Ecological opportunity shapes a large Arctic charr species radiation

Differential Stage-Specific Mortality as a Mechanism for Diversification

AbstractIndividual variability in mortality is widespread in nature. The general rule is that larger organisms have a greater chance of survival than smaller conspecifics. There is growing evidence that differential mortality between developmental stages has important consequences for the ecology and evolution of populations and communities. However, we know little about how it can influence diversification. Using an eco-evolutionary model of diversification that considers individual variability in mortality, I show that commonly observed differences in mortality between juveniles and adults can facilitate adaptive diversification. In particular, diversification is expected to be less restricted when mortality is more biased toward juveniles. Additionally, I find stage-specific differences in metabolic cost and foraging capacity to further facilitate diversification when adults are slightly superior competitors, due to either a lower metabolic cost or a higher foraging capacity, than juveniles. This is because by altering the population composition, differential stage-specific mortality and competitive ability can modulate the strength of intraspecific competition, which in turn determines the outcome of diversification. These results demonstrate the strong influence that ecological differences between developmental stages have on diversification and highlight the need for integrating developmental processes into diversification theory.

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.

Genomic underpinnings of head and body shape in Arctic charr ecomorph pairs

Across its Holarctic range, Arctic charr (Salvelinus alpinus) populations have diverged into distinct trophic specialists across independent replicate lakes. The major aspect of divergence between ecomorphs is in head shape and body shape, which are ecomorphological traits reflecting niche use. However, whether the genomic underpinnings of these parallel divergences are consistent across replicates was unknown but key for resolving the substrate of parallel evolution. We investigated the genomic basis of head shape and body shape morphology across four benthivore-planktivore ecomorph pairs of Arctic charr in Scotland. Through genome-wide association analyses, we found genomic regions associated with head shape (89 SNPs) or body shape (180 SNPs) separately and 50 of these SNPs were strongly associated with both body and head shape morphology. For each trait separately, only a small number of SNPs were shared across all ecomorph pairs (3 SNPs for head shape and 10 SNPs for body shape). Signs of selection on the associated genomic regions varied across pairs, consistent with evolutionary demography differing considerably across lakes. Using a comprehensive database of salmonid QTLs newly augmented and mapped to a charr genome, we found several of the head- and body-shape-associated SNPs were within or near morphology QTLs from other salmonid species, reflecting a shared genetic basis for these phenotypes across species. Overall, our results demonstrate how parallel ecotype divergences can have both population-specific and deeply shared genomic underpinnings across replicates, influenced by differences in their environments and demographic histories.

The role of fish predators and their foraging traits in shaping zooplankton community structure

Differentiation of foraging traits among predator populations may help explain observed variation in the structure of prey communities. However, few studies have investigated the phenotypic effects of predators on their prey in natural communities. Here, we use a comparative analysis of 78 Greenlandic lakes to examine how foraging trait variation among threespine stickleback populations can help explain variation in zooplankton community composition among lakes. We find that landscape-scale variation in zooplankton composition was jointly explained by lake properties, such as size and water chemistry, and the presence and absence of both stickleback and arctic char. Additional variation in zooplankton community structure can be explained by stickleback jaw protrusion, a trait with known utility for foraging on zooplankton, but only in lakes where stickleback co-occur with arctic char. Overall, our results illustrate how trait variation of predators, alongside other ecosystem properties, can influence the composition of prey communities in nature.

Otolith-inferred patterns of marine migration frequency in Nunavik Arctic charr

Alternative migratory tactics in salmonids reflect the large observed interindividual variation in spatial behaviour which may range from strict freshwater residency to uninterrupted anadromy. In Salvelinus, sea migrations are performed during the ice-free period as freshwater overwintering is thought to be obligatory due to physiological constraints. As a result, individuals can either migrate the next spring or remain in freshwater, as anadromy is generally considered facultative. In Arctic charr (Salvelinus alpinus), skipped migrations are known to occur, but limited data are available regarding their frequencies within and among populations. Here, the authors used an otolith microchemistry approach relying on strontium (88 Sr) to infer movements between freshwater and marine habitats, and annual oscillations in zinc (64 Zn) to help with age identification. They determined the age-at-first-migration and the occurrence of subsequent annual migrations in two Nunavik Arctic charr populations sampled in Deception Bay (Salluit) and river systems linked to Hopes Advance Bay (Aupaluk), northern Québec, Canada. The mode for age-at-first-migration was 4+ for both populations, although it exhibited large variation (range: 0+ to 8+). Skipped migrations constituted a rare event, as 97.7% and 95.6% of the examined Arctic charr at Salluit (n = 43, mean age = 10.3 ± 2.0 years) and Aupaluk (n = 45, mean age = 6.0 ± 1.9 years), respectively, were found to have performed uninterrupted annual migrations after initiation of the behaviour. The consistency of the annual migrations suggests that the tactic is sufficiently fitness rewarding to be maintained under current environmental conditions. From a fisheries management perspective, these repeated migrations combined with low site fidelity in this species may lead to large interannual variations in abundance at the local scale, which may represent a challenge for monitoring Arctic charr demographics on a river-by-river basis.

The transcriptional state and chromatin landscape of cichlid jaw shape variation across species and environments

Adaptive phenotypes are shaped by a combination of genetic and environmental forces, but how they interact remains poorly understood. Here, we utilize the cichlid oral jaw apparatus to better understand these gene-by-environment effects. First, we employed RNA-seq in bony and ligamentous tissues important for jaw opening to identify differentially expressed genes between species and across foraging environments. We used two Lake Malawi species adapted to different foraging habitats along the pelagic-benthic ecomorphological axis. Our foraging treatments were designed to force animals to employ either suction or biting/scraping, which broadly mimic pelagic or benthic modes of feeding. We found a large number of differentially expressed genes between species, and while we identified relatively few differences between environments, species differences were far more pronounced when they were challenged with a pelagic versus benthic foraging mode. Expression data carried the signature of genetic assimilation, and implicated cell cycle regulation in shaping the jaw across species and environments. Next, we repeated the foraging experiment and performed ATAC-seq procedures on nuclei harvested from the same tissues. Cross-referencing results from both analyses revealed subsets of genes that were both differentially expressed and differentially accessible. This reduced dataset implicated notable candidate genes including the Hedgehog effector, KIAA0586 and the ETS transcription factor, etv4, which connects environmental stress and craniofacial morphogenesis. Taken together, these data provide novel insights into the epigenetic, genetic and cellular bases of species- and environment-specific bone shapes.

Temporal stability of polymorphic Arctic charr parasite communities reflects sustained divergent trophic niches

Polymorphic Arctic charr Salvelinus alpinus populations frequently display distinct differences in habitat use, diet, and parasite communities. Changes to the relative species densities and composition of the wider fish community have the potential to alter the habitat niche of sympatric Arctic charr populations. This study evaluated the temporal stability of the parasite community, diet, and stable isotopes (δ¹³C, δ¹⁵N) of three sympatric Arctic charr morphs (piscivore, benthivore, and planktivore) from Loch Rannoch, Scotland, in relation to changes to the fish community. All Arctic charr morphs displayed distinct differences in parasite communities, diet, and stable isotope signatures over time, despite the establishment of four new trophically transmitted parasite taxa, and increased fish and zooplankton consumption by the piscivorous and planktivore morphs, respectively. Native parasite prevalence also increased in all Arctic charr morphs. Overall, Loch Rannoch polymorphic Arctic charr morph populations have maintained their distinct trophic niches and parasite communities through time despite changes in the fish community. This result indicates that re‐stocking a native fish species has the potential to induce shifts in the parasite community and diet of Arctic charr morphs.

Variation in egg size and offspring phenotype among and within seven Arctic charr morphs

Maternal effects have the potential to alter early developmental processes of offspring and contribute to adaptive diversification. Egg size is a major contributor to offspring phenotype, which can influence developmental trajectories and potential resource use. However, to what extent intraspecific variation in egg size facilitates evolution of resource polymorphism is poorly understood. We studied multiple resource morphs of Icelandic Arctic charr, ranging from an anadromous morph-with a phenotype similar to the proposed ancestral phenotype-to sympatric morphs that vary in their degree of phenotypic divergence from the ancestral anadromous morph. We characterized variation in egg size and tested whether egg size influenced offspring phenotype at early life stages (i.e., timing of- and size at- hatching and first feeding [FF]). We predicted that egg size would differ among morphs and be less variable as morphs diverge away from the ancestral anadromous phenotype. We also predicted that egg size would correlate with offspring size and developmental timing. We found morphs had different egg size, developmental timing, and size at hatching and FF. Egg size increased as phenotypic proximity to the ancestral anadromous phenotype decreased, with larger eggs generally giving rise to larger offspring, especially at FF, but egg size had no effect on developmental rate. The interaction between egg size and the environment may have a profound impact on offspring fitness, where the resulting differences in early life-history traits may act to initiate and/or maintain resource morphs diversification.

Life-history variation as a source of diversity for endemic white charr (Salmonidae) of the lower Kamchatka River

Sympatric fish morphs diversifying in their feeding pattern in fresh waters typically implement alternative migratory tactics so that omnivores become migrants and specialists-residents. Charrs of the genus Salvelinus populating the lower Kamchatka River (Northeast Asia) are a rare example wherein two related sympatric morphs both implement a variety of life-history tactics in parallel. Here the authors analyse the ecological diversity in the endemic piscivorous "white" morph that exploits resources of the Kamchatka River in sympatry with the partially anadromous invertivorous "Dolly Varden" (DV) morph. Eco-morphological criteria allowed the authors to validate the morph identification. The white charr (WC) was found to subdivide into the small-sized (up to 1.6 kg) fish inhabiting the lacustrine part of the ecosystem and the large-sized (up to 3.4 kg) fish inhabiting the main river channel. The persistent spatial segregation of the sub-groups was confirmed by significant differences in the life span, muscle δ¹³ С signature and parasite load. According to contrasting patterns of strontium accumulation in otoliths, the riverine WC is represented by resident and semi-anadromous individuals. At the same time, the lack of microsatellite DNA differentiation and allometric nature of the morphometric discrepancy point to the intra-population source of the WC polymorphism. The authors suggest that WC diverged from DV as a result of feeding specialization on the threespine stickleback numerous in the ecosystem since the temporary flooding by marine waters in the middle Holocene. The modern stickleback division into local stocks following the ecosystem differentiation into a river, side lake and estuary resulted in the WC life-history split and ecological radiation.

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.

Genetic Causes and Consequences of Sympatric Morph Divergence in Salmonidae: A Search for Mechanisms

Repeatedly and recently evolved sympatric morphs exhibiting consistent phenotypic differences provide natural experimental replicates of speciation. Because such morphs are observed frequently in Salmonidae, this clade provides a rare opportunity to uncover the genomic mechanisms underpinning speciation. Such insight is also critical for conserving salmonid diversity, the loss of which could have significant ecological and economic consequences. Our review suggests that genetic differentiation among sympatric morphs is largely nonparallel apart from a few key genes that may be critical for consistently driving morph differentiation. We discuss alternative levels of parallelism likely underlying consistent morph differentiation and identify several factors that may temper this incipient speciation between sympatric morphs, including glacial history and contemporary selective pressures. Our synthesis demonstrates that salmonids are useful for studying speciation and poses additional research questions to be answered by future study of this family. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The interaction of resource use and gene flow on the phenotypic divergence of benthic and pelagic morphs of Icelandic Arctic charr (Salvelinus alpinus)

Conceptual models of adaptive divergence and ecological speciation in sympatry predict differential resource use, phenotype-environment correlations, and reduced gene flow among diverging phenotypes. While these predictions have been assessed in past studies, connections among them have rarely been assessed collectively. We examined relationships among phenotypic, ecological, and genetic variation in Arctic charr (Salvelinus alpinus) from six Icelandic localities that have undergone varying degrees of divergence into sympatric benthic and pelagic morphs. We characterized morphological variation with geometric morphometrics, tested for differential resource use between morphs using stable isotopes, and inferred the amount of gene flow from single nucleotide polymorphisms. Analysis of stable isotopic signatures indicated that sympatric morphs showed similar difference in resource use across populations, likely arising from the common utilization of niche space within each population. Carbon isotopic signature was also a significant predictor of individual variation in body shape and size, suggesting that variation in benthic and pelagic resource use is associated with phenotypic variation. The estimated percentage of hybrids between sympatric morphs varied across populations (from 0% to 15.6%) but the majority of fish had genotypes (ancestry coefficients) characteristic of pure morphs. Despite evidence of reduced gene flow between sympatric morphs, we did not detect the expected negative relationship between divergence in resource use and gene flow. Three lakes showed the expected pattern, but morphs in the fourth showed no detectable hybridization and had relatively low differences in resource use between them. This coupled with the finding that resource use and genetic differentiation had differential effects on body shape variation across populations suggests that reproductive isolation maintains phenotypic divergence between benthic and pelagic morphs when the effects of resource use are relatively low. Our ability to assess relationships between phenotype, ecology, and genetics deepens our understanding of the processes underlying adaptive divergence in sympatry.

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.

A brain and a head for a different habitat: Size variation in four morphs of Arctic charr (Salvelinus alpinus (L.)) in a deep oligotrophic lake

Adaptive radiation is the diversification of species to different ecological niches and has repeatedly occurred in different salmonid fish of postglacial lakes. In Lake Tinnsjøen, one of the largest and deepest lakes in Norway, the salmonid fish, Arctic charr (Salvelinus alpinus (L.)), has likely radiated within 9,700 years after deglaciation into ecologically and genetically segregated Piscivore, Planktivore, Dwarf, and Abyssal morphs in the pelagial, littoral, shallow-moderate profundal, and deep-profundal habitats. We compared trait variation in the size of the head, the eye and olfactory organs, as well as the volumes of five brain regions of these four Arctic charr morphs. We hypothesised that specific habitat characteristics have promoted divergent body, head, and brain sizes related to utilized depth differing in environmental constraints (e.g., light, oxygen, pressure, temperature, and food quality). The most important ecomorphological variables differentiating morphs were eye area, habitat, and number of lamellae. The Abyssal morph living in the deepest areas of the lake had the smallest brain region volumes, head, and eye size. Comparing the olfactory bulb with the optic tectum in size, it was larger in the Abyssal morph than in the Piscivore morph. The Piscivore and Planktivore morphs that use more illuminated habitats have the largest optic tectum volume, followed by the Dwarf. The observed differences in body size and sensory capacities in terms of vision and olfaction in shallow and deepwater morphs likely relates to foraging and mating habitats in Lake Tinnsjøen. Further seasonal and experimental studies of brain volume in polymorphic species are needed to test the role of plasticity and adaptive evolution behind the observed differences.

Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish

Understanding the extent to which ecological divergence is repeatable is essential for predicting responses of biodiversity to environmental change. Here we test the predictability of evolution, from genotype to phenotype, by studying parallel evolution in a salmonid fish, Arctic charr (Salvelinus alpinus), across eleven replicate sympatric ecotype pairs (benthivorous-planktivorous and planktivorous-piscivorous) and two evolutionary lineages. We found considerable variability in eco-morphological divergence, with several traits related to foraging (eye diameter, pectoral fin length) being highly parallel even across lineages. This suggests repeated and predictable adaptation to environment. Consistent with ancestral genetic variation, hundreds of loci were associated with ecotype divergence within lineages of which eight were shared across lineages. This shared genetic variation was maintained despite variation in evolutionary histories, ranging from postglacial divergence in sympatry (ca. 10-15kya) to pre-glacial divergence (ca. 20-40kya) with postglacial secondary contact. Transcriptome-wide gene expression (44,102 genes) was highly parallel across replicates, involved biological processes characteristic of ecotype morphology and physiology, and revealed parallelism at the level of regulatory networks. This expression divergence was not only plastic but in part genetically controlled by parallel cis-eQTL. Lastly, we found that the magnitude of phenotypic divergence was largely correlated with the genetic differentiation and gene expression divergence. In contrast, the direction of phenotypic change was mostly determined by the interplay of adaptive genetic variation, gene expression, and ecosystem size. Ecosystem size further explained variation in putatively adaptive, ecotype-associated genomic patterns within and across lineages, highlighting the role of environmental variation and stochasticity in parallel evolution. Together, our findings demonstrate the parallel evolution of eco-morphology and gene expression within and across evolutionary lineages, which is controlled by the interplay of environmental stochasticity and evolutionary contingencies, largely overcoming variable evolutionary histories and genomic backgrounds.

Marine trophic niche use and life history diversity among Arctic charr Salvelinus alpinus in southwestern Greenland

Life history strategies and potential marine niche use of Arctic charr Salvelinus alpinus (n = 237, 84-652 mm, total body length, L_T ) were determined during the ice-free season (2012) at three different watercourses in south-western Greenland. All Arctic charr were collected from freshwater habitats. Based on stable isotopes of δ³⁴ S, the Arctic charr were categorized as either marine- or freshwater-dependent feeders. The use of time-integrated trophic tracers (stable isotopes of δ¹³ C, δ¹⁵ N, δ³⁴ S) suggested that several trophic groups of Arctic charr operate alongside within each fjord system. The groups suggested were one group that specialized in the marine habitat, in addition to two freshwater resident morphs (small-sized resident and/or large-growing cannibalistic individuals). Stomach contents consisted entirely of freshwater and terrestrial prey (i.e., insects), indicating that marine-dependent feeders also fed in freshwater habitats after return from their marine migration. Growth and maturity patterns further supported variable life history strategies within each watercourse. The life history strategy patterns and marine trophic niche use were consistent across the watercourses along several hundred kilometres of coastline. This study represents the first ecological baseline for partially anadromous populations of Greenland Arctic charr.

Ecological opportunity shapes a large Arctic charr species radiation

Ecological opportunity is considered a crucial factor for adaptive radiation. Here, we combine genetic, morphological and ecological data to assess species and ecomorphological diversity of Artic charr in six lakes of a catchment in southernmost Greenland, where only charr and stickleback occur. Because the diversity of habitats and resources increases with lake size, we predict a positive association between lake size and the extent of ecomorphological diversity. The largest lake of the catchment harbours the largest Arctic charr assemblage known today. It consists of six genetically differentiated species belonging to five ecomorphs (anadromous, littoral benthic, profundal dwarf, planktivorous, piscivorous), of which the latter comprises two ecomorphologically extremely similar species. Lakes of intermediate size contain two ecomorphologically and genetically distinct species. Small lakes harbour one genetically homogeneous, yet sometimes ecomorphologically variable population. Supporting our prediction, lake size is positively correlated with the extent of ecomorphological specialization towards profundal, pelagic and piscivorous lifestyle. Furthermore, assemblage-wide morphospace increases sharply when more than one genetic cluster is present. Our data suggest that ecological opportunity and speciation jointly determine phenotypic expansion in this charr radiation.