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Abstract Overfishing remains a threat to coral reef fishes worldwide, with large carnivores often disproportionately vulnerable. Marine protected areas (MPAs) can restore fish populations and biodiversity, but their effect has been understudied in mesophotic coral ecosystems (MCEs), particularly in the Coral Triangle.Videos were analysed from baited remote underwater video systems deployed in 2016 to investigate the assemblage structure of large carnivorous fishes at shallow (4–12 m) and mesophotic (45–96 m) depths in two of the largest and most isolated MPAs in the Philippines: an uninhabited, fully no‐take MPA enacted in 1988 (Tubbataha Reefs Natural Park) and an archipelagic municipality surrounded by an extensive but not fully no‐take MPA declared in 2016 (Cagayancillo). Taxa focused on were groupers (Serranidae), snappers (Lutjanidae), emperors (Lethrinidae), jacks (Carangidae) and the endangeredCheilinus undulatus(Labridae).Mean abundance and species richness were not greater in TRNP than in Cagayancillo regardless of depth despite long‐term protection in the former. Limited impacts of fishing in Cagayancillo may explain this result. Differentiation of fish assemblages was evident between TRNP and Cagayancillo but more obvious between depths at each location, probably due more to habitat than MPA effects. In Cagayancillo, overall carnivorous reef fish, grouper and jack mean abundance were 2, 2 and 10 times higher, respectively, at mesophotic depths, suggesting that MCEs can serve as deep refugia from fishing.These findings of differentiation between depths and higher abundance of certain taxa in mesophotic depths emphasize that MCEs are distinct from shallow reefs, serve as important habitat for species susceptible to overfishing and, thus, must be explicitly included in the design of MPAs. This study also highlights the value of maintaining strict protection of MPAs like TRNP for the Coral Triangle and an opportunity to safeguard intact fish assemblages in Cagayancillo by expanding its no‐take zones. 

Interactions among selection, gene flow, and drift affect the trajectory of adaptive evolution. In natural populations, the direction and magnitude of these processes can be variable across different spatial, temporal, or ontogenetic scales. Consequently, variability in evolutionary processes affects the predictability or stochasticity of microevolutionary outcomes. We studied an intertidal fish, Bathygobius cocosensis (Bleeker, 1854), to understand how space, time, and life stage structure genetic and phenotypic variation in a species with potentially extensive dispersal and a complex life cycle (larval dispersal preceding benthic recruitment). We sampled juvenile and adult life stages, at three sites, over three years. Genome-wide SNPs uncovered a pattern of chaotic genetic patchiness, that is, weak-but-significant patchy spatial genetic structure that was variable through time and between life stages. Outlier locus analyses suggested that targets of spatially divergent selection were mostly temporally variable, though a significant number of spatial outlier loci were shared between life stages. Head shape, a putatively ecologically responsive (adaptive) phenotype in B. cocosensis also exhibited high temporal variability within sites. However, consistent spatial relationships between sites indicated that environmental similarities among sites may generate predictable phenotype distributions across space. Our study highlights the complex microevolutionary dynamics of marine systems, where consideration of multiple ecological dimensions can reveal both predictable and stochastic patterns in the distributions of genetic and phenotypic variation. Such considerations probably apply to species that possess short, complex life cycles, have large dispersal potential and fecundities, and that inhabit heterogeneous environments. 

Abstract AimHumans are unintentionally affecting the evolution of fishery species directly through exploitation and indirectly by altering climate. We aim to test for a relationship between biogeographic patterns in the shell phenotypes of an over‐exploited shellfish and the presence of humans to identify human‐mediated adaptive trade‐offs. The implications of these trade‐offs are discussed with respect to the sustainability of the fishery. TaxonThe endemic Hawaiian intertidal limpet, ‘opihi makaiauli (Patellagastropoda, Nacellidae, Cellana exarata) MethodsWe surveyed phenotypic characters associated with temperature and predation avoidance across the entire species range and tested for differences in the relationship between these characters and latitude, on islands with and without humans. ResultsAmong all limpets surveyed, there was a bimodal distribution in shell colour (light, dark) and a parapatric pattern of shell coloration across the archipelago with lighter shells being prevalent on the uninhabited islands and darker, more camouflaged shells being prevalent on the inhabited islands. On the cooler, uninhabited islands, all morphometric characters associated with thermal avoidance (surface area, height and doming) increased with decreasing latitude. On the hotter, inhabited islands, however, shells were flatter, less variable and less adapted for avoiding thermal stress than predation. Main ConclusionsThe biogeographic patterns in shell phenotype and previous genetic studies suggest that the population is beginning to bifurcate in response to disruptive and directional selection as well as geographic isolation between the islands with and without humans. Decreased phenotypic and genetic diversity on the inhabited islands despite much larger populations of ‘opihi suggests a prominent historical bottleneck. The prevalence of maladaptive dark, flat phenotypes for thermal avoidance on the inhabited islands suggests that predation is a stronger selective force, driving adaptive trade‐offs in shape and colour. We propose that this is likely a case of fisheries‐induced evolution and a millennium of harvesting is the most likely selective pressure driving the observed biogeographic patterns in shell morphology. The flatter, darker shells will allow body temperatures to rise higher in direct sunlight, therefore we hypothesize that the thermal niche of ‘opihi is narrower on inhabited islands and will continue to narrow as Earth warms.