Comparative population genomics provide new insight into the evolutionary history and adaptive potential of World Ocean krill

Abstract Genetic variation is instrumental for adaptation to new or changing environments but it is poorly understood how it is structured and contributes to adaptation in pelagic species without clear barriers to gene flow. Here we use extensive transcriptome datasets from 20 krill species collected across the Atlantic, Indian, Pacific and Southern Oceans and compare genetic variation both within and between species across thousands of genes. We resolve phylogenetic interrelationships and uncover genomic evidence in support of elevating the cryptic Euphausia similis var. armata into species. We estimate levels of genetic variation and rates of adaptive protein evolution among species and find that these are comparably low in large Southern Ocean species endemic to cold environments, including the Antarctic krill Euphausia superba , suggesting their adaptive potential to rapid climate change may also be low. We uncover hundreds of candidate loci with signatures of adaptive divergence between krill native to cold and warm waters and identify candidates for cold-adaptation that have also been detected in Antarctic fish, including genes that govern thermal reception such as TrpA1 . Our results suggest parallel genetic responses to similar selection pressures across Antarctic taxa and provide new insights into the adaptive potential of important zooplankton that are already strongly affected by climate change.