Contrasting genomic responses of hydrothermal vent animals and their symbionts to population decline after the Hunga volcanic eruption

Genetic bottlenecks are evolutionary events that reduce the effective size and diversity of natural populations, often limiting a population’s ability to adapt to environmental change. Given the accelerating human impact on ecosystems worldwide, understanding how populations evolve after a genetic bottleneck is becoming increasingly important for species conservation. Ash deposits from the 2022 Hunga volcanic eruption in the Southwest Pacific led to a drastic decline of animal symbioses associated with hydrothermal vents in this region, allowing insights into the effects of population bottlenecks in the deep sea. Here, we applied metagenomic sequencing to pre- and post-eruption samples of mollusk-microbial symbioses from the Lau Basin to investigate patterns of genetic variation and effective population size. Our data indicate that animal host populations currently show only small changes in genome-wide diversity but in most cases experienced a long-term decline in effective size that was likely intensified by the volcanic impact. By contrast, symbiont populations exhibited a notable decrease in genomic variation, including loss of certain habitat-specific strains. However, detection of environmental symbiont sequences suggests that lost strain diversity might be recovered from the free-living symbiont pool. The differences between host and symbiont populations might be related to their contrasting genetic structures and levels of gene flow, although the full extent of population bottlenecks in the host animals might only be recognizable after a few generations. These results add to our understanding of the evolutionary dynamics of animal-microbe populations following a natural disturbance and help assess their resilience to potential future anthropogenic impacts.