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Apes were a variety of primate found on Earth and beyond.
Following Miracle Day in 2011, it was observed that apes, among other species, were still dying as usual, demonstrating that only humans had become immortal. (TV: The New World)
Apes were listed in the Avalonian Bestiary of all animal life on the Earth colony Avalon. (PROSE: The Sorcerer's Apprentice)
Human evolution
In 1883, Reverend Ernest Matthews was turned into an ape by Josiah Samuel Smith because he didn't believe that man evolved from apes. (TV: Ghost Light) This sentiment was not shared by the Silurians, who had witnessed the evolution, and therefore frequently called humans "apes". (COMIC: Twilight of the Silurians, TV: Doctor Who and the Silurians, Cold Blood, and many others)
Earth apes
In ancient times, Silurian scientists Nagara and Guruz attempted to force pre-human apes to learn and display intelligence. Kin, leader of the apes, strangled Guruz in response to another beating. Nagura returned to set the Apes free. Believing the Apes to be thanking him for the discipline he offered them, he accepted a woven headband like Kin's. Only when the headband was in place did he realised his third eye was blocked by a stone at the front and he was powerless. The apes exacted their revenge for their brutal captivity. (COMIC: Twilight of the Silurians)
In 1605, the Lord Chamberlain brought forth a Barbary ape as one of the many entertainments provided to King James I at the Palace of Whitehall. (PROSE: The Plotters)
A species of ape known as "Ice Apes" lived under the Antarctic ice cap. (COMIC: Ice Cap Terror)
The Yeti species Mih-teh and Dzu-teh were closely related to apes. (PROSE: Downtime)
Apes from elsewhere
One planet was home to apes, some of which were captured by giant birds, apparently as pets. They captured John and Gillian as well when they visited the planet. (COMIC: Kingdom of the Animals)
Lord Eskdale owned many sentient apes who he kept as slaves. He freed them after his daughter Charlotte Eskdale demanded he did. (COMIC: Sky Manor)
As a slur
A Kish captain called Enkidu an ape. (PROSE: Timewyrm: Genesys)
The Ninth Doctor called humans "stupid apes" on a few occasions. (TV: Rose, Father's Day) Indeed, according to the Eighth Doctor, his own kind "wasn't descended from anything even remotely embarrassing" in contrast to humans being "ape descendants". He suggested this was one of the causes of the Time Lords' arrogance. (PROSE: Interference - Book Two)
Trevor Ridgely called Palmer an annoying ape. (AUDIO: The Nowhere Place)
Silurians referred to humans as apes. Silurians would use a virus on their crops to get rid of them. (TV: Doctor Who and the Silurians) Alaya indicated that she used to hunt apes for sport. (TV: Cold Blood) A female Silurian, Vastra, once commented that "people are apes, men are monkeys." (TV: Deep Breath)
Other
Strax once claimed to have a hoard of samurai apes. (COMIC: The Adventures of Strax & the Time Shark)