Complete mitogenomes reveal high diversity and recent population dynamics in Antarctic krill

The Antarctic krill (Euphausia superba) is a keystone species in the Southern Ocean ecosystem, influencing food web dynamics and ecosystem functionality. Despite its ecological importance, further exploration is essential to understand their population dynamics.

In this study, we present the complete mitogenome of the Antarctic krill. The assembly is 18,926 bp, including a notably large 3,952 bp control region (CR). The CR features a satellite repeat spanning 2,289 bp, showcasing the effectiveness of long-read sequencing in resolving complex genomic regions. Additionally, we identified 900 nuclear-mitochondrial segments (NUMTs) totaling 2.79 Mb, shedding light on the dynamic integration of mitochondrial DNA (mtDNA) into the nuclear genomes. By establishing a dataset comprising 80 krill mitogenomes, we unveil substantial mitochondrial diversity, particularly within the ND4 gene. While our analysis reveals no significant differentiation among four geographically distinct groups, we identify at least four maternal genetic clusters. Haplotype network analysis and demographic reconstructions suggest a recent population expansion, likely driven by favorable environmental conditions during the late Pleistocene. Furthermore, our investigation into selection pressures on mitochondrial genes reveals evidence of purifying selection across all 13 protein-coding genes, underscoring the pivotal role of mtDNA conservation in maintaining mitochondrial function under extreme environments.

This study provides a repository of Antarctic krill mitogenomes and insights into the population genetics and evolutionary history of this ecologically important species from a mitogenomic perspective, with implications for krill conservation and management in the Southern Ocean.