Integrating intraspecific genetic variation and species distribution models to predict the potential impacts of climate change on Sepia pharaonis

Abstract Incorporating intraspecific genetic variation into species distribution models (SDMs) can improve the accuracy of species distribution predictions. However, few studies have evaluated its importance for SDMs. The pharaoh cuttlefish (Sepia pharaonis), widely distributed across the Indo-Pacific, exhibits genetic differentiation. In this study, we investigated intraspecific genetic variation based on mitochondrial COI and 16S rRNA sequences and integrated genetic information into SDMs to predict distribution shifts and ecological vulnerability at the lineage level. Phylogeographic analysis identified five lineages: Red Sea (RE), Australian (AU), Persian Gulf and Oman Sea (PE), central Indian Ocean (CE), and western Pacific (WE) lineages. These lineages exhibited substantial niche differentiation. At the species level, S. pharaonis preferred waters with high primary productivity. Suitable habitats were projected to expand southward, and relatively high ecological vulnerability was predicted in the Persian Gulf, the South China Sea, and Malaysian coastal waters. Lineage-level models revealed divergent climate responses masked by the species-level model. The CE and PE lineages preferred high productivity environments, consistent with the species-level SDM prediction, whereas the AU and WE lineages exhibited stronger tolerance to low-productivity environments. The WE and CE lineages faced higher risks of range contraction under SSP5-8.5. The WE lineage also harbored lower genetic diversity, potentially increasing its vulnerability to climate change. In contrast, the AU and PE lineages were projected to expand their suitable habitats eastward under most climate scenarios, reflecting their greater climate tolerances. This study provides crucial information for climate-adaptive conservation and management based on more precise taxonomic units for S. pharaonis.