Wild or domestic
Every mob is origin-tagged the moment it spawns. Natural spawns and worldgen are wild, and so is anything that predates the plugin. Anything a player caused is domestic: breeding, thrown eggs, spawn eggs, spawners, curing, allay duplication, commands. The only way for an animal to be domestic is to be born of a player.
Every wild death counts
When a wild mob dies, its species' count drops by one, whatever the cause: player, fox, lava, cliff, cactus. Domestic deaths never touch the count, and nothing raises it except slow natural regeneration. A drop-crusher farm is not a loophole; it is the fastest extinction machine on the server, with your name on it.
Tip: Farm domestic animals. Breed two wild cows and the calves are yours; the parents still count as wild.
The wild thins out
As a population falls, natural spawning of that species thins in proportion. Below the critical line, 10% of the starting population, it stops entirely: fresh chunks generate without them, and the world simply runs out.
Regeneration and the endling rule
Populations heal slowly on their own, one point per species every 45 real minutes by default, but only while at least one wild member survives. Zero is terminal: regeneration never resurrects a species, and one survivor is enough for it to claw all the way back. That is the endling rule, and it makes the last individual of a species the most important animal on the server.
Relict names
When a species is down to its last few, five by default, the survivors get names in gold over their heads: Willow, Clover, Maple, Juniper, Sage, Rowan. The names are applied retroactively to wild-origin mobs and removed again if the population recovers. Killing Meadow is supposed to feel different, and it does.
Tip: A gold name is the plugin telling you, personally, to put the sword away.
The broadcasts
The server announces the milestones: endangered at 25%, critically endangered at 10% when spawning stops, and recovery on the way back up. Extinction gets the full treatment: a chat line naming exactly who or what killed the last one, a full-screen EXTINCT title for everyone online, and a small melodramatic dirge.
The Naturalist's Journal
Crafted shapeless from a book and an emerald. Right-click a creature to see its species' census over your hotbar; use it in the air for a summary of everything extinct, critical and endangered; sneak-use in the air for the full list, rarest first. Point it at something untracked, like a zombie, and it answers that the wild population is beyond counting.
Transformations
A wild mob that transforms away counts as a wild loss: a pig struck by lightning, a mooshroom sheared into a cow, a villager zombified. Whatever it becomes is domestic, so one animal can never cost two species.