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Migratory jackpot individuals fuel rapid ecotype shifts in Galaxias fishes


Abstract

Adaptation is considered essential for species facing environmental change, but our understanding of the evolution of complex ecotypes remains limited. We show that a substantial genomic cluster of co-adapted alleles has repeatedly fuelled complex life-history shifts in fishes. Specifically, the majority of strong outlier loci underpinning repeated landlocking of formerly marine-migratory Galaxias lineages are co-located on a single chromosome. Phenotypic, behavioural and genomic comparisons reveal a strong parallel basis for multi-trait ecotype shifts (osmoregulation; musculature; locomotion; reproduction) across eight independently landlocked populations. Critically, migratory populations house ‘jackpot’ individuals carrying intact sequences essential for rapid multi-trait life-history switches. The observed high frequencies of these migratory jackpot carriers explain the rapid ecotype shifts detected in Galaxias populations isolated by recent catastrophic landslides in New Zealand. These findings represent a complete example of complex ecotype evolution, highlighting the key role of modular genomic variation in facilitating rapid adaptive change.

Acknowledgements

This research was primarily conducted in Aotearoa New Zealand. We strive to uphold the Treaty of Waitangi, which guarantees rights to the indigenous Māori people of this land. We are grateful for the guidance and trust of Te Rūnanga o Ōtākou, Kāti Huirapa Rūnaka ki Puketeraki, Te Rūnanga o Makaawhio, and Ngāti Apa ki te Rā Tō for their trust and guidance with this research. Similarly, we acknowledge that the Galaxias brevipinnis specimen obtained for genome sequencing, and the freshwater ecosystem it inhabited, are part of a living landscape that holds deep cultural, spiritual, and ecological significance for the Palawa/Pakana peoples, the traditional custodians of lutruwita/Tasmania. We wish to acknowledge the use of New Zealand eScience Infrastructure (NeSI) high performance computing facilities, consulting support and/or training services as part of this research (https://www.nesi.org.nz.). Richard Allibone and Graham Wallis provided samples and contributed evolutionary genetic context on this system. All specimen collection and animal handling were approved by the Animal Ethics Committee of the University of Otago (permits AUP-19-64; AUP-59-2016; AUP-103-2013; AEC-64-14) and by the Department of Conservation (permits 39843-RES; 51959-RES).

Funding

This research was supported by University of Otago Department of Zoology funding allocations to J.W., G.M., G.C., T.I., L.D. and M. L. Postgraduate researchers M.D. and J.A. were supported by University of Otago Doctoral Scholarships, and A.I. was supported by a University of Otago Māori Master’s Research Scholarship.

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Jonathan M. Waters.

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Iwikau, A., Augspurger, J., Bailie, M.A. et al. Migratory jackpot individuals fuel rapid ecotype shifts in Galaxias fishes.
Nat Commun (2026). https://doi.org/10.1038/s41467-026-74946-5

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