Children of Time is a 2015 science fiction novel by Adrian Tchaikovsky.
In the distant future, humanity seeks to create new habitats for itself on distant planets, terraforming them and seeding them with life. Dr. Avrana Kern is heading one such project, orbiting the tentatively named "Kern's World", where the plan is to release monkeys 
infected with a nanovirus that will accelerate their evolution. Through an act of sabotage from an anti-technology group that has also destroyed much of Earth, the monkeys are never released, and the virus instead infects a species of spider, Portia labiata. The book follows the evolution of the spiders and their eventual civilisation, as well as a remnant of humanity that fled to Kern's World hoping to find paradise.
also children of ruin and children of memory, the sequels, are really good
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also had to look up what konohagakure was since I'm dub only