Trans-Acting Genotypes Associated with mRNA Expression Affect Metabolic and Thermal Tolerance Traits.

Evolutionary processes driving physiological trait variation depend on the underlying genomic mechanisms. Evolution of these mechanisms depends on the genetic complexity (involving many genes) and how gene expression impacting the traits is converted to phenotype. Yet, genomic mechanisms that impact physiological traits are diverse and context dependent (e.

Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, .

Pallas's cat, or the manul cat (), is a small felid native to the grasslands and steppes of central Asia. Population strongholds in Mongolia and China face growing challenges from climate change, habitat fragmentation, poaching, and other sources. These threats, combined with 's zoo collection popularity and value in evolutionary biology, necessitate improvement of species genomic resources.

Feeling the heat: variation in thermal sensitivity within and among populations.

Physiology defines individual responses to global climate change and species distributions across environments. Physiological responses are driven by temperature on three time scales: acute, acclimatory and evolutionary. Acutely, passive temperature effects often dictate an expected 2-fold increase in metabolic processes for every 10°C change in temperature (Q10).

Sequencing Bait: Nuclear and Mitogenome Assembly of an Abundant Coastal Tropical and Subtropical Fish, Atherinomorus stipes.

Genetic data from nonmodel species can inform ecology and physiology, giving insight into a species' distribution and abundance as well as their responses to changing environments, all of which are important for species conservation and management. Moreover, reduced sequencing costs and improved long-read sequencing technology allows researchers to readily generate genomic resources for nonmodel species. Here, we apply Oxford Nanopore long-read sequencing and low-coverage (∼1x) whole genome short-read sequencing technology (Illumina) to assemble a genome and examine population genetics of an abundant tropical and subtropical fish, the hardhead silverside (Atherinomorus stipes).

Transcriptomic analysis provides insights into molecular mechanisms of thermal physiology.

Physiological trait variation underlies health, responses to global climate change, and ecological performance. Yet, most physiological traits are complex, and we have little understanding of the genes and genomic architectures that define their variation. To provide insight into the genetic architecture of physiological processes, we related physiological traits to heart and brain mRNA expression using a weighted gene co-expression network analysis.

Interindividual plasticity in metabolic and thermal tolerance traits from populations subjected to recent anthropogenic heating.

To better understand temperature's role in the interaction between local evolutionary adaptation and physiological plasticity, we investigated acclimation effects on metabolic performance and thermal tolerance among natural (small estuarine fish) populations from different thermal environments. populations experience large daily and seasonal temperature variations, as well as local mean temperature differences across their large geographical cline. In this study, we use three populations: one locally heated (32°C) by thermal effluence (TE) from the Oyster Creek Nuclear Generating Station, NJ, and two nearby reference populations that do not experience local heating (28°C).

Paradoxical whole genome DNA methylation dynamics of 5'aza-deoxycytidine in chronic low-dose exposure in mice.

Decitabine (5-aza-2'deoxycytidine; DAC) is a DNA methyltransferase inhibitor used to hypomethylate the epigenome. Current dosing regimens of DAC for use in mice vary widely and their hypomethylating ability has not been robustly characterized, despite reliable results of hypomethylation of the epigenome with cell lines and tissue specificity . We investigated the effects on the DNA methylome and gene expression within mice exposed to chronic low doses of DAC ranging from 0 to 0.

Evolutionary conservation of DNA methylation in CpG sites within ultraconserved noncoding elements.

Ultraconserved noncoding elements (UCNEs) constitute less than 1 Mb of vertebrate genomes and are impervious to accumulating mutations. About 4000 UCNEs exist in vertebrate genomes, each at least 200 nucleotides in length, sharing greater than 95% sequence identity between human and chicken. Despite extreme sequence conservation over 400 million years of vertebrate evolution, we show both ordered interspecies and within-species interindividual variation in DNA methylation in these regions.