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I'm currently working on a world where there are two groups of dragons, Continent dragons and island dragons. The basic story is that long ago there was one massive population of dragons that lived on the continent, before some kind of natural disaster or predator forced some of the dragons to flee to an island far out in the ocean.

The continent dragons evolved into three main subspecies, which all appear slightly similar, while the island dragons evolved into eight main subspecies that are each highly specialized to the environments they live in, and all look very different. The island dragons lay smaller nests and grow larger and slower than continent dragons. The continent dragons are more intelligent and civilized than the island dragons.

My question is, why would a smaller population be more specialized to their environment than a large population that reproduces faster?

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Assuming there was no mass extinction event involved on the mainland, what you'd be looking at is adaptive radiation. Darwin's finches are the stereotypical example here. When the first tanagers (Galapagos finches are not true finches) arrived on the Galapagos, they were in an environment with a lot of open niches for small birds because there were no small birds existing there already (or at least none in significant numbers), and so you had rapid speciation and diversification as the tanagers exploited the wide-open ecological terrain.

Your dragons would have a similar history. On the mainland, dragons would have existed in a mature ecological environment, with a defined place in the food chain and so on. There wouldn't have been as much opportunity to change lifestyles and assume other niches because those niches would already have been filled by something non-dragon. Assuming the islands only recently formed, there would likely have been a lot of open spaces in the environment that dragons could, and did, fill. That would have allowed them to diversify and specialize to an extent that the continental species could not.

An artificial version of this is the dog. The wolf is a pretty basic canine, and despite there being (currently) 38 subspecies of timber wolf, they all look very similar, occupy similar ecological niches, and so on. Wolves are not going to specialize as, say, low-slung, short-legged predators that chase prey into burrows, because that role is already filled by animals such as weasels and their relatives. However, humans in their artificial environment, have bred dogs that fill that role. If wolves were dropped into an environment where weasels and such didn't exist, but burrowing rodents did, what humans did artificially could happen to wolves naturally, and you might still have the big, rangy, running pack predators, and a separate species that was built more like a dachshund.

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Evolutionary pressure

Evolution is driven, primarily, by external pressures on the groups of organisms, regardless of their breeding rates or starting population numbers.

A large group, or a small group, that reproduces quickly, or slowly, will stay relatively the same over long periods of time, as long as it has no real reason to change (no evolutionary pressure).

A large group, or a small group, that reproduces quickly, or slowly, will change rapidly (or it will go extinct completely) if the pressures are strong enough.

On a continent, if things change in one location, a group might evolve slightly, but they also have the option to simply walk (or fly) to another, more favorable, location on that continent, rather than evolve.

The option to relocate is much more restricted on a remote island, so any change to the environment will require drastic and (relatively) immediate evolution or evacuation. So you end up with islands that have either been abandoned completely, or have specialized species of anything that was there before the change to the environment.

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"Short" Answer

(special environments require higher specialization)

The continent dragons don't need to evolve because there is enough space to sustain all dragons. While on the islands there is little space (compared to the continent) and the dragons have to compete more which is why natural selection actually does occur on a way larger scale than on the continent as there even the weak ones survive.

"Long" Answer

Continent

On the continent the variety of food and terrain is huge so being a generalist is the optimal choice. While specialization might even be bad for the dragons because it removes some food options from the menu while (possibly) also decreasing the habitat of the dragon. Because food and area are abundant even weaker dragons can exist and evolution might not cause the dragons on the continent to change as much because better and worse mutations don't cause the dragon to survive or die differently. (at least in most cases)

Island

On the islands the variety of food and terrain per island will be way smaller and as such require higher specialization. On different Islands the environment changes enough to require differences in the species. Also because land area is not as abundant only the fastest, strongest and most capable survive and thereby dragons on the islands change and adapt way faster than on the continent.

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Of note: this condition is intimately connected with Charles Darwin's original observations of finches' beaks whilst traversing islands on HMS Beagle - those observations were amplified and augmented with other later observations and thinking to become On the Origin of Species.

Divergent evolution of otherwise related species is in fact accelerated in island conditions, due to paucity of resources, highly specific forms of competition and predation, and the (presumable) lack of ability simply remove to other resource pools when times are lean.

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