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I visited the Zoo this afternoon, and the lion-tailed macaques were, indeed, off exhibit, with a "Wildlife Off Exhibit" sign up in place of the macaque signage...
My last visits were June 13th, and the 17th.

On ZTL it has been reported that they are now deceased, and a mere couple of weeks after I last saw them :( very sad if true. They were one of my favorite animals to see at the zoo and due to the almost-complete collapse of the Lion-tailed Macaque population in North America I doubt they will be replaced anytime soon, if ever.

I have some photos I took of them during my visit in May, I will make a point to upload them sometime soon.
 
Here are some updates from June 13, some of these might not be confirmed or already mentioned.
  • Sadly, Kenny the coconut crab has died a month or two ago. The keeper I asked said he was believed to be between 20-40 years of age. He was a confiscation and the zoo doesn't plan to acquire another coconut crab, his exhibit is empty for now and no animals are planned for it I believe.
  • A Lord Howe stick insect might have died, though the body may have just been a molt.
  • Due to aggression, only a single hummingbird, a male Anna's, is on display in the hummingbird aviary.
  • There were many unsigned species in the reptile house, such as the Asian giant toads, several snakes, and a mixed exhibit for ashy and mangrove pit vipers.
  • A purplish colored crayfish is in the circular aquatic tank with the reptiles behind the pygmy hippos. Perhaps it might be a yabby?
  • Elephant odyssey currently holds Mexican alligator lizards, rosy boas, sunburst diving beetles, and island night lizards Xantusia riversiana. The rattlesnake habitat holds mexican beaded lizards, red diamond, southwestern speckled, and southern Pacific rattlesnakes.
  • I believe this has been mentioned but the marsh aviary in the tiger area holds some unsigned species such as crowned pigeons, redhead ducks, northern shovelers, and ring necked ducks.
  • I overheard two reptile keepers stating how New Zealand would not allow the tuataras to be displayed until they have bred, not sure if this is true.
  • The blue duiker is no longer separated from the gerenuk I believe, I also saw the red flanked duiker on display.
  • As mentioned earlier, the "hidden aviaries" behind the polar bears currently hold species like some of the birds from the bus stop aviary like Kagu, Guianan cock of the rock, several pigeons and doves, white naped pheasant pigeon, blue coua, what looked like a white rumped shama, and more.
 
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  • Sadly, Kenny the coconut crab has died a month or two ago. The keeper I asked said he was believed to be between 20-40 years of age. He was a confiscation and the zoo doesn't plan to acquire another coconut crab, his exhibit is empty for now and no animals are planned for it I believe.
  • There were many unsigned species in the reptile house, such as the Asian giant toads, several snakes, and a mixed exhibit for ashy and mangrove pit vipers.
It’s unfortunate to hear about the passing of the coconut crab! He was always a highlight of Spineless Marvels. The last I had heard he was in molt, but I guess he did not reemerge this time :(

The unsigned animals in the Reptile House is not unusual. I feel like more animals in that building are unsigned than signed :p The on-display collection also changes quite regularly.

What happened to the maned wolf?
It also passed away. It was another elderly animal.
 
Something else I noticed during my visit last month is that the Black Crested Mangabey enclosure in Lost Forest had a Vervet in it instead... does anyone know if this is a permanent arrangement? Does the zoo not have mangabey anymore?

Also I heard there might be Island Foxes on display now in Northern Frontier, can anyone confirm or deny that?

I believe this has been mentioned but the marsh aviary in the tiger area holds some unsigned species such as crowned pigeons, redhead ducks, northern shovelers, and ring necked ducks.

As far as I could tell they are all birds from Owens and Arctic that got redistributed while renovations are done on those aviaries. Some of the Owens refugees do have signage at Tiger River, though - the Collared Kingfisher for instance.
 
Something else I noticed during my visit last month is that the Black Crested Mangabey enclosure in Lost Forest had a Vervet in it instead... does anyone know if this is a permanent arrangement? Does the zoo not have mangabey anymore?
This is a permanent arrangement, yes. The vervet troop had splintered into two groups that couldn’t be housed together anymore. Moving this troop to the Lost Forest allowed both groups to be on exhibit at the same time. The Zoo does still have black crested mangabey, though. The remaining mangabeys are now with the second Angolan colobus troop in the old lion-tailed macaque exhibit in Sun Bear Forest.

Also I heard there might be Island Foxes on display now in Northern Frontier, can anyone confirm or deny that?
This is at least not yet the case. On my visit on Tuesday the Canada lynxes were still in the exhibit on the right side of the old reindeer exhibit, and the black-billed magpie was still signed for the left side exhibit (although I did not see it).

As far as I could tell they are all birds from Owens and Arctic that got redistributed while renovations are done on those aviaries. Some of the Owens refugees do have signage at Tiger River, though - the Collared Kingfisher for instance.
That is correct, yes. The collared kingfishers were in there prior to the closing of the Owens, however.
 
Such a shame about Kenny and Annie & Frankie the lion tailed macaques. They were for sure among my favorites. :( First the Golden takins going off exhibit (with no plans to bring them back?), and then the secretary birds completely gone from both parks, and now this. It feels like SDZ has lost so much in such a short amount of time, it’s depressing. :( Speaking of which, does anyone know what happened to two of the cheetahs in Urban Jungle? I don’t think I’ve seen Roketi or Maggie at all since December of last year/January of this year. As much as I love seeing Ayana and Jabula, it has me worried once again. I haven’t seen any new pictures of Roketi or Maggie pop up anywhere, either. I’m also curious to know what happened to the maned wolf and if they ever plan to exhibit that species again.
 
Between discussions in the last couple pages, I feel like you could write a really fun thread just by going over rarities San Diego has held at its parks in the last two or three decades, the individuals, where they lived at the parks and when they passed away.
 
If someone could make a complete list with all the species that the SDZ has had in the las two decades, and saying the species that the zoo has lost over the years, I would be so thankful.
Thanks for everything.
(Maybe we could do it in another thread.)
 
If someone could make a complete list with all the species that the SDZ has had in the las two decades, and saying the species that the zoo has lost over the years, I would be so thankful.
Thanks for everything.
(Maybe we could do it in another thread.)
San Diego Zoo Species History [San Diego Zoo] - ZooChat This isn't exactly what you were looking for, but your comment inspired me to finally post this. It covers the last decade.
 
Official announcement of the new female Baird's Tapir calf:

June 25 (UPI) -- The San Diego Zoo announced the birth of a female Baird's tapir, an endangered animal native to Mexico and Central America.

The zoo said the calf, born June 3 to mother Luna, is now on display alongside the facility's capybaras in an enclosure located in the Elephant Odyssey section of the zoo.

"Luna is bonding with her calf by vocalizing to her, licking her and keeping a close eye on her at all times," the zoo said in the announcement. "The calf is starting to get 'zoomies' and likes to mouth and play with leaves and food even if she's not eating it. They spend their time grooming, nursing and laying together."

The birth was hailed as a milestone for conservation efforts for the Baird's tapir, which is listed as Endangered on the International Union for Conservation of Nature Red List of Threatened Species. The animals are threatened by sport hunting in Costa Rica and habitat loss due to farming, cattle grazing, and palm oil and rubber plantations, the zoo said.
Watch: San Diego Zoo celebrates birth of endangered Baird's tapir - UPI.com

 
Does anybody know whether or not the zoo still keeps or displays Eastern Hooded Scaly-foot (Pygopus schraderi) and where the zoo's different beaded lizard taxa are kept? Thank you.
 
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