Migratory behaviour patterns in animals are controlled by a complex genetic architecture. Rainbow trout (Oncorhynchus mykiss) is a salmonid fish that spawns in streams but exhibits three primary life history pathways: stream‐resident (fluvial), lake‐migrant (adfluvial) and ocean‐migrant (anadromous). Previous studies examining fluvial and anadromous O. mykiss have identified several genes associated with life history divergence including the presence of an inversion complex within chromosome 5 (Omy05) that appears to maintain a suite of linked genes controlling migratory behaviour. However, adfluvial trout are migratory without being anadromous, and the genetic basis for this life history has not been investigated from evolutionary perspectives. We sampled wild, native nonanadromous rainbow trout occupying connected stream and lake habitats in a southwest Alaskan watershed to determine whether these fish exhibit genetic divergence between fluvial and adfluvial ecotypes, and whether that divergence parallels that documented in fluvial and anadromous O. mykiss. Data from restriction site‐associated DNA (RAD) sequencing revealed an association between frequencies of both the Omy05 inversion complex and other single nucleotide polymorphisms (SNPs) with habitat type (stream or lake), supporting the genetic divergence of fluvial and adfluvial individuals in sympatry. The presence of a genetic basis for migration into lakes, analogous to that documented for anadromy, indicates that the adfluvial ecotype must be recognized separately from the fluvial form of O. mykiss even though neither is anadromous. These results highlight the genetic architecture underlying migration and the importance of chromosomal inversions in promoting and sustaining intraspecific diversity.

The blue marlin (Makaira nigricans) is a highly migratory pelagic predator of tropical and subtropical seas. Information on the habitat use of marine species is fundamental to understanding their ecology and population dynamics and is needed to inform responsible management strategies. Using a long‐term satellite tagging data set from The International Game Fish Association Great Marlin Race, we examined habitat use and how oxygen and temperature influence the horizontal and vertical distributions of blue marlin in the Central Pacific. Blue marlin primarily occurred in warm waters (26–30°C) and exhibited a diel bimodal depth distribution across the 5‐year data record (2009–2013), with fish spending the majority of their time near the surface at night and at deeper depths during the day (25–100 m). The depth distribution of blue marlin was limited in areas where low oxygen and/or temperature conditions occur closer to the surface, with the extent of habitat compression being greatest when both oxygen and temperature were limiting. The migrations of blue marlin appeared restricted during the 2010 La Niña, when increased equatorial upwelling resulted in an extension of the cold, low oxygen waters of the cold tongue into the Central Pacific, creating a barrier to the trans‐equatorial migrations that occurred during all other tagging years. If the frequency and intensity of La Niña events increases and the oxygen minimum layer continues to expand as has been predicted under certain climate change scenarios, the migratory behavior and habitat availability of blue marlin may be impacted.

Many large marine predators make excursions from surface waters to the deep ocean below 200 m. Moreover, the ability to access meso- and bathypelagic habitats has evolved independently across marine mammals, reptiles, birds, teleost fishes, and elasmobranchs. Theoretical and empirical evidence suggests a number of plausible functional hypotheses for deep-diving behavior. Developing ways to test among these hypotheses will, however, require new ways to quantify animal behavior and biophysical oceanographic processes at coherent spatiotemporal scales. Current knowledge gaps include quantifying ecological links between surface waters and mesopelagic habitats and the value of ecosystem services provided by biomass in the ocean twilight zone. Growing pressure for ocean twilight zone fisheries creates an urgent need to understand the importance of the deep pelagic ocean to large marine predators.

Salmonid fishes may reside within or migrate between stream and lake habitats, or undergo anadromous migrations between freshwater and the ocean. While the degree of anadromy of salmonids has been thoroughly compared, no analogous review has examined the degree of lake use. To assess the extent of reliance on lake habitat in this family, we considered 16 species of salmon, trout and charr from the genera Oncorhynchus, Salmo and Salvelinus, comparing their (a) use of lakes as spawning habitat, (b) rearing strategies in lakes, and (c) occurrence and diversity of lacustrine trophic polymorphism. In identifying the primary life‐history patterns of each species and exploring the lesser‐known lacustrine behaviours, we found that the extent of reliance on lakes exhibits a negative association with the degree of anadromy. Oncorhynchus rely least on lakes, Salmo to an intermediate level and Salvelinus the most, opposite of the general prevalence of anadromy among these genera. Lakes are critical to adfluvial and lake‐resident salmonids, but they also support anadromous and fluvial life histories by providing spawning, rearing, overwintering and/or summer refuge habitat. Adfluviality, although a non‐anadromous life history, consists of similar migration‐related traits and behaviours as anadromy, including the parr–smolt transformation, sex‐biased patterns of migration and residency, and the presence of precocious males. Lakes support life‐history variants, reproductive ecotypes and trophic morphs unique to lacustrine habitat. Therefore, conservation of salmonids is dependent on maintaining the diversity and quality of their habitats, including lakes.