Optimal sampling methods for modelling the occupancy of Arctic grayling (Thymallus arcticus) in the Canadian Barrenlands

© Canadian Science Publishing or its licensors. Baker, LF, KJ Artym and HK Swanson (2017). Optimal sampling methods for modelling the occupancy of Arctic grayling (Thymallus arcticus) in the Canadian Barrenlands. Canadian Journal of Fisheries and Aquatic Sciences. doi/10.1139/cjfas-2016-0429. Published by NRC Research Press, the final published version is available at: http://dx.doi.org/10.1139/cjfas-2016-0429In occupancy models, imperfect detectability of animals is usually corrected for by using temporally-repeated surveys to estimate probability of detection. Substituting spatial replicates for temporal replicates could be an advantageous sampling strategy in remote Arctic regions, but may lead to serious violations of model assumptions. Using a case study of site occupancy of adfluvial young-of-year Arctic Grayling in Barrenland tundra streams, we assessed reliability and efficiency of alternative sampling strategies; i) randomly distributed vs sequential adjacent spatial replicates; ii) visual vs electrofishing surveys; and, iii) spatial vs temporal replicates. Sequential, adjacent spatial replicates produced spatially auto-correlated data. Autocorrelation was relieved using randomly distributed spatial replicates, but using these randomly distributed spatial replicates introduced significant error into estimates of the probability of occupancy in streams. Models designed for spatially-autocorrelated data could minimize this bias. Visual and electrofishing surveys produced comparable probabilities of detection. Spatially-replicated surveys performed better than temporal replicates. The easiest and relatively most cost-effective sampling methods performed as well as, or better than, the more established, expensive, and logistically difficult alternatives for occupancy estimation.De Beers Canada Ltd Natural Sciences and Engineering Research Council CRD || CRDPJ 469307 - 1

Species and Life History Affect the Utility of Otolith Chemical Composition for Determining Natal Stream of Origin for Pacific Salmon

To test the utility of otolith chemical composition as a tool for determining the natal stream of origin for salmon, we examined water chemistry and otoliths of juvenile and adult Chum Salmon Oncorhynchus keta and Coho Salmon O. kisutch from three watersheds (five rivers) in the Norton Sound region of Alaska. The two species are characterized by different life histories: Coho Salmon rear in freshwater for up to 3years, whereas Chum Salmon emigrate from freshwater shortly after emergence. We used laser ablation (LA) inductively coupled plasma (ICP) mass spectrometry (MS) to quantify element: Ca ratios for Mg, Mn, Zn, Sr, and Ba, and we used multicollector LA-ICP-MS to determine Sr-⁸⁷:Sr-⁸⁶ ratios in otolith regions corresponding to the period of freshwater residence. Significant differences existed in both water and otolith elemental composition, suggesting that otolith composition could be used to discriminate the natal origin of Coho Salmon and Chum Salmon but only when Sr-⁸⁷:Sr-⁸⁶ ratios were included in the discriminant function analyses. The best discriminant model included Sr-⁸⁷:Sr-⁸⁶ ratios, and without Sr-⁸⁷:Sr-⁸⁶ ratios it was difficult to discriminate among watersheds and rivers. Classification accuracy was 80% for Coho Salmon and 68% for Chum Salmon, indicating that this method does not provide sufficient sensitivity to estimate straying rates of Pacific salmon at the scale we studied.Keywords: Plasma mass spectrometry, Fish otoliths, Stock identification, Chemistry, Oncorhynchus tshawytscha, Population structure, Microchemistry, Elemental analysis, Describe movements, Trace element

Contributions and perspectives of Indigenous Peoples to the study of mercury in the Arctic

Arctic Indigenous Peoples are among the most exposed humans when it comes to foodborne mercury (Hg). In response, Hg monitoring and research have been on-going in the circumpolar Arctic since about 1991; this work has been mainly possible through the involvement of Arctic Indigenous Peoples. The present overview was initially conducted in the context of a broader assessment of Hg research organized by the Arctic Monitoring and Assessment Programme. This article provides examples of Indigenous Peoples' contributions to Hg monitoring and research in the Arctic, and discusses approaches that could be used, and improved upon, when carrying out future activities. Over 40 mercury projects conducted with/by Indigenous Peoples are identified for different circumpolar regions including the U.S., Canada, Greenland, Sweden, Finland, and Russia as well as instances where Indigenous Knowledge contributed to the understanding of Hg contamination in the Arctic. Perspectives and visions of future Hg research as well as recommendations are presented. The establishment of collaborative processes and partnership/co-production approaches with scientists and Indigenous Peoples, using good communication practices and transparency in research activities, are key to the success of research and monitoring activities in the Arctic. Sustainable funding for community-driven monitoring and research programs in Arctic countries would be beneficial and assist in developing more research/ monitoring capacity and would promote a more holistic approach to understanding Hg in the Arctic. These activities should be well connected to circumpolar/international initiatives to ensure broader availability of the information and uptake in policy development

Circumpolar patterns of Arctic freshwater fish biodiversity : A baseline for monitoring

1. Climate change, biological invasions, and anthropogenic disturbance pose a threat to the biodiversity and function of Arctic freshwater ecosystems. Understanding potential changes in fish species distribution and richness is necessary, given the great importance of fish to the function of freshwater ecosystems and as a resource to humans. However, information gaps limit large-scale studies and our ability to determine patterns and trends in space and time. This study takes the first step in determining circumpolar patterns of fish species richness and composition, which provides a baseline to improve both monitoring and conservation of Arctic freshwater biodiversity. 2. Information on species presence/absence was gathered from the Circumpolar Biodiversity Monitoring Program's Freshwater Database and used to examine patterns of freshwater fish γ-, α-, and β-diversity across 234° of longitude in the Arctic. The metrics of diversity provided information on species richness and composition across hydrobasins, ecoregions, and Arctic zones. 3. Circumpolar patterns of fish species biodiversity varied with latitude, isolation, and coarse ecoregion characteristics; patterns were consistent with historic and contemporary barriers to colonisation and environmental characteristics. Gamma-diversity was lower in the high Arctic compared to lower latitude zones, but α-diversity did not decrease with increasing latitude below 71°N, reflecting glacial history. Alpha-diversity was reduced to a single species, Arctic charr Salvelinus alpinus, in ecoregions above 71°N, where γ-diversity was the lowest. Beta-diversity indicated little variation in the composition and richness of species across the High Arctic; at lower latitudes, ecoregions contained more species, although species composition turned over across large spatial extents. 4. In an analysis of five ecoregions in the circumpolar Arctic, physical isolation, and ecoregion area and topography were identified as strong drivers of γ-, α-, and β-diversity. Physical isolation reduced the γ- and α-diversity, and changes in β-diversity between adjacent locations were due mainly to losses in species richness, rather than due to differences in species composition. Heterogeneity of habitats, environmental gradients, and geographic distance probably contributed to patterns of fish dissimilarity within and across ecoregions. 5. This study presents the first analysis of large-scale patterns of freshwater fish biodiversity in the circumpolar Arctic. However, information gaps in space, time, and among taxonomic groups remain. Future inclusion of extensive archive and new data will allow future studies to test for changes and drivers of the observed patterns of biodiversity. This is important given the potential impacts of ongoing and accelerating climate change, land use, and biotic exchange on Arctic fish biodiversity

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

Following the domestication of maize over the past ∼10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that there are several hundred CNV sequences among the two genotypes, as well as several thousand PAV sequences that are present in B73 but not Mo17. Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop