The Lie Tree by Frances Hardinge

The Lie Tree begins with a gloomy, wet boat journey to a gloomy, wet island in the English Channel.  Fourteen-year-old Faith Sunderly, our protagonist, is moving with her family to the Isle of Vane, so that her father, the Reverend Erasmus Sunderly, can consult on an archaeological dig.  It's the 1860s, and amateur natural scientists like Erasmus are grappling with the new, controversial theory