Learn English – How to use “for the first and only time”

by which time refers to a specific time that has previously been mentioned. It's typically the end of a process or event, so in your example 2010 would be the likely referent.

Had they intended to refer to the entire time period, they would more properly have used during which time.

Furthermore, the context makes it unlikely that lionfish accounted for the same percentage during the entire period. The sentence emphasizes an increase. While it's conceivable that the lionfish population increased proportionately with all the rest of the predators, so that the percentage stayed the same, it doesn't seem to fit with the sense of the sentence.

Since this is in the domain of biology, the word might be evolve. Evolve (v.): to change or develop slowly often into a better, more complex, or more advanced state. [ref] Example: The North-American crows have evolved to adapt to urbanization.

To describe a change over time of a part of an animal (e.g. beak), you can try the word morph. Example: The wings of these birds morphed over millenniums as atmospheric pressure changes.

To describe a change in habitat location over time, you can try the word shift. Example: After Seattle became a city, the Pacific wren and the Swainson’s thrush shifted their habitat. [ref]

Suggestion after asker added an example: trend. Example: The trend of population size over the last decade.