@Fantastic Yeah, Fluttershy does seem pretty self sufficent, taking care of all those animals by herself. She’s probably relatively used to not having other ponies around. And she seems to have a reasonable amount of medical training. So out of the Mane Six (except Applejack), I would say she would be the best prepared for surviving this type of thing.

Sounds like you’ve really thought this through. I’ll leave you to it.

Oh, and there was a questionable sighting of Applejack in a dark part of a cave. I still need to address that, too.

I’ve thought about all of that, it’s all being addressed as and when I draw a scene that demands it or can offer a bit of insight on it. I’ve just got to hurry my ass up, and start drawing and writing more scenes, so all of that information can be covered.
 
That said, out of all of the scenes I’ve currently drawn and wrote for, Dragons, Diamond Dogs (and their burly, warrior-like cousins, known as Hounds), Timberwolves (very brief cameo), Spike, and Fluttershy are about the extent of known survivors right now.
 
There is a scene I could draw next that could more or less address what other races are left… hmm… In fact, I should draw it.

Are there still Gryphons, Diamond Dogs, or Zebras? Is the giant menagerie of sentient beings that also inhabit the equestrian territories inexplicably absent?

She seems to do pretty good living on her own in that shack of hers. She doesn’t seem to leave unless she’s asked to by other ponies. If the world became completely devoid of other ponies, she probably wouldn’t notice for weeks.

“Uncle Owen, Aunt Peru?!”

”‘What happened?’
 
“I dizzily came to in the tipped-over carriage. My eyes slid into focus and revealed a mess of shattered glass and scattered luggage. My head hurt, several places of my body stung from cuts, and I could feel bruises all over myself from where I had hit something while being bounced around like a rubber ball.
 
“I had been knocked unconscious in the crash, and I was still dazed. I spent a moment verbally trying to pace my way through my foggy memories up until now. ‘I was sat down, I… I received a letter from Twilight through Spike, and then there… there was a bright light and a shockwave. Everypony fell silent, or I was deafened, or…’
 
“My eyes widened and I scrambled onto my hooves in alarm. ‘The other passengers!’
 
“I limped my way all over the carriage, searching for other ponies who may have been hurt. I moved luggage away in case there was anypony trapped underneath, and looked high and low. But there was nopony else in this carriage. Quickly, I negotiated with the lopsided train and searched all of the cars. the locomotive, and the caboose. Each one turned up empty, save for various belongings laying around.
 
“I began to panic; what if I had been unconscious for so long, that nopony saw me, and they all left together to get help? I clambered outside into the desert Sun, and broke out into an awkward, pained run. I ran up to the top of the nearest dune and looked over the other side. There was no sign of anypony. I looked around, hoping to catch a silhouette in the horizon, but only sand and sky were all I could see. Desperately, I called for help, but no response came.
 
“Tears formed in my eyes, I called for help, again and again, until my throat was sore and I was coughing on sand.
 
“Everypony was gone, and I had been left alone.”