Early detection and recovery of river herring spawning habitat use in response to a mainstem dam removal.

Historical loss of river and stream habitats due to impassable dams has contributed to the severe decline of many fish species. Anadromous fishes that migrate from the sea to freshwater streams to spawn have been especially impacted as dams restrict these fish from accessing ancestral spawning grounds. In 2018, Bloede Dam was removed from the Patapsco River near Baltimore, Maryland, restoring approximately 100 km of potential habitat for migratory fish.

Cross-Hemispheric Genetic Diversity and Spatial Genetic Structure of Reovirus 1 (CsRV1).

The movement of viruses in aquatic systems is rarely studied over large geographic scales. Oceanic currents, host migration, latitude-based variation in climate, and resulting changes in host life history are all potential drivers of virus connectivity, adaptation, and genetic structure. To expand our understanding of the genetic diversity of Callinectes sapidus reovirus 1 (CsRV1) across a broad spatial and host life history range of its blue crab host (), we obtained 22 complete and 96 partial genomic sequences for CsRV1 strains from the US Atlantic coast, Gulf of Mexico, Caribbean Sea, and the Atlantic coast of South America.

Genome-wide analysis of natural and restored eastern oyster populations reveals local adaptation and positive impacts of planting frequency and broodstock number.

The release of captive-bred plants and animals has increased worldwide to augment declining species. However, insufficient attention has been given to understanding how neutral and adaptive genetic variation are partitioned within and among proximal natural populations, and the patterns and drivers of gene flow over small spatial scales, which can be important for restoration success. A seascape genomics approach was used to investigate population structure, local adaptation, and the extent to which environmental gradients influence genetic variation among natural and restored populations of Chesapeake Bay eastern oysters .

Genome-wide analysis of acute low salinity tolerance in the eastern oyster Crassostrea virginica and potential of genomic selection for trait improvement.

As the global demand for seafood increases, research into the genetic basis of traits that can increase aquaculture production is critical. The eastern oyster (Crassostrea virginica) is an important aquaculture species along the Atlantic and Gulf Coasts of the United States, but increases in heavy rainfall events expose oysters to acute low salinity conditions, which negatively impact production. Low salinity survival is known to be a moderately heritable trait, but the genetic architecture underlying this trait is still poorly understood.

Chromosome-level genome assembly of the blue crab, Callinectes sapidus.

The blue crab, Callinectes sapidus (Rathbun, 1896) is an economically, culturally, and ecologically important species found across the temperate and tropical North and South American Atlantic coast. A reference genome will enable research for this high-value species. Initial assembly combined 200× coverage Illumina paired-end reads, a 60× 8 kb mate-paired library, and 50× PacBio data using the MaSuRCA assembler resulting in a 985 Mb assembly with a scaffold N50 of 153 kb.

Are bivalves susceptible to domestication selection? Using starvation tolerance to test for potential trait changes in eastern oyster larvae.

Conservation efforts are increasingly being challenged by a rapidly changing environment, and for some aquatic species the use of captive rearing or selective breeding is an attractive option. However, captivity itself can impose unintended artificial selection known as domestication selection (adaptation to culture conditions) and is relatively understudied for most marine species. To test for domestication selection in marine bivalves, we focused on a fitness-related trait (larval starvation resistance) that could be altered under artificial selection.

Tracking genetic diversity in a large-scale oyster restoration program: effects of hatchery propagation and initial characterization of diversity on restored vs. wild reefs.

The release of hatchery-propagated fish and shellfish is occurring on a global scale, but the genetic impacts of these practices are often not fully understood and rarely monitored. Slow recovery of depleted eastern oyster populations in the Chesapeake Bay, USA has prompted a hatchery-based restoration program focused in the Choptank River, Maryland consisting of the mass release of hatchery-produced juveniles from local, wild broodstock. To evaluate potential genetic effects of this program, we (1) examined changes in genetic diversity (allelic richness, heterozygosity) and the effective number of breeders (N) over the hatchery production cycle with microsatellite-based parentage of natural, mass- and controlled-spawned cohorts, and (2) compared genetic diversity and effective population size (N) of a restored reef to wild source populations.

Environmental DNA analysis of river herring in Chesapeake Bay: A powerful tool for monitoring threatened keystone species.

Environmental DNA (eDNA) sampling has emerged as a powerful tool to detect and quantify species abundance in aquatic environments. However, relatively few studies have compared the performance of eDNA-based abundance estimates to traditional catch or survey approaches in the field. Here, we have developed and field-tested a qPCR assay to detect eDNA from alewife and blueback herring (collectively known as 'river herring'), comparing eDNA-based presence and abundance data to traditional methods of quantification (ichthyoplankton sampling and adult observations).

Genetic load in marine animals: a review.

Marine invertebrates and fish are well known for their remarkable genetic diversity, which is commonly explained by large population size and the characteristic dispersive nature of their early, planktonic life history. Other potential sources of diversity in marine animals, such as a higher mutation rate, have been much less considered, though evidence for a high genetic load in marine bivalves has been accumulating for nearly half a century. In this review, I examine evidence for a higher genetic load in marine animals from studies of molecular marker segregation and linkage over the last 40 years, and survey recent work examining mutational load with molecular evolution approaches.

Density drives polyandry and relatedness influences paternal success in the Pacific gooseneck barnacle, Pollicipes elegans.

Background: Polyandry is a common mating strategy in animals, increasing female fitness through direct (material) and indirect (genetic) benefits. Most theories about the benefits of polyandry come from studies of terrestrial animals, which have relatively complex mating systems and behaviors; less is known about the potential benefits of polyandry in sessile marine animals, for which potential mates may be scarce and females have less control over pre-copulatory mate choice. Here, we used microsatellite markers to examine multiple paternity in natural aggregations of the Pacific gooseneck barnacle Pollicipes elegans, testing the effect of density on paternity and mate relatedness on male reproductive success.

Characterization of microsatellite loci and repeat density in the gooseneck barnacle, Pollicipes elegans, using next generation sequencing.

Pollicipes elegans is a commercially important and biogeographically significant rocky-shore gooseneck barnacle found along the eastern Pacific coasts of Peru, El Salvador, and Mexico. Little is known about its reproductive biology, and no genetic resources exist despite its growing importance as a fisheries species in the region. Next generation sequencing methods can provide rapid and cost-effective development of molecular markers such as microsatellites, which can be applied to studies of paternity, parentage, and population structure in this understudied species.

Environmental stress increases selection against and dominance of deleterious mutations in inbred families of the Pacific oyster Crassostrea gigas.

The deleterious effects of inbreeding are well documented and of major concern in conservation biology. Stressful environments have generally been shown to increase inbreeding depression; however, little is known about the underlying genetic mechanisms of the inbreeding-by-stress interaction and to what extent the fitness of individual deleterious mutations is altered under stress. Using microsatellite marker segregation data and quantitative trait locus (QTL) mapping methods, I performed a genome scan for deleterious mutations affecting viability (viability or vQTL) in two inbred families of the Pacific oyster Crassostrea gigas, reared in a stressful, nutrient-poor diet and a favourable, nutrient-rich diet, which had significant effects on growth and survival.

Quantitative trait locus analysis of stage-specific inbreeding depression in the Pacific oyster Crassostrea gigas.

Inbreeding depression and genetic load have been widely observed, but their genetic basis and effects on fitness during the life cycle remain poorly understood, especially for marine animals with high fecundity and high, early mortality (type-III survivorship). A high load of recessive mutations was previously inferred for the Pacific oyster Crassostrea gigas, from massive distortions of zygotic, marker segregation ratios in F(2) families. However, the number, genomic location, and stage-specific onset of mutations affecting viability have not been thoroughly investigated.