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The Atlantic surfclam (Spisula solidissima solidissima) is an economically valuable clam species that supports a major US fishery. Until recently, fishery efforts along the southern edge of the surfclam range were low due to clam mortalities there in the 1990s. Recent surfclam fishing efforts off Virginia raised questions of whether the surfclam population has returned in the southern region or if a single cohort is supporting the fishery there. Questions have also arisen about whetherS. s. similisis among the population fished off the coast of VA.Spisula solidissima similisis a warm-water cryptic subspecies of the Atlantic surfclam. Although morphologically indistinguishable,S. s. similisgrows to a smaller size and is genetically distinct. Atlantic surfclams (n = 103) were collected from the fishing grounds off the coast of VA. Each surfclam was aged, and shell length and tissue weight recorded for comparison to surfclams of the same age from the center of the population. Analyses of mitochondrial (mtCOI) sequences suggests that the two groups sampled off VA are genetically homogeneous, both groups contain two divergent mitochondrial lineages, and one surfclam sampled shares theS. s. similismtCOI sequence. There are multiple cohorts of surfclams, suggesting that environmental conditions may have improved for surfclams in the south, or that this population has acclimated to altered conditions. Further research should investigate the potential for subspecies hybridization.

 

Genome assembly can be challenging for species that are characterized by high amounts of polymorphism, heterozygosity, and large effective population sizes. High levels of heterozygosity can result in genome mis-assemblies and a larger than expected genome size due to the haplotig versions of a single locus being assembled as separate loci. Here, we describe the first chromosome-level genome for the eastern oyster, Crassostrea virginica. Publicly released and annotated in 2017, the assembly has a scaffold N50 of 54 mb and is over 97.3% complete based on BUSCO analysis. The genome assembly for the eastern oyster is a critical resource for foundational research into molluscan adaptation to a changing environment and for selective breeding for the aquaculture industry. Subsequent resequencing data suggested the presence of haplotigs in the original assembly, and we developed a post hoc method to break up chimeric contigs and mask haplotigs in published heterozygous genomes and evaluated improvements to the accuracy of downstream analysis. Masking haplotigs had a large impact on SNP discovery and estimates of nucleotide diversity and had more subtle and nuanced effects on estimates of heterozygosity, population structure analysis, and outlier detection. We show that haplotig masking can be a powerful tool for improving genomic inference, and we present an open, reproducible resource for the masking of haplotigs in any published genome.