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Whole genome duplication (WGD) is often considered to be mechanistically associated with species diversification. Such ideas have been anecdotally attached to a WGD at the stem of the salmonid fish family, but remain untested. Here, we characterized an extensive set of gene paralogues retained from the salmonid WGD, in species covering the major lineages (subfamilies Salmoninae, Thymallinae and Coregoninae). By combining the data in calibrated relaxed molecular clock analyses, we provide the first well-constrained and direct estimate for the timing of the salmonid WGD. Our results suggest that the event occurred no later in time than 88 Ma and that 40–50 Myr passed subsequently until the subfamilies diverged. We also recovered a Thymallinae–Coregoninae sister relationship with maximal support. Comparative phylogenetic tests demonstrated that salmonid diversification patterns are closely allied in time with the continuous climatic cooling that followed the Eocene–Oligocene transition, with the highest diversification rates coinciding with recent ice ages. Further tests revealed considerably higher speciation rates in lineages that evolved anadromy—the physiological capacity to migrate between fresh and seawater—than in sister groups that retained the ancestral state of freshwater residency. Anadromy, which probably evolved in response to climatic cooling, is an established catalyst of genetic isolation, particularly during environmental perturbations (for example, glaciation cycles). We thus conclude that climate-linked ecophysiological factors, rather than WGD, were the primary drivers of salmonid diversification.

Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss. Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.

The Arctic climate is changing rapidly, yet predicting how aquatic species will respond to these changes remains challenging given the lack of empirical data for most high-latitude taxa. Acoustic telemetry has recently emerged as an important methodology for understanding horizontal and vertical space-use patterns in fishes. Here, we used acoustic telemetry to document marine habitat use and depth/temperature preference of 26 anadromous Arctic char Salvelinus alpinus within the Kitikmeot Sea region of the Canadian central Arctic over 4 yr (2013−2016). Most detections (~70%) were within the top 3 m of the water column, and most were in estuarine (72.6%) vs. marine (27.4%) habitats. Arctic char preferred deeper waters later in the summer, but the temperature they occupied remained relatively constant throughout the marine feeding season (~5−8°C). Most Arctic char exhibited some degree of repetitive diving behavior, with individuals diving to 35 m. Diving activity increased later in the summer marine feeding season and is likely a response to the seasonal transition of their preferred prey to deeper waters as the season progresses. Finally, Arctic char preferred deeper waters with less ice cover and during the day, the latter suggesting potential diel patterns to marine habitat use. Finally, year-to-year variation in Arctic char depth and temperature use was very modest despite differences in climatic and ice conditions. This result suggests that habitat use is relatively fixed and may reflect their thermal and osmoregulatory physiology, which has important implications for forecasting the impacts of a changing Arctic on this economically valuable species.

Habitats along migratory routes may provide key resources for migratory species (e.g. stopover habitat). For example, migratory juvenile salmon transit through estuaries on their way from freshwaters out to the ocean, but they may also reside and feed in these habitats. Here we examined the amount of time that juvenile salmon feed and reside in the estuary of the Skeena River (British Columbia, Canada), the second-largest salmon-bearing watershed in Canada. We implemented a novel application of stable isotopes of sulfur, carbon, and nitrogen as clocks to estimate the days since estuary entry. Salmon estuary residency varied across species; 25% of individuals spent at least 33, 22, 30, and 5 d in the estuary for Chinook Oncorhynchus tshawytscha, coho O. kisutch, pink O. gorbuscha, and sockeye salmon O. nerka, respectively. Larger pink and Chinook salmon resided in the estuary for longer durations, growing at an estimated 0.2 and 0.5 mm d−1, respectively, evidence that estuary residency provides growth opportunities. A negative relationship between size and estuary residency in coho salmon suggests the potential existence of an estuary fry life history. Genetic stock assignment indicated that different populations of sockeye salmon may reside in the estuary for different amounts of time. Collectively, these results reveal that estuaries can represent stopover habitats for salmon, and that the extent varies across salmon species and populations. These data address a knowledge gap in assessment of environmental risks of proposed industrial developments. This study indicates the importance of considering the fundamental nature of habitats through which migratory species move.

Arctic charr have a circumpolar distribution, persevere under extreme environmental conditions, and reach ages unknown to most other salmonids. The Salvelinus genus is primarily composed of species with genomes that are structured more like the ancestral salmonid genome than most Oncorhynchus and Salmo species of sister genera. It is thought that this aspect of the genome may be important for local adaptation (due to increased recombination) and anadromy (the migration of fish from saltwater to freshwater). In this study, we describe the generation of a new genetic map, the sequencing and assembly of the Arctic charr genome (GenBank accession: GCF_002910315.2) using the newly created genetic map and a previous genetic map, and present several analyses of the Arctic charr genes and genome assembly. The newly generated genetic map consists of 8,574 unique genetic markers and is similar to previous genetic maps with the exception of three major structural differences. The N50, identified BUSCOs, repetitive DNA content, and total size of the Arctic charr assembled genome are all comparable to other assembled salmonid genomes. An analysis to identify orthologous genes revealed that a large number of orthologs could be identified between salmonids and many appear to have highly conserved gene expression profiles between species. Comparing orthologous gene expression profiles may give us a better insight into which genes are more likely to influence species specific phenotypes.

Migration of fishes between habitats influences population dynamics and ecological interactions. Some “partially migratory” populations include both migratory and non-migratory individuals, adding complexity to these dynamics. For partially migratory fishes with diadromous life histories, freshwater and marine habitats can differ greatly in availability of prey and physical conditions conducive to growth, predation risk, and exposure to fisheries and to contaminants. Therefore, understanding patterns of migratory behavior can inform population biology and conservation. Using otolith microchemistry, we describe observations of partial anadromy in a threatened, iteroparous salmonid species, bull trout (Salvelinus confluentus), in the Skagit River basin of Washington State, USA. We found that 59% of the fish sampled (> 338 mm fork length) in the river had not been to marine water, despite easy access. The other 41% had migrated to salt water, typically every year beginning at age 2 or 3. We also observed overwintering in marine waters by some individuals, and extended time in fresh water between otherwise annual migrations to marine waters in others. Additionally, there was no obligatory relationship between anadromy in mothers and their offspring. The facultative nature of migration in this species, and the lack of tight connection between maternal and offspring life history patterns are consistent with studies of other Salvelinus species but contrast with the more rigid controls on migration in semelparous salmonids.

In mobile animals, selection pressures resulting from spatio-temporally varying ecological factors often drive adaptations in migration behavior and associated physiological phenotypes. These adaptations may manifest in ecologically and genetically distinct ecotypes within populations. We studied a meta-population of northern pike (Esox lucius) in brackish environments and examined intrapopulation divergence along environmental gradients. Behavioral phenotypes in habitat use were characterized via otolith microchemistry in 120 individuals sampled from brackish lagoons and adjacent freshwater tributaries. We genotyped 1514 individual pike at 33 highly informative genetic markers. The relationship between behavioral phenotype and genotype was examined in a subset of 101 pikes for which both phenotypic and genomic data were available. Thermosaline differences between juvenile and adult life stages indicated ontogenetic shifts from warm, low-saline early habitats towards colder, higher-saline adult habitats. Four behavioral phenotypes were found: Freshwater residents, anadromous, brackish residents, and cross-habitat individuals, the latter showing intermediary habitat use between brackish and freshwater areas. Underlying the behavioral phenotypes were four genotypes, putative freshwater, putative anadromous, and two putatively brackish genotypes. Through phenotype-genotype matching, three ecotypes were identified: (i) a brackish resident ecotype, (ii) a freshwater ecotype expressing freshwater residency or anadromy, and (iii) a previously undescribed intermediary cross-habitat ecotype adapted to intermediate salinities, showing limited reliance on freshwater. Life-time growth of all ecotypes was similar, suggesting comparable fitness. By combining genetic data with lifelong habitat use and growth as a fitness surrogate, our study revealed strong differentiation in response to abiotic environmental gradients, primarily salinity, indicating ecotype diversity in coastal northern pike is higher than previously believed.

Multiple studies in a range of taxa have found links between structural variants and the development of ecologically important traits. Such variants are becoming easier to find due, in large part, to the increase in the amount of genome-wide sequence data in nonmodel organisms. The salmonids (salmon, trout, and charr) are a taxonomic group with abundant genome-wide datasets due to their importance in aquaculture, fisheries, and variation in multiple ecologically important life-history traits. Previous research on rainbow trout (Oncorhynchus mykiss) has documented a large pericentric (∼55 Mb) chromosomal inversion (CI) on chromosome 5 (Omy05) and a second smaller (∼14 Mb) chromosome inversion on Omy20. While the Omy05 inversion appears to be associated with multiple adaptive traits, the inversion on Omy20 has received far less attention. In this study, we re-analyze RAD-seq and amplicon data from several populations of rainbow trout (O. mykiss) to better document the structure and geographic distribution of variation in the Omy20 CI. Moreover, we utilize phylogenomic techniques to characterize both the age- and the protein-coding gene content of the Omy20 CI. We find that the age of the Omy20 inversion dates to the early stages of O. mykiss speciation and predates the Omy05 inversion by ∼450,000 years. The 2 CIs differ further in terms of the frequency of the homokaryotypes. While both forms of the Omy05 CI are found across the eastern Pacific, the ancestral version of the Omy20 CI is restricted to the southern portion of the species range in California. Furthermore, the Omy20 inverted haplotype is comparable in genetic diversity to the ancestral form, whereas derived CIs typically show substantially reduced genetic diversity. These data contribute to our understanding of the age and distribution of a large CI in rainbow trout and provide a framework for researchers looking to document CIs in other nonmodel species.

Arctic char (Salvelinus alpinus) and Dolly Varden (S. malma) are two closely related species in the genus Salvelinus. Both species show substantial intra-specific variation in ecology, morphology, and post-glacial history across their distributional ranges, which has presented substantial challenges for conservation and management and has led to the coining of the term, ‘the charr problem’. Arctic char and Dolly Varden have been studied extensively by scientists since the 1700s, not only because these fishes play important ecological roles within ecosystems, but also because they are culturally, economically, and recreationally valuable. While several detailed reviews have been published on Arctic char over the past 40 years, Dolly Varden remain understudied. In addition, advances in the fields of genetics, ecology, and morphometrics have improved our understanding of the behavior, feeding, habitat requirements, post-glacial histories and intraspecific diversity of each of these two species. Herein, we present an updated review that focuses on placing findings from more recently published (through 2022) phylogenetic, ecological and morphometric studies within the foundational context of earlier papers and reviews (since 1943). We also review anticipated effects of climate change on both species. Across their ranges, Arctic char and Dolly Varden can display a variety of life history types, with many populations exhibiting anadromy and/or potadromy; due to their use of distinct habitats at specific life stages, migratory chars are vulnerable to climate-induced changes to habitat quantity and quality. In addition to reviewing the existing literature, we highlight knowledge gaps and research priorities that, when addressed, will enable more informed conservation and management initiatives for these highly valued fishes.

Although theory predicts that dispersal has a pivotal influence on speciation and extinction rates, it can have contradictory effects on each, such that empirical quantification of its role is required. In many studies, dispersal reduction appears to promote diversification, although some comparisons of migratory and nonmigratory species suggest otherwise. We tested for a relationship between migratory status and diversification rate within the dominant radiation of temperate Southern Hemisphere freshwater fishes, the Galaxiidae. We reconstructed a molecular phylogeny comprising >95% of extant taxa, and applied State-dependent Speciation Extinction models to estimate speciation, extinction, and diversification rates. In contrast to some previous studies, we revealed higher diversification rates in nonmigratory lineages. The reduced gene flow experienced by nonmigratory galaxiids appears to have increased diversification under conditions of allopatry or local adaptation. Migratory galaxiid lineages, by contrast, are genetically homogeneous within landmasses, but may also be rarely able to diversify by colonizing other landmasses in the temperate Southern Hemisphere. Apparent contradictions among studies of dispersal-diversification relationships may be explained by the spatial context of study systems relative to species dispersal abilities, by means of the “intermediate dispersal” model; the accurate quantification of dispersal abilities will aid in the understanding of these proposed interactions.