Resistance to avian malaria in Hawai’i amakihi

Genomics of tolerance to avian malaria among Hawaii amakihi:

Avian malaria was introduced to Hawaii in the 1930s and caused devastating population declines in many native Hawaiian birds, driving some to extinction.   Some species, notably the Hawai’i amakihi (Hemignathus virens), were able to persist in small, isolated populations and have developed the ability to survive malaria infection.  Recently, amakihi populations have begun to rebound despite the widespread presence of malaria.  It is our goal to characterize the genomic changes that are involved in resistance and/or tolerance to avian malaria.

To do this, we are using an amakihi reference genome developed by T. Callicrate and others, along with the annotated zebrafinch genome, to identify SNPs that are associated with malaria survival.  Using a capture approach, we have recovered ~60,000 high-quality SNPs located randomly across the genome. The figure below depicts coverage depth across the genome (lines are sliding window averages).

We are using an Fst-outlier approach to detect loci that are strongly differentiated between elevations, as well as direct tests of selection (e.g., Tajima’s D and selective sweeps).   We complement this spatial approach with genome-wide association methods to detect sites that are associated with survivorship from malaria in experimental infection studies. 

More to come soon!  In the meantime, you can watch my recent Evolution talk on YouTube:


Rob Fleischer, Smithsonian National Zoo

Taylor Callicrate, Smithsonian National Zoo & University of Maryland

Low-elevation populations have evolved under the recent selection pressure of avian malaria, whereas high-elevation populations (which are too cold for the mosquito vector) have not.  Because amakihi individuals disperse much farther within an elevation than across elevation, there is genetic differentiation between low- and high-elevation populations (below, differentiation between one low- and one high-elevation population).