Matthew P. Hare
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View article: Range-wide climate risk and adaptive potential in a cold-water fish species
Range-wide climate risk and adaptive potential in a cold-water fish species Open
Predicting extinction risk from climate change requires understanding adaptive variation and local adaptation across species' ranges. We combine experimental and -omics approaches with climate change modeling to identify molecular mechanis…
View article: Microgeographic variation in gene expression plasticity under osmotic stress in wild eastern oyster juveniles (Crassostrea virginica)
Microgeographic variation in gene expression plasticity under osmotic stress in wild eastern oyster juveniles (Crassostrea virginica) Open
Gene expression plasticity is an essential mechanism of physiological acclimation. In adult eastern oysters, Crassostrea virginica (Gmelin, 1791), transcriptomic responses to experimental osmotic stress differ between oyster bed sources wi…
View article: Hindcasting Estuarine Bottom Salinity Using Observing Systems Data and Nonlinear Regression, as Applied to Oysters in Delaware Bay
Hindcasting Estuarine Bottom Salinity Using Observing Systems Data and Nonlinear Regression, as Applied to Oysters in Delaware Bay Open
Salinity is a major environmental factor that influences the population dynamics of fish and shellfish along coasts and estuaries, yet empirical methods for hindcasting salinity at specific sampling stations are not widely available. The s…
View article: Consequences of domestication in eastern oyster: Insights from whole genomic analyses
Consequences of domestication in eastern oyster: Insights from whole genomic analyses Open
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 al…
View article: A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference
A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference Open
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 tha…
View article: Immune priming prior to pathogen exposure sheds light on the relationship between host, microbiome and pathogen in disease
Immune priming prior to pathogen exposure sheds light on the relationship between host, microbiome and pathogen in disease Open
Dynamic interactions between host, pathogen and host-associated microbiome dictate infection outcomes. Pathogens including Batrachochytrium dendrobatidis (Bd) threaten global biodiversity, but conservation efforts are hindered by limited u…
View article: Reproductive phenology of the eastern oyster,<i>Crassostrea virginica</i>(Gmelin, 1791), along a temperate estuarine salinity gradient
Reproductive phenology of the eastern oyster,<i>Crassostrea virginica</i>(Gmelin, 1791), along a temperate estuarine salinity gradient Open
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 predict…
View article: A second unveiling: haplotig masking of the eastern oyster genome improves population-level inference
A second unveiling: haplotig masking of the eastern oyster genome improves population-level inference Open
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 tha…
View article: Aquatic <scp>eDNA</scp> can advance monitoring of a small‐bodied terrestrial salamander and amphibian pathogen
Aquatic <span>eDNA</span> can advance monitoring of a small‐bodied terrestrial salamander and amphibian pathogen Open
Successful conservation efforts for threatened species depend on accurate characterization of their distribution, habitat use, and threats. However, surveillance can be challenging for species with small size, cryptic coloring, or elusive …
View article: Does a complex life cycle affect adaptation to environmental change? Genome-informed insights for characterizing selection across complex life cycle
Does a complex life cycle affect adaptation to environmental change? Genome-informed insights for characterizing selection across complex life cycle Open
Complex life cycles, in which discrete life stages of the same organism differ in form or function and often occupy different ecological niches, are common in nature. Because stages share the same genome, selective effects on one stage may…
View article: Environmental DNA‐derived pathogen gene sequences can expand surveillance when pathogen titers are decoupled in eDNA and hosts
Environmental DNA‐derived pathogen gene sequences can expand surveillance when pathogen titers are decoupled in eDNA and hosts Open
Environmental DNA (eDNA) collection has emerged as a powerful and noninvasive wildlife population and pathogen‐monitoring tool. Ranavirus is an emerging pathogen linked to die‐offs in amphibian species. Applications of eDNA detection for r…
View article: Population Genetics of Sugar Kelp Throughout the Northeastern United States Using Genome-Wide Markers
Population Genetics of Sugar Kelp Throughout the Northeastern United States Using Genome-Wide Markers Open
© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mao, X., Augyte, S., Huang, M., Hare, M. P., Bailey, D., Umanzor, S., Marty-Rivera, M.,…
View article: Are bivalves susceptible to domestication selection? Using starvation tolerance to test for potential trait changes in eastern oyster larvae
Are bivalves susceptible to domestication selection? Using starvation tolerance to test for potential trait changes in eastern oyster larvae Open
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 unintende…
View article: Population genetics of sugar kelp in the Northwest Atlantic region using genome-wide markers
Population genetics of sugar kelp in the Northwest Atlantic region using genome-wide markers Open
An assessment of genetic diversity of marine populations is critical not only for the understanding and preservation of natural biodiversity but also for its economic potential. As commercial demand rises for marine resources, it is critic…
View article: Are bivalves susceptible to domestication selection? Using starvation tolerance to test for potential trait changes in eastern oyster larvae
Are bivalves susceptible to domestication selection? Using starvation tolerance to test for potential trait changes in eastern oyster larvae Open
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 unintende…
View article: Correction: Restoring oysters to urban estuaries: Redefining habitat quality for eastern oyster performance near New York City
Correction: Restoring oysters to urban estuaries: Redefining habitat quality for eastern oyster performance near New York City Open
[This corrects the article DOI: 10.1371/journal.pone.0207368.].
Restoring oysters to urban estuaries: Redefining habitat quality for eastern oyster performance near New York City Open
[This corrects the article DOI: 10.1371/journal.pone.0207368.].
View article: Large-scale variation in density of an aquatic ecosystem indicator species
Large-scale variation in density of an aquatic ecosystem indicator species Open
Monitoring indicator species is a pragmatic approach to natural resource assessments, especially when the link between the indicator species and ecosystem state is well justified. However, conducting ecosystem assessments over representati…
View article: Examining the occupancy–density relationship for a low‐density carnivore
Examining the occupancy–density relationship for a low‐density carnivore Open
Summary The challenges associated with monitoring low‐density carnivores across large landscapes have limited the ability to implement and evaluate conservation and management strategies for such species. Non‐invasive sampling techniques a…
View article: Accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering
Accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering Open
Error-tolerant likelihood-based match calling presents a promising technique to accurately identify recapture events in genetic mark–recapture studies by combining probabilities of latent genotypes and probabilities of observed genotypes, …
View article: Examining the occupancy-density relationship for a low density carnivore
Examining the occupancy-density relationship for a low density carnivore Open
The challenges associated with monitoring low-density carnivores across large landscapes have limited the ability to implement and evaluate conservation and management strategies for such species. Noninvasive sampling techniques and advanc…
View article: Supplementary material from "Accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering"
Supplementary material from "Accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering" Open
Error-tolerant likelihood-based match calling presents a promising technique to accurately identify recapture events in genetic mark–recapture studies by combining probabilities of latent genotypes and probabilities of observed genotypes, …