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7. Development and Evaluation of High-Density SNP Arrays for the Eastern Oyster Crassostrea virginica

Author

Guo, Ximing, Puritz, Jonathan B., Wang, Zhenwei, Proestou, Dina, Allen, Jr., Standish, Small, Jessica, Verbyla, Klara, Zhao, Honggang, Haggard, Jaime, Chriss, Noah, Zeng, Dan, Lundgren, Kathryn, Allam, Bassem, Bushek, David, Gomez-Chiarri, Marta, Hare, Matthew, Hollenbeck, Christopher, La Peyre, Jerome, Liu, Ming, Lotterhos, Katie E., Plough, Louis, Rawson, Paul, Rikard, Scott, Saillant, Eric, Varney, Robin, Wikfors, Gary, and Wilbur, Ami

Published
2023
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10. Type 2 diabetes after a pregnancy with gestational diabetes among first nations women in Australia: The PANDORA study

Author

Wood, Anna J., Boyle, Jacqueline A., Barr, Elizabeth L.M., Barzi, Federica, Hare, Matthew J.L., Titmuss, Angela, Longmore, Danielle K., Death, Elizabeth, Kelaart, Joanna, Kirkwood, Marie, Graham, Sian, Connors, Christine, Moore, Elizabeth, O'Dea, Kerin, Oats, Jeremy J.N., McIntyre, Harold D., Zimmet, Paul Z., Lu, Zhong X., Brown, Alex, Shaw, Jonathan E., and Maple-Brown, Louise J.

Published
2021
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13. Consequences of domestication in eastern oyster: Insights from whole genomic analyses.

Author

Zhao, Honggang, Guo, Ximing, Wang, Wenlu, Wang, Zhenwei, Rawson, Paul, Wilbur, Ami, and Hare, Matthew

Subjects
AMERICAN oyster, GENOMICS, FISH breeding, HOMOZYGOSITY, LINKAGE disequilibrium, GENETIC variation, RANDOM forest algorithms, POPULATION genetics
Abstract

Selective breeding for production traits has yielded relatively rapid successes with high‐fecundity aquaculture species. Discovering the genetic changes associated with selection is an important goal for understanding adaptation and can also facilitate better predictions about the likely fitness of selected strains if they escape aquaculture farms. Here, we hypothesize domestication as a genetic change induced by inadvertent selection in culture. Our premise is that standardized culture protocols generate parallel domestication effects across independent strains. Using eastern oyster as a model and a newly developed 600K SNP array, this study tested for parallel domestication effects in multiple independent selection lines compared with their progenitor wild populations. A single contrast was made between pooled selected strains (1–17 generations in culture) and all wild progenitor samples combined. Population structure analysis indicated rank order levels of differentiation as [wild − wild] < [wild − cultured] < [cultured − cultured]. A genome scan for parallel adaptation to the captive environment applied two methodologically distinct outlier tests to the wild versus selected strain contrast and identified a total of 1174 candidate SNPs. Contrasting wild versus selected strains revealed the early evolutionary consequences of domestication in terms of genomic differentiation, standing genetic diversity, effective population size, relatedness, runs of homozygosity profiles, and genome‐wide linkage disequilibrium patterns. Random Forest was used to identify 37 outlier SNPs that had the greatest discriminatory power between bulked wild and selected oysters. The outlier SNPs were in genes enriched for cytoskeletal functions, hinting at possible traits under inadvertent selection during larval culture or pediveliger setting at high density. This study documents rapid genomic changes stemming from hatchery‐based cultivation of eastern oysters, identifies candidate loci responding to domestication in parallel among independent aquaculture strains, and provides potentially useful genomic resources for monitoring interbreeding between farm and wild oysters. [ABSTRACT FROM AUTHOR]

Published
2024
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19. Population History and Genetic Structure in the Western Atlantic Surfclam Subspecies (Spisula solidissima spp.).

Author

Fletcher, Nicholas K. and Hare, Matthew P.

Abstract

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. similis 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. [ABSTRACT FROM AUTHOR]

Published
2024
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24. A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference.

Author

Puritz, Jonathan B., Guo, Ximing, Hare, Matthew, He, Yan, Hillier, LaDeana W., Jin, Shubo, Liu, Ming, Lotterhos, Katie E., Minx, Pat, Modak, Tejashree, Proestou, Dina, Rice, Edward S., Tomlinson, Chad, Warren, Wesley C., Witkop, Erin, Zhao, Honggang, and Gomez‐Chiarri, Marta

Subjects
AMERICAN oyster, GENOME size, GENOMES, HETEROZYGOSITY, OUTLIER detection, AUDITORY masking, AQUACULTURE industry, FISH breeding
Abstract

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]

Published
2024
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35. The prevalence of diabetes distress and its association with glycaemia in young people living with insulin‐requiring‐diabetes in a regional centre in Australia.

Author

Stapleton, Ciara, Watkins, Elizabeth, Hare, Matthew J L, Timms, Francesca, Wood, Anna J, and Titmuss, Angela

Subjects
YOUNG adults, PSYCHOLOGICAL distress, DIABETES, INSULIN therapy, HOSPITAL records
Abstract

Aim: Emotional responses, such as feeling overwhelmed with diabetes‐related treatment, burnt‐out and anxiety, are known as 'diabetes distress'. This study aimed to determine diabetes distress among children, adolescents and parents/carers managing insulin‐requiring diabetes in a regional Australian setting, and to assess association with glycaemia. Methods: All children, adolescents and their parents/carers attending a regional hospital outpatient diabetes clinic between March 2018 and June 2019 were invited to complete a validated child, adolescent or parent/carer diabetes distress questionnaire. Demographics and time‐matched clinical data were obtained from hospital records. A cross‐sectional analysis was performed. Results: A total of 43 young people and 30 parents/carers completed a diabetes distress questionnaire during the study period. Diabetes distress was common, with 63% of young people and 67% of parents/carers nominating at least one serious concern. After adjustment for potential confounding factors, higher glycaemia (HbA1c%) was associated with higher distress scores among both young people (ß 6.2, 95% confidence interval (CI): 3.2–9.2, P < 0.001) and carers/parents (ß 5.6, 95% CI:1.5–9.8, P < 0.001). Diabetes distress did not differ by child age, duration of diagnosis or mode of insulin administration. For children, adolescents and carers, 'serious concerns' most commonly related to the impact of diabetes upon family and peer relationships. Conclusions: Diabetes distress was common and associated with sub‐optimal glycaemia. Routine screening for diabetes distress should be considered in paediatric services. Development of strategies to minimise diabetes distress for youth and families is required. [ABSTRACT FROM AUTHOR]

Published
2022
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37. Consequences of Salinity Change, Salinity History, and Shell Morphology on Early Growth of Juvenile Oysters.

Author

Manuel, Emily C., Hare, Matthew P., and Munroe, Daphne

Abstract

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. [ABSTRACT FROM AUTHOR]

Published
2023
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