How populations of aquatic fauna persist in extreme desert environments
is an enigma. Individuals often breed and disperse during favourable
conditions. However, theory predicts that adaptive capacity should be
low in small populations, such as in desert fishes. We integrated
satellite-derived surface water data, neutral population dynamics and
adaptive evolution to understand metapopulation persistence across the
range of the desert rainbowfish, central Australia. Desert rainbowfish
showed very small population sizes, especially at peripheral
populations, and low connectivity between river catchments. Yet, there
was no evidence of population-level inbreeding and there was adaptive
divergence associated with aridity. Candidate adaptive genes included
functions related to environmental cues and stressful conditions.
Evolutionary modelling showed that selection in refugial sub-populations
combined with connectivity during flood periods can enable retention of
adaptive diversity. Our study demonstrates that adaptive evolution can
occur in small populations and integrate with neutral metapopulation
processes to allow persistence in the desert.