Estuarine gradients and climate stressors: Divergent population responses and management implications for coastal species across the Yangtze Estuary barrier.

The Yangtze Estuary, a critical biogeographic barrier and major biogeographic transition zone, is under escalating pressure from climate change. This study integrates species distribution modeling, niche analysis, and multi-period future climate projections to quantify how the estuary's environmental gradients shape the vulnerability and fate of intraspecific populations in two key coastal species: the hairfin anchovy (Setipinna tenuifilis) and the Chinese mitten crab (Eriocheir sensu stricto). Results reveal that the estuary acts as an ecological filter shaped by river-sea mixing, turbidity and nutrient delivery, which form strong north-south gradients in chlorophyll-a and primary productivity. These gradients underpin distinct niche adaptations: maximum chlorophyll contributes 58.1% to the distribution of the northern anchovy population, which is mainly constrained by this factor, while minimum primary productivity dominates the niche of southern anchovy population with a contribution rate of 62.0%. Under the high-emission RCP8.5 climate scenario, intraspecific climate responses diverge sharply by 2100. The southern EJC crab lineage emerges as a "climate winner" with a net suitable habitat gain of 919,698.44 km2. In contrast, two threatened populations are identified as typical "climate losers": the southern anchovy population, where 17.17% (751,217.84 km2) of its current suitable habitat will contract with a net habitat loss of 8.91% (389,930.16 km2) after offsetting newly expanded areas; the ES crab lineage exhibits a gross habitat contraction proportion of 27.00% (287,601.94 km2) and a net habitat loss rate of 21.28% (-226,707.23 km2). Crucially, climate change will drastically reconfigure intraspecific competitive interactions. For E. sensu stricto, niche overlap area between the EJC and ES lineages surges by 103.0% (from 263,118.50 km2 to 534,084.26 km2), shifting most inter-lineage competitive pressure toward the expanding EJC lineage. For S. tenuifilis, strong inherent niche divergence and the estuary's persistent geographic barrier buffer inter-population competition, their Schoener's D niche overlap index remains consistently low, rising only slightly from the current 0.15 to 0.23 by 2100 and maintaining stable ecological isolation. These findings demonstrate that estuarine gradients pre-determine population-specific climate vulnerability and future ecological outcomes. We therefore propose an evolutionarily significant unit (ESU)-based adaptive management framework, with a core actionable policy recommendation: the southern anchovy population and ES crab lineage should be independently classified, assessed and protected as separated conservation units during marine spatial planning.