Evolutionary history of alpine and subalpine Daphnia in western North America

Studying adaptation within a multispecies complex can be challenging due to uncertainty about the evolutionary relationships among populations. An accurate phylogenetic context is especially important for drawing conclusions about phenotypic evolution for species used as model organisms in ecological and evolutionary research. Within the zooplankton genus Daphnia, carapace melanin pigmentation has often been suggested as an adaptation to ultraviolet radiation exposure in clear-water habitats. However, the evolutionary history of melanism has been obscured because of phylogenetic uncertainty. We inferred a molecular phylogeny based on the mitochondrial ND5 and COI loci and used it to explore the evolutionary history of populations belonging to the Daphnia pulex species complex that inhabit alpine and subalpine lakes and ponds in western North America. Our analysis confirms the existence of a distinct mitochondrial clade for Daphnia melanica within the D. pulex species complex and shows it to be more geographically widespread than previously thought and includes populations from several disjunct sites. We show that melanism, once used as a diagnostic character for identifying Daphnia species, is polymorphic within the D. melanica clade. This polymorphism suggests the possibility of independent parallel evolutionary losses and gains of melanism in this species complex.