Abstract
Rafting dispersal has been proposed as a way for coastal species to track climate-driven niche shifts. However, little information exists on how rafting species disperse and adapt to shifting environmental conditions, particularly ocean currents and salinity. Here, we integrate dispersal simulations, ecological genomics, and salinity stress experiments to investigate rafting dynamics and adaptive shifts in widely distributed crustaceans across the Indo-Australian Archipelago. We develop a quantified model to examine asymmetric gene flow between populations driven by recent seasonal oceanographic shifts. Our climatic and dispersal models suggest that rafting populations must cope with increasing salinity fluctuation caused by rapidly-shifting oceanic connectivity patterns. Our genomic data provide evidence for recent selective sweeps at osmoregulatory loci, and key duplications at glycoside hydrolase gene families. Our experimental data reveal plastic expression of osmoregulatory genes required for survival during long-distance rafting voyages. These synergies between rafting dispersal and genomic change highlight the potential for rafting species to adapt to rapidly shifting oceanographic conditions.
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Data availability
All the raw RNA-seq (SRR34777140, SRR34777151–SRR34777186, SRR34777191, SRR34777202, SRR34777213, SRR34777215–SRR34777246, SRR34777256, SRR34777267, SRR34777278, SRR34777289, SRR34777300, SRR34777311–SRR34777313, SRR36240034–SRR36240062), and genome resequencing data (SRR34777130–SRR34777139, SRR34777141–SRR34777150, SRR34777187–SRR34777190, SRR34777192–SRR34777201, SRR34777203–SRR34777212, SRR34777214, SRR34777247–SRR34777255, SRR34777257–SRR34777266, SRR34777268–SRR34777277, SRR34777279–SRR34777288, SRR34777290–SRR34777299, SRR34777301–SRR34777310), and the genome assembly generated in this study has been deposited in the NCBI under the accession number GCA_054095995.1, datasets used to generate the assembly are available under the accession number PRJNA1297316. Sanger sequences have been deposited in GenBank with accession numbers in Supplementary Data 1. Other genomes used in this study include Hyalella azteca (GCA_000764305.4)94, Parhyale hawaiensis (GCA_001587735.2)37, Hirondellea gigas (CNGBdb Project ID CNP0005374)95, Trinorchestia longiramus (GCA_006783055.1)96, Morinoia aosen (GCA_030386875.1)71, Floresorchestia mkomani (SRR23898670 under PRJNA938803)71, Cochinorchestia sp. (SRR23898667 under PRJNA938803)71, Platorchestia pacifica (SRR23898669 under PRJNA938803)71. Four annual mean environmental variables (sea surface temperature, sea surface salinity, ocean current direction, and ocean current velocity) are from Bio-ORACLE (https://www.bio-oracle.org/), the variable “distance from shore” from the MARSPEC database (http://marspec.weebly.com). Sea surface ocean currents data from Global Ocean Ensemble Physics Reanalysis (GOEPR) are available in Copernicus Marine Environment Monitoring Service (CMEMS; https://marine.copernicus.eu/). The bathymetric data can be obtained from the ETOPO1 database (https://www.ngdc.noaa.gov/mgg/global/relief/ETOPO1/). Sampling data can be found in Supplementary Data 1. Results of genetic offsets are available in Supplementary Data 2–6, and gene family can be found in Supplementary Data 7. Source data are provided in this paper.
Code availability
Analysis scripts can be found at Figshare (https://doi.org/10.6084/m9.figshare.29614727)100, and Code Ocean deposition (https://doi.org/10.24433/CO.2066999.v1).
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Acknowledgements
We thank Baocheng Guo, Yilin Chen, Dezhi Zhang, Bingyue Zhu, Tongyao Jiang, Zhe Zhao, Fengyuan Li, and Pengyu Jin for helpful discussion; Zeyu Liu and Wenpei Xin for help in salinity experiments; Knut-Frode Dagestad for help in OpenDrift analysis; Zilong Bai and O. Alfaruq for assistance in field collection. This study was supported by the National Natural Science Foundation of China (grant number 32470474 for Z.H., 32500387 for H.L.), the International Partnership Program of the Chinese Academy of Sciences (grant number 073GJHZ2024043MI for Z.H. and H.L.), the Institute of Zoology, Chinese Academy of Sciences (2023IOZ0104 and 2024IOZ0108 for Z.H.), Beijing Natural Science Foundation (grant number 5244045 for H.L.).
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H.L. and Z.H. designed research; H.L., M.H., and Z.W. performed research; W.J.C. and S.L. collected samples and participated in discussions; H.L. and Z.H. wrote the manuscript; J.M.W. reviewed and edited the manuscript. All authors proofread and approved the manuscript.
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Liu, H., Waters, J.M., Huang, M. et al. Genomics of rafting crustaceans reveals adaptation to climate change in tropical oceans. Nat Commun (2026). https://doi.org/10.1038/s41467-026-69173-x
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DOI: https://doi.org/10.1038/s41467-026-69173-x
