Extinction

Extinction is the end of a species caused either the death of the entire population or over a long period of time in which the species is slowly reduced in number until the last members eventually die.

During the 41st century, the Astrophia Tribe died out during the Valhalla Wars. Its lone survivor of the tribe, became a hunter collecting the last members of several extinct species. (IDW: Agent Provocateur)

The Museum of the Last Ones was a museum that preserved and kept a single living specimen of an every extinct species. (NSA: The Last Dodo)

The Silurians were capable of bringing species back from extinction, such as many species of dinosaurs. (DW: Doctor Who and the Silurians, NA: Blood Heat)

Before the destruction of Gallifrey no animal native to the planet had gone extinct. (NSA: The Last Dodo) This is likely due to the Time Lords as they would have brought the species back

The Endangered Dangerous Species Society was an organization that was created to hunt down and wipe out dangerous species. (NSA: The Doctor Trap)

Extinctions and Near-Extinctions

 * The Last Great Time War caused the extinctions of many species and the near-extinction of the Time Lords except The Doctor and The Master. The Doctor destroyed Gallifrey and the Time Lords using The Moment despite an attempt by Rassilon to break the Time Lock and initiate The End of Time (DW: The End of Time).
 * The Doctor's use of the moment also caused the near extinction of the Daleks, all killed except for a single Dalek (DW: Dalek),The Dalek Emperor and his Mothership (DW: Bad Wolf (TV story)/The Parting of the Ways) and the Cult of Skaro who's last surviving member broke the Time-Lock and rescued Davros (DW: Doomsday/Evolution of the Daleks/The Stolen Earth. All of the survivors (with the possible exception of Davros) are known to be dead. However it is known the Daleks are not extinct. (DW: Victory of the Daleks)
 * All of Eve's species apart from herself died when their homeworld was exterminated by the Daleks. Eve's parents sent her on a Ship to escape. (SJA: The Mad Woman in the Attic)
 * At the end of the universe in 100'000'000'000'000 almost all species were extinct except for Humans,Malmooth,Futurekind and possibly the Sycorax(DWF: The Sycorax). Yana worked on the Utopia project to humanity. The humans on Malcassairo left to find Utopia but when they reached it, it was uninhabitable. The Master turned the last humans into the Toclafane who worked with them to take over the Earth of 2009. However after the alternate timeline was negated the Toclafane were left trapped in the end of the universe resulting in their extinction. (DW: Utopia (TV story)/Last of the Time Lords)
 * When Yana became the Master he murdered Chantho, the last surviving Malmooth.(DW: Utopia (TV story))
 * The Futurekind and the Sycorax most likely went extinct at the end of the universe.(DW: Utopia (TV story))
 * A human freighter from the year 2526 caused the extinction of the various species of Dinosaur on Earth when it was sent 65'000'000 years back in time and crashed to the planet. (DW: Earthshock)
 * By the 29th century the Star Whales were driven to near-extinction. Only one survived and offered help to Starship UK however it was captured and tortured by its leaders. 300 years later Its intent was realised and it was released by Amy Pond however it continued to serve Starship UK. (DW: The Beast Below)
 * The Veil became near-extinct when their planet's star was extinguished. The last member of the race, Androvax went on a vengful vendetta destroying 12 planets before finally being arrested by the Judoon when he attempted to destroy Earth. (SJA: Prisoner of the Judoon)
 * Baaraddelskelliumfatrexius Beasts were hunted to extinction by the Raxacoricofallapatorians. (SJA: Revenge of the Slitheen)
 * Perganon and Ascinta were two extinct civilizations referred to by Brother Lassar. (DW: School Reunion)
 * Cirranin were wiped out in a war except for one individual, Hr'oln.All the Animals native to the Cirranin homeworld including the Elipigs,Fuffoxes,Fruzin,Vish and the Kivurd were also wiped out in the war. (NSA: The Last Dodo)
 * The Cybershades, an experimental type of Cybermen created when the Cybermen were sent to 1851 became extinct when the Cybermen were destroyed. (DW: The Next Doctor)
 * The Arkellis flower,native to Skaro became extinct.(DWA: The Dalek Book)
 * The Dals a race which were native to Skaro. Died out before Davros was born. (BFA: Purity)
 * Human Badgers were created when the European badgers became extinct. (NSA: The Pirate Loop)
 * Tigers went extinct before 2148. (NA: St Anthony's Fire)
 * All species of Cat became extinct before 2157. (NA: Lucifer Rising)
 * The Benelisans became extinct the Beast traveled to Benelisa and fed on them. Before they became extinct, the Benelisans sent Azoth to locate and destroy the Beast. (EDA: The Taint)
 * The Khorlthochloi went extinct in the Distant Past. (PDA: Synthespians™)
 * The Dax were driven to near-extinction by the Daleks when they destroyed their homeworld of Daxus. However some managed to escape to Earth.(DYD: The Corinthian Project)
 * 200 species including Irradiate Grinderstag and the Stellar Raptors were driven to extinction by the Endangered Dangerous Species Society]. ([[NSA: The Doctor Trap)
 * Sheep became extinct before 2106. (NA: Lucifer Rising)
 * The Ostrich and the Black rhinoceros became extinct in 2051. (REF Doctor Who: Monsters and Villains)
 * The Thains became extinct in 6000 BC. (EDA: Placebo Effect)
 * The Tytheg became extinct by the 26th century. (NA: St Anthony's Fire)
 * The Valnaxi were driven to near-extinction in 118 A.D. at the end of the Valnaxi-Wurm War.(NSA: The Art of Destruction)