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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: Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus
Dryad
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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Has anyone seen my plasmid? Probing the dark corners of metagenome-assembled genomes
Banff International Research Station for Mathematical Innovation and Discovery
Beiko, Robert — 2020-03-16 Metagenomic analyses typically produce millions of short reads, sampled from the entire diversity of genomes present in a particular sample. While direct analysis of these reads can yield useful information about the diversity of microorganisms and functions present, a great deal of information can be learned by merging short reads into longer assemblies. Algorithms to reconstruct metagenome-assembled genomes (MAGs) draw from different types of evidence, including the relative abundance of particular reads in a sample, and the similarity of â wordsâ of length k (known as k-mers). Reconstruction of MAGs has shed new light on heretofore unknown deep lineages of bacteria, and revealed the degree of diversity of closely related organisms in different habitats. MAGs can also be very useful for the reconstruction of entire metabolic pathways and networks. However, the effectiveness of MAG assembly is not uniform, and stretches of DNA that deviate from the expected frequency or k-mer distribution can be difficult or impossible to correctly assign. This problem is especially acute in unusual constituents of the genome such as plasmids and genomic islands (GIs); since these elements often harbour useful information about antimicrobial resistance and other important pathways, their absence from a MAG can lead to underestimation of their abundance. We assessed the extent of the problem using a simulated 250 base-pair paired-end metagenome of 30 genomes displaying a broad range of GI abundance and numbers of plasmids. Across a range of methods, a median of 66.2% of all chromosomal sequence was binned into MAGs; however, only 23.1% of plasmids and 31.7% of GIs were similarly present in any bin. When assessing the percentage of GIs and plasmids that were correctly assigned to the same bin as the rest of their source genome this performance is even worse (median 32.5% of GIs and 6.9% of plasmids). These results on a relatively simple simulated community point to (possibly fundamental) limitations of existing methods in assigning exotic elements to their correct source genome. Although further improvements will undoubtedly be realized through better algorithms and statistics, high accuracy may depend on the integration of additional DNA sequencing data, and better use of known reference genomes. Non UBC Unreviewed Author affiliation: Dalhousie University Faculty http://creativecommons.org/licenses/by-nc-nd/4.0/

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(Author: Beiko, Robert)

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