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Data from: Climate change and pathways of vessel traffic create marine protected area networks of invasion
Iacarella, Josephine; Lyons, Devin; Burke, Lily; Davidson, Ian; Therriault, Thomas; Dunham, Anya; DiBacco, Claudio — 2020-05-04 <ol> <li>Establishment of protected areas to maintain biodiversity requires identification, prioritization, and management of stressors that may undermine conservation goals. Nonindigenous species and climate change are critical ecosystem stressors that need greater attention in the context of spatial planning and management of protected areas. Risk of invasion into protected areas needs to be quantified under current and projected climate conditions in conjunction with prioritization of key vectors and vulnerable areas to enable development of effective management strategies.</li> <li>We assessed the likelihood of invasion across networks of marine protected areas (MPAs) to determine how invaded MPAs may compromise MPA networks by sharing nonindigenous species. We evaluated invasion risk in 83 MPAs along Canada’s Pacific coast for eight nonindigenous species based on environmental suitability under current and future (average conditions from 2041-2070) climate conditions and association with shipping and boating pathways. We applied species distribution models and network analysis of vessel tracking data for 805 vessels in 2016 that connected MPAs.</li> <li>The probability of occurrence within MPAs and the proportion of MPA area that is suitable to the modelled species significantly increased under future climate conditions, with six species reaching over 90% predicted occurrence across MPAs and over 70% of suitable area within MPAs. Vessel traffic created four network clusters of 61 highly connected MPAs that spanned the coastline. Occupancy of over 90% of the MPAs within the clusters was predicted for most species.</li> <li> <i>Synthesis and applications.</i> Our results indicate a high likelihood of marine protected area (MPA) network invasion based on current and future environmental conditions and vectors of spread, and the potential for extensive nonindigenous species distributions within MPAs. Our approach highlights how interacting stressors can exacerbate MPA susceptibility to nonindigenous species, adding further challenges for protected area management. Management planning that invests in understanding connectivity and vector processes (human behaviors) is more likely to derive effective policies to stem the flow of nonindigenous species under both current and future conditions. In particular, biosecurity measures including vessel biofouling regulations and MPA- and MPA network-specific plans for prevention, monitoring, and mitigation of nonindigenous species are needed.</li> </ol>
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Data from: Genomic evidence of hybridization between two independent invasions of European green crab (Carcinus maenas) in the Northwest Atlantic
Jeffery, Nicholas W.; DiBacco, Claudio; Wringe, Brendan F.; Stanley, Ryan R.E.; Hamilton, Lorraine C.; Ravindran, Praveen N.; Bradbury, Ian R. — 2017-03-22 Invasive species have been associated with significant negative impacts in their introduced range often outcompeting native species, yet the long-term evolutionary dynamics of biological invasions are not well understood. Hybridization, either among waves of invasion or between native and introduced populations, could alter the ecological and evolutionary impacts of invasions yet has rarely been studied in marine invasive species. The European green crab (Carcinus maenas) invaded eastern North America twice from northern and southern locations in its native range. Here we examine the frequency of hybridization among these two distinct invasions at locations from New Jersey, USA to Newfoundland, Canada using restriction-site associated DNA sequencing (RAD-seq), microsatellite loci, and COI mtDNA sequences. We used Bayesian clustering and hybrid assignment analyses to investigate hybridization between the northern and southern populations. Of the samples analyzed, six locations contained at least one hybrid individual, while two locations were characterized by extensive hybridization, with 95% of individuals collected from Placentia Bay, Newfoundland being hybrids (mostly F2), and 90% of individuals from Kejimkujik, Nova Scotia being classified as hybrids, mostly backcrosses to the northern ecotype. The presence of both F2 hybrids and backcrossed individuals suggests that these hybrids are viable and introgression is occurring between invasions. Our results provide insight into the demographic and evolutionary consequences of hybridization between independent invasions, and will inform the management of green crabs in eastern North America.
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Data from: RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic
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Jeffery, Nicholas W.; DiBacco, Claudio; Van Wyngaarden, Mallory; Hamilton, Lorraine C.; Stanley, Ryan R. E.; Bernier, Renée; FitzGerald, Jennifer; Matheson, K.; McKenzie, C. H.; Nadukkalam Ravindran, Praveen; Beiko, Robert; Bradbury, Ian R. — 2017-03-22 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.
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Data from: Temporal dynamics of the genetic clines of invasive European green crab (Carcinus maenas) in eastern North America
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Lehnert, Sarah J.; DiBacco, Claudio; Jeffery, Nicholas W.; Blakeslee, April M.H.; Isaksson, Jonatan; Roman, Joe; Wringe, Brendan F.; Stanley, Ryan R.E.; Matheson, Kyle; McKenzie, Cynthia H.; Hamilton, Lorraine C.; Bradbury, Ian R.; Stanley, Ryan R. E.; Blakeslee, April M. H. — 2018-06-05 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, ~39-49°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.
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Data from: Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus
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Van Wyngaarden, Mallory; Snelgrove, Paul V. R.; DiBacco, Claudio; Hamilton, Lorraine C.; Rodriguez-Ezpeleta, Naiara; Zhan, Luyao; Beiko, Robert; Bradbury, Ian R.; Beiko, Robert G. — 2019-01-02 Environmental factors can influence diversity and population structure in marine species and accurate understanding of this influence can both improve fisheries management and help predict responses to environmental change. We used 7163 SNPs derived from restriction site-associated DNA sequencing genotyped in 245 individuals of the economically important sea scallop, Placopecten magellanicus, to evaluate the correlations between oceanographic variation and a previously identified latitudinal genomic cline. Sea scallops span a broad latitudinal area (>10 degrees), and we hypothesized that climatic variation significantly drives clinal trends in allele frequency. Using a large environmental dataset, including temperature, salinity, chlorophyll a, and nutrient concentrations, we identified a suite of SNPs (285–621, depending on analysis and environmental dataset) potentially under selection through correlations with environmental variation. Principal components analysis of different outlier SNPs and environmental datasets revealed similar northern and southern clusters, with significant associations between the first axes of each (R2adj = .66–.79). Multivariate redundancy analysis of outlier SNPs and the environmental principal components indicated that environmental factors explained more than 32% of the variance. Similarly, multiple linear regressions and random-forest analysis identified winter average and minimum ocean temperatures as significant parameters in the link between genetic and environmental variation. This work indicates that oceanographic variation is associated with the observed genomic cline in this species and that seasonal periods of extreme cold may restrict gene flow along a latitudinal gradient in this marine benthic bivalve. Incorporating this finding into management may improve accuracy of management strategies and future predictions.
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Data from: Genome-wide evidence of environmentally mediated secondary contact of European green crab (Carcinus maenas) lineages in eastern North America
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Jeffery, Nicholas W.; Bradbury, Ian R.; Stanley, Ryan R.E.; Wringe, Brendan F.; Van Wyngaarden, Mallory; Lowen, J. Ben; McKenzie, Cynthia H.; Matheson, Kyle; Sargent, Philip S.; DiBacco, Claudio; Stanley, Ryan R. E. — 2018-01-19 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 9137 genome-wide 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<0.0001) 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.
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Data from: Identifying patterns of dispersal, connectivity, and selection in the sea scallop, Placopecten magellanicus, using RAD-seq derived SNPs
Dryad
Van Wyngaarden, Mallory; Snelgrove, Paul V.R.; DiBacco, Claudio; Hamilton, Lorraine C.; Rodríguez-Ezpeleta, Naiara; Jeffery, Nicholas W.; Stanley, Ryan R.; Bradbury, Ian R.; Stanley, Ryan R. E.; Snelgrove, Paul V. R. — 2016-08-29 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 range-wide 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.

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(auteur : DiBacco, Claudio)

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