Biology subjects

Hare, M. P.

Publications and source records attributed to Hare, M. P..

5 recordsLinked to original sources

bioRxiv2026

Genomic Population Structure of Atlantic surfclams: Cryptic Taxonomic Units and Population Connectivity

The Atlantic surfclam, Spisula solidissima solidissima supports multimillion dollar harvests in the western North Atlantic, including Georges Bank and Mid-Atlantic Bight populations along the continental shelf. Surfclam populations in this part of the Exclusive Economic Zone (3-200 nm from shore) are managed as a single unit, but demographic connectivity has never been tested directly. This study analyzed >8,500 SNPs in 548 Atlantic surfclams sampled across the USA harvested range to infer population structure, genomic diversity, and gene flow patterns. Genomic analyses included eight sampled and 10 reference Spisula solidissima similis samples, a morphologically cryptic nominal subspecies previously known only from nearshore habitats. Novel morphologically cryptic population structure was identified in S.s. solidissima. One operational taxonomic unit (OTU-A) was found only in the inshore region of southern New England, south of Cape Cod. The other population unit, OTU-B, was found offshore and in Cape Cod Bay. The federal fishing grounds only had OTU-B clams. Populations within each OTU were connected by gene flow, justifying current fishery management practices. Nearshore state waters had mixed OTU stocks. Hybridization was analyzed between the two OTUs and between the two subspecies based on nuclear SNPs and asymmetrical mitochondrial DNA introgression. Finally, we demonstrated the utility of a novel SNP panel for diagnosing all three taxa and their hybrids.

evolutionary biology↗

bioRxiv2022

Reproductive phenology of the eastern oyster, Crassostrea virginica (Gmelin, 1791), along a temperate estuarine salinity gradient

Low salinity can negatively affect reproduction in estuarine bivalves. The spatial and temporal extent of these effects are important to inform models of population dynamics, environmental risk assessments, restoration efforts, and predictions of climate change effects. We hypothesized that oysters at low salinity sites would have delayed gametogenesis compared to their higher salinity counterparts in downstream experimental cages. The timing of gametogenesis and spawning was observed June - August for 2-year-old oysters from three distinct ancestries (Native, Hatchery, Aquaculture), outplanted at age 1 month along the salinity gradient (3-30 psu) of a temperate estuary. A second season of data was collected from 3-year-old Aquaculture oysters (comparable to year 1 data) and Native adult oysters transplanted one year prior. Dermo was very low both years. A delay in gametogenesis and spawning was observed for all ancestries at low salinity relative to higher salinity sites during July and August of the first year but not the second year. In contrast, June showed the reverse pattern with northern low salinity sites having more advanced gonad index (2.65) than a high salinity site (1.46). This difference in average gonad index was 2.65 vs 1.46, respectively, for the Native line and 2.62 vs 2.08 for Aquaculture. Low salinity seemed to not only induce earlier gametogenesis in June, but also extended the reproductive season relative to higher salinity sites. Among oyster ancestries, the Aquaculture line stood out as having 30 - 48% lower gametogenic synchrony within sites, but only in 2018. Despite some dependence of reproductive phenology on salinity variation, the Native low salinity population demonstrates notable reproductive plasticity in the completion of a reproductive cycle across a wide range of salinities, an encouraging result for potential future restoration strategies.

ecology↗

bioRxiv2022

Nucleotide and structural polymorphisms of the eastern oyster genome paint a mosaic of divergence, selection, and human impacts

The eastern oyster, Crassostrea virginica, is a valuable fishery and aquaculture species that provides critical services as an ecosystem engineer. Oysters have a life-history that promotes high genetic diversity and gene flow while also occupying a wide range of habitats in variable coastal environments from the southern Gulf of Mexico to the southern waters of Atlantic Canada. To understand the interplay of genetic diversity, gene flow, and intense environmental selection, we used whole genome re-sequencing data from 90 individuals across the eastern United States and Gulf of Mexico, plus 5 selectively bred lines. Our data confirmed a large phylogeographic break between oyster populations in the Gulf of Mexico and the Atlantic coast of the USA. We also demonstrated that domestication has artificially admixed genetic material between the two ocean basins, and selected lines with admixed ancestry continue to maintain heterozygosity at these sites through several generations post admixture, possibly indicating relevance to desirable aquaculture traits. We found that genetic and structural variation are high in both wild and selected populations, but we also demonstrated that, when controlling for domestication admixture across ocean basins, wild populations do have significantly higher levels of nucleotide diversity and copy number variation than selected lines. Within the Atlantic coast, we detected subtle but distinct population structure, introgression of selected lines within wild individuals, an interaction between structural variation and putatively adaptive population structure, and evidence of candidate genes responding to selection from salinity. Our study highlights the potential for applying whole genome sequencing to highly polymorphic species and provides a road map for future work examining the genome variation of eastern oyster populations.

evolutionary biology↗

bioRxiv2022

A second unveiling: haplotig masking of the eastern oyster genome improves population-level inference

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.

genomics↗

bioRxiv2020

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). For most marine species, it is not known to what degree domestication selection affects traits related to fitness in the wild. To test for domestication selection in a marine bivalve, we focused on a fitness-related trait (larval starvation resistance) that could be altered under artificial selection. Using larvae produced from a wild population of Crassostrea virginica and a selectively bred, disease-resistant line we measured growth and survival during starvation versus standard algal diet (control) conditions. Larvae from both lineages showed a remarkable resilience to food limitation, possibly mediated by an ability to uptake and utilize dissolved organic matter for somatic maintenance. Water chemistry analysis showed dissolved organic carbon in filtered tank water to be at concentrations similar to natural river water. We observed that survival in larvae produced from the aquaculture line was significantly lower compared to larvae produced from wild broodstock (8 {+/-} 3% and 21 {+/-} 2%, respectively) near the end of a 10-day period with no food (phytoplankton). All larval cohorts had arrested growth during the starvation period and took at least two days to recover once food was reintroduced before resuming growth. Phenotypic differences between the wild and aquaculture lines suggest potential differences in the capacity to sustain extended food limitation, but this work requires replication with multiple selection lines and wild populations to make more general inferences about domestication selection. With this contribution we explore the potential for domestication selection in bivalves, discuss the physiological and fitness implications of reduced starvation tolerance, and aim to inspire further research on the topic.

evolutionary biology↗