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Understanding population history and genetic connectivity is important for assessing the long-term viability of populations. The Atlantic surfclam (Spisula solidissima) has historically been subdivided into two subspecies: lesser-known S.s. simitis in the South Atlantic Bight and Gulf of Mexico, and commercially important S.s. solidissima mostly north of Cape Hatteras. Novel populations of the 'southern' S.s. similis subspecies were previously identified far north of their historical range limit. Here, to test a hypothesis of recency and isolation in the North, population samples from Southern New England S..s. similis were compared for the first time to a population sample from Georgia, as well as to S.s. solidissima. Population structure and demographic history were inferred using genetic variation at a combination of microsatellite, mtDNA, and nuclear intron loci. The Southern New England populations of S.s. similis had slightly lower nuclear DNA diversity than in Georgia. Genetic differentiation between Massachusetts and Georgia S.s. similis was weak and only significant for microsatellite markers. Consistent with weak differentiation, coalescent modeling of nuclear sequence variation indicated high levels of gene flow. All S.s. similis populations had extremely low mtDNA diversity, with only two mitochondrial cytochrome oxidase I haplotypes found in contrast to 15 haplotypes in S.s. solidissima. Collectively, the population genetic patterns are more parsimoniously explained by the northern S.s. similis populations originating from a postglacial expansion rather than recent colonization. KEY WORDS: Spisula solidissima, population structure, gene flow, marine phylogeography, mitochondrial DNA, COI, intron, microsatellites, coalescent model, demographic history, INTRODUCTION It is valuable to assess the population history and genetic connectivity of populations to assess their long-term viability and threat of extinction (Allendorf & Luikart 2009, Hellberg 2009, Nance [...]

Estuaries provide valuable habitat for the eastern oyster (Crassostrea virginica). Although salinity at a given location fluctuates regularly with tides, upbay and downbay salinity differences span a broad estuarine salinity gradient. Higher salinity habitats downbay support faster oyster growth, whereas lower salinities upbay act as a refuge from predation and disease but slows growth. Two experiments were performed to investigate the effect of salinity, postsettlement salinity changes, and shell morphology on juvenile oyster growth. One experiment used wild oyster spat collected from three distinct Delaware Bay salinity zones that were then transplanted into various salinity conditions in the laboratory, where growth was monitored. Transplanting into low salinity led to decreased growth compared with transplanting to higher salinity, and growth of oyster spat was overall highest for spat from the lowest salinity source. Growth did not differ among shell morphologies. A second experiment used hatchery reared larvae set in one of four different salinity conditions. Those spat were maintained in settlement salinities 22, 16, 10, and 6 for 2-3 wk postsettlement, then measured before fully factorial transfer into new salinity conditions with measurement 3 wk later. Lower final salinity treatments were associated with lower growth, lower initial salinity treatments were associated with faster final treatment growth, and final growth depended on the interaction between initial and final salinity. Therefore, in addition to the effects of acute salinity changes on growth, early postsettlement hyposalinity stress can generate compensatory juvenile oyster growth. As increased freshwater events due to climate change are expected in the Delaware Bay and regionally in the Northeast, these results indicate that nonlinear early life stress responses are important to quantify to better understand oyster stock resilience and plan management. KEY WORDS: Oyster, spat morphology, salinity, growth, carryover effects, INTRODUCTION Oysters (Crassostrea virginica Gmelin, 1791) provide many economic benefits and ecosystem services to the east coast of the Americas. They are euryhaline and can sustain populations in salinities ranging [...]

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. [ABSTRACT FROM AUTHOR]

Cisco (Coregonus artedi) are an important component of native food webs in the Great Lakes, and their restoration is instrumental to the recovery of lake trout (Salvelinus namaycush) and Atlantic salmon (Salmo salar). Difficulties with visual identification of larvae can confound early life history surveys, as cisco are often difficult to distinguish from lake whitefish (Coregonus clupeaformis). We compared traditional visual species identification methods with genetic identifications based on barcoding of the mitochondrial cytochrome c oxidase I gene for 726 coregonine larvae caught in Chaumont Bay, Lake Ontario. We found little agreement between the visual characteristics of cisco identified by genetic barcoding and the most widely used dichotomous key, and the considerable overlap in ranges of traditionally utilized metrics suggests that visual identification of coregonine larvae from Chaumont Bay is impractical. Coregonines are highly variable and plastic species and often display wide variations in morphometric characteristics across their broad range. This study highlights the importance of developing accurate, geographically appropriate larval identification methods to best inform cisco restoration and management efforts. Les ciscos de lacs (Coregonus artedi) constituent un element important des reseaux trophiques indigenes dans les Grands Lacs, et leur regeneration est utile pour le retablissement des touladis (Salvelinus namaycush) et des saumons atlantiques (Salmo salar). Les difficultes que presente l'identification visuelle des larves peuvent fausser les evaluations des premiers stades de vie, les ciscos etant souvent difficiles a distinguer des grands coregones (Coregonus clupeaformis). Nous avons compare des methodes traditionnelles d'identification visuelle des especes a l'identification genetique reposant sur le codage a barres du gene de la cytochrome c oxydase I mitochondriale pour 726 larves de coregonine capturees dans la baie de Chaumont du lac Ontario. Nous avons note peu de concordance entre les caracteristiques visuelles de ciscos identifies par codage a barres genetique et a l'aide de la cle dichotomique la plus largement utilisee, et le chevauchement considerable des fourchettes de parametres utilises traditionnellement indiquerait que l'identification visuelle de larves de coregonine de la baie de Chaumont n'est pas une approche pratique. Les coregonines sont des especes tres variables et plastiques dont les caracteristiques morphometriques presentent souvent de grandes variations a l'echelle de leur grande aire de repartition. L'etude souligne l'importance du developpement de methodes d'identification des larves adaptees a l'emplacement afin de mieux eclairer les efforts de regeneration et de gestion des ciscos. [Traduit par la Redaction], Introduction Cisco (Coregonus artedi) were an important component of both native food webs and commercial fisheries in the Laurentian Great Lakes before their collapse in the middle of the 20th [...]