Ape

Apes were a variety of primate native to Earth, evolutionarily close to humans.

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)

Subspecies
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)

Extra-terrestrial apes
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)

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)