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As climate change transforms marine environments globally, species distributions correspondingly shift to locations where conditions have become or remain favourable. The ability to model these distributional shifts has been facilitated by species distribution models (SDMs). However, current SDM approaches have largely ignored climate‐driven changes in species interactions, which ultimately can have an important influence on species distributions. In this study, we utilize a long‐term, large‐scale dataset spanning 48 years and approximately 30 degrees latitude across the Canadian Atlantic shelf. We examine how climate influences the distribution and predation patterns of two invertebrates, northern shrimp Pandalus borealis and snow crab Chionoecetes opilio, aiming to evaluate the impacts of climate change on prey distributions. We found that both invertebrate species have a pronounced predicted response to climate change, with a northern shift in the distribution of northern shrimp and an overall reduction in abundance of both snow crab and shrimp associated with warming temperatures. Including predatory interactions as predictors in the SDMs (either directly via predator densities or via estimated predation rates) improved prediction accuracy for northern shrimp but not for snow crab. This is consistent with the ecology of these two species, as northern shrimp is more vulnerable to predation than snow crab. We found that the projections of future northern shrimp distributions are sensitive to the predicted spatial distribution and abundance of predators, highlighting the inherent complexity of predicting species response to climate change. Collectively, these results contribute to a broader literature that seeks to improve the capabilities of models to predict the effects of species interactions on species distributions under changing ecological conditions. [ABSTRACT FROM AUTHOR]

Species with widespread distributions play a crucial role in our understanding of climate change impacts on population structure. In marine species, population structure is often governed by both high connectivity potential and selection across strong environmental gradients. Despite the complexity of factors influencing marine populations, studying species with broad distribution can provide valuable insights into the relative importance of these factors and the consequences of climate‐induced alterations across environmental gradients. We used the northern shrimp Pandalus borealis and its wide latitudinal distribution to identify current drivers of population structure and predict the species' vulnerability to climate change. A total of 1514 individuals sampled across 24° latitude were genotyped at high geographic (54 stations) and genetic (14,331 SNPs) resolutions to assess genetic variation and environmental correlations. Four populations were identified in addition to finer substructure associated with local adaptation. Geographic patterns of neutral population structure reflected predominant oceanographic currents, while a significant proportion of the genetic variation was associated with gradients in salinity and temperature. Adaptive landscapes generated using climate projections suggest a larger genomic offset in the southern extent of the P. borealis range, where shrimp had the largest adaptive standing genetic variation. Our genomic results combined with recent observations point to further deterioration in southern regions and an impending vulnerable status in the regions at higher latitudes for P. borealis. They also provide rare insights into the drivers of population structure and climatic vulnerability of a widespread meroplanktonic species, which is crucial to understanding future challenges associated with invertebrates essential to ecosystem functioning. [ABSTRACT FROM AUTHOR]

A global decline in seagrass populations has led to renewed calls for their conservation as important providers of biogenic and foraging habitat, shoreline stabilization and carbon storage. Eelgrass (Zostera marina) occupies the largest geographic range among seagrass species spanning a commensurately broad spectrum of environmental conditions. In Canada, eelgrass is managed as a single phylogroup despite occurring across three oceans and a range of ocean temperatures and salinity gradients. Previous research has focused on applying relatively few markers to reveal population structure of eelgrass, whereas a whole‐genome approach is warranted to investigate cryptic structure among populations inhabiting different ocean basins and localized environmental conditions. We used a pooled whole‐genome re‐sequencing approach to characterize population structure, gene flow and environmental associations of 23 eelgrass populations ranging from the Northeast United States to Atlantic, subarctic and Pacific Canada. We identified over 500,000 SNPs, which when mapped to a chromosome‐level genome assembly revealed six broad clades of eelgrass across the study area, with pairwise FST ranging from 0 among neighbouring populations to 0.54 between Pacific and Atlantic coasts. Genetic diversity was highest in the Pacific and lowest in the subarctic, consistent with colonization of the Arctic and Atlantic oceans from the Pacific less than 300 kya. Using redundancy analyses and two climate change projection scenarios, we found that subarctic populations are predicted to be potentially more vulnerable to climate change through genomic offset predictions. Conservation planning in Canada should thus ensure that representative populations from each identified clade are included within a national network so that latent genetic diversity is protected, and gene flow is maintained. Northern populations, in particular, may require additional mitigation measures given their potential susceptibility to a rapidly changing climate. [ABSTRACT FROM AUTHOR]

Ongoing effects of climate change create a dual challenge of shifting distributions of organisms and concerns about the fate of organic carbon in nature. Marine sediments store vast amounts of organic carbon, but the fate of that material hinges on the biology of organisms associated with the seafloor and how they influence rates of carbon decomposition and burial. Shifts in large megafauna that disturb and thus help to oxygenate sediments could have important ramifications regarding whether sediments release or store carbon for long periods of time. We consider snow crab and lobster, two commercially important seafloor species in the Northeastern Atlantic, and the potential effects of ongoing changes in their distributions and that of their fisheries for future climate scenarios. These ongoing biogeographic shifts, considered in tandem with areas of seabed legislatively protected from fishing impacts and thus not confounded by cumulative effects of fishing gear disturbance, offer an opportunity to study how newly arrived species that disturb large areas of the seafloor might influence the global carbon cycle. [ABSTRACT FROM AUTHOR]

Marine classification schemes based on abiotic surrogates often inform regional marine conservation planning in lieu of detailed biological data. However, these schemes may poorly represent ecologically relevant biological patterns required for effective design and management strategies. We used a community‐level modeling approach to characterize and delineate representative mesoscale (tens to thousands of kilometers) assemblages of demersal fish and benthic invertebrates in the Northwest Atlantic. Hierarchical clustering of species occurrence data from four regional annual multispecies trawl surveys revealed three to six groupings (predominant assemblage types) in each survey region, broadly associated with geomorphic and oceanographic features. Indicator analyses identified 3–34 emblematic taxa of each assemblage type. Random forest classifications accurately predicted assemblage distributions from environmental covariates (AUC > 0.95) and identified thermal limits (annual minimum and maximum bottom temperatures) as important predictors of distribution in each region. Using forecasted oceanographic conditions for the year 2075 and a regional classification model, we projected assemblage distributions in the southernmost bioregion (Scotian Shelf‐Bay of Fundy) under a high emissions climate scenario (RCP 8.5). Range expansions to the northeast are projected for assemblages associated with warmer and shallower waters of the Western Scotian Shelf over the 21st century as thermal habitat on the relatively cooler Eastern Scotian Shelf becomes more favorable. Community‐level modeling provides a biotic‐informed approach for identifying broadscale ecological structure required for the design and management of ecologically coherent, representative, well‐connected networks of Marine Protected Areas. When combined with oceanographic forecasts, this modeling approach provides a spatial tool for assessing sensitivity and resilience to climate change, which can improve conservation planning, monitoring, and adaptive management. [ABSTRACT FROM AUTHOR]

A high‐resolution coastal Finite‐Volume Community Ocean Model (FVCOM) has been configured to simulate the water circulation in the Eastern Shore Islands (ESI) archipelago on the coastal Scotian Shelf. Circulation in this area is characterized by complex interactions between the irregular coastline, a dense archipelago, tides, wind, and subtidal currents. Model outputs show close agreement with the tides, subtidal current, and hydrographic observations. Two circulation regimes within the study area were identified "inshore" and "offshore" of the 60‐m isobath. The balance between pressure gradient and Coriolis effect controls the dominant southwestward current (Nova Scotia Current) in the offshore. Rotary spectra and numerical experiments showed that the tidal current was an important component to the circulation in the inshore. Within the study area there are several clockwise and counter‐clockwise gyres related to the Coriolis effect, surface wind stress, pressure gradient, and the interaction between the irregular topography and current. The combined effects of topography, wind, tide, and Nova Scotia Current regulate the inshore circulation. The topographic features complex the cross‐shore transport. The increased bathymetric slope and strengthened relative vorticity contribute to the inshore cross‐shore current. Here, we found that the joint effect of baroclinicity and bottom relief drives the cross‐isobath transport. The ability of our model to resolve complex coastal circulation patterns provides an important basis on which to better understand how physical oceanography influences the unique ecological processes of this coastal archipelago and ultimately will help to evaluate dispersal and connectivity of coastal species in this area. Plain Language Summary: The Eastern Shore Islands archipelago is characterized by the highest density of islands in the coastal Scotian Shelf. Here, we establish a high‐resolution coastal ocean model to describe the water circulation in this unique area. Using numerical model results, we demonstrate persistent southwestward alongshore flows in the offshore area agreeing with previous observations. Interactions between currents, stratification and topography jointly regulate the cross‐shore transport in the area. We found a strong tidal influence on circulation in inshore waters at both hourly and seasonal timescales. Our model will provide an invaluable resource to understand key physical processes and ultimately help evaluate the important biological characteristics and functions in this area. Key Points: Two circulation regimes are identified in the Eastern Shore Islands Area of Interest (AOI) on the costal Scotian ShelfThe cross‐shore geostrophic balance controls the water circulation in the offshore component of the study areaIrregular topography influences the flow pattern between the coastline and the 60‐m isobath [ABSTRACT FROM AUTHOR]

Two genetically distinct lineages of European green crabs (Carcinus maenas) were independently introduced to eastern North America, the first in the early 19th century and the second in the late 20th century. These lineages first came into secondary contact in southeastern Nova Scotia, Canada (NS), where they hybridized, producing latitudinal genetic clines. Previous studies have documented a persistent southward shift in the clines of different marker types, consistent with existing dispersal and recruitment pathways. We evaluated current clinal structure by quantifying the distribution of lineages and fine‐scale hybridization patterns across the eastern North American range (25 locations, ~39 to 49°N) using informative single nucleotide polymorphisms (SNPs; n = 96). In addition, temporal changes in the genetic clines were evaluated using mitochondrial DNA and microsatellite loci (n = 9–11) over a 15‐year period (2000–2015). Clinal structure was consistent with prior work demonstrating the existence of both northern and southern lineages with a hybrid zone occurring between southern New Brunswick (NB) and southern NS. Extensive later generation hybrids were detected in this region and in southeastern Newfoundland. Temporal genetic analysis confirmed the southward progression of clines over time; however, the rate of this progression was slower than predicted by forecasting models, and current clines for all marker types deviated significantly from these predictions. Our results suggest that neutral and selective processes contribute to cline dynamics, and ultimately, highlight how selection, hybridization, and dispersal can collectively influence invasion success. [ABSTRACT FROM AUTHOR]

Abstract: Genetic‐environment associations are increasingly revealed through population genomic data and can occur through a number of processes, including secondary contact, divergent natural selection, or isolation by distance. Here, we investigate the influence of the environment, including seasonal temperature and salinity, on the population structure of the invasive European green crab (Carcinus maenas) in eastern North America. Green crab populations in eastern North America are associated with two independent invasions, previously shown to consist of distinct northern and southern ecotypes, with a contact zone in southern Nova Scotia, Canada. Using a RAD‐seq panel of 9,137 genomewide SNPs, we detected 41 SNPs (0.49%) whose allele frequencies were highly correlated with environmental data. A principal components analysis of 25 environmental variables differentiated populations into northern, southern, and admixed sites in concordance with the observed genomic spatial structure. Furthermore, a spatial principal components analysis conducted on genomic and geographic data revealed a high degree of global structure (p < .0001) partitioning a northern and southern ecotype. Redundancy and partial redundancy analyses revealed that among the environmental variables tested, winter sea surface temperature had the strongest association with spatial structuring, suggesting that it is an important factor defining range and expansion limits of each ecotype. Understanding environmental thresholds associated with intraspecific diversity will facilitate the ability to manage current and predict future distributions of this aquatic invasive species. [ABSTRACT FROM AUTHOR]

The ability to detect and characterize hybridization in nature has long been of interest to many fields of biology and often has direct implications for wildlife management and conservation. The capacity to identify the presence of hybridization, and quantify the numbers of individuals belonging to different hybrid classes, permits inference on the magnitude of, and timescale over which, hybridization has been or is occurring. Here, we present an r package and associated workflow developed for the detection, with estimates of efficiency and accuracy, of multigenerational hybrid individuals using genetic or genomic data in conjunction with the program newhybrids. This package includes functions for the identification and testing of diagnostic panels of markers, the simulation of multigenerational hybrids, and the quantification and visualization of the efficiency and accuracy with which hybrids can be detected. Overall, this package delivers a streamlined hybrid analysis platform, providing improvements in speed, ease of use and repeatability over current ad hoc approaches. The latest version of the package and associated documentation are available on GitHub (). [ABSTRACT FROM AUTHOR]

Abstract: Genomic studies of invasive species can reveal both invasive pathways and functional differences underpinning patterns of colonization success. The European green crab (Carcinus maenas) was initially introduced to eastern North America nearly 200 years ago where it expanded northwards to eastern Nova Scotia. A subsequent invasion to Nova Scotia from a northern European source allowed further range expansion, providing a unique opportunity to study the invasion genomics of a species with multiple invasions. Here, we use restriction‐site‐associated DNA sequencing‐derived SNPs to explore fine‐scale genomewide differentiation between these two invasions. We identified 9137 loci from green crab sampled from 11 locations along eastern North America and compared spatial variation to mitochondrial COI sequence variation used previously to characterize these invasions. Overall spatial divergence among invasions was high (pairwise FST ~0.001 to 0.15) and spread across many loci, with a mean FST ~0.052 and 52% of loci examined characterized by FST values >0.05. The majority of the most divergent loci (i.e., outliers, ~1.2%) displayed latitudinal clines in allele frequency highlighting extensive genomic divergence among the invasions. Discriminant analysis of principal components (both neutral and outlier loci) clearly resolved the two invasions spatially and was highly correlated with mitochondrial divergence. Our results reveal extensive cryptic intraspecific genomic diversity associated with differing patterns of colonization success and demonstrates clear utility for genomic approaches to delineating the distribution and colonization success of aquatic invasive species. [ABSTRACT FROM AUTHOR]

Advances in genetic sequencing technologies and techniques have made large, genome-wide data sets comprised of hundreds or even thousands of individuals and loci the norm rather than the exception even for nonmodel organisms. While such data present new opportunities for evaluating population structure and demographic processes, the large size of these genomic data sets brings new computational challenges for researchers needing to parse, convert and manipulate data often into a variety of software-specific formats required of genomic analyses. We developed genepopedit as a flexible tool for the manipulation of multilocus molecular data sets. Functionality can be divided among diagnostic-, manipulation-, sampling-, simulation-, and transformation-based tools. Metadata from large genomic data sets can be efficiently extracted, without the need to view data in a text-editing program. genepopedit provides tools to manipulate loci, individual samples and populations included in genomic data sets, in addition to the ability to convert directly to a variety of software formats. Functions are compiled as an R package, which can integrate into existing analysis workflows. Importantly, genepopedit provides a simple yet robust code-based tool for repeatable genomic data manipulation, which has been proven to be stable for data sets in excess of 200 000 SNPs. The latest version of the package and associated documentation are available on Github (github.com/rystanley/genepopedit). [ABSTRACT FROM AUTHOR]

Hybridization among populations and species is a central theme in many areas of biology, and the study of hybridization has direct applicability to testing hypotheses about evolution, speciation and genetic recombination, as well as having conservation, legal and regulatory implications. Yet, despite being a topic of considerable interest, the identification of hybrid individuals, and quantification of the (un)certainty surrounding the identifications, remains difficult. Unlike other programs that exist to identify hybrids based on genotypic information, newhybrids is able to assign individuals to specific hybrid classes (e.g. F1, F2) because it makes use of patterns of gene inheritance within each locus, rather than just the proportions of gene inheritance within each individual. For each comparison and set of markers, multiple independent runs of each data set should be used to develop an estimate of the hybrid class assignment accuracy. The necessity of analysing multiple simulated data sets, constructed from large genomewide data sets, presents significant computational challenges. To address these challenges, we present parallelnewhybrid, an r package designed to decrease user burden when undertaking multiple newhybrids analyses. parallelnewhybrid does so by taking advantage of the parallel computational capabilities inherent in modern computers to efficiently and automatically execute separate newhybrids runs in parallel. We show that parallelization of analyses using this package affords users several-fold reductions in time over a traditional serial analysis. parallelnewhybrid consists of an example data set, a readme and three operating system-specific functions to execute parallel newhybrids analyses on each of a computer's c cores. parallelnewhybrid is freely available on the long-term software hosting site github (). [ABSTRACT FROM AUTHOR]

Understanding patterns of dispersal and connectivity among marine populations can directly inform fisheries conservation and management. Advances in high-throughput sequencing offer new opportunities for estimating marine connectivity. We used restriction-site-associated DNA sequencing to examine dispersal and realized connectivity in the sea scallop Placopecten magellanicus, an economically important marine bivalve. Based on 245 individuals sampled rangewide at 12 locations from Newfoundland to the Mid-Atlantic Bight, we identified and genotyped 7163 single nucleotide polymorphisms; 112 (1.6%) were identified as outliers potentially under directional selection. Bayesian clustering revealed a discontinuity between northern and southern samples, and latitudinal clines in allele frequencies were observed in 42.9% of the outlier loci and in 24.6% of neutral loci. Dispersal estimates derived using these clines and estimates of linkage disequilibrium imply limited dispersal; 373.1 ± 407.0 km (mean ± SD) for outlier loci and 641.0 ± 544.6 km (mean ± SD) for neutral loci. Our analysis suggests restricted dispersal compared to the species range (>2000 km) and that dispersal and effective connectivity differ. These observations support the hypothesis that limited effective dispersal structures scallop populations along eastern North America. These findings can help refine the appropriate scale of management and conservation in this commercially valuable species. [ABSTRACT FROM AUTHOR]

Verrucous carcinoma, because of its oftentimes unusual clinical appearance, may be misdiagnosed if there is not good communication between the surgeon and the pathologist. We have reviewed our series of 20 cases of verrucous carcinoma from 1964 through 1974 and have analyzed the results of our therapy. We have concluded that verrucous carcinoma is a slow-growing, locally invasive lesion that does not metastasize to the cervical lymph nodes. Radiation therapy does not seem to be an effective method of treatment; the recurrence rate is high. Conservative laryngeal surgery is the preferred method of treatment in these patients and should prevent loss of life and spare laryngeal function.