Multi-generation selective landscapes and sub-lethal injuries in stickleback.

The interaction between predation landscape and phenotypic variability within prey populations is of substantial significance in evolutionary biology. Extending from several decades of studies at a remote freshwater lake on Haida Gwaii, western Canada, we analyze the incidence of predator-induced sub-lethal injuries in 8,069 wild-captured threespine stickleback (Gasterosteus aculeatus) and using cohort analyses test whether the distribution of injuries informs the selective landscape influencing the bell-shaped frequency distribution of the traits. Our results indicate that (1) the incidence of injuries varies among phenotypes differing in the number and position of lateral plates, (2) these differences occur only among younger fish, (3) the incidence of injuries is inversely related to the estimated population frequencies of plate phenotypes, with the modal phenotype generally having the fewest injuries, (4) direct estimates of selective differentials and relative fitness based on analyses of 1,735 fish from 6 independent yearly cohorts indicates statistically informative elevated differentials in phenotypes with greater number of plates and elevated relative fitness of non-modal phenotypes, and (5) there are significant differences among yearly cohorts in strength and direction of selection, and an increased prevalence of diversifying versus stabilizing selection despite longer-term stasis (4 decades) in trait means. We conclude that the presence of multiple "optimal" phenotypes complements the renewed interests in quantifying short-term temporal or spatial variation in ecological processes in studies of fitness landscapes and intrapopulation variability.

Evolution of stickleback spines through independent cis-regulatory changes at HOXDB.

Understanding the mechanisms leading to new traits or additional features in organisms is a fundamental goal of evolutionary biology. We show that HOXDB regulatory changes have been used repeatedly in different fish genera to alter the length and number of the prominent dorsal spines used to classify stickleback species. In Gasterosteus aculeatus (typically 'three-spine sticklebacks'), a variant HOXDB allele is genetically linked to shortening an existing spine and adding an additional spine. In Apeltes quadracus (typically 'four-spine sticklebacks'), a variant HOXDB allele is associated with lengthening a spine and adding an additional spine in natural populations. The variant alleles alter the same non-coding enhancer region in the HOXDB locus but do so by diverse mechanisms, including single-nucleotide polymorphisms, deletions and transposable element insertions. The independent regulatory changes are linked to anterior expansion or contraction of HOXDB expression. We propose that associated changes in spine lengths and numbers are partial identity transformations in a repeating skeletal series that forms major defensive structures in fish. Our findings support the long-standing hypothesis that natural Hox gene variation underlies key patterning changes in wild populations and illustrate how different mutational mechanisms affecting the same region may produce opposite gene expression changes with similar phenotypic outcomes.

Innervation and structure of the adipose fin of a lanternfish.

Adipose fins of teleost fishes have been shown to function as mechanosensory organs that respond to minute bending forces created by turbulence in fast-flowing streams. Nonetheless, adipose fins also exist in some fishes that occupy still waters, including lanternfish (Myctophidae) in the deep sea. The authors examined adipose fin structure in northern lampfish, Stenobrachius leucopsarus, from coastal British Columbia. After fixation, embedding and sectioning of the adipose and supporting tissue, it was evident that lanternfish adipose fins are stiffened by compound actinotrichia, acting like fin rays, that would create a higher aspect ratio. The actinotrichia converge at the base of the fin in a hinge point complex that anteriorly interacts with a cartilaginous endoskeletal rod, controlled by skeletal muscles. Afferent nerves enter the fin at this point and form fine branches as they track deeper alongside actinotrichia. The authors propose that the vertical nightly migration to surface waters, as well as predator evasion within large schools, results in microturbulence. In these circumstances, the adipose fin acts as a mechanosensor providing feedback to the caudal fin, as it occurs in salmonids and catfish.

Genomic changes underlying repeated niche shifts in an adaptive radiation.

In adaptive radiations, single lineages rapidly diversify by adapting to many new niches. Little is known yet about the genomic mechanisms involved, that is, the source of genetic variation or genomic architecture facilitating or constraining adaptive radiation. Here, we investigate genomic changes associated with repeated invasion of many different freshwater niches by threespine stickleback in the Haida Gwaii archipelago, Canada, by resequencing single genomes from one marine and 28 freshwater populations. We find 89 likely targets of parallel selection in the genome that are enriched for old standing genetic variation. In contrast to theoretical expectations, their genomic architecture is highly dispersed with little clustering. Candidate genes and genotype-environment correlations match the three major environmental axes predation regime, light environment, and ecosystem size. In a niche space with these three dimensions, we find that the more divergent a new niche from the ancestral marine habitat, the more loci show signatures of parallel selection. Our findings suggest that the genomic architecture of parallel adaptation in adaptive radiation depends on the steepness of ecological gradients and the dimensionality of the niche space.

Behavioural responses of threespine stickleback with lateral line asymmetries to experimental mechanosensory stimuli.

Behavioural asymmetry, typically referred to as laterality, is widespread among bilaterians and is often associated with asymmetry in brain structure. However, the influence of sensory receptor asymmetry on laterality has undergone limited investigation. Here we used threespine stickleback (Gasterosteus aculeatus) to investigate the influence of lateral line asymmetry on laterality during lab simulations of three mechanosensation-dependent behaviours: predator evasion, prey localization and rheotaxis. We recorded the response of stickleback to impacts at the water surface and water flow in photic conditions and low-frequency oscillations in the dark, across four repeat trials. We then compared individuals' laterality with asymmetry in the number of neuromasts on either side of their body. Stickleback hovered with their right side against the arena wall 57% of the time (P<0.001) in illuminated surface impact trials and 56% of the time (P=0.085) in dark low-frequency stimulation trials. Light regime modulated the effect of neuromast count on laterality, as fish with more neuromasts were more likely to hover with the wall on their right during illumination (P=0.007) but were less likely to do so in darkness (P=0.025). Population-level laterality diminished in later trials across multiple behaviours and individuals did not show a consistent side bias in any behaviours. Our results demonstrate a complex relationship between sensory structure asymmetry and laterality, suggesting that laterality is modulated by multiple sensory modalities and is temporally dynamic.

Regional heterogeneity in coral species richness and hue reveals novel global predictors of reef fish intra-family diversity.

Habitat heterogeneity shapes biological communities, a well-known process in terrestrial ecosystems but substantially unresolved within coral reef ecosystems. We investigated the extent to which coral richness predicts intra-family fish richness, while simultaneously integrating a striking aspect of reef ecosystems-coral hue. To do so, we quantified the coral richness, coral hue diversity, and species richness within 25 fish families in 74 global ecoregions. We then expanded this to an analysis of all reef fishes (4465 species). Considering coral bleaching as a natural experiment, we subsequently examined hue's contribution to fish communities. Coral species and hue diversity significantly predict each family's fish richness, with the highest correlations (> 80%) occurring in damselfish, butterflyfish, emperors and rabbitfish, lower (60-80%) in substrate-bound and mid-water taxa such as blennies, seahorses, and parrotfish, and lowest (40-60%) in sharks, morays, grunts and triggerfish. The observed trends persisted globally. Coral bleaching's homogenization of reef colouration revealed hue's contribution to maintaining fish richness, abundance, and recruit survivorship. We propose that each additional coral species and associated hue provide added ecological opportunities (e.g. camouflage, background contrast for intraspecific display), facilitating the evolution and co-existence of diverse fish assemblages.

Intrapopulation foraging niche variation between phenotypes and genotypes of Spirit bear populations.

Foraging niche variation within a species can contribute to the maintenance of phenotypic diversity. The multiniche model posits that phenotypes occupying different niches can contribute to the maintenance of balanced polymorphisms. Using coastal populations of black bears (Ursus americanus kermodei) from British Columbia, Canada, we examined potential foraging niche divergence between phenotypes (black and white "Spirit" coat color) and between genotypes (black-coated homozygote and heterozygous). We applied the Bayesian multivariate models, with biotracers of diet (δ13C and δ15N) together comprising the response variable, to draw inference about foraging niche variation. Variance-covariance matrices from multivariate linear mixed-effect models were visualized as the Bayesian standard ellipses in δ13C and δ15N isotopic space to assess potential seasonal and annual niche variation between phenotypes and genotypes. We did not detect a difference in annual isotopic foraging niche area in comparisons between genotypes or phenotypes. Consistent with previous field experimental and isotopic analyses, however, we found that white phenotype Spirit bears were modestly more enriched in δ15N during the fall foraging season, though with our modest sample sizes these results were not significant. Although also not statistically significant, variation in isotopic niches between genotypes revealed that heterozygotes were moderately more enriched in δ13C along hair segments grown during fall foraging compared with black-coated homozygotes. To the extent to which the pattern of elevated δ15N and δ13C may signal the consumption of salmon (Oncorhynchus spp.), as well as the influence of salmon consumption on reproductive fitness, these results suggest that black-coated heterozygotes could have a minor selective advantage in the fall compared with black-coated homozygotes. More broadly, our multivariate approach, coupled with knowledge of genetic variation underlying a polymorphic trait, provides new insight into the potential role of a multiniche mechanism in maintaining this rare morph of conservation priority in Canada's Great Bear Rainforest and could offer new understanding into polymorphisms in other systems.

Right nostril biases to experimental scents in Canis familiaris.

Although olfactory laterality in canids has been demonstrated experimentally, the extent to which nostril bias occurs in "nature" is not well known. We tested whether there was olfactory laterality of untrained dogs in various off-leash dog parks within Victoria, British Columbia to manipulated scents placed at the tail base of full-size dog replica. Using video-playback, we found that of 192 separate approaches (N = 119 different subjects), dogs used the right nostril first greater than 66% of the time and for longer periods when investigating estrous dog secretions, deer urine and coyote urine. Similar trends were observed when using scents on a similar-sized box rather than the dog model. There was no side preference for the scent of commercial pet food. These results support right hemisphere control of the sympathetic-hypothalamic-pituitary-adrenal axis and encourage more detailed evaluations of olfactory laterality in wild canids and other carnivores where olfaction is the major sensory modality.

Salmonid species diversity predicts salmon consumption by terrestrial wildlife.

Resource waves-spatial variation in resource phenology that extends feeding opportunities for mobile consumers-can affect the behaviour and productivity of recipient populations. Interspecific diversity among Pacific salmon species (Oncorhynchus spp.) creates staggered spawning events across space and time, thereby prolonging availability to terrestrial wildlife. We sought to understand how such variation might influence consumption by terrestrial predators compared with resource abundance and intra- and interspecific competition. Using stable isotope analysis, we investigated how the proportion of salmon in the annual diet of male black bears (Ursus americanus; n = 405) varies with species diversity and density of spawning salmon biomass, while also accounting for competition with sympatric black and grizzly bears (U. arctos horribilis), in coastal British Columbia, Canada. We found that the proportion of salmon in the annual diet of black bears was ≈40% higher in the absence of grizzly bears, but detected little effect of relative black bear density and salmon biomass density. Rather, salmon diversity had the largest positive effect on consumption. On average, increasing diversity from one salmon species to ~four (with equal biomass contributions) approximately triples the proportion of salmon in diet. Given the importance of salmon to bear life histories, this work provides early empirical support for how resource waves may increase the productivity of consumers at population and landscape scales. Accordingly, terrestrial wildlife management might consider maintaining not only salmon abundance but also diversity.

DNA fragility in the parallel evolution of pelvic reduction in stickleback fish.

Evolution generates a remarkable breadth of living forms, but many traits evolve repeatedly, by mechanisms that are still poorly understood. A classic example of repeated evolution is the loss of pelvic hindfins in stickleback fish (Gasterosteus aculeatus). Repeated pelvic loss maps to recurrent deletions of a pelvic enhancer of the Pitx1 gene. Here, we identify molecular features contributing to these recurrent deletions. Pitx1 enhancer sequences form alternative DNA structures in vitro and increase double-strand breaks and deletions in vivo. Enhancer mutability depends on DNA replication direction and is caused by TG-dinucleotide repeats. Modeling shows that elevated mutation rates can influence evolution under demographic conditions relevant for sticklebacks and humans. DNA fragility may thus help explain why the same loci are often used repeatedly during parallel adaptive evolution.

Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation.

A substantial part of biodiversity is thought to have arisen from adaptive radiations in which one lineage rapidly diversified into multiple lineages specialized to many different niches. However, selection and drift reduce genetic variation during adaptation to new niches and may thus prevent or slow down further niche shifts. We tested whether rapid adaptation is still possible from a highly derived ecotype in the adaptive radiation of threespine stickleback on the Haida Gwaii archipelago, Western Canada. In a 19-year selection experiment, we let giant sticklebacks from a large blackwater lake evolve in a small clearwater pond without vertebrate predators. A total of 56 whole genomes from the experiment and 26 natural populations revealed that adaptive genomic change was rapid in many small genomic regions and encompassed 75% of the change between 12,000-year-old ecotypes. Genomic change was as fast as phenotypic change in defence and trophic morphology, and both were largely parallel between the short-term selection experiment and long-term natural adaptive radiation. Our results show that functionally relevant standing genetic variation can persist in derived radiation members, allowing adaptive radiations to unfold very rapidly.

Fish Parasite Dinoflagellates Haidadinium ichthyophilum and Piscinoodinium Share a Recent Common Ancestor.

The dinoflagellate Haidadinium ichthyophilum Buckland-Nicks, Reimchen and Garbary 1997 is an ectoparasite of the spine-deficient, three-spine stickleback Gasterosteus aculeatus L. Reimchen 1984, a fish endemic to Rouge Lake, Haida Gwaii. Haidadinium ichthyophilum proved difficult to assign taxonomically because its morphology and complex life cycle exhibited defining characteristics of both autotrophic and heterotrophic dinoflagellates, and was tentatively assigned to the Phytodiniales. Here, we characterized a 492 bp fragment of the small subunit ribosomal RNA (SSU rRNA) from preserved H. ichthyophilum cysts. In SSU phylogeny, H. ichthyophilum branches with the fish parasites, Piscinoodinium sp., strongly supporting the inclusion of H. ichthyophilum within the Suessiales.

Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments.

Repeated adaptation to a new environment often leads to convergent phenotypic changes whose underlying genetic mechanisms are rarely known. Here, we study adaptation of color vision in threespine stickleback during the repeated postglacial colonization of clearwater and blackwater lakes in the Haida Gwaii archipelago. We use whole genomes from 16 clearwater and 12 blackwater populations, and a selection experiment, in which stickleback were transplanted from a blackwater lake into an uninhabited clearwater pond and resampled after 19 y to test for selection on cone opsin genes. Patterns of haplotype homozygosity, genetic diversity, site frequency spectra, and allele-frequency change support a selective sweep centered on the adjacent blue- and red-light sensitive opsins SWS2 and LWS. The haplotype under selection carries seven amino acid changes in SWS2, including two changes known to cause a red-shift in light absorption, and is favored in blackwater lakes but disfavored in the clearwater habitat of the transplant population. Remarkably, the same red-shifting amino acid changes occurred after the duplication of SWS2 198 million years ago, in the ancestor of most spiny-rayed fish. Two distantly related fish species, bluefin killifish and black bream, express these old paralogs divergently in black- and clearwater habitats, while sticklebacks lost one paralog. Our study thus shows that convergent adaptation to the same environment can involve the same genetic changes on very different evolutionary time scales by reevolving lost mutations and reusing them repeatedly from standing genetic variation.

Opsin gene repertoires in northern archaic hominids.

The Neanderthals' northern distribution, hunting techniques, and orbit breadths suggest that they were more active in dim light than modern humans. We surveyed visual opsin genes from four Neanderthals and two other archaic hominids to see if they provided additional support for this hypothesis. This analysis was motivated by the observation that alleles responsible for anomalous trichromacy in humans are more common in northern latitudes, by data suggesting that these variants might enhance vision in mesopic conditions, and by the observation that dim light active species often have fewer opsin genes than diurnal relatives. We also looked for evidence of convergent amino acid substitutions in Neanderthal opsins and orthologs from crepuscular or nocturnal species. The Altai Neanderthal, the Denisovan, and the Ust'-Ishim early modern human had opsin genes that encoded proteins identical to orthologs in the human reference genome. Opsins from the Vindija Cave Neanderthals (three females) had many nonsynonymous substitutions, including several predicted to influence colour vision (e.g., stop codons). However, the functional implications of these observations were difficult to assess, given that "control" loci, where no substitutions were expected, differed from humans to the same extent. This left unresolved the test for colour vision deficiencies in Vindija Cave Neanderthals.

HUMAN IMPACTS. The unique ecology of human predators.

Paradigms of sustainable exploitation focus on population dynamics of prey and yields to humanity but ignore the behavior of humans as predators. We compared patterns of predation by contemporary hunters and fishers with those of other predators that compete over shared prey (terrestrial mammals and marine fishes). Our global survey (2125 estimates of annual finite exploitation rate) revealed that humans kill adult prey, the reproductive capital of populations, at much higher median rates than other predators (up to 14 times higher), with particularly intense exploitation of terrestrial carnivores and fishes. Given this competitive dominance, impacts on predators, and other unique predatory behavior, we suggest that humans function as an unsustainable "super predator," which­unless additionally constrained by managers­will continue to alter ecological and evolutionary processes globally.

Role of the iridescent eye in stickleback female mate choice.

Many vertebrates exhibit prominent body colours that are used in courtship and territorial communication. Some fishes also have an eye whose iris becomes iridescent during the mating season, as in the threespine stickleback. Behavioural studies in this species have focused on the redness of the throat/jaw as the primary determinant of female mate choice. Unlike the iridescent eye, however, the red throat/jaw is not present in all stickleback populations, suggesting that the colour of the eye may be equally important for female mate choice. Here, we used data on photoreceptors and environmental light to assess body conspicuousness and the colour contrast of courtship signals for stickleback populations living in a range of waters, from clear (mesotrophic) to red light shifted (dystrophic). This analysis indicated that the redness of the throat/jaw is expressed to enhance the contrast of the eye. To test the importance of eye colour as a courtship signal, we carried out mate choice experiments in which females were presented with identical videos of a courting male but for the colour of the eye and/or the throat/jaw. Females did not choose based on differences in throat/jaw redness between videos, but preferred males with the highest contrast between the eye and the throat/jaw. This result points to the blue iridescent eye as a primary courtship signal in stickleback female mate choice.

Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide single nucleotide polymorphism genotyping.

Threespine stickleback populations are model systems for studying adaptive evolution and the underlying genetics. In lakes on the Haida Gwaii archipelago (off western Canada), stickleback have undergone a remarkable local radiation and show phenotypic diversity matching that seen throughout the species distribution. To provide a historical context for this radiation, we surveyed genetic variation at >1000 single nucleotide polymorphism (SNP) loci in stickleback from over 100 populations. SNPs included markers evenly distributed throughout genome and candidate SNPs tagging adaptive genomic regions. Based on evenly distributed SNPs, the phylogeographic pattern differs substantially from the disjunct pattern previously observed between two highly divergent mtDNA lineages. The SNP tree instead shows extensive within watershed population clustering and different watersheds separated by short branches deep in the tree. These data are consistent with separate colonizations of most watersheds, despite underlying genetic connections between some independent drainages. This supports previous suppositions that morphological diversity observed between watersheds has been shaped independently, with populations exhibiting complete loss of lateral plates and giant size each occurring in several distinct clades. Throughout the archipelago, we see repeated selection of SNPs tagging candidate freshwater adaptive variants at several genomic regions differentiated between marine-freshwater populations on a global scale (e.g. EDA, Na/K ATPase). In estuarine sites, both marine and freshwater allelic variants were commonly detected. We also found typically marine alleles present in a few freshwater lakes, especially those with completely plated morphology. These results provide a general model for postglacial colonization of freshwater habitat by sticklebacks and illustrate the tremendous potential of genome-wide SNP data sets hold for resolving patterns and processes underlying recent adaptive divergences.

Salmon subsidize an escape from a size spectrum.

A general rule in ecology is that the abundance of species or individuals in communities sharing a common energy source decreases with increasing body size. However, external energy inputs in the form of resource subsidies can modify this size spectrum relationship. Here, we provide the first test of how a marine resource subsidy can affect size spectra of terrestrial communities, based on energy derived from Pacific salmon carcasses affecting a forest soil community beside streams in western Canada. Using both species-based and individual approaches, we found size structuring in this forest soil community, and transient community-wide doubling of standing biomass in response to energy pulses from Pacific salmon carcasses. One group of species were clear outliers in the middle of the size spectrum relationship: larval calliphorid and dryomyzid flies, which specialize on salmon carcasses, and which showed a tenfold increase in biomass in their size class when salmon were available. Thus, salmon subsidize their escape from the size spectrum. These results suggest that using a size-based perspective of resource subsidies can provide new insights into the structure and functioning of food webs.

Pronounced heritable variation and limited phenotypic plasticity in visual pigments and opsin expression of threespine stickleback photoreceptors.

Vertebrate colour vision is mediated by the differential expression of visual pigment proteins (opsins) in retinal cone photoreceptors. Many species alter opsin expression during life, either as part of development or as a result of changes in habitat. The latter, a result of phenotypic plasticity, appears common among fishes, but its cellular origin and ecological significance are unknown. Here, we used adult threespine stickleback fish from different photic regimes to investigate heritable variability and phenotypic plasticity in opsin expression. Fish from clear waters had double cones that expressed long (LWS) and middle (RH2) wavelength opsins, one per double cone member. In contrast, fish from red light-shifted lakes had double cones that were >95% LWS/LWS pairs. All fish had single cones that predominantly expressed a short wavelength (SWS2) opsin but ultraviolet cones, expressing a SWS1 opsin, were present throughout the retina. Fish from red light-shifted lakes, when transferred to clear waters, had a ∼2% increase in RH2/LWS double cones, though double cone density remained constant. Comparison of visual pigment absorbance and light transmission in the environment indicated that the opsin complements of double cones maximized sensitivity to the background light, whereas single cones had visual pigments that were spectrally offset from the dominant background wavelengths. Our results indicate that phenotypic plasticity in opsin expression is minor in sticklebacks and of questionable functional significance.

Population genomics of parallel phenotypic evolution in stickleback across stream-lake ecological transitions.

Understanding the genetics of adaptation is a central focus in evolutionary biology. Here, we use a population genomics approach to examine striking parallel morphological divergences of parapatric stream-lake ecotypes of threespine stickleback fish in three watersheds on the Haida Gwaii archipelago, western Canada. Genome-wide variation at greater than 1000 single nucleotide polymorphism loci indicate separate origin of giant lake and small-bodied stream fish within each watershed (mean F(ST) between watersheds = 0.244 and within = 0.114). Genome scans within watersheds identified a total of 21 genomic regions that are highly differentiated between ecotypes and are probably subject to directional selection. Most outliers were watershed-specific, but genomic regions undergoing parallel genetic changes in multiple watersheds were also identified. Interestingly, several of the stream-lake outlier regions match those previously identified in marine-freshwater and benthic-limnetic genome scans, indicating reuse of the same genetic loci in different adaptive scenarios. We also identified multiple new outlier loci, which may contribute to unique aspects of differentiation in stream-lake environments. Overall, our data emphasize the important role of ecological boundaries in driving both local and broadly occurring parallel genetic changes during adaptation.