the lower legs. It's one version of Dun that most interests me though. It's called Grulla, and it's a unique kind of dove grey with dark mane and tail, along with dark ears, muzzle, and lower legs, not unlike a Siamese Cat. There's also a line from the nape of the neck down the back to the tail, called an Eel Stripe. It's possible that in isolation, this color pattern propagated and became the most common one. The mane and tail might also be stiffer and coarser. More prone to standing straight up if cut short or "roached."

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Indeed, quite an interesting story...

great discussion