In estuary and coastal systems, human demand for freshwater, climate change‐driven precipitation variability, and extreme weather impact salinity levels, reducing connectivity between mesohaline coastal fish populations and potentially contributing to genomic divergence. We examined gill transcriptome responses to salinity in wild‐caught juveniles from two populations of Sacramento splittail (Pogonichthys macrolepidotus), a species of conservation concern that is endemic to the San Francisco Estuary, USA, and the lower reaches of its tributaries. Recent extreme droughts have led to salinities above the tolerance limits for this species, creating a migration barrier between these populations, which potentially contributed to population divergence. We identified transcripts involved in a conserved response to salinity; however, the more salinity‐tolerant San Pablo population had greater transcriptome plasticity (3.6‐fold more transcripts responded than the Central Valley population) and a response consistent with gill remodeling after 168 hr of exposure to elevated salinity. The reorganization of the gill in response to changing osmotic gradients is a process critical for acclimation and would facilitate enhanced salinity tolerance. We detected an upregulation of receptors that control the Wnt (wingless‐type) cell signaling pathway that may be required for an adaptive response to increases in salinity, patterns not observed in the relatively salinity‐sensitive Central Valley population. We detected 62 single nucleotide polymorphisms (SNPs) in coding regions of 26 transcripts that differed between the populations. Eight transcripts that contained SNPs were associated with immune responses, highlighting the importance of diversity in immune gene sequences as a defining characteristic of genomic divergence between these populations. Our data demonstrate that these populations have divergent transcriptomic responses to salinity, which is consistent with observed physiological differences in salinity tolerance.

The considerable quantities of dead wood in the intertidal zone of mature mangrove forests are tunnelled by bivalves of the family Teredinidae. When the surface of heavily tunnelled wood is broken open, cryptofauna are able to use tunnels as refuges. In this study, the exploitation of this niche during low tide by the dartfish Parioglossus interruptus was investigated. The majority of tunnels offer a close fit falling within the range of typical dartfish diameters. The fish found within wood tended to be smaller than fish found swimming between mangrove roots at high tide. Dartfish were found in tunnelled wood even where it was emersed for over 11 h d −1 , but favoured wood in the lower intertidal. Within the wood, daytime thermal maxima were reduced by 6.5°C compared with adjacent tidepools. Wind-tunnel observations indicated that this lowering could be due to evaporative cooling. However, dartfish were found to be notably tolerant of high temperatures, with a critical thermal maximum that exceeded temperatures reached in tunnelled wood and pools. Nonetheless, such tolerance may impose a metabolic cost that would be reduced by occupying tunnels. Teredinid tunnels are also likely to give dartfish protection from desiccation and predation. During high-tide, free-swimming dartfish were observed to favour areas of Rhizophora roots over open creeks. In aquaria, fish swam actively during the day, but took refuge in teredinid tunnels at night. Sampling of wood at low tide and direct observations at high tide indicate that a substantial proportion of the dartfish population takes refuge in wood during low tide. Thus, teredinid-tunnelled wood is a key low-tide refuge especially for younger fish, which would otherwise be exposed to predators. This study provides an example of a mechanism whereby mangrove forests support intertidal biodiversity.

Genetically-distinct populations of the Sacramento Splittail, a minnow endemic to the San Francisco Estuary, exhibit different physiological responses and tolerances to salinity as juveniles. Population-level responses correspond with known salinity habitat differences suggesting some degree of local adaptation. Further studies are needed to elucidate these differences, but these data suggest a potential need for population-specific conservation and management strategies.

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