Adaptive Evolution of Nearctic Deepwater Fish Vision: Implications for Assessing Functional Variation for Conservation.

Intraspecific functional variation is critical for adaptation to rapidly changing environments. For visual opsins, functional variation can be characterized in vitro and often reflects a species' ecological niche but is rarely considered in the context of intraspecific variation or the impact of recent environmental changes on species of cultural or commercial significance. Investigation of adaptation in postglacial lakes can provide key insight into how rapid environmental changes impact functional evolution. Here, we report evidence for molecular adaptation in vision in 2 lineages of Nearctic fishes that are deep lake specialists: ciscoes and deepwater sculpin. We found depth-related variation in the dim-light visual pigment rhodopsin that evolved convergently in these 2 lineages. In vitro characterization of spectral sensitivity of the convergent deepwater rhodopsin alleles revealed blue-shifts compared with other more widely distributed alleles. These blue-shifted rhodopsin alleles were only observed in deep clear postglacial lakes with underwater visual environments enriched in blue light. This provides evidence of remarkably rapid and convergent visual adaptation and intraspecific functional variation in rhodopsin. Intraspecific functional variation has important implications for conservation, and these fishes are of conservation concern and great cultural, commercial, and nutritional importance to Indigenous communities. We collaborated with the Saugeen Ojibway Nation to develop and test a metabarcoding approach that we show is efficient and accurate in recovering the ecological distribution of functionally relevant variation in rhodopsin. Our approach bridges experimental analyses of protein function and genetics-based tools used in large-scale surveys to better understand the ecological extent of adaptive functional variation.

Prediction of protein structure from ideal forms.

For many years it has been accepted that the sequence of a protein can specify its three-dimensional structure. However, there has been limited progress in explaining how the sequence dictates its fold and no attempt to do this computationally without the use of specific structural data has ever succeeded for any protein larger than 100 residues. We describe a method that can predict complex folds up to almost 200 residues using only basic principles that do not include any elements of sequence homology. The method does not simulate the folding chain but generates many thousands of models based on an idealized representation of structure. Each rough model is scored and the best are refined. On a set of five proteins, the correct fold score well and when tested on a set of larger proteins, the correct fold was ranked highest for some proteins more than 150 residues, with others being close topological variants. All other methods that approach this level of success rely on the use of templates or fragments of known structures. Our method is unique in using a database of ideal models based on general packing rules that, in spirit, is closer to an ab initio approach.

Climate change influences on environment as a determinant of Indigenous health: Relationships to place, sea ice, and health in an Inuit community.

This paper contributes to the literature on Indigenous health, human dimensions of climate change, and place-based dimensions of health by examining the role of environment for Inuit health in the context of a changing climate. We investigated the relationship between one key element of the environment - sea ice - and diverse aspects of health in an Inuit community in northern Canada, drawing on population health and health geography approaches. We used a case study design and participatory and collaborative approach with the community of Nain in northern Labrador, Canada. Focus groups (n = 2), interviews (n = 22), and participant observation were conducted in 2010-11. We found that an appreciation of place was critical for understanding the full range of health influences of sea ice use for Inuit. Negative physical health impacts were reported on less frequently than positive health benefits of sea ice use, which were predominantly related to mental/emotional, spiritual, social, and cultural health. We found that sea ice means freedom for sea ice users, which we suggest influences individual and collective health through relationships between sea ice use, culture, knowledge, and autonomy. While sea ice users reported increases in negative physical health impacts such as injuries and stress related to changing environmental conditions, we suggest that less tangible climate change impacts related to losses of health benefits and disruptions to place meanings and place attachment may be even more significant. Our findings indicate that climate change is resulting in and compounding existing environmental dispossession for Inuit. They also demonstrate the necessity of considering place meanings, culture, and socio-historical context to assess the complexity of climate change impacts on Indigenous environmental health.

Contemporary programs in support of traditional ways: Inuit perspectives on community freezers as a mechanism to alleviate pressures of wild food access in Nain, Nunatsiavut.

Rapid socio-cultural, economic, and environmental changes are challenging wild food access and thus food security for Inuit in the Canadian Arctic. In response to the continued value and practice of harvesting wild foods, communities are establishing "wild food support" initiatives. This study evaluated how one such initiative, a community freezer, in Nain, Nunatsiavut supported wild food access for community members. Data were collected through: interviews and focus groups with users, freezer managers, and active harvesters; participant observation; and document analysis. Results indicated that the community freezer supported socio-cultural, economic and local access to wild foods. However, there were issues associated with supply, dependency, social exclusion, and tension between feasibility and traditional values and practices. Communities, governments, and policymakers are urged to consider social and physical location as factors when investing in and monitoring such initiatives. The Nunatsiavut Government and the Nain Inuit Community Government have since worked together to modify this early freezer initiative due, in part, to this study's findings.

Investigating environmental determinants of injury and trauma in the Canadian north.

Unintentional injury and trauma rates are disproportionately high in Inuit regions, and environmental changes are predicted to exacerbate injury rates. However, there is a major gap in our understanding of the risk factors contributing to land-based injury and trauma in the Arctic. We investigated the role of environmental and other factors in search and rescue (SAR) incidents in a remote Inuit community in northern Canada using a collaborative mixed methods approach. We analyzed SAR records from 1995 to 2010 and conducted key consultant interviews in 2010 and 2011. Data showed an estimated annual SAR incidence rate of 19 individuals per 1,000. Weather and ice conditions were the most frequent contributing factor for cases. In contrast with other studies, intoxication was the least common factor associated with SAR incidents. The incidence rate was six times higher for males than females, while land-users aged 26-35 had the highest incidence rate among age groups. Thirty-four percent of individuals sustained physical health impacts. Results demonstrate that environmental conditions are critical factors contributing to physical health risk in Inuit communities, particularly related to travel on sea ice during winter. Age and gender are important risk factors. This knowledge is vital for informing management of land-based physical health risk given rapidly changing environmental conditions in the Arctic.

Effects-based marine ecological risk assessment at a polychlorinated biphenyl-contaminated site in Saglek, Labrador, Canada.

Although the presence and distribution of polychlorinated biphenyls (PCBs) in Arctic marine environments has been well documented, the implications for the health of biota are poorly understood. In the present study, multiple lines of evidence, including site-specific effects data, were used to assess PCB-related risks to marine biota at a contaminated military site in Saglek Bay, Labrador, Canada, from 1997 to 1999. Risks were evaluated for three components of the ecosystem: benthic invertebrates, a bottom-feeding fish (shorthorn sculpin, Myoxocephalus scorpius), and a diving seabird (black guillemot, Cepphus grylle). Average sediment PCB concentrations exceeded the Canadian interim sediment quality guideline level by 41-fold. However, sediment toxicity testing and a benthic community survey showed no evidence of adverse effects. In contrast, shorthorn sculpin and black guillemot PCB exposures (measured as sum of 55 congeners) were elevated enough to pose risks to survival or reproduction. Based on the collective evidence, the authors estimated that risks were posed by sediment PCB concentrations greater than 77 ng/g dry weight for black guillemots and 750 ng/g dry weight for shorthorn sculpins. The present study, along with two parallel studies, provided information to support the management decisions concerning potential remedial action on the contaminated sediments. This ecological risk assessment describes the steps and rationale taken to evaluate the risk posed by an area of PCB-contaminated marine sediments in an otherwise relatively pristine northern coastal environment.

Parasites of the deepwater sculpin (Myoxocephalus thompsonii) across its Canadian range.

Deepwater sculpin (Myoxocephalus thompsonii) were collected from 19 lakes across the species' distribution in Canada and examined for parasites. Six helminth species (Crepidostomum farionis, Bothriocephalus cuspidatus, Proteocephalus sp., Cyathocephalus truncatus, Raphidascaris acus, and Echinorhynchus salmonis), 1 crustacean species (Ergasilus nerkae), and 1 molluscan species (glochidia) parasitized these hosts. Crepidostomum farionis, Proteocephalus sp., R. acus, E. nerkae, and the glochidia represent new parasite records for this host species. Overall parasite prevalence was 78.0% while mean intensity was 6.1 +/- 7.1 SD. Bothriocephalus cuspidatus was the most prevalent parasite and was recorded from 62.2% of the deepwater sculpin and found in 17 of the 19 lakes. The low-productivity habitat of this host limits the parasites available for transmission, and the infra- and component communities were generally species poor. With the exception of the Proteocephalus sp., all of the helminth parasites recovered have been reported as adults in lake trout (Salvelinus namaycush) or burbot (Lota lota), suggesting that, in the lakes where they occur, deepwater sculpin may play an important role in energetic transfer and parasitic transmission to higher trophic levels.

Reduction of PCB contamination in an Arctic coastal environment: a first step in assessing ecosystem recovery after the removal of a point source.

Studies have documented the presence of organic contaminants in Arctic marine environments due to local point sources, but little long-term data is known of the recovery process once those contaminants are removed. In this study, natural recovery of a local marine food web from a historic terrestrial source of polychlorinated biphenyls (PCBs) at Saglek Bay is examined. PCBs were measured in marine sediments, shorthorn sculpin (Myoxocephalus scorpius), and black guillemots (Cepphus grylle) to assess ecosystem recovery over an eight-year period after cleanup of the source. Surface sediment measurements indicate decreases in both the extent and average concentrations of PCBs throughout Saglek Bay. Sculpin collected near the former contaminated beach in 2006 had significantly lower PCB burdens than those collected in 1998/ 99. PCB levels have also decreased significantly in black guillemot nestlings collected from the former contaminated beach area, as well as Island (6-8 km from the source) and Reference (greater than 18 km from the source) locations. This study demonstrates the utility of using indicator species, especially the black guillemot, to monitor PCB uptake in benthic food webs. The rapid decreases in the physical and biotic PCB concentrations from the local ecosystem at Saglek Bay demonstratethe efficiency with which natural ecosystem recovery can take place in a highly energetic coastal marine environment once a chronic contaminant source is removed.

All three variable regions of the TRIM5alpha B30.2 domain can contribute to the specificity of retrovirus restriction.

Recent studies have revealed the contribution of TRIM5alpha to retrovirus restriction in cells from a variety of primate species. TRIM5alpha consists of a tripartite motif (the RBCC domain) followed by a B30.2 domain. The B30.2 domain is thought to be involved in determination of restriction specificity and contains three variable regions. To investigate the relationship between the phylogeny of primate TRIM5alpha and retrovirus restriction specificity, a series of chimeric TRIM5alpha consisting of the human RBCC domain followed by the B30.2 domain from various primates was constructed. These constructs showed restriction profiles largely consistent with the origin of the B30.2 domain. Restriction specificity was further investigated with a variety of TRIM5alphas containing mixed or mutated B30.2 domains. This study revealed the importance of all three variable regions for determining restriction specificity. Based on the molecular structures of other PRYSPRY domains solved recently, a model for the molecular structure of the B30.2 domain of TRIM5alpha was developed. The model revealed that the variable regions of the B30.2 domain are present as loops located on one side of the B30.2 core structure. It is hypothesized that these three loops form a binding surface for virus and that evolutionary changes in any one of the loops can alter restriction specificity.