Mechanisms of thermal adaptation and evolutionary potential of conspecific populations to changing environments

Beyond latitude: thermal tolerance and vulnerability of a broadly distributed salmonid across a habitat temperature gradient

Salmonid fishes are a focal point of conservation physiology due to their high value to humans and ecosystems, and their susceptibility to decline from climate change. A significant challenge in conserving these fishes is that populations of the same species can be locally adapted to vastly different habitats within their wild ranges and can therefore have unique tolerance or vulnerability to environmental stressors within those habitats. Within the state of Oregon, USA, summer steelhead (Oncorhynchus mykiss) inhabit both cool, coastal waters most typically associated with Pacific salmonids and arid, inland environments where temperatures are more extreme. Here, we utilized streamside physiological experiments paired with habitat temperature monitoring to assess the thermal tolerance and vulnerability of four populations of summer steelhead from distinct thermal habitats. All populations had unique responses of critical thermal maximum, aerobic scope and exercise recovery to temperature. Despite populations from warm habitats exhibiting higher thermal tolerance than populations from cooler habitats, summer steelhead from warm habitats appear to be more vulnerable to the physiological consequences of warming based on the extreme temperatures they already experience during the summer. These results demonstrate an example of thermal physiology varying between populations within the same portion of their latitudinal range and highlight the need for habitat-specific conservation strategies for this species.

Narrow Margins: Aerobic Performance and Temperature Tolerance of Coral Reef Fishes Facing Extreme Thermal Variability

Climate change is driving rising average sea temperatures and the intensification of thermal variability. Tropical coral reef fishes have evolved under thermally stable conditions to function optimally within a narrow temperature range, with many currently living close to their upper thermal limits. However, recent work has demonstrated that some species possess additional capacity, such as reductions in basal metabolic rates (i.e., 'plastic floors'), to compensate for the acute effects of thermal challenges when assessed over multigenerational timeframes. In this study, we use the 'plastic floors and concrete ceilings' hypothesis to generate and then test predictions regarding the thermal physiology of reef fishes in the world's hottest and most thermally variable coral reef ecosystem (southern Arabian/Persian Gulf). By comparing three species of reef fishes (Scolopsis ghanam, Ecsenius pulcher and Cheilodipterus novemstriatus) from the southern Arabian/Persian Gulf, with an annual temperature range of 18.0°C-36.5°C, to conspecifics from nearby but more thermally benign (~21.0°C-32.0°C) reefs in the Gulf of Oman, we find enhanced upper thermal limits and a broadening of the temperature performance curves for aerobic scope in the Arabian/Persian Gulf, but no evidence for changes in basal metabolic rates ('plastic floors'). Despite these conserved increases in temperature tolerance, the summer thermal safety margins of Arabian/Persian Gulf fishes were 1.47°C lower than those of conspecifics from the Gulf of Oman, demonstrating that while the temperature tolerance of tropical coral reef fishes is somewhat plastic over multigenerational timeframes, its rate of change is likely insufficient to keep pace with the rising average temperatures and growing thermal variability expected under climate change.

Broad thermal tolerance and high mitochondrial genetic connectivity in the pinfish (Lagodon rhomboides)

Pinfish (Lagodon rhomboides) are highly abundant in coastal ecosystems of the Gulf of Mexico and western Atlantic Ocean and serve as a crucial link in marine food webs. Despite their ecological relevance, little is known about this species' susceptibility to anthropogenic climate change. Here, we characterized patterns of mitochondrial genetic divergence and examined the upper thermal tolerance of pinfish across a large portion of the species' range. We found little evidence of population genetic differentiation among distant localities with divergent temperature regimes (e.g., Mexico and North Carolina), using two mitochondrial markers (cytochrome b [CytB] and cytochrome c oxidase I [COI]). This suggests high genetic connectivity, which implies low potential for local adaptation of populations to different thermal conditions along a latitudinal gradient. To further examine population-scale differences in thermal tolerance, we assessed the critical thermal maxima (CTmax) of pinfish from four localities: North Carolina, Florida Keys, Alabama, and Texas. We found that CTmax was similar across sites, with all localities showing an average CTmax within a 1°C temperature range (34.5-35.5°C). This suggests that southern populations of pinfish may be more susceptible to the detrimental effects of ocean warming, as individuals in lower latitudes regularly experience temperatures within a few degrees of their CTmax. Finally, we examined the influence of varying salinity on the upper thermal limit of the pinfish and found that pinfish show no variation in CTmax under salinity conditions ranging from hypo- to hypersaline (15-35 ppt). These results show that pinfish can tolerate a wide range of environmental parameters but may rely on phenotypic plasticity, rather than local adaptation, to distinct conditions to cope with different environmental regimes.

(Limited) Predictability of thermal adaptation in invertebrates

Evolutionary genomic approaches provide powerful tools to understand variation in and evolution of physiological processes. Untargeted genomic or transcriptomic screens can identify functionally annotated candidate genes linked to specific physiological processes, in turn suggesting evolutionary roles for these processes. Such studies often aim to inform modeling of the potential of natural populations to adapt to climate change, but these models are most accurate when evolutionary responses are repeatable, and thus predictable. Here, we synthesize the evolutionary genetic and comparative transcriptomic literature on terrestrial and marine invertebrates to assess whether evolutionary responses to temperature are repeatable within populations, across populations and across species. There is compelling evidence for repeatability, sometimes even across species. However, responses to laboratory selection and geographic variation across thermal gradients appear to be highly idiosyncratic. We also survey whether genetic/transcriptomic studies repeatedly identify candidate genes in three functional groups previously associated with the response to thermal stress: heat shock protein (Hsp) genes, proteolysis genes and immunity genes. Multiple studies across terrestrial and marine species identify candidates included in these gene sets. Yet, each of the gene sets are identified in only a minority of studies. Together, these patterns suggest that there is limited predictability of evolutionary responses to natural selection, including across studies within species. We discuss specific patterns for the candidate gene sets, implications for predictive modeling, and other potential applications of evolutionary genetics in elucidating physiology and gene function. Finally, we discuss limitations of inferences from available evolutionary genetic studies and directions for future research.

Temperature-Related Effects on Disease Susceptibility and Immune Response in Redband Trout (Oncorhynchus mykiss gairdneri) Following Challenge With Flavobacterium columnare

Heat stress can increase disease risk in fishes by reducing immune function. Interactions between redband trout (Oncorhynchus mykiss gairdneri) and Flavobacterium columnare, a causative agent of columnaris disease, provide an opportunity to investigate the effects of temperature on immune function and disease resistance during periods of thermal stress. We conducted three trials to characterise differences in immune function and mortality between redband trout held at 18°C and 21°C following challenge with F. columnare. In trial 1, cumulative per cent mortality (CPM) was low and not statistically different between 18°C and 21°C. In trials 2 and 2, we administered higher challenge doses and observed increased CPM overall and significantly greater CPM at 21°C than 18°C. Redband trout upregulated il-8, tnf-α, igm and igt following infection by F. columnare, suggesting that all of these genes may be involved in immune responses to F. columnare infection. We found no differences in the strength of the immune responses between fish held at 21°C versus 18°C. This indicated that 21°C did not elicit sufficient thermal stress to impair immune function and that increased CPM at 21°C versus 18°C was due to enhanced F. columnare virulence.

Local conditions drive interpopulation variation in field-based critical thermal maximum of brook trout

Individual- and population-level responses to thermal change will be pivotal for species' resilience and adaptive responses to climate change. Thermal tolerance of ectotherms has been extensively studied under laboratory conditions, but comparatively few studies have assessed intra- and interpopulation variation under natural conditions or in situ. We measured field critical thermal maximum (CTmax) of brook trout (Salvelinus fontinalis) populations at twenty sites across Ontario, Canada, to assess their thermal tolerance in situ and examine potential factors underlying intraspecific variation in thermal performance. We modelled CTmax as a function of acclimation using short-term stream temperature data to assess interpopulation variation, and used full-season stream temperatures to calculate thermal safety margins (TSM) for each population. CTmax ranged between 27.41 and 30.46°C and acclimation periods between 4 and 40 days were strong predictors of site CTmax, aligning closely with lab-based studies. Seasonal temperature profiles varied substantially among sites, with mean 30-day stream temperature accounting for 66% of the among-site variation in CTmax. TSMs ranged between 0.51 and 15.51°C and reflected differences among site thermal regimes. Streams in watersheds with more urban or agricultural development had the lowest TSMs in addition to those that were fed by lake surface water. This work emphasizes the importance of locally based conservation and management practices that act at or below the population level, as local factors beyond acclimation temperature were partly responsible for variation in thermal tolerance and thus dictate the resiliency of brook trout under climate change.

Measuring maximum heart rate to study cardiac thermal performance and heat tolerance in fishes

The thermal sensitivity of heart rate (fH) in fishes has fascinated comparative physiologists for well over a century. We now know that elevating fH is the primary mechanism through which fishes increase convective oxygen delivery during warming to meet the concomitant rise in tissue oxygen consumption. Thus, limits on fH can constrain whole-animal aerobic metabolism. In this Review, we discuss an increasingly popular methodology to study these limits, the measurement of pharmacologically induced maximum fH (fH,max) during acute warming of an anaesthetized fish. During acute warming, fH,max increases exponentially over moderate temperatures (Q10∼2-3), but this response is blunted with further warming (Q10∼1-2), with fH,max ultimately reaching a peak (Q10≤1) and the heartbeat becoming arrhythmic. Because the temperatures at which these transitions occur commonly align with whole-animal optimum and critical temperatures (e.g. aerobic scope and the critical thermal maximum), they can be valuable indicators of thermal performance. The method can be performed simultaneously on multiple individuals over a few hours and across a broad size range (<1 to >6000 g) with compact equipment. This simplicity and high throughput make it tractable in lab and field settings and enable large experimental designs that would otherwise be impractical. As with all reductionist approaches, the method does have limitations. Namely, it requires anaesthesia and pharmacological removal of extrinsic cardiac regulation. Nonetheless, the method has proven particularly effective in the study of patterns and limits of thermal plasticity and holds promise for helping to predict and mitigate outcomes of environmental change.

Upper thermal limits are 'hard-wired' across body mass but not populations of an estuarine fish

Climate warming is seeing temperatures breach exceptional thresholds as the frequency and intensity of heat waves increase. Efforts to forecast species vulnerability to climate warming often focus on upper thermal limits threatening survival, overlooking the role of intraspecific variation in determining vulnerability. Using an estuarine fish (black bream, Acanthopagrus butcheri) as a model, we explore how intraspecific variation in body mass and among populations affects upper thermal tolerance. Upper thermal limits were quantified using critical thermal maxima (CTmax) of wild fish. We used a ∼500 g (mean = 52.4 g, range = 0.57-541 g) mass range to test the relationship between body mass and thermal tolerance. Four distinct black bream populations were chosen along a 5° latitudinal cline to explore population differences in thermal limits. Contrary to expectations, there was no effect of body mass on upper thermal limits. However, significant population differences in thermal tolerance were observed that correlate with mean habitat temperatures. Specifically, the southern population had a significantly lower CTmax (35.57 ± 0.43 °C) compared to northern (36.32 ± 0.70 °C) and mid-latitude (36.36 ± 1.15 °C) populations. These data underscore the importance of observing intraspecific variation in thermal limits to reveal the capabilities of individuals within a species to cope with climate warming and improve the management of at-risk life stages and populations.

Thermal tolerance of cultured and wild Icelandic arctic charr (Salvelinus alpinus) at self-selected flow rates

Climate change is predicted to change not only the temperature of many freshwater systems but also flow dynamics. Understanding how fishes will fare in the future requires knowing how they will respond to both extended variations of temperature and flow. Arctic charr have had their thermal tolerance measured, but never with respect to flow. Additionally, this circumpolar species has multiple populations exhibiting dramatic phenotypic plasticity which may mean that regional differences in thermal tolerance are unaccounted for. In Iceland, Arctic charr populations have experienced highly variable flow and temperature conditions over the past 10,000 years. The Icelandic climate, topography and geothermal activity have created a mosaic of freshwater habitats inhabited by charr that vary substantially in both temperature and flow. Our purpose was to test whether populations from these varied environments had altered thermal tolerance and whether phenotypic plasticity of thermal tolerance in charr depends on flow. We raised cultured Icelandic charr from hatch under a 2 X 2 matrix of flow and temperature and compared them to wild charr captured from matching flow and temperature environments. Wild fish were more thermally tolerant than cultured fish at both acclimation temperatures and were more thermally plastic. Icelandic Arctic charr were more thermally tolerant than comparison charr populations across Europe and North America, but only when acclimated to 13 °C; fish acclimated to 5 °C compared equably with comparison charr populations. Icelandic Arctic charr were also more thermally plastic than all but one other salmonine species. Neither flow of rearing or the flow selected during a thermal tolerance (CTmax) test factored into thermal tolerance. Thermal tolerance was also independent of body size, condition factor, heart and gill size. In summary, wild Icelandic Arctic charr have greater thermal tolerance and plasticity than predicted from the literature and their latitude, but artificial selection for properties like growth rate or fecundity may be breeding that increased tolerance out of cultured fish. As the world moves toward a warmer climate and increased dependence on cultured fish, this is a noteworthy result and merits further study.

Efficient species identification for Pacific salmon genetic monitoring programs

Genetic monitoring of Pacific salmon in the Columbia River basin provides crucial information to fisheries managers that is otherwise challenging to obtain using traditional methods. Monitoring programs such as genetic stock identification (GSI) and parentage-based tagging (PBT) involve genotyping tens of thousands of individuals annually. Although rare, these large sample collections inevitably include misidentified species, which exhibit low genotyping success on species-specific Genotyping-in-Thousands by sequencing (GT-seq) panels. For laboratories involved in large-scale genotyping efforts, diagnosing non-target species and reassigning them to the appropriate monitoring program can be costly and time-consuming. To address this problem, we identified 19 primer pairs that exhibit consistent cross-species amplification among salmonids and contain 51 species informative variants. These genetic markers reliably discriminate among 11 salmonid species and two subspecies of Cutthroat Trout and have been included in species-specific GT-seq panels for Chinook Salmon, Coho Salmon, Sockeye Salmon, and Rainbow Trout commonly used for Pacific salmon genetic monitoring. The majority of species-informative amplicons (16) were newly identified from the four existing GT-seq panels, thus demonstrating a low-cost approach to species identification when using targeted sequencing methods. A species-calling script was developed that is tailored for routine GT-seq genotyping pipelines and automates the identification of non-target species. Following extensive testing with empirical and simulated data, we demonstrated that the genetic markers and accompanying script accurately identified species and are robust to missing genotypic data and low-frequency, shared polymorphisms among species. Finally, we used these tools to identify Coho Salmon incidentally caught in the Columbia River Chinook Salmon sport fishery and used PBT to determine their hatchery of origin. These molecular and computing resources provide a valuable tool for Pacific salmon conservation in the Columbia River basin and demonstrate a cost-effective approach to species identification for genetic monitoring programs.

Long non-coding RNAs mediate fish gene expression in response to ocean acidification

The majority of the transcribed genome does not have coding potential but these non-coding transcripts play crucial roles in transcriptional and post-transcriptional regulation of protein-coding genes. Regulation of gene expression is important in shaping an organism's response to environmental changes, ultimately impacting their survival and persistence as population or species face global change. However, the roles of long non-coding RNAs (lncRNAs), when confronted with environmental changes, remain largely unclear. To explore the potential role of lncRNAs in fish exposed to ocean acidification (OA), we analyzed publicly available brain RNA-seq data from a coral reef fish Acanthochromis polyacanthus. We annotated the lncRNAs in its genome and examined the expression changes of intergenic lncRNAs (lincRNAs) between A. polyacanthus samples from a natural CO2 seep and a nearby control site. We identified 4728 lncRNAs, including 3272 lincRNAs in this species. Remarkably, 93.03% of these lincRNAs were species-specific. Among the 125 highly expressed lincRNAs and 403 differentially expressed lincRNAs in response to elevated CO2, we observed that lincRNAs were either neighboring or potentially trans-regulating differentially expressed coding genes associated with pH regulation, neural signal transduction, and ion transport, which are known to be important in the response to OA in fish. In summary, lncRNAs may facilitate fish acclimation and mediate the responses of fish to OA by modulating the expression of crucial coding genes, which offers insight into the regulatory mechanisms underlying fish responses to environmental changes.

Body size and temperature affect metabolic and cardiac thermal tolerance in fish

Environmental warming is associated with reductions in ectotherm body sizes, suggesting that larger individuals may be more vulnerable to climate change. The mechanisms driving size-specific vulnerability to temperature are unknown but are required to finetune predictions of fisheries productivity and size-structure community responses to climate change. We explored the potential metabolic and cardiac mechanisms underlying these body size vulnerability trends in a eurythermal fish, barred surfperch. We acutely exposed surfperch across a large size range (5-700 g) to four ecologically relevant temperatures (16 °C, 12 °C, 20 °C, and 22 °C) and subsequently, measured their metabolic capacity (absolute and factorial aerobic scopes, maximum and resting metabolic rates; AAS, FAS, MMR, RMR). Additionally, we estimated the fish's cardiac thermal tolerance by measuring their maximum heart rates (fHmax) across acutely increasing temperatures. Barred surfperch had parallel hypoallometric scaling of MMR and RMR (exponent 0.81) and a weaker hypoallometric scaling of fHmax (exponent - 0.05) across all test temperatures. In contrast to our predictions, the fish's aerobic capacity was maintained across sizes and acute temperatures, and larger fish had greater cardiac thermal tolerance than smaller fish. These results demonstrate that thermal performance may be limited by different physiological constraints depending on the size of the animal and species of interest.

Differential effects of parental and developmental temperatures on larval thermal adaptation in oviparous and viviparous model fish species

Phenotypic plasticity has been identified as a major mechanism of response to changing temperatures. Parental effects are potentially important drivers of ecological and evolutionary dynamics, while developmental plasticity also plays a key role in generating phenotypic variation. However, little is known of the interaction between parental effects and developmental plasticity on the thermal phenotypes of fishes with different reproductive modes (i.e. oviparous vs. viviparous). To understand the contributions of inter- and intra-generational plasticity of thermal phenotypes (preferred temperature, avoidance temperatures, critical thermal thresholds) in fishes with different reproductive modes, we carried out a factorial experiment in which both breeding parents and offspring were exposed to lower (22 °C) or higher (28 °C) temperatures, using zebrafish (Danio rerio) and guppies (Poecilia reticulata) as representative oviparous and viviparous species. We found that offspring thermal preference and avoidance of both species were significantly influenced by parental effects and developmental plasticity, with higher thermal preference and avoidance consistent with higher background (parental) temperature treatments. However, parental effects were only found to impose significant effect on the thermal tolerances of guppies. The findings suggest that phenotypic plasticity, both within and across generations, may be an important mechanism to adapt to rapid climate changes, and that future temperature fluctuations may impose more profound effects on viviparous fish species in general.

Thermal tolerance and vulnerability to warming differ between populations of wild Oncorhynchus mykiss near the species' southern range limit

Fish habitat temperatures are increasing due to human impacts including climate change. For broadly distributed species, thermal tolerance can vary at the population level, making it challenging to predict which populations are most vulnerable to warming. Populations inhabiting warm range boundaries may be more resilient to these changes due to adaptation or acclimatization to warmer temperatures, or they may be more vulnerable as temperatures may already approach their physiological limits. We tested functional and critical thermal tolerance of two populations of wild Oncorhynchus mykiss near the species' southern range limit and, as predicted, found population-specific responses to temperature. Specifically, the population inhabiting the warmer stream, Piru Creek, had higher critical thermal maxima and higher functional thermal tolerance compared to the population from the cooler stream, Arroyo Seco. Arroyo Seco O. mykiss are more likely to experience a limitation of aerobic scope with warming. Piru Creek O. mykiss, however, had higher resting metabolic rates and prolonged exercise recovery, meaning that they could be more vulnerable to warming if prey or dissolved oxygen become limited. Temperature varies widely between streams near the O. mykiss southern range limit and populations will likely have unique responses to warming based on their thermal tolerances and metabolic requirements.

A homology guide for Pacific salmon genus Oncorhynchus resolves patterns of ohnolog retention, resolution and local adaptation following the salmonid-specific whole-genome duplication event

Salmonid fishes have emerged as a tractable model to study whole-genome duplications (WGDs) as this group has undergone four rounds of WGDs. While most of the salmonid genome has returned to a diploid state, a significant proportion of genes are maintained as duplicates and are referred to as ohnologs. The fact that much of the modern salmonid gene repertoire is comprised of ohnologs, while other genes have returned to their singleton state creates complications for genetic studies by obscuring homology relationships. The difficulty this creates is particularly prominent in Pacific salmonids belonging to genus Oncorhynchus who are the focus of intense genetics-based conservation and management efforts owing to the important ecological and cultural roles these fish play. To address this gap, we generated a homology guide for six species of Oncorhynchus with available genomes and used this guide to describe patterns of ohnolog retention and resolution. Overall, we find that ohnologs comprise approximately half of each species modern gene repertoires, which are functionally enriched for genes involved in DNA binding, while the less numerous singleton genes are heavily enriched in dosage-sensitive processes such as mitochondrial metabolism. Additionally, by reanalyzing published expression data from locally adapted strains of O. mykiss, we show that numerous ohnologs exhibit adaptive expression profiles; however, ohnologs are not more likely to display adaptive signatures than either paralogs or singletons. Finally, we demonstrate the utility of our homology guide by investigating the evolutionary relationship among genes highlighted as playing a role in salmonid life-history traits or gene editing targets.

Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout

Aquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence of climate conditions on body temperature. We investigated local adaptation in redband trout (Oncorhynchus mykiss gairdneri) using genome scans for 547 samples from 11 populations across a wide range of habitats and thermal gradients in the interior Columbia River. We estimated allele frequencies for millions of single nucleotide polymorphism loci (SNPs) across populations using low-coverage whole genome resequencing, and used population structure outlier analyses to identify genomic regions under divergent selection between populations. Twelve genomic regions showed signatures of local adaptation, including two regions associated with genes known to influence migration and developmental timing in salmonids (GREB1L, ROCK1, SIX6). Genotype-environment association analyses indicated that diurnal temperature variation was a strong driver of local adaptation, with signatures of selection driven primarily by divergence of two populations in the northern extreme of the subspecies range. We also found evidence for adaptive differences between high-elevation desert vs. montane habitats at a smaller geographical scale. Finally, we estimated vulnerability of redband trout to future climate change using ecological niche modelling and genetic offset analyses under two climate change scenarios. These analyses predicted substantial habitat loss and strong genetic shifts necessary for adaptation to future habitats, with the greatest vulnerability predicted for high-elevation desert populations. Our results provide new insight into the complexity of local adaptation in salmonids, and important predictions regarding future responses of redband trout to climate change.

Thermal physiology integrated species distribution model predicts profound habitat fragmentation for estuarine fish with ocean warming

Species distribution models predict a poleward migration for marine ectotherms with ocean warming. However, a key limitation in current species distribution models (SDM) is that they do not account for population-specific heterogeneity in physiological responses to temperature change resulting from local adaptations and acclimatization. To address this gap, we developed a novel, Physiology Integrated BioClimate Model (PIBCM) that combines habitat-specific metabolic thermal physiological tolerance of a species into a bioclimate envelope model. Using a downscaling approach, we also established a fine-resolution coastal sea-surface temperature data set for 2050-2080, that showed a high degree of location-specific variability in future thermal regimes. Combining predicted temperature data with the PIBCM model, we estimated habitat distribution for a highly eurythermal intertidal minnow, the Atlantic killifish (Fundulus heteroclitus), a species that likely presents a best-case-scenario for coastal vertebrates. We show that the killifish northern boundary shifts southwards, while distinct habitat fragmentation occurs in the southern sub-population (due to migration of adjacent fish populations to the nearest metabolically optimal thermal habitat). When compared to current SDMs (e.g., AquaMaps), our results emphasize the need for thermal physiology integrated range shift models and indicate that habitat fragmentation for coastal fishes may reshape nursery habitats for many commercially and ecologically important species.

Temperature-dependent plasticity mediates heart morphology and thermal performance of cardiac function in juvenile Atlantic salmon (Salmo salar)

In many fishes, upper thermal tolerance is thought to be limited in part by the heart's ability to meet increased oxygen demands during periods of high temperature. Temperature-dependent plasticity within the cardiovascular system may help fishes cope with the thermal stress imposed by increasing water temperatures. In this study, we examined plasticity in heart morphology and function in juvenile Atlantic salmon (Salmo salar) reared under control (+0°C) or elevated (+4°C) temperatures. Using noninvasive Doppler echocardiography, we measured the effect of acute warming on maximum heart rate, stroke distance, and derived cardiac output. A 4°C increase in average developmental temperature resulted in a>5°C increase in the Arrhenius breakpoint temperature for maximum heart rate and enabled the hearts of these fish to continue beating rhythmically to temperatures approximately 2°C higher than control fish. However, these differences in thermal performance were not associated with plasticity in maximum cardiovascular capacity, as peak measures of heart rate, stroke distance, and derived cardiac output did not differ between temperature treatments. Histological analysis of the heart revealed that while ventricular roundness and relative ventricle size did not differ between treatments, the proportion of compact myocardium in the ventricular wall was significantly greater in fish raised at elevated temperatures. Our findings contribute to the growing understanding of how the thermal environment can affect phenotypes later in life and identifies a morphological strategy that may help fishes cope with acute thermal stress.

ddRAD-Seq reveals evolutionary insights into population differentiation and the cryptic phylogeography of Hyporhamphus intermedius in Mainland China

Species differentiation and local adaptation in heterogeneous environments have attracted much attention, although little is known about the mechanisms involved. Hyporhamphus intermedius is an anadromous, brackish-water halfbeak that is widely distributed in coastal areas and hyperdiverse freshwater systems in China, making it an interesting model for research on phylogeography and local adaptation. Here, 156 individuals were sampled at eight sites from heterogeneous aquatic habitats to examine environmental and genetic contributions to phenotypic divergence. Using double-digest restriction-site-associated DNA sequencing (ddRAD-Seq) in the specimens from the different watersheds, 5498 single nucleotide polymorphisms (SNPs) were found among populations, with obvious population differentiation. We find that present-day Mainland China populations are structured into distinct genetic clusters stretching from southern and northern ancestries, mirroring geography. Following a transplant event in Plateau Lakes, there were virtually no variations of genetic diversity occurred in two populations, despite the fact two main splits were unveiled in the demographic history. Additionally, dorsal, and anal fin traits varied widely between the southern group and the others, which highlighted previously unrecognized lineages. We then explore genotype-phenotype-environment associations and predict candidate loci. Subgroup ranges appeared to correspond to geographic regions with heterogeneous hydrological factors, indicating that these features are likely important drivers of diversification. Accordingly, we conclude that genetic and phenotypic polymorphism and a moderate amount of genetic differentiation occurred, which might be ascribed to population subdivision, and the impact of abiotic factors.

Invasive Widow Spiders Perform Differently At Low Temperatures than Conspecifics from the Native Range

Temperature challenges are one of the leading abiotic causes of success or failure of non-native species in a novel environment, and this is particularly true for low temperatures. Establishing and reproducing in a novel thermal environment can alter survival, behaviour, and traits related to fitness. It has been proposed that plasticity or adaptation of thermal tolerance may allow an introduced species to thrive, or that successful invaders may be those with a thermal breadth in their native habitat that encompasses their new environment. Here, we tested these hypotheses using native and invasive populations of Australian redback spiders (Latrodectus hasselti). We measured how exposure to temperatures (exposure to 15°C and 25°C, respectively) common to invasive and native range habitats affected behavioural and life-history traits and tradeoffs that may underlie fitness in an invasive population detected in 1995 in Japan and a native population from Australia. We found that the critical thermal minimum (CTmin) was higher in the invasive population from Japan than in the native population, but critical thermal maximum (CTmax) did not differ between populations. Compared to the invasive population, eggs from the native population had a longer development time and lower hatching success at 15°C. Both populations performed equally well at 25 °C, as measured by egg development time and hatching success. Invasive juveniles that developed at 15 °C were slower to explore a novel environment and less bold when tested at 25 °C vs. 15 °C. In comparison, the native population showed faster average exploration, with no differences in response at the two development or testing temperatures. Overall, L. hasselti from Japan maintained hatching success and development across a wider temperature range than the native population, indicating greater thermal breadth and higher behavioural plasticity. These results support the importance of plasticity in thermal tolerance and behaviour for a successful invasion under novel environmental temperatures.

Turning the tide on sex and the microbiota in aquatic animals

Sex-based differences in animal microbiota are increasingly recognized as of biological importance. While most animal biomass is found in aquatic ecosystems and many water-dwelling species are of high economic and ecological value, biological sex is rarely included as an explanatory variable in studies of the aquatic animal microbiota. In this opinion piece, we argue for greater consideration of host sex in studying the microbiota of aquatic animals, emphasizing the many advancements that this information could provide in the life sciences, from the evolution of sex to aquaculture.

Copper exposure improves the upper thermal tolerance in a sex-specific manner, irrespective of fish thermal history

Ectotherms can respond to climate change via evolutionary adaptation, usually resulting in an increase of their upper thermal tolerance. But whether such adaptation influences the phenotypic plasticity of thermal tolerance when encountering further environmental stressors is not clear yet. This is crucial to understand because organisms experience multiple stressors, besides warming climate, in their natural environment and pollution is one of those. Here, we studied the phenotypic plasticity of thermal tolerance in three-spined stickleback populations inhabiting spatially replicated thermally polluted and pristine areas before and after exposing them to a sublethal concentration of copper for one week. We found that the upper thermal tolerance and its phenotypic plasticity after copper exposure did not depend on the thermal history of fish, suggesting that five decades of thermal pollution did not result in evolutionary adaptation to thermal tolerance. The upper thermal tolerance of fish was, on the other hand, increased by ∼ 1.5 °C after 1-week copper exposure in a sex-specific manner, with males having higher plasticity. To our knowledge this is the first study that shows an improvement of the upper thermal tolerance as a result of metal exposure. The results suggest that three-spined sticklebacks are having high plasticity and they are capable of surviving in a multiple-stressor scenario in the wild and that male sticklebacks seem more resilient to fluctuating environmental conditions than female.

An unusually high upper thermal acclimation potential for rainbow trout

Thermal acclimation, a compensatory physiological response, is central to species survival especially during the current era of global warming. By providing the most comprehensive assessment to date for the cardiorespiratory phenotype of rainbow trout (Oncorhynchus mykiss) at six acclimation temperatures from 15°C to 25°C, we tested the hypothesis that, compared with other strains of rainbow trout, an Australian H-strain of rainbow trout has been selectively inbred to have an unusually high and broad thermal acclimation potential. Using a field setting at the breeding hatchery in Western Australia, thermal performance curves were generated for a warm-adapted H-strain by measuring growth, feed conversion efficiency, specific dynamic action, whole-animal oxygen uptake (ṀO₂) during normoxia and hypoxia, the critical maximum temperature and the electrocardiographic response to acute warming. Appreciable growth and aerobic capacity were possible up to 23°C. However, growth fell off drastically at 25°C in concert with increases in the time required to digest a meal, its total oxygen cost and its peak ṀO₂. The upper thermal tipping points for appetite and food conversion efficiency corresponded with a decrease in the ability to increase heart rate during warming and an increase in the cost to digest a meal. Also, comparison of upper thermal tipping points provides compelling evidence that limitations to increasing heart rate during acute warming occurred well below the critical thermal maximum (CT_max) and that the faltering ability of the heart to deliver oxygen at different acclimation temperatures is not reliably predicted by CT_max for the H-strain of rainbow trout. We, therefore, reasoned the remarkably high thermal acclimation potential revealed here for the Australian H-strain of rainbow trout reflected the existing genetic variation within the founder Californian population, which was then subjected to selective inbreeding in association with severe heat challenges. This is an encouraging discovery for those with conservation concerns for rainbow trout and other fish species. Indeed, those trying to predict the impact of global warming should more fully consider the possibility that the standing intra-specific genetic variation within a fish species could provide a high thermal acclimation potential, similar to that shown here for rainbow trout.

Applying genomics in assisted migration under climate change: Framework, empirical applications, and case studies

The rate of global climate change is projected to outpace the ability of many natural populations and species to adapt. Assisted migration (AM), which is defined as the managed movement of climate-adapted individuals within or outside the species ranges, is a conservation option to improve species' adaptive capacity and facilitate persistence. Although conservation biologists have long been using genetic tools to increase or maintain diversity of natural populations, genomic techniques could add extra benefit in AM that include selectively neutral and adaptive regions of the genome. In this review, we first propose a framework along with detailed procedures to aid collaboration among scientists, agencies, and local and regional managers during the decision-making process of genomics-guided AM. We then summarize the genomic approaches for applying AM, followed by a literature search of existing incorporation of genomics in AM across taxa. Our literature search initially identified 729 publications, but after filtering returned only 50 empirical studies that were either directly applied or considered genomics in AM related to climate change across taxa of plants, terrestrial animals, and aquatic animals; 42 studies were in plants. This demonstrated limited application of genomic methods in AM in organisms other than plants, so we provide further case studies as two examples to demonstrate the negative impact of climate change on non-model species and how genomics could be applied in AM. With the rapidly developing sequencing technology and accumulating genomic data, we expect to see more successful applications of genomics in AM, and more broadly, in the conservation of biodiversity.

Fish out of water: Genomic insights into persistence of rainbowfish populations in the desert

How populations of aquatic fauna persist in extreme desert environments is an enigma. Individuals often breed and disperse during favorable conditions. Theory predicts that adaptive capacity should be low in small populations, such as in desert fishes. We integrated satellite-derived surface water data and population genomic diversity from 20,294 single-nucleotide polymorphisms across 344 individuals to understand metapopulation persistence of the desert rainbowfish (Melanotaenia splendida tatei) in central Australia. Desert rainbowfish showed very small effective population sizes, especially at peripheral populations, and low connectivity between river catchments. Yet, there was no evidence of population-level inbreeding and a signal of possible adaptive divergence associated with aridity was detected. Candidate genes for local adaptation included functions related to environmental cues and stressful conditions. Eco-evolutionary modeling showed that positive selection in refugial subpopulations combined with connectivity during flood periods can enable retention of adaptive diversity. Our study suggests that adaptive variation can be maintained in small populations and integrate with neutral metapopulation processes to allow persistence in the desert.

Intraspecific variation in thermal tolerance differs between tropical and temperate fishes

How ectothermic animals will cope with global warming is a critical determinant of the ecological impacts of climate change. There has been extensive study of upper thermal tolerance limits among fish species but how intraspecific variation in tolerance may be affected by habitat characteristics and evolutionary history has not been considered. Intraspecific variation is a primary determinant of species vulnerability to climate change, with implications for global patterns of impacts of ongoing warming. Using published critical thermal maximum (CT_max) data on 203 fish species, we found that intraspecific variation in upper thermal tolerance varies according to a species’ latitude and evolutionary history. Overall, tropical species show a lower intraspecific variation in thermal tolerance than temperate species. Notably, freshwater tropical species have a lower variation in tolerance than freshwater temperate species, which implies increased vulnerability to impacts of thermal stress. The extent of variation in CT_max among fish species has a strong phylogenetic signal, which may indicate a constraint on evolvability to rising temperatures in tropical fishes. That is, in addition to living closer to their upper thermal limits, tropical species may have higher sensitivity and lower adaptability to global warming compared to temperate counterparts. This is evidence that freshwater tropical fish communities, worldwide, are especially vulnerable to ongoing climate change.

Transcriptome analysis reveals the molecular mechanisms of heterosis on thermal resistance in hybrid abalone

BACKGROUND

Heterosis has been exploited for decades in different animals and crops due to it resulting in dramatic increases in yield and adaptability. Hybridization is a classical breeding method that can effectively improve the genetic characteristics of organisms through heterosis. Abalone has become an increasingly economically important aquaculture resource with high commercial value. However, due to changing climate, abalone is now facing serious threats of high temperature in summer. Interspecific hybrid abalone (Haliotis gigantea ♀ × H. discus hannai ♂, SD) has been cultured at large scale in southern China and has been shown high survival rates under heat stress in summer. Therefore, SD has become a good model material for heterosis research, but the molecular basis of heterosis remains elusive.

RESULTS

Heterosis in thermal tolerance of SD was verified through Arrhenius break temperatures (ABT) of cardiac performance in this study. Then RNA-Sequencing was conducted to obtain gene expression patterns and alternative splicing events at control temperature (20 °C) and heat stress temperature (30 °C). A total of 356 (317 genes), 476 (435genes), and 876 (726 genes) significantly diverged alternative splicing events were identified in H. discus hannai (DD), H. gigantea (SS), and SD in response to heat stress, respectively. In the heat stress groups, 93.37% (20,512 of 21,969) of the expressed genes showed non-additive expression patterns, and over-dominance expression patterns of genes account for the highest proportion (40.15%). KEGG pathway enrichment analysis showed that the overlapping genes among common DEGs and NAGs were significantly enriched in protein processing in the endoplasmic reticulum, mitophagy, and NF-κB signaling pathway. In addition, we found that among these overlap genes, 39 genes had undergone alternative splicing events in SD. These pathways and genes may play an important role in the thermal resistance of hybrid abalone.

CONCLUSION

More alternative splicing events and non-additive expressed genes were detected in hybrid under heat stress and this may contribute to its thermal heterosis. These results might provide clues as to how hybrid abalone has a better physiological regulation ability than its parents under heat stress, to increase our understanding of heterosis in abalone.

Antibiotics Shift the Temperature Response Curve of Escherichia coli Growth

Temperature variation-through time and across climatic gradients-affects individuals, populations, and communities. Yet how the thermal response of biological systems is altered by environmental stressors is poorly understood. Here, we quantify two key features-optimal temperature and temperature breadth-to investigate how temperature responses vary in the presence of antibiotics. We use high-throughput screening to measure growth of Escherichia coli under single and pairwise combinations of 12 antibiotics across seven temperatures that range from 22°C to 46°C. We find that antibiotic stress often results in considerable changes in the optimal temperature for growth and a narrower temperature breadth. The direction of the optimal temperature shifts can be explained by the similarities between antibiotic-induced and temperature-induced damage to the physiology of the bacterium. We also find that the effects of pairs of stressors in the temperature response can often be explained by just one antibiotic out of the pair. Our study has implications for a general understanding of how ecological systems adapt and evolve to environmental changes. IMPORTANCE The growth of living organisms varies with temperature. This dependence is described by a temperature response curve that is described by an optimal temperature where growth is maximized and a temperature range (termed breadth) across which the organism can grow. Because an organism's temperature response evolves or acclimates to its environment, it is often assumed to change over only evolutionary or developmental timescales. Counter to this, we show here that antibiotics can quickly (over hours) change the optimal growth temperature and temperature breadth for the bacterium Escherichia coli. Moreover, our results suggest a shared-damage hypothesis: when an antibiotic damages similar cellular components as hot (or cold) temperatures do, this shared damage will combine and compound to more greatly reduce growth when that antibiotic is administered at hot (or cold) temperatures. This hypothesis could potentially also explain how temperature responses are modified by stressors other than antibiotics.

Separating the Wheat from the Chaff: The Use of Upstream Regulator Analysis to Identify True Differential Expression of Single Genes within Transcriptomic Datasets

The development of DNA microarray and RNA-sequencing technology has led to an explosion in the generation of transcriptomic differential expression data under a wide range of biologic systems including those recapitulating the monogenic muscular dystrophies. Data generation has increased exponentially due in large part to new platforms, improved cost-effectiveness, and processing speed. However, reproducibility and thus reliability of data remain a central issue, particularly when resource constraints limit experiments to single replicates. This was observed firsthand in a recent rare disease drug repurposing project involving RNA-seq-based transcriptomic profiling of primary cerebrocortical cultures incubated with clinic-ready blood-brain penetrant drugs. Given the low validation rates obtained for single differential expression genes, alternative approaches to identify with greater confidence genes that were truly differentially expressed in our dataset were explored. Here we outline a method for differential expression data analysis in the context of drug repurposing for rare diseases that incorporates the statistical rigour of the multigene analysis to bring greater predictive power in assessing individual gene modulation. Ingenuity Pathway Analysis upstream regulator analysis was applied to the differentially expressed genes from the Care4Rare Neuron Drug Screen transcriptomic database to identify three distinct signaling networks each perturbed by a different drug and involving a central upstream modulating protein: levothyroxine (DIO3), hydroxyurea (FOXM1), dexamethasone (PPARD). Differential expression of upstream regulator network related genes was next assessed in in vitro and in vivo systems by qPCR, revealing 5× and 10× increases in validation rates, respectively, when compared with our previous experience with individual genes in the dataset not associated with a network. The Ingenuity Pathway Analysis based gene prioritization may increase the predictive value of drug-gene interactions, especially in the context of assessing single-gene modulation in single-replicate experiments.

Intraspecific variation in tolerance of warming in fishes

Intraspecific variation in key traits such as tolerance of warming can have profound effects on ecological and evolutionary processes, notably responses to climate change. The empirical evidence for three primary elements of intraspecific variation in tolerance of warming in fishes is reviewed. The first is purely mechanistic that tolerance varies across life stages and as fishes become mature. The limited evidence indicates strongly that this is the case, possibly because of universal physiological principles. The second is intraspecific variation that is because of phenotypic plasticity, also a mechanistic phenomenon that buffers individuals' sensitivity to negative impacts of global warming in their lifetime, or to some extent through epigenetic effects over successive generations. Although the evidence for plasticity in tolerance to warming is extensive, more work is required to understand underlying mechanisms and to reveal whether there are general patterns. The third element is intraspecific variation based on heritable genetic differences in tolerance, which underlies local adaptation and may define long-term adaptability of a species in the face of ongoing global change. There is clear evidence of local adaptation and some evidence of heritability of tolerance to warming, but the knowledge base is limited with detailed information for only a few model or emblematic species. There is also strong evidence of structured variation in tolerance of warming within species, which may have ecological and evolutionary significance irrespective of whether it reflects plasticity or adaptation. Although the overwhelming consensus is that having broader intraspecific variation in tolerance should reduce species vulnerability to impacts of global warming, there are no sufficient data on fishes to provide insights into particular mechanisms by which this may occur.

The role of mechanistic physiology in investigating impacts of global warming on fishes

Warming of aquatic environments as a result of climate change is already having measurable impacts on fishes, manifested as changes in phenology, range shifts and reductions in body size. Understanding the physiological mechanisms underlying these seemingly universal patterns is crucial if we are to reliably predict the fate of fish populations with future warming. This includes an understanding of mechanisms for acute thermal tolerance, as extreme heatwaves may be a major driver of observed effects. The hypothesis of gill oxygen limitation (GOL) is claimed to explain asymptotic fish growth, and why some fish species are decreasing in size with warming; but its underlying assumptions conflict with established knowledge and direct mechanistic evidence is lacking. The hypothesis of oxygen- and capacity-limited thermal tolerance (OCLTT) has stimulated a wave of research into the role of oxygen supply capacity and thermal performance curves for aerobic scope, but results vary greatly between species, indicating that it is unlikely to be a universal mechanism. As thermal performance curves remain important for incorporating physiological tolerance into models, we discuss potentially fruitful alternatives to aerobic scope, notably specific dynamic action and growth rate. We consider the limitations of estimating acute thermal tolerance by a single rapid measure whose mechanism of action is not known. We emphasise the continued importance of experimental physiology, particularly in advancing our understanding of underlying mechanisms, but also the challenge of making this knowledge relevant to the more complex reality.

Whole genome resequencing reveals genomic regions associated with thermal adaptation in redband trout

Adaptation to local environments involves evolution of ecologically important traits and underlying physiological processes. Here, we used low coverage whole-genome resequencing (lcWGR) on individuals to identify genome regions involved in thermal adaptation in wild redband trout Oncorhynchus mykiss gairdneri, a subspecies of rainbow trout that inhabits ecosystems ranging from cold montane forests to high elevation deserts. This study includes allele frequency-based analyses for selective sweeps among populations, followed by multiple association tests for specific sets of phenotypes measured under thermal stress (acute and chronic survival/mortality; high or low cardiac performance groups). Depending on the groups in each set of analyses, sequencing reads covered 43%-75% of the genome at ≥15× and each analysis included millions of SNPs across the genome. In tests for selective sweeps among populations, a total of six chromosomal regions were significant. The further association tests for specific phenotypes revealed that the region on chromosome 4 was consistently the most significant and contains the cerk gene (ceramide kinase). This study provides insight into a potential genetic mechanism of local thermal adaptation and suggests cerk may be an important candidate gene. However, further validation of this cerk gene is necessary to determine if the association with cardiac performance results in a functional role to influence thermal performance when exposed to high water temperatures and hypoxic conditions.

Predicting Thermal Adaptation by Looking Into Populations' Genomic Past

Molecular evolution offers an insightful theory to interpret the genomic consequences of thermal adaptation to previous events of climate change beyond range shifts. However, disentangling often mixed footprints of selective and demographic processes from those due to lineage sorting, recombination rate variation, and genomic constrains is not trivial. Therefore, here we condense current and historical population genomic tools to study thermal adaptation and outline key developments (genomic prediction, machine learning) that might assist their utilization for improving forecasts of populations' responses to thermal variation. We start by summarizing how recent thermal-driven selective and demographic responses can be inferred by coalescent methods and in turn how quantitative genetic theory offers suitable multi-trait predictions over a few generations via the breeder's equation. We later assume that enough generations have passed as to display genomic signatures of divergent selection to thermal variation and describe how these footprints can be reconstructed using genome-wide association and selection scans or, alternatively, may be used for forward prediction over multiple generations under an infinitesimal genomic prediction model. Finally, we move deeper in time to comprehend the genomic consequences of thermal shifts at an evolutionary time scale by relying on phylogeographic approaches that allow for reticulate evolution and ecological parapatric speciation, and end by envisioning the potential of modern machine learning techniques to better inform long-term predictions. We conclude that foreseeing future thermal adaptive responses requires bridging the multiple spatial scales of historical and predictive environmental change research under modern cohesive approaches such as genomic prediction and machine learning frameworks.

Heat acclimation mediated cardioprotection is controlled by mitochondrial metabolic remodeling involving HIF-1α

Heat acclimation (HA) induces metabolic plasticity to resist the effects of environmental heat with cross-tolerance to novel stressors such as oxygen supply perturbations, exercise, and alike. Our previous results indicated that hypoxia inducible transcription factor (HIF-1α) contributes to this adaptive process. In the present study, we link functional studies in isolated cardiomyocytes, with molecular and biochemical studies of cardiac mitochondria and demonstrate that HA remodels mitochondrial metabolism and performance. We observed the significant role that HIF-1α plays in the HA heart, as HA reduces oxidative stress during ischemia by shifting mitochondrial substrate preference towards pyruvate, with elevated level and activity of mitochondrial LDH (LDHb), acting a pivotal role. Increased antioxidative capacity to encounter hazards is implicated. These results deepen our understanding of heat acclimation-mediated cross tolerance (HACT), in which adaptive bioenergetic-mechanisms counteract the hazards of oxidative stress.

Adaptation of plasticity to projected maximum temperatures and across climatically defined bioregions

Resilience to environmental stressors due to climate warming is influenced by local adaptations, including plastic responses. The recent literature has focused on genomic signatures of climatic adaptation, but little is known about how plastic capacity may be influenced by biogeographic and evolutionary processes. We investigate phenotypic plasticity as a target of climatic selection, hypothesizing that lineages that evolved in warmer climates will exhibit greater plastic adaptive resilience to upper thermal stress. This was experimentally tested by comparing transcriptomic responses within and among temperate, subtropical, and desert ecotypes of Australian rainbowfish subjected to contemporary and projected summer temperatures. Critical thermal maxima were estimated, and ecological niches delineated using bioclimatic modeling. A comparative phylogenetic expression variance and evolution model was used to assess plastic and evolved changes in gene expression. Although 82% of all expressed genes were found in the three ecotypes, they shared expression patterns in only 5 out of 236 genes that responded to the climate change experiment. A total of 532 genes showed signals of adaptive (i.e., genetic-based) plasticity due to ecotype-specific directional selection, and 23 of those responded to projected summer temperatures. Network analyses demonstrated centrality of these genes in thermal response pathways. The greatest adaptive resilience to upper thermal stress was shown by the subtropical ecotype, followed by the desert and temperate ecotypes. Our findings indicate that vulnerability to climate change will be highly influenced by biogeographic factors, emphasizing the value of integrative assessments of climatic adaptive traits for accurate estimation of population and ecosystem responses.

Genomic Signatures of Selection along a Climatic Gradient in the Northern Range Margin of the White-Footed Mouse (Peromyscus leucopus)

Identifying genetic variation involved in thermal adaptation is likely to yield insights into how species adapt to different climates. Physiological and behavioral responses associated with overwintering (e.g., torpor) are thought to serve important functions in climate adaptation. In this study, we use 2 isolated Peromyscus leucopus lineages on the northern margin of the species range to identify single nucleotide polymorphisms (SNPs) showing a strong environmental association and test for evidence of parallel evolution. We found signatures of clinal selection in each lineage, but evidence of parallelism was limited, with only 2 SNPs showing parallel allele frequencies across transects. These parallel SNPs map to a gene involved in protection against iron-dependent oxidative stress (Fxn) and to a gene with unknown function but containing a forkhead-associated domain (Fhad1). Furthermore, within transects, we find significant clinal patterns in genes enriched for functions associated with glycogen homeostasis, synaptic function, intracellular Ca2+ balance, H3 histone modification, as well as the G2/M transition of cell division. Our results are consistent with recent literature on the cellular and molecular basis of climate adaptation in small mammals and provide candidate genomic regions for further study.

How repeatable is CTmax within individual brook trout over short- and long-time intervals?

As stream temperatures increase due to factors such as heated runoff from impervious surfaces, deforestation, and climate change, fish species adapted to cold water streams are forced to move to more suitable habitat, acclimate or adapt to increased thermal regimes, or die. To estimate the potential for adaptation, a (within individual) repeatable metric of thermal tolerance is imperative. Critical thermal maximum (CT_max) is a dynamic test that is widely used to measure thermal tolerance across many taxa and has been used in fishes for decades, but its repeatability in most species is unknown. CT_max tests increase water temperature steadily over time until loss of equilibrium (LOE) is achieved. To determine if CT_max is a consistent metric within individual fish, we measured CT_max on the same lab-held individually-marked adult brook trout Salvelinus fontinalis at three different times (August & September 2016, September 2017). We found that CT_max is a repeatable trait (Repeatability ± S.E.: 0.48 ± 0.14). CT_max of individuals males was consistent over time, but the CT_max of females increased slightly over time. This result indicates that CT_max is a robust, repeatable estimate of thermal tolerance in a cold-water adapted fish.

Northern European Salmo trutta (L.) populations are genetically divergent across geographical regions and environmental gradients

The salmonid fish Brown trout is iconic as a model for the application of conservation genetics to understand and manage local interspecific variation. However, there is still scant information about relationships between local and large-scale population structure, and to what extent geographical and environmental variables are associated with barriers to gene flow. We used information from 3,782 mapped SNPs developed for the present study and conducted outlier tests and gene-environment association (GEA) analyses in order to examine drivers of population structure. Analyses comprised >2,600 fish from 72 riverine populations spanning a central part of the species' distribution in northern Europe. We report hitherto unidentified genetic breaks in population structure, indicating strong barriers to gene flow. GEA loci were widely spread across genomic regions and showed correlations with climatic, abiotic and geographical parameters. In some cases, individual loci showed consistent GEA across the geographical regions Britain, Europe and Scandinavia. In other cases, correlations were observed only within a sub-set of regions, suggesting that locus-specific variation was associated with local processes. A paired-population sampling design allowed us to evaluate sampling effects on detection of outlier loci and GEA. Two widely applied methods for outlier detection (pcadapt and bayescan) showed low overlap in loci identified as statistical outliers across sub-sets of data. Two GEA analytical approaches (LFMM and RDA) showed good correspondence concerning loci associated with specific variables, but LFMM identified five times more statistically significant associations than RDA. Our results emphasize the importance of carefully considering the statistical methods applied for the hypotheses being tested in outlier analysis. Sampling design may have lower impact on results if the objective is to identify GEA loci and their population distribution. Our study provides new insights into trout populations, and results have direct management implications in serving as a tool for identification of conservation units.

Local cold adaption increases the thermal window of temperate mussels in the Arctic

Species expand towards higher latitudes in response to climate warming, but the pace of this expansion is related to the physiological capacity to resist cold stress. However, few studies exist that have quantified the level of inter-population local adaptation in marine species freeze tolerance, especially in the Arctic. We investigated the importance of cold adaptation and thermal window width towards high latitudes from the temperate to the Arctic region. We measured upper and lower lethal air temperatures (i.e. LT and LT50) in temperate and Arctic populations of blue mussels (Mytilus edulis), and analysed weather data and membrane fatty acid compositions, following emersion simulations. Both populations had similar upper LT (~38 °C), but Arctic mussels survived 4°C colder air temperatures than temperate mussels (-13 vs. -9°C, respectively), corresponding to an 8% increase in their thermal window. There were strong latitudinal relationships between thermal window width and local air temperatures, indicating Arctic mussels are highly adapted to the Arctic environment where the seasonal temperature span exceeds 60°C. Local adaptation and local habitat heterogeneity thus allow leading-edge M. edulis to inhabit high Arctic intertidal zones. This intraspecific pattern provides insight into the importance of accounting for cold adaptation in climate change, conservation and biogeographic studies.

The effect of acute warming and thermal acclimation on maximum heart rate of the common killifish Fundulus heteroclitus

Common killifish Fundulus heteroclitus were acclimated to ecologically relevant temperatures (5, 15 and 33°C) and their maximum heart rate (f_Hmax ) was measured at each acclimation temperature during an acute warming protocol. Acclimation to 33°C increased peak f_Hmax by up to 32% and allowed the heart to beat rhythmically at a temperature 10°C higher when compared with acclimation to 5°C. Independent of acclimation temperature, peak f_Hmax occurred about 3°C cooler than the temperature that first produced cardiac arrhythmias. Thus, when compared with previously published values for the critical thermal maximum of F. heteroclitus, the temperature for peak f_Hmax was cooler and the temperature that first produced cardiac arrhythmias was similar to these critical thermal maxima. The considerable thermal plasticity of f_Hmax demonstrated in the present study is entirely consistent with eurythermal ecology of killifish, as shown previously for another eurythermal fish Gillichthys mirabilis.

Plasticity in Standard and Maximum Aerobic Metabolic Rates in Two Populations of an Estuarine Dependent Teleost, Spotted Seatrout (Cynoscion nebulosus)

We studied the effects of metabolic cold adaptation (MCA) in two populations of a eurythermal species, spotted seatrout (Cynoscion nebulosus) along the U.S. East Coast. Fish were captured from their natural environment and acclimated at control temperatures 15 °C or 20 °C. Their oxygen consumption rates, a proxy for metabolic rates, were measured using intermittent flow respirometry during acute temperature decrease or increase (2.5 °C per hour). Mass-specific standard metabolic rates (SMR) were higher in fish from the northern population across an ecologically relevant temperature gradient (5 °C to 30 °C). SMR were up to 37% higher in the northern population at 25 °C and maximum metabolic rates (MMR) were up to 20% higher at 20 °C. We found evidence of active metabolic compensation in the southern population from 5 °C to 15 °C (Q₁₀ < 2), but not in the northern population. Taken together, our results indicate differences in metabolic plasticity between the northern and southern populations of spotted seatrout and provide a mechanistic basis for predicting population-specific responses to climate change.

Deep transcriptome analysis of the heat shock response in an Atlantic sturgeon (Acipenser oxyrinchus) cell line

Despite efforts to restore Atlantic sturgeon in European rivers, aquaculture techniques result in animals with high post-release mortality due to, among other reasons, their low tolerance to increasing water temperature. Marker genes to monitor heat stress are needed in order to identify heat-resistant fish. Therefore, an Atlantic sturgeon cell line was exposed to different heat shock protocols (30 °C and 35 °C) and differences in gene expression were investigated. In total 3020 contigs (∼1.5%) were differentially expressed. As the core of the upregulated contigs corresponded to heat shock proteins (HSP), the heat shock factor (HSF) and the HSP gene families were annotated in Atlantic sturgeon and mapped via Illumina RNA sequencing to identify heat-inducible family members. Up to 6 hsf and 76 hsp genes were identified in the Atlantic sturgeon transcriptome resources, 16 of which were significantly responsive to the applied heat shock. The previously studied hspa1 (hsp70) gene was only significantly upregulated at the highest heat shock (35 °C), while a set of 5 genes (hspc1, hsph3a, hspb1b, hspb11a, and hspb11b) was upregulated at all conditions. Although the hspc1 (hsp90a) gene was previously used as heat shock-marker in sturgeons, we found that hspb11a is the most heat-inducible gene, with up to 3296-fold higher expression in the treated cells, constituting the candidate gene markers for in vivo trials.

Heat Waves, the New Normal: Summertime Temperature Extremes Will Impact Animals, Ecosystems, and Human Communities

A consequence of climate change is the increased frequency and severity of extreme heat waves. This is occurring now as most of the warmest summers and most intense heat waves ever recorded have been during the past decade. In this review, I describe the ways in which animals and human populations are likely to respond to increased extreme heat, suggest how to study those responses, and reflect on the importance of those studies for countering the devastating impacts of climate change.

Chum salmon migrating upriver adjust to environmental temperatures through metabolic compensation

Ectotherms adjust their thermal performance to various thermal ranges by altering their metabolic rates. These metabolic adjustments involve plastic and/or genetic traits and pathways depend on species-specific ecological contexts. Chum salmon (Oncorhynchus keta) are ecologically unique among the Pacific salmonids as early-run and late-run populations are commonly observed in every part of their range. In the Sanriku coastal area, Japan, early-run adults experience high water temperatures (12-24°C) during their migration, compared with those of the late-run adults (4-15°C), suggesting that the two populations might have different thermal performance. Here, we found population-specific differences in the thermal sensitivities of metabolic rates [resting metabolic rate, RMR, and maximum (aerobic) metabolic rate, MMR] and critical temperature maxima. Using these parameters, we estimated thermal performance curves of absolute aerobic scope (AAS). The populations had different thermal performance curves of AAS, and in both populations high values of AAS were maintained throughout the range of ecologically relevant temperatures. However, the populations did not vary substantially in the peak (AAS at optimal temperature, T _optAAS) or breadth (width of sub-optimal temperature range) of the performance curves. The AAS curve of early-run fish was shifted approximately 3°C higher than that of late-run fish. Furthermore, when the data for RMR and MMR were aligned to the thermal differences from T _optAAS, it became clear that the populations did not differ in the temperature dependence of their metabolic traits. Our results indicate that chum salmon thermally accommodate through compensatory alterations in metabolic rates. Our results imply that metabolic plasticity and/or the effect of genetic variance on plasticity might play a pivotal role in their thermal accommodation.

Different Transcriptomic Responses to Thermal Stress in Heat-Tolerant and Heat-Sensitive Pacific Abalones Indicated by Cardiac Performance

The Pacific abalone Haliotis discus hannai is one of the most economically important mollusks in China. Even though it has been farmed in southern China for almost 20 years, summer mortality remains the most challengeable problem for Pacific abalone aquaculture recently. Here, we determined the different heat tolerance ability for five selective lines of H. discus hannai by measuring the cardiac performance and Arrhenius breakpoint temperature (ABT). The Red line (RL) and Yangxia line (YL) were determined as the most heat-sensitive and most heat-tolerant line, respectively. Heart rates for RL were significantly lower than those of the YL at the same temperature (p < 0.05). The differentially expressed genes (DEGs), which were enriched in several pathways including cardiac muscle contraction, glutathione metabolism and oxidative phosphorylation, were identified between RL and YL at control temperature (20°C) and heat stress temperature (28.5°C, the ABT of the RL) by RNA-seq method. In the RL, 3370 DEGs were identified between the control and the heat-stress temperature, while only 1351 DEGs were identified in YL between these two temperature tests. Most of these DEGs were enriched in the pathways such as protein processing in endoplasmic reticulum, nucleotide binding and oligomerization domain (NOD) like receptor signaling, and ubiquitin mediated proteolysis. Notably, the most heat-tolerant line YL used an effective heat-protection strategy based on moderate transcriptional changes and regulation on the expression of key genes.

Temperature effects on performance and physiology of two prairie stream minnows

Earth's atmosphere has warmed by ~1°C over the past century and continues to warm at an increasing rate. Effects of atmospheric warming are already visible in most major ecosystems and are evident across all levels of biological organization. Linking functional responses of individuals to temperature is critical for predicting responses of populations and communities to global climate change. The southern redbelly dace Chrosomus erythrogaster and the central stoneroller Campostoma anomalum are two minnows (Cyprinidae) that commonly occur in the Flint Hills region of the USA but show different patterns of occurrence, with dace largely occupying headwater reaches and stonerollers persisting in both headwater and intermediate-sized streams. We tested for differences between species in critical thermal maximum, energy metabolism, sustained swimming and activity over an ecologically relevant temperature gradient of acclimation temperatures. Typically, metrics increased with acclimation temperature for both species, although stoneroller activity decreased with temperature. We observed a significant interaction between species and temperature for critical thermal maxima, where stonerollers only had higher critical thermal maxima at the coldest temperature and at warm temperatures compared to the dace. We did not find evidence suggesting differences in the energy metabolism of dace and stonerollers. We detected interspecific differences in sustained swimming performance, with dace having higher swimming speed than stonerollers regardless of acclimation temperature. Finally, there was a significant interaction between temperature and species for activity; dace activity was higher at intermediate and warm temperatures compared to stonerollers. We observed subtle interspecific differences in how performance metrics responded to temperature that did not always align with observed patterns of distribution for these species. Thus, other ecological factors likely are important drivers of distributional patterns in these species.

Tolerance traits related to climate change resilience are independent and polygenic

The resilience of organisms to climate change through adaptive evolution is dependent on the extent of genetically based variation in key phenotypic traits and the nature of genetic associations between them. For aquatic animals, upper thermal tolerance and hypoxia tolerance are likely to be a important determinants of sensitivity to climate change. To determine the genetic basis of these traits and to detect associations between them, we compared naturally occurring populations of two subspecies of Atlantic killifish, Fundulus heteroclitus, that differ in both thermal and hypoxia tolerance. Multilocus association mapping demonstrated that 47 and 35 single nucleotide polymorphisms (SNPs) explained 43.4% and 51.9% of variation in thermal and hypoxia tolerance, respectively, suggesting that genetic mechanisms underlie a substantial proportion of variation in each trait. However, no explanatory SNPs were shared between traits, and upper thermal tolerance varied approximately linearly with latitude, whereas hypoxia tolerance exhibited a steep phenotypic break across the contact zone between the subspecies. These results suggest that upper thermal tolerance and hypoxia tolerance are neither phenotypically correlated nor genetically associated, and thus that rates of adaptive change in these traits can be independently fine-tuned by natural selection. This modularity of important traits can underpin the evolvability of organisms to complex future environmental change.

Physiological and genomic signatures of evolutionary thermal adaptation in redband trout from extreme climates

Temperature is a master environmental factor that limits the geographical distribution of species, especially in ectotherms. To address challenges in biodiversity conservation under ongoing climate change, it is essential to characterize relevant functional limitations and adaptive genomic content at population and species levels. Here, we present evidence for adaptive divergence in cardiac function and genomic regions in redband trout (Oncorhynchus mykiss gairdneri) populations from desert and montane streams. Cardiac phenotypes of individual fish were measured in the field with a custom-built electrocardiogram apparatus. Maximum heart rate and its rate limiting temperature during acute warming were significantly higher in fish that have evolved in the extreme of a desert climate compared to a montane climate. Association mapping with 526,301 single nucleotide polymorphisms (SNPs) across the genome revealed signatures of thermal selection both within and among ecotypes. Among desert and montane populations, 435 SNPs were identified as putative outliers under natural selection and 20 of these loci showed significant association with average summer water temperatures among populations. Phenotypes for cardiac performance were variable within each ecotype, and 207 genomic regions were strongly associated with either maximum heart rate or rate limiting temperatures among individuals. Annotation of significant loci provided candidate genes that underlie thermal adaptation, including pathways associated with cardiac function (IRX5, CASQ1, CAC1D, and TITIN), neuroendocrine system (GPR17 and NOS), and stress response (SERPH). By integrating comparative physiology and population genomics, results here advance our knowledge on evolutionary processes of thermal adaptation in aquatic ectotherms.