RNA-seq analysis pipeline

mosquitoes and Plasmodium relictum introduced to Hawai‘i have resulted in extinctions and catastrophic population declines due to avian malaria, particularly in the diverse clade of Hawaiian honeycreepers. However, some species such as the Hawai‘i ‘amakihi (Chlorodrepanis virens) can survive infection. Immunity exists in low-elevation populations where mosquitoes are abundant, whereas high-elevation, unexposed populations of ‘amakihi display greatly reduced immunity. To explore the basis of adaptation to P. relictum in low-elevation ‘amakihi, we sequenced transcriptomes from 24 low-elevation and 15 high-elevation ‘amakihi. We tested for differential gene expression between (i) infected and uninfected birds and (ii) low- and high-elevation birds.