Resource polymorphism and diversity of Arctic charr Salvelinus alpinus in a series of isolated lakes

Foraging-induced craniofacial plasticity is associated with an early, robust and dynamic transcriptional response

Phenotypic plasticity is the ability of a single genotype to vary its phenotype in response to the environment. Plasticity of the skeletal system in response to mechanical input is widely studied, but the timing of its transcriptional regulation is not well understood. Here, we used the cichlid feeding apparatus to examine the transcriptional dynamics of skeletal plasticity over time. Using three closely related species that vary in their ability to remodel bone and a panel of 11 genes, including well-studied skeletal differentiation markers and newly characterized environmentally sensitive genes, we examined plasticity at one, two, four and eight weeks following the onset of alternate foraging challenges. We found that the plastic species exhibited environment-specific bursts in gene expression beginning at one week, followed by a sharp decline in levels, while the species with more limited plasticity exhibited consistently low levels of gene expression. This trend held across nearly all genes, suggesting that it is a hallmark of the larger plasticity regulatory network. We conclude that plasticity of the cichlid feeding apparatus is not the result of slowly accumulating gene expression difference over time, but rather is stimulated by early bursts of environment-specific gene expression followed by a return to homeostatic levels.

Global investigation of lake habitat coupling by fishes

Habitat coupling, where consumers acquire resources from different habitats, plays an important role in ecosystem functioning. In this study, we provide a global investigation of lake habitat coupling by freshwater fishes between littoral (nearshore) and pelagic (open water) zones and elucidate the extent to which magnitude of coupling varies according to environmental context and consumer traits. We consider the influence of lake factors (surface area, depth, shoreline complexity, and annual temperature), relative trophic position of consumers, fish community species richness, and fish morphological traits on habitat coupling by fishes. Using a worldwide dataset consisting of fish stable isotope values (δ¹³C and δ¹⁵N), we developed an index of habitat coupling, and used Bayesian hierarchical and non-hierarchical beta regressions to estimate the effects of environmental lake context and morphological traits on habitat coupling by fishes. Our results show high rates of habitat coupling among fishes globally with marked taxonomic differences in the magnitude and variation. Habitat coupling was higher in lower elevation lakes and in regions characterized by relatively colder climates, whereas other environmental context factors had little or no effects on habitat coupling. Furthermore, habitat coupling was associated with several locomotion and feeding traits, but independent from species maximum body length. Overall, we highlight the prevalence of multiple resources supporting fish populations and suggest future research identify implications to ecosystem functioning that may result from alterations to habitat coupling by fishes.

Variation in the genomic basis of parallel phenotypic and ecological divergence in benthic and pelagic morphs of Icelandic Arctic charr (Salvelinus alpinus)

Sympatric adaptive phenotypic divergence should be underlain by genomic differentiation between sub-populations. When divergence drives similar patterns of phenotypic and ecological variation within species we expect evolution to draw on common allelic variation. We investigated divergence histories and genomic signatures of adaptive divergence between benthic and pelagic morphs of Icelandic Arctic charr. Divergence histories for each of four populations were reconstructed using coalescent modelling and 14,187 single nucleotide polymorphisms. Sympatric divergence with continuous gene flow was supported in two populations while allopatric divergence with secondary contact was supported in one population; we could not differentiate between demographic models in the fourth population. We detected parallel patterns of phenotypic divergence along benthic-pelagic evolutionary trajectories among populations. Patterns of genomic differentiation between benthic and pelagic morphs were characterized by outlier loci in many narrow peaks of differentiation throughout the genome, which may reflect the eroding effects of gene flow on nearby neutral loci. We then used genome-wide association analyses to relate both phenotypic (body shape and size) and ecological (carbon and nitrogen stable isotopes) variation to patterns of genomic differentiation. Many peaks of genomic differentiation were associated with phenotypic and ecological variation in the three highly divergent populations, suggesting a genomic basis for adaptive divergence. We detected little evidence for a parallel genomic basis of differentiation as most regions and outlier loci were not shared among populations. Our results show that adaptive divergence can have varied genomic consequences in populations with relatively recent common origins, similar divergence histories, and parallel phenotypic divergence.

Genomic basis of deep-water adaptation in Arctic Charr (Salvelinus alpinus) morphs

The post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Colonization of deep-water (>50 m) habitats often requires extensive adaptation to cope with novel environmental challenges from high hydrostatic pressure, low temperature, and low light, but the genomic mechanisms underlying evolution in these environments are rarely known. Here, we compare genomic divergence between a deep-water morph adapted to depths of up to 288 m and a larger, piscivorous pelagic morph occupying shallower depths. Using both a SNP array and resequencing of whole nuclear and mitochondrial genomes, we find clear genetic divergence (F_ST  = 0.11-0.15) between deep and shallow water morphs, despite an absence of morph divergence across the mitochondrial genome. Outlier analyses identified many diverged genomic regions containing genes enriched for processes such as gene expression and DNA repair, cardiac function, and membrane transport. Detection of putative copy number variants (CNVs) uncovered 385 genes with CNVs distinct to piscivorous morphs, and 275 genes with CNVs distinct to deep-water morphs, enriched for processes associated with synapse assembly. Demographic analyses identified evidence for recent and local morph divergence, and ongoing reductions in diversity consistent with postglacial colonization. Together, these results show that Arctic Charr morph divergence has occurred through genome-wide differentiation and elevated divergence of genes underlying multiple cellular and physiological processes, providing insight into the genomic basis of adaptation in a deep-water habitat following postglacial recolonization.

Investigating the morphological and genetic divergence of arctic char (Salvelinus alpinus) populations in lakes of arctic Alaska

Polymorphism facilitates coexistence of divergent morphs (e.g., phenotypes) of the same species by minimizing intraspecific competition, especially when resources are limiting. Arctic char (Salvelinus sp.) are a Holarctic fish often forming morphologically, and sometimes genetically, divergent morphs. In this study, we assessed the morphological and genetic diversity and divergence of 263 individuals from seven populations of arctic char with varying length-frequency distributions across two distinct groups of lakes in northern Alaska. Despite close geographic proximity, each lake group occurs on landscapes with different glacial ages and surface water connectivity, and thus was likely colonized by fishes at different times. Across lakes, a continuum of physical (e.g., lake area, maximum depth) and biological characteristics (e.g., primary productivity, fish density) exists, likely contributing to characteristics of present-day char populations. Although some lakes exhibit bimodal size distributions, using model-based clustering of morphometric traits corrected for allometry, we did not detect morphological differences within and across char populations. Genomic analyses using 15,934 SNPs obtained from genotyping by sequencing demonstrated differences among lake groups related to historical biogeography, but within lake groups and within individual lakes, genetic differentiation was not related to total body length. We used PERMANOVA to identify environmental and biological factors related to observed char size structure. Significant predictors included water transparency (i.e., a primary productivity proxy), char density (fish·ha-1), and lake group. Larger char occurred in lakes with greater primary production and lower char densities, suggesting less intraspecific competition and resource limitation. Thus, char populations in more productive and connected lakes may prove more stable to environmental changes, relative to food-limited and closed lakes, if lake productivity increases concomitantly. Our findings provide some of the first descriptions of genomic characteristics of char populations in arctic Alaska, and offer important consideration for the persistence of these populations for subsistence and conservation.

Ontogenetic and ecotypic variation in the coloration and morphology of rainbow trout (Oncorhynchus mykiss) in a stream–lake system

Alternative ecotypes of diverse animal taxa exhibit distinct, habitat-specific phenotypes. Rainbow trout (Oncorhynchus mykiss), a salmonid fish, exhibits stream-resident (fluvial), lake-migrant (adfluvial) and ocean-migrant (anadromous) ecotypes throughout its range. We investigated the coloration, and morphology associated with swimming performance of wild, native non-anadromous rainbow trout in connected stream and lake habitats of a south-west Alaskan watershed to assess if they exhibited phenotypic diversity consistent with the presence of alternative fluvial and adfluvial ecotypes. Colour differences among rainbow trout of different size classes and habitats (stream or lake) indicated ecotype-specific pathways, diverging at the same point in ontogeny and resulting in different terminal coloration patterns. Specifically, lake-caught fish exhibited distinct silvering of the body, whereas stream-caught fish displayed banded coloration when small and bronze colour when larger. The morphology of lake-caught rainbow trout also differed from that of stream-caught fish in features associated with swimming performance, and they exhibited both shared and unique morphological patterns compared to sympatric Salvelinus species in those habitats [Dolly Varden (S. malma) in streams, and Arctic char (S. alpinus) in the lake]. Greater morphological variation within stream- than lake-caught rainbow trout, and their limited overlap in morphology, suggested population-specific partial migration. This study highlights the intraspecific diversity of migratory behaviour and how conservation of particular phenotypes depends on managing both for genotypes and for habitats.

Intraspecific brain size variation between coexisting sunfish ecotypes

Variation in spatial complexity and foraging requirements between habitats can impose different cognitive demands on animals that may influence brain size. However, the relationship between ecologically related cognitive performance and brain size is not well established. We test whether variation in relative brain size and brain region size is associated with habitat use within a population of pumpkinseed sunfish composed of different ecotypes that inhabit either the structurally complex shoreline littoral habitat or simpler open-water pelagic habitat. Sunfish using the littoral habitat have on average 8.3% larger brains than those using the pelagic habitat. We found little difference in the proportional sizes of five brain regions between ecotypes. The results suggest that cognitive demands on sunfish may be reduced in the pelagic habitat given no habitat-specific differences in body condition. They also suggest that either a short divergence time or physiological processes may constrain changes to concerted, global modifications of brain size between sunfish ecotypes.

Hybridization between char species (Salvelinus alpinus and Salvelinus fontinalis): a fast track for novel allometric trajectories

Hybridization between closely related species can generate genetic and phenotypic variation, providing valuable biological material to assess the physiological impact of the structural or functional variability of different organs. In the present study, we examined growth rates of various organs and whole body in brook char, Arctic char and their reciprocal hybrids over a period of 281 days. Parental species achieved significantly higher body mass than their hybrids. Hybridization significantly reduced the relative size of the heart, liver and spleen. The relative size of pyloric caeca did not differ among the four groups. The observed lower growth performance of the hybrids compared to parental species strongly suggests that divergence in the relative size of digestive organs, liver and heart partly dictate growth capacity. Our results also suggest that the increased variability achieved through hybridization may prove useful in a genetic selection program.

Trophic ecology of nonanadromous rainbow trout in a post-glacial lake system: partial convergence of adfluvial and fluvial forms

The rainbow trout (Oncorhynchus mykiss (Walbaum, 1792)) is one of many salmonid species exhibiting a gradient of life histories including fluvial (stream-resident), anadromous (ocean-migrant), and adfluvial (lake-migrant) forms, the last of which is less extensively studied than the other two. Our goal was to determine the extent of diet segregation between fluvial and adfluvial rainbow trout. We collected stomach content and stable isotope data on rainbow trout sampled in stream and lake habitats in a southwestern Alaska watershed during summer and compared them with data on sympatric stream- and lake-specialist char species, Dolly Varden (Salvelinus malma (Walbaum in Artedi, 1792)) and Arctic char (Salvelinus alpinus (Linnaeus, 1758)), respectively. Rainbow trout in streams fed largely on aquatic insects, while those in the lake ate primarily benthic snails and amphipods. The trophic segregation of stream-resident and lake-migrant rainbow trout mirrored but was less extreme than the divergence of lotic Dolly Varden and lentic Arctic char in the same system. Spawning sockeye salmon (Oncorhynchus nerka (Walbaum in Artedi, 1792)) provided a nutrient subsidy in the form of eggs that supported rainbow trout in both stream and lake (littoral) habitats, causing their isotopic signatures to converge. This study augments knowledge of partial migration and trophic divergence within populations.

Trophic biology and migratory patterns of sympatric Dolly Varden (Salvelinus malma) and Arctic char (Salvelinus alpinus)

The trophic ecology (diet and head morphology) and migration patterns of two closely related salmonid fishes, Arctic char (Salvelinus alpinus (L., 1758)) and Dolly Varden (Salvelinus malma (Walbaum, 1792)), were examined in tributaries of Lake Aleknagik, southwestern Alaska, to test for differentiation between species. Schoener’s index of proportional overlap and multivariate analyses of diets suggested that these species had significantly different trophic niches. Arctic char and the largest individuals of both species had the most diverse diets, and sockeye salmon (Oncorhynchus nerka (Walbaum, 1792)) eggs dominated the diet of both species, especially Arctic char. Arctic char had larger jaws and wider heads than Dolly Varden of similar body length, which may contribute to interspecific diet difference. The species also differed in migration patterns; otolith microchemistry indicated that juvenile Arctic char were produced by nonanadromous mothers, whereas the mothers of the Dolly Varden had been to sea in the season prior to spawning. The species also segregate in spawning habitat (Arctic char in the lakes and Dolly Varden in streams), as well as in juvenile rearing habitat. Our study provides the first evidence of divergent feeding and migratory ecology between sympatric juvenile Arctic char and Dolly Varden, differences that may constrain hybridization and introgression between them.

Morphological divergence between three Arctic charr morphs - the significance of the deep-water environment

Morphological divergence was evident among three sympatric morphs of Arctic charr (Salvelinus alpinus (L.)) that are ecologically diverged along the shallow-, deep-water resource axis in a subarctic postglacial lake (Norway). The two deep-water (profundal) spawning morphs, a benthivore (PB-morph) and a piscivore (PP-morph), have evolved under identical abiotic conditions with constant low light and temperature levels in their deep-water habitat, and were morphologically most similar. However, they differed in important head traits (e.g., eye and mouth size) related to their different diet specializations. The small-sized PB-morph had a paedomorphic appearance with a blunt head shape, large eyes, and a deep body shape adapted to their profundal lifestyle feeding on submerged benthos from soft, deep-water sediments. The PP-morph had a robust head, large mouth with numerous teeth, and an elongated body shape strongly related to their piscivorous behavior. The littoral spawning omnivore morph (LO-morph) predominantly utilizes the shallow benthic–pelagic habitat and food resources. Compared to the deep-water morphs, the LO-morph had smaller head relative to body size. The LO-morph exhibited traits typical for both shallow-water benthic feeding (e.g., large body depths and small eyes) and planktivorous feeding in the pelagic habitat (e.g., streamlined body shape and small mouth). The development of morphological differences within the same deep-water habitat for the PB- and PP-morphs highlights the potential of biotic factors and ecological interactions to promote further divergence in the evolution of polymorphism in a tentative incipient speciation process. The diversity of deep-water charr in this study represents a novelty in the Arctic charr polymorphism as a truly deep-water piscivore morph has to our knowledge not been described elsewhere.