DNA methylation correlates with transcriptional noise in response to elevated pCO in the eastern oyster ().

Ocean acidification significantly affects marine calcifiers like oysters, warranting the study of molecular mechanisms like DNA methylation that contribute to adaptive plasticity in response to environmental change. However, a consensus has not been reached on the extent to which methylation modules gene expression, and in turn plasticity, in marine invertebrates. In this study, we investigated the impact of pCO on gene expression and DNA methylation in the eastern oyster, .

The accuracy of predicting maladaptation to new environments with genomic data.

Rapid environmental change poses unprecedented challenges to species persistence. To understand the extent that continued change could have, genomic offset methods have been used to forecast maladaptation of natural populations to future environmental change. However, while their use has become increasingly common, little is known regarding their predictive performance across a wide array of realistic and challenging scenarios.

Dipping Your Toe in The CURE Pool: Longitudinal Tracking of Instructors Suggests Use of a Short-Duration CURE Can Catalyze Expansion to Longer CURE Experiences.

Course-based undergraduate research experiences (CUREs) are an effective method of engaging large numbers of students in authentic research but are associated with barriers to adoption. Short CURE modules may serve as a low-barrier entryway, but their effectiveness in promoting expansion has not been studied. The Prevalence of Antibiotic Resistance in the Environment (PARE) project is a modular CURE designed to be a low-barrier gateway into CURE use.

Interpretation issues with "genomic vulnerability" arise from conceptual issues in local adaptation and maladaptation.

As climate change causes the environment to shift away from the local optimum that populations have adapted to, fitness declines are predicted to occur. Recently, methods known as (GOs) have become a popular tool to predict population responses to climate change from landscape genomic data. Populations with a high GO have been interpreted to have a high "genomic vulnerability" to climate change.

Lighting pathways to success in STEM: a virtual Laboratory Meeting Programme (LaMP) mutually benefits mentees and host laboratories.

Developing robust professional networks can help shape the trajectories of early career scientists. Yet, historical inequities in science, technology, engineering, and mathematics (STEM) fields make access to these networks highly variable across academic programmes, and senior academics often have little time for mentoring. Here, we illustrate the success of a virtual Laboratory Meeting Programme (LaMP).

Physiologically informed organismal climatologies reveal unexpected spatiotemporal trends in temperature.

Body temperature is universally recognized as a dominant driver of biological performance. Although the critical distinction between the temperature of an organism and its surrounding habitat has long been recognized, it remains common practice to assume that trends in air temperature-collected via remote sensing or weather stations-are diagnostic of trends in animal temperature and thus of spatiotemporal patterns of physiological stress and mortality risk. Here, by analysing long-term trends recorded by biomimetic temperature sensors designed to emulate intertidal mussel temperature across the US Pacific Coast, we show that trends in maximal organismal temperature ('organismal climatologies') during aerial exposure can differ substantially from those exhibited by co-located environmental data products.

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.

The paradox of adaptive trait clines with nonclinal patterns in the underlying genes.

Multivariate climate change presents an urgent need to understand how species adapt to complex environments. Population genetic theory predicts that loci under selection will form monotonic allele frequency clines with their selective environment, which has led to the wide use of genotype-environment associations (GEAs). This study used a set of simulations to elucidate the conditions under which allele frequency clines are more or less likely to evolve as multiple quantitative traits adapt to multivariate environments.

Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species.

Methylation of cytosines is a prototypic epigenetic modification of the DNA. It has been implicated in various regulatory mechanisms across the animal kingdom and particularly in vertebrates. We mapped DNA methylation in 580 animal species (535 vertebrates, 45 invertebrates), resulting in 2443 genome-scale DNA methylation profiles of multiple organs.

A parasite outbreak in notothenioid fish in an Antarctic fjord.

Climate changes can promote disease outbreaks, but their nature and potential impacts in remote areas have received little attention. In a hot spot of biodiversity on the West Antarctic Peninsula, which faces among the fastest changing climates on Earth, we captured specimens of two notothenioid fish species affected by large skin tumors at an incidence never before observed in the Southern Ocean. Molecular and histopathological analyses revealed that X-cell parasitic alveolates, members of a genus we call , are the etiological agent of these tumors.

Seeing the forest for the trees: Assessing genetic offset predictions from gradient forest.

Gradient Forest (GF) is a machine learning algorithm designed to analyze spatial patterns of biodiversity as a function of environmental gradients. An offset measure between the GF-predicted environmental association of adapted alleles and a new environment (GF Offset) is increasingly being used to predict the loss of environmentally adapted alleles under rapid environmental change, but remains mostly untested for this purpose. Here, we explore the robustness of GF Offset to assumption violations, and its relationship to measures of fitness, using SLiM simulations with explicit genome architecture and a spatial metapopulation.

Disturbance decreases genotypic diversity by reducing colonization: Implications for disturbance-diversity feedbacks.

One objective of eco-evolutionary dynamics is to understand how the interplay between ecology and evolution on contemporary timescales contributes to the maintenance of biodiversity. Disturbance is an ecological process that can alter species diversity through both ecological and evolutionary effects on colonization and extinction dynamics. While analogous mechanisms likely operate among genotypes within a population, empirical evidence demonstrating the relationship between disturbance and genotypic diversity remains limited.

The impacts of mangrove range expansion on wetland ecosystem services in the southeastern United States: Current understanding, knowledge gaps, and emerging research needs.

Climate change is transforming ecosystems and affecting ecosystem goods and services. Along the Gulf of Mexico and Atlantic coasts of the southeastern United States, the frequency and intensity of extreme freeze events greatly influence whether coastal wetlands are dominated by freeze-sensitive woody plants (mangrove forests) or freeze-tolerant grass-like plants (salt marshes). In response to warming winters, mangroves have been expanding and displacing salt marshes at varying degrees of severity in parts of north Florida, Louisiana, and Texas.

Adaptations and Diversity of Antarctic Fishes: A Genomic Perspective.

Antarctic notothenioid fishes are the classic example of vertebrate adaptive radiation in a marine environment. Notothenioids diversified from a single common ancestor ∼22 Mya to between 120 and 140 species today, and they represent ∼90% of fish biomass on the continental shelf of Antarctica. As they diversified in the cold Southern Ocean, notothenioids evolved numerous traits, including osteopenia, anemia, cardiomegaly, dyslipidemia, and aglomerular kidneys, that are beneficial or tolerated in their environment but are pathological in humans.

Meta-analysis of salt marsh vegetation impacts and recovery: a synthesis following the Deepwater Horizon oil spill.

Marine oil spills continue to be a global issue, heightened by spill events such as the 2010 Deepwater Horizon spill in the Gulf of Mexico, the largest marine oil spill in US waters and among the largest worldwide, affecting over 1,000 km of sensitive wetland shorelines, primarily salt marshes supporting numerous ecosystem functions. To synthesize the effects of the oil spill on foundational vegetation species in the salt marsh ecosystem, Spartina alterniflora and Juncus roemerianus, we performed a meta-analysis using data from 10 studies and 255 sampling sites over seven years post-spill. We examined the hypotheses that the oil spill reduced plant cover, stem density, vegetation height, aboveground biomass, and belowground biomass, and tracked the degree of effects temporally to estimate recovery time frames.

The aquaculture supply chain in the time of covid-19 pandemic: Vulnerability, resilience, solutions and priorities at the global scale.

The COVID-19 global pandemic has had severe, unpredictable and synchronous impacts on all levels of perishable food supply chains (PFSC), across multiple sectors and spatial scales. Aquaculture plays a vital and rapidly expanding role in food security, in some cases overtaking wild caught fisheries in the production of high-quality animal protein in this PFSC. We performed a rapid global assessment to evaluate the effects of the COVID-19 pandemic and related emerging control measures on the aquaculture supply chain.

Modulation of bioelectric cues in the evolution of flying fishes.

Changes to allometry, or the relative proportions of organs and tissues within organisms, is a common means for adaptive character change in evolution. However, little is understood about how relative size is specified during development and shaped during evolution. Here, through a phylogenomic analysis of genome-wide variation in 35 species of flying fishes and relatives, we identify genetic signatures in both coding and regulatory regions underlying the convergent evolution of increased paired fin size and aerial gliding behaviors.

Novel and disappearing climates in the global surface ocean from 1800 to 2100.

Marine ecosystems are experiencing unprecedented warming and acidification caused by anthropogenic carbon dioxide. For the global sea surface, we quantified the degree that present climates are disappearing and novel climates (without recent analogs) are emerging, spanning from 1800 through different emission scenarios to 2100. We quantified the sea surface environment based on model estimates of carbonate chemistry and temperature.

Fluctuating selection and global change: a synthesis and review on disentangling the roles of climate amplitude, predictability and novelty.

A formidable challenge for global change biologists is to predict how natural populations will respond to the emergence of conditions not observed at present, termed novel climates. Popular approaches to predict population vulnerability are based on the expected degree of novelty relative to the amplitude of historical climate fluctuations experienced by a population. Here, we argue that predictions focused on amplitude may be inaccurate because they ignore the predictability of environmental fluctuations in driving patterns of evolution and responses to climate change.

Bone microstructure and bone mineral density are not systemically different in Antarctic icefishes and related Antarctic notothenioids.

Ancestors of the Antarctic icefishes (family Channichthyidae) were benthic and had no swim bladder, making it energetically expensive to rise from the ocean floor. To exploit the water column, benthopelagic icefishes were hypothesized to have evolved a skeleton with "reduced bone," which gross anatomical data supported. Here, we tested the hypothesis that changes to icefish bones also occurred below the level of gross anatomy.

Refining Convergent Rate Analysis with Topology in Mammalian Longevity and Marine Transitions.

The quest to map the genetic foundations of phenotypes has been empowered by the modern diversity, quality, and availability of genomic resources. Despite these expanding resources, the abundance of variation within lineages makes it challenging to associate genetic change to specific phenotypes, without an a priori means of isolating the changes from background genomic variation. Evolution provides this means through convergence-that is, the shared variation that may result from replicate evolutionary experiments across independent trait occurrences.