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

   https://doi.org/10.1093/gbe/evad123  

   Drown, Melissa K; Oleksiak, Marjorie F; Crawford, Douglas L (July 2023, Genome Biology and Evolution)

   Betancourt, Andrea (Ed.)

   Abstract 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.g., vary by environment and tissues), making them difficult to discern. We examine the relationships between genotype, mRNA expression, and physiological traits to discern the genetic complexity and whether the gene expression affecting the physiological traits is primarily cis- or trans-acting. We use low-coverage whole genome sequencing and heart- or brain-specific mRNA expression to identify polymorphisms directly associated with physiological traits and expressed quantitative trait loci (eQTL) indirectly associated with variation in six temperature specific physiological traits (standard metabolic rate, thermal tolerance, and four substrate specific cardiac metabolic rates). Focusing on a select set of mRNAs belonging to co-expression modules that explain up to 82% of temperature specific traits, we identified hundreds of significant eQTL for mRNA whose expression affects physiological traits. Surprisingly, most eQTL (97.4% for heart and 96.7% for brain) were trans-acting. This could be due to higher effect size of trans- versus cis-acting eQTL for mRNAs that are central to co-expression modules. That is, we may have enhanced the identification of trans-acting factors by looking for single nucleotide polymorphisms associated with mRNAs in co-expression modules that broadly influence gene expression patterns. Overall, these data indicate that the genomic mechanism driving physiological variation across environments is driven by trans-acting heart- or brain-specific mRNA expression. 

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2. Genetic differences in thermal tolerance among colonies of threatened coral Acropora cervicornis: potential for adaptation to increasing temperature

   https://doi.org/10.3354/meps13407  

   Yetsko, K; Ross, M; Bellantuono, A; Merselis, D; Rodriquez-Lanetty, M; Gilg, MR (July 2020, Marine Ecology Progress Series)

   null (Ed.)

   Climate change is resulting in warmer temperatures that are negatively impacting corals. Understanding how much individuals within a population vary in their thermal tolerance and whether this variation is heritable is important in determining whether a species can adapt to climate change. To address this, Acropora cervicornis fragments from 20 genetically distinct colonies collected from the Coral Restoration Foundation Tavernier nursery (Florida, USA) were kept at either ambient (28 ± 1°C) or elevated (32 ± 1°C) temperatures, and mortality was monitored for 26 d. Both broad-sense ( H 2 ) and narrow-sense ( h 2 ) heritability of thermal tolerance were estimated to determine the amount of genetic variation underlying survival to elevated temperature. To understand the physiological basis of thermal tolerance, tissue from both treatments was taken 12 h after the start of the experiment to investigate gene expression at the mRNA and protein level between tolerant and susceptible colonies. Results revealed that this population has considerable total genetic variation in thermal tolerance ( H 2 = 0.528), but low variance in relatedness among colonies prevented us from making any conclusions regarding h 2 . Despite high transcriptomic variability among and within colonies, 40 genes were consistently and significantly different between tolerant and susceptible colonies, and could be potential biomarkers for thermal tolerance should they be verified in a larger sample. Overall, the results suggest that this population has substantial genetic variation for traits that directly impact thermal tolerance; however, their response to projected increases in temperature will depend on more precise estimates of the additive components of this variation ( h 2 ). 

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

   https://doi.org/10.1242/jeb.244831  

   DeLiberto, Amanda N.; Drown, Melissa K.; Ehrlich, Moritz A.; Oleksiak, Marjorie F.; Crawford, Douglas L. (November 2022, Journal of Experimental Biology)

   ABSTRACT 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). Yet, these acute responses often are mitigated through acclimation within an individual or evolutionary adaptation within populations over time. Natural selection can influence both responses and often reduces interindividual variation towards an optimum. However, this interindividual physiological variation is not well characterized. Here, we quantified responses to a 16°C temperature difference in six physiological traits across nine thermally distinct Fundulus heteroclitus populations. These traits included whole-animal metabolism (WAM), critical thermal maximum (CTmax) and substrate-specific cardiac metabolism measured in approximately 350 individuals. These traits exhibited high variation among both individuals and populations. Thermal sensitivity (Q10) was determined, specifically as the acclimated Q10, in which individuals were both acclimated and assayed at each temperature. The interindividual variation in Q10 was unexpectedly large: ranging from 0.6 to 5.4 for WAM. Thus, with a 16°C difference, metabolic rates were unchanged in some individuals, while in others they were 15-fold higher. Furthermore, a significant portion of variation was related to habitat temperature. Warmer populations had a significantly lower Q10 for WAM and CTmax after acclimation. These data suggest that individual variation in thermal sensitivity reflects different physiological strategies to respond to temperature variation, providing many different adaptive responses to changing environments. 

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4. Evolutionary Physiology and Genomics in the Highly Adaptable Killifish (Fundulus heteroc

   https://doi.org/10.1002/cphy.c190004  

   Crawford, D. L. Schulte (April 2020, Comprehensive physiology)

   By investigating evolutionary adaptations that change physiological functions, we can enhance our understanding of how organisms work, the importance of physiological traits, and the genes that influence these traits. This approach of investigating the evolution of physiological adaptation has been used with the teleost fish Fundulus heteroclitus and has produced insights into (i) how protein polymorphisms enhance swimming and development; (ii) the role of equilibrium enzymes in modulating metabolic flux; (iii) how variation in DNA sequences and mRNA expression patterns mitigate changes in temperature, pollution, and salinity; and (iv) the importance of nuclear-mitochondrial genome interactions for energy metabolism. Fundulus heteroclitus provides so many examples of adaptive evolution because their local population sizes are large, they have significant standing genetic variation, and they experience large ranges of environmental conditions that enhance the likelihood that adaptive evolution will occur. Thus, F. heteroclitus research takes advantage of evolutionary changes associated with exposure to diverse environments, both across the North American Atlantic coast and within local habitats, to contrast neutral versus adaptive divergence. Based on evolutionary analyses contrasting neutral and adaptive evolution in F. heteroclitus populations, we conclude that adaptive evolution can occur readily and rapidly, at least in part because it depends on large amounts of standing genetic variation among many genes that can alter physiological traits. These observations of polygenic adaptation enhance our understanding of how evolution and physiological adaptation progresses, thus informing both biological and medical scientists about genotype-phenotype relationships 

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5. Genome‐wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia

   https://doi.org/10.1111/tpj.15592  

   De La Torre, Amanda R.; Sekhwal, Manoj K.; Puiu, Daniela; Salzberg, Steven L.; Scott, Alison D.; Allen, Brian; Neale, David B.; Chin, Alana R. O.; Buckley, Thomas N. (December 2021, The Plant Journal)

   SUMMARY Drought is a major limitation for survival and growth in plants. With more frequent and severe drought episodes occurring due to climate change, it is imperative to understand the genomic and physiological basis of drought tolerance to be able to predict how species will respond in the future. In this study, univariate and multitrait multivariate genome‐wide association study methods were used to identify candidate genes in two iconic and ecosystem‐dominating species of the western USA, coast redwood and giant sequoia, using 10 drought‐related physiological and anatomical traits and genome‐wide sequence‐capture single nucleotide polymorphisms. Population‐level phenotypic variation was found in carbon isotope discrimination, osmotic pressure at full turgor, xylem hydraulic diameter, and total area of transporting fibers in both species. Our study identified new 78 new marker × trait associations in coast redwood and six in giant sequoia, with genes involved in a range of metabolic, stress, and signaling pathways, among other functions. This study contributes to a better understanding of the genomic basis of drought tolerance in long‐generation conifers and helps guide current and future conservation efforts in the species. 

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