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Genomic signatures of cold adaptation in a Himalayan drosophilid.

Drosophila nepalensis is a cold-adapted drosophilid endemic to the Himalayan region. Its ability to survive in harsh, cold conditions makes it a valuable Drosophila model for investigating how adaptation to thermal extremes may influence species persistence under future climate change. Here, we report the first de novo genome assembly of D. nepalensis, based on a hybrid sequencing strategy that combines Illumina short reads and Oxford Nanopore long reads. Illumina sequencing generated 49.88 million 150 bp paired-end reads (∼14.96 Gbp), while Nanopore sequencing produced 1.35 million long reads totaling ∼0.76 Gbp. The assembled genome spanned ∼178 Mb with an N50 of 83.6 kb and 98% BUSCO completeness, comparable to other well-annotated Drosophila genomes. Annotation identified 10,560 protein-coding genes, including transcription factor-rich and stress-related domains such as zinc fingers, WD40 repeats, and ankyrin motifs. Comparative orthology analysis across 6 Drosophila species identified 14,168 orthologous clusters, of which 9,173 were shared among all 6 species, indicating a conserved core genomic set across the sampled taxa. D. nepalensis showed 83 unique orthogroups and 50 singletons, suggesting some lineage-specific gene expansions associated with cold adaptation and endemicity, including families encoding caspase-family apoptotic regulators, chromatin remodeling proteins (HMGB/protamine-like), and SNARE-domain vesicle trafficking factors. Gene family evolution analysis revealed the highest expansions in the cold-tolerant Himalayan drosophilid, D. nepalensis, including significant expansions in serine protease, chaperone, and neurotransmitter transporter families, alongside dramatic contractions of core histone gene families, suggesting lineage-specific chromatin remodeling and ecological specialization.

Drosophila nepalensis

Quantifying the evolutionary potential for Delta Smelt persistence in a warming habitat.

Long-term persistence of managed species will depend, in part, on whether the species harbors the physiological or genetic potential to adjust to warming temperatures, and whether relevant genetic variation is modified by management practices. The critically endangered Delta Smelt (Hypomesus transpacificus) is intensively managed, but little is known about the presence of genetic variation for resistance to elevated temperature, which will be important to maintain for their persistence in a rapidly warming future. Using a pedigree and whole genome sequencing data, we characterized the genetic variation and genomic architecture for CTMax (as a metric of upper thermal tolerance) across control and elevated rearing temperatures, alongside covarying traits (body size, degree of hatchery ancestry). Warmer rearing temperatures increased CTMax through acclimation but also resulted in reduced additive genetic variation for the trait, which could constrain adaptation under thermal stress. We found that larger fish had reduced CTMax, although this effect was diminished at elevated temperatures. We observed modest heritability for CTMax at rearing temperatures of 15°C and 18°C (0.26 and 0.16, respectively), but only a limited number of loci were identified that had consistent effects on CTMax across rearing temperatures. Instead, the genomic basis of thermal tolerance was highly dependent on rearing temperature (many loci detected with a GxE effect). The influence of domestication selection was indicated by changes in allele frequency, and divergence in upper thermal tolerance and plasticity, between low and high hatchery ancestry groups. Minimal overlap between loci associated with domestication and CTMax suggests that these traits possess separate genetic underpinnings. Knowledge of genetic variation supporting ecologically relevant physiological variation may be useful for refuge management and may inform supplementation in an ever-warming environment.

conservation physiology

Integrated physiological and transcriptomic analyses reveal coordinated gill responses to heat stress in pikeperch (Sander lucioperca).

Climate change-driven warming of aquatic environments has made thermal stress an increasingly important factor influencing fish physiological homeostasis. Given their central roles in respiration and osmoregulation, gills are particularly responsive to variations in ambient temperature. Histological examination, physiological measurements, and transcriptome profiling were integrated to investigate the mechanisms associated with heat stress-induced gill injury in pikeperch (Sander lucioperca). Histological analysis revealed that exposure to 29 °C directly caused structural damage to the gills of pikeperch. Oxidative status was evaluated by measuring malondialdehyde (MDA) levels and the activities of antioxidant enzymes, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). MDA accumulation was significantly enhanced under heat stress, while antioxidant enzyme activities (SOD, POD, and CAT) displayed a transient increase followed by a subsequent decline. Transcriptome profiling showed marked enrichment of the protein processing in endoplasmic reticulum pathway after heat stress, suggesting activation of endoplasmic reticulum (ER) stress in pikeperch gills. With increasing stress duration, the unfolded protein response (UPR) appeared unable to re-establish ER homeostasis, shifting ire1 and atf6 toward a pro-apoptotic state. Protein-protein interaction (PPI) analysis further highlighted hub genes potentially involved in heat stress-induced ER stress and apoptosis. TUNEL staining and western blotting collectively confirmed that heat stress triggered apoptosis in pikeperch gill tissue. Overall, this study provides new insights into the physiological and molecular responses of pikeperch gills to heat stress and enhances our understanding of thermal stress adaptation in cold-water aquaculture species under climate change.

Animals

Further studies on the adaptation of fish myofibrillar ATPases to different cell temperatures.

Previous studies on fish Mg2+Ca2+ activated myofibrillar ATPases have been extended to species inhabiting diverse thermal environments. Cold adapted ATPases have considerably higher catalytic centred activities at low temperatures than warm adapted ATPases. Differences in cell temperature have also lead to evolutionary modifications in thermodynamic activation parameters. The free energies (deltaG2+), enthalpies (deltaH2+) and entropies (deltaS2+) of activation of the Mg2+Ca2+ myofibrillar ATPase are positively correlated with adaptation temperature. Myofibrils with CaATP-2 as substrate in the absence of Mg2+ will hydrolyse ATP by a mechanism not associated with fibril shortening. Differences in activation enthalpies (deltaHH) between cold and warm adapted Ca2+-activated myofibrillar ATPases are less pronounced than for the physiological ATPase. Furthermore the Ca2+-activated ATPase showed no relationship between environmental temperature and substrate turnover number or free energy of activation (deltaG2+).

Acclimatization

Whole-genome sequencing reveals divergent and shared selection signatures of heat stress adaptation in indigenous Ethiopian zebu cattle from dry-hot and humid-hot environments.

African zebu cattle (Bos indicus) exhibit remarkable adaptations to extreme thermal conditions, yet the genomic basis of this resilience remains incompletely characterized. Ethiopia provides a unique natural setting in which closely related zebu populations have adapted divergently to dry-hot (DHETZ) and humid-hot (HHETZ) climates. In this study, we reanalyzed publicly available whole-genome sequencing datasets from 46 Ethiopian zebu cattle from five populations and compared them with Asian zebu, Sudanese zebu, African taurine, and European taurine breeds. By integrating genome-wide SNP analysis, population genetic structure assessment, and multiple selection scans (iHS, Hp, XP-EHH, and XP-CLR), we identified distinct and shared selection signatures between DHETZ and HHETZ. We detected 33.7 million and 34.2 million biallelic autosomal SNPs in DHETZ and HHETZ, respectively. Ethiopian zebu clustered closely with Sudanese zebu but showed clear divergence from Asian zebu and taurine breeds. DHETZ and HHETZ exhibited very low genetic differentiation (FST = 0.0063), consistent with their shared ancestry; however, each group displayed unique selection signals. In DHETZ, iHS and Hp detected 298 and 113 candidate regions, respectively, whereas in HHETZ, they detected 244 and 138 regions, respectively. Cross-population XP-EHH and XP-CLR analyses identified 163 and 227 divergent regions between DHETZ and HHETZ, respectively. Integration of the four selection scans identified 19 high-confidence candidate regions in DHETZ and 13 in HHETZ. DHETZ showed strong selection in genes involved in oxidative stress regulation, protein folding, mitochondrial function, and vascular remodeling, including SESN2, DNAJC8, GRPEL2, ABLIM3, and AFAP1L1. In contrast, HHETZ displayed signatures in genes associated with immune responses, energy metabolism, and angiogenesis inhibition, including MYD88, PRKACA, PRKACB, and WIF1. Several genes, including VEGFC, TNIP3, and DMXL2, were under selection in both groups, suggesting conserved mechanisms of thermotolerance and reproductive adaptation. The shared VEGFC signal and the HHETZ-specific WIF1 signal may indicate a distinct vascular regulatory mechanism in the dry-hot and humid-hot environments. Our results reveal a dual pattern of genomic adaptation in Ethiopian zebu cattle and provide candidate loci for future validation and climate-resilient livestock breeding.

Animals

Long-term heat exposure reshapes muscle molecular regulation and enhances thermal tolerance in Clarias fuscus.

Rapid fluctuations in water temperature driven by global warming have become a major abiotic stressor affecting muscle function in teleost fish. This study examined the effects of long-term thermal conditions on heat tolerance in Clarias fuscus. Fish were maintained for 90 days at either a normal temperature group (NT, 26 °C) or a high-temperature group (HT, 34 °C). Subsequently, muscle histology, and transcriptomic profiles were observed following acute high-temperature exposure (34 °C) and after temperature recovery (26 °C). Histological analysis showed that fish from the NT under acute high-temperature stress exhibited severe muscle damage (atrophy, myofilament disruption, and myolysis), whereas fish from the HT displayed markedly reduced lesions. RNA-seq profiling revealed 5769 differentially expressed genes (DEGs) in the NT and 3292 DEGs in the HT following acute temperature challenges. Functional enrichment indicated that, in the HT, modulation of key cell cycle regulators (e.g., ccna, ccnb, cdk1, cdk2) contributed to alleviating muscle damage caused by temperature fluctuations. In the NT, genes associated with ribosome biogenesis (e.g., nop56, riok2, riok1) were up-regulated and then down-regulated during temperature fluctuation, whereas p53 in the cell cycle pathway showed the opposite expression pattern. These findings demonstrate long-term heat exposure reshapes molecular expression and regulatory mechanisms in the muscle of C. fuscus, thereby enhancing thermal tolerance and adaptability, and providing a theoretical basis for breeding heat-resistant, high-quality aquaculture strains.

Animals

Experimental evolution reveals contrasting adaptive landscapes in lab and field environments.

Experimental evolution is widely used to infer microbial responses to environmental change, yet most laboratory studies impose constant, well-mixed conditions that differ fundamentally from fluctuating, spatially structured field environments. We compared genomic evolution in the leaf litter-associated bacterium Curtobacterium strain MMLR14_002 under control and warming treatments in laboratory culture and in a complementary field experiment. Laboratory-derived isolates accumulated more mutations per genome and exhibited stronger locus-level parallelism, with mutations recurring in a small number of coding loci. Field-derived isolates accumulated fewer mutations per genome, and these mutations rarely occurred in the same coding loci across replicate populations. Instead, field isolates exhibited a higher proportion of intergenic mutations, with mutations recurring in the same intergenic regions across independent field deployments. When coding mutations were detected in the field, they were distributed across functionally diffuse targets and more often involved metabolic pathways than the core cellular processes repeatedly targeted during laboratory evolution. Warming itself did not consistently influence mutation accumulation or the genomic distribution of mutations; instead, laboratory and field contexts primarily shaped the accumulation, targets, and repeatability of genomic change. These results suggest that laboratory thermal evolution identifies adaptive routes favored under sustained selection but may overestimate coding-level parallelism under heterogeneous field conditions. Bridging laboratory and field evolution will likely require experimental designs that incorporate temporal variability and spatial heterogeneity characteristic of natural systems.IMPORTANCEA central goal of experimental evolution is to infer how microbes evolve in nature from laboratory studies. Here, we evaluate this assumption by comparing genomic evolution of a leaf litter-associated Curtobacterium strain in laboratory and field warming experiments to identify broad patterns rather than isolate the contribution of any single environmental factor. We find that the strong parallelism at coding loci observed under laboratory conditions is reduced in the field, while mutations recurring in the same intergenic regions across field deployments suggest that parallel evolution in nature may more often involve regulatory noncoding regions rather than coding targets. These results show that environmental context reshapes adaptive landscapes and may limit the parallelism of coding-level genomic responses inferred from homogeneous laboratory conditions.

experimental evolution

[Isolation and detection of avian adenoviruses on cell cultures].

It is important, from the hygienic and epizootological view-point, to detect the presence of various microbiological agents in birds. The authors present the results of the virological examination of poultry, avian adenoviruses being the main object of investigation. Ninety-eight virus strains were isolated from chickens of different age categories and were included in the group of avian adenoviruses according to the form of cytopathic changes on the cell cultures of hen kidneys, according to the need for adaptation passages, chloroform, thermal, and pH resistance, character of nucleic acid, formation of intranuclear inclusions, and joint precipitation antigen, shared with the reference virus.

Adenoviridae

The role of cutaneous mechanoreceptors in thermal sensation and pain.

The functional behavior of slowly adapting cutaneous mechanoreceptors under combined thermal-mechanical stimulation was investigated by single-unit recordings from the lumbar dorsal roots of the cat. Increased sensitivity to bimodal stimulation was observed in 24 of the 28 units studied, employing stimulus-response functional behavior as the basis for judgment. Low-threshold receptors generally did not exhibit increased spontaneous firing as accompaniment to heightened sensitivity, while such enhanced basal activity was usually observed in moderate-threshold units in addition to increased reactivity. Information theory calculations performed on these stimulus-response data revealed that 15 of the 24 "heat-sensitive" receptors were additionally characterized by an enhanced ability to transmit neural information under bimodal stimulation. These results were interpreted as supporting pattern theories of pain as opposed to the concept of receptor specificity. No contradiction was observed, however, between the present results and those of other investigators. The present conclusions derive from new criteria for thermal reactivity based upon innovative stimulus conditions.

Animals

The dynamic response of warm units in human skin nerves.

Electrophysiological recordings were made from 12 specific warm receptors in the sensory nerves of human hairy skin. In all cases examined, single warm fibers were spontaneously active at normal skin temperature from about 32 degrees C upwards, while touch, stretching, vibration or pricking the skin did not elicit any response within the receptive fields of warm units. Moderate warming of the skin using linear temperature rates from 0.5 degrees C/s to 1.5 degrees C/s caused a transient overshoot in the frequency of discharge with peak frequencies depending on the rate of change of temperature (dT/dt), the magnitude of thermal increment (deltaT) and the adapting temperature (TA). Cooling the skin caused a transient inhibition of discharge.

Adult

Evolutionary adaptation of membranes to temperature.

The "fluidity" of brain synaptosomal membrane preparations of arctic and hot-springs fish species, two temperature water fish species acclimated to different seasonal temperatures, and two mammals was estimated using the fluorescence polarization technique. At all measurement temperatures, the fluidity decreased in the order: arctic sculpin, 5 degrees-acclimated goldfish, 25 degrees-acclimated goldfish, desert pupfish, and rat. This correlated with increasing adaptation or body (i.e., cellular) temperatures of 0 degrees, 5 degrees, 25 degrees, 34 degrees, and 37 degrees and suggested a partial compensation of membrane fluidity for environmental temperature that occurs over the evolutionary time period as well as during laboratory (seasonal) acclimation. Evolutionary adaptation of relatively stenothermal species to constant thermal environments resulted in a more complete compensation than laboratory (seasonal) acclimation. Each compensation is accompanied by differences in the saturation of membrane phosphoglycerides. At increased cellular temperatures the proportion of saturated fatty acids increased and the unsaturation index decreased; the correlation between these indices and the measured expression of membrane dynamic structure was highly significant. It is concluded that the homeoviscous compensation of synaptic membrane function is an important component of temperature adaptation.

Adaptation, Physiological

Epitranscriptomic erasers in bivalves: Evolutionary divergence and species-specific transcriptional plasticity of the ALKBH family under acute thermal stress.

The AlkB homolog (ALKBH) family of Fe(II)/α-ketoglutarate-dependent dioxygenases mediates nucleic acid demethylation, thereby governing RNA metabolism and genomic stability. Despite their pivotal roles in epitranscriptomic regulation across vertebrates, the evolutionary dynamics and functional significance of ALKBH proteins in bivalve mollusks remain largely unexplored. Here, we present a comprehensive phylogenomic analysis of 210 ALKBH genes identified across 35 bivalve species. Our analyses reveal a distinct evolutionary trajectory characterized by the lineage-specific loss of ALKBH4 and the restricted distribution of ALKBH5 to the Mytilidae family, contrasting sharply with vertebrate repertoires. Using the noble scallop (Chlamys nobilis) and Pacific oyster (Crassostrea gigas) as model systems, we demonstrate that ALKBH genes exhibit conserved spatiotemporal expression patterns, with pronounced enrichment in gonadal tissues and during metamorphic transitions, implicating these enzymes in gametogenesis and larval development. Furthermore, comparative thermal stress experiments reveal divergent transcriptional plasticity: the subtropical scallop C. nobilis mounts rapid, transient induction of ALKBH1/2/6 under heat shock, whereas the eurythermal oyster C. gigas maintains sustained ALKBH3 expression, potentially underpinning its superior thermal tolerance. Conversely, cold stress elicits bimodal regulation in C. nobilis, with ALKBH1/2 upregulation contrasting with ALKBH6/7/8 suppression. These findings illuminate the functional diversification of bivalve ALKBH genes and their potential utility as molecular biomarkers for assessing developmental competence and thermal resilience in shellfish aquaculture.

Animals

Maternal and developmental temperature modulate adult response to temperature in Drosophila melanogaster.

Beyond inherited genes and environmentally induced changes in gene expression, phenotypes can also be shaped by parental effects-an effect from a parental phenotype that causes modifications in offspring traits, which cannot be solely explained by the parental or offspring genomes. Such effects may prepare offspring for future environmental conditions and contribute to phenotypic plasticity, including responses to temperature. While temperature-induced plasticity has been extensively studied, the relative contributions of parental versus direct environmental cues remain poorly understood. The fruit fly Drosophila melanogaster is a powerful model for studying physiological and behavioral adaptation to temperature. Flies inhabit environments spanning broad thermal ranges and show evidence of parental effects, such as increased heat tolerance in offspring from warm-reared parents. Here, we exposed mothers to two experimental temperatures and split their broods between the same two temperatures to estimate the relative importance of maternal and developmental effects on adult physiological and developmental responses to temperature. We find that the reaction norms of locomotor activity under gradually increasing temperatures, responses to heat-shock and cold-shock, and fecundity are mostly governed by direct plastic responses to developmental environment. We detected comparatively weak maternal effects in the response to heat-shock, fecundity, and grand-offspring survival where matched environments counteracted the effects of direct offspring experience. We conclude that thermal experience during development is the primary determinant of phenotypic plasticity in D. melanogaster, while maternal experience contributes a small but non-negligible component.

Animals

A review of selected biological effects and dosimetric data useful for development of radiofrequency safety standards for human exposure.

This report examines the bases for developing radiofrequency exposure standards which can be related to the thermogenic properties of electromagnetic fields. A review of selected biological effects, including dosimetric data and simulation of human thermodyanmic characteristics that are pertinent to standards development, is presented. Based on the analogy of thermal-stress standards that have been developed for hot industrial environments, limits on increases of body temperature are proposed as criteria for limiting exposure to radiofrequency fields, i.e., occupational exposures involving deep heating of the whole body should not increase core temperature in excess of 1 degree C. Since energy deposition from exposure to some RF fields is likely to be non-uniform and may be high in tissues that are not adapted to high rates of absorption or dissipation of thermalizing energy, means are needed to adjust focal thermal loading against the whole-body averages. A limit on core temperature is inadequate when focal elevations of temperature are close to the limits for protein denaturation, as may well occur even though the core temperature may rise less than 1 degree C. Safety limits for the general population are also discussed and here the permissible thermal load should be low enough to cause no more than an insignificant increase in core temperature. Areas needing further research to reduce the uncertainties in developing safe exposure limits for man are delineated. Even in highly adverse environmental conditions the gross thermal load and consequential heat stress from exposure to radiofrequency fields at the 10 mW/cm2 level will be small compared with that generated by any physical effort. On the basis of available data, it is concluded that the safe value for continuous exposure to 10 mW/cm2, widely used in Western countries, appears to provide an adequate margin of safety for both occupational and environmental exposure for frequencies above about 1 GHz. This limit may well be too high (perhaps by an order of magnitude) for some frequencies below 1 GHz where body resonances cause a significant increase in energy deposition and where local temperature rises occur. At the same time the present averaging period of 0.1 h seems unjustifiably short.

Animals

Changes in hypothalamic noradrenaline and 5-hydroxytryptamine levels during the development of warm- and cold-adaptation in the rat.

Hypothalamic 5-hydroxytryptamine (5-HT) and noradrenaline (NA) as well as plasma corticosterone levels were studied in male rats after 1, 2, 4 and 6 weeks of exposure to 4--7 or 30--31 degrees C. An increase of the NA concentration and a decrease of the 5-HT level was observed after the first week in both cold and warm environment together with an increase of plasma corticosterone levels in both groups. NA, 5-HT and plasma corticosterone levels returned to normal in cold-exposed animals by the 6th week whereas in warm-acclimated rats NA and corticosterone levels regained their initial values and 5-HT concentrations remained low. Changes by the end of the first week of exposure may result from the thermal stress. The low 5-HT levels of warm-adapted animals at the end of the 6th week were probably secondary to the process of adaptation.

Adaptation, Physiological

Thermoregulatory behaviour after repetitive cooling of the preoptic area and of the spinal cord in the rat.

The thermoregulatory behaviour of 6 rats was studied during exposure to cold and warm ambient temperatures after either the preoptic area or the cervical spinal cord had been intermittently cooled for an average of 130 h. The precooled animals worked more for heat in cold environments and for cool air in a warm environment than the control animals. This behaviour, probably due to a decreased ability of the precooled animals to retain heat, suggested that the precooled animals were not fully adapted to cold. 1974) will learn to press a lever to modify their thermal environment, and this paper describes the thermoregulatory behaviour of rats after prolonged cooling of the preoptic area, and of the spinal cord. The thermoregulatory behaviour of cold exposed and cold adapted animals has already been studied in several species (Carlton and Marks, 1958; Laties and Weiss, 1960; Revusky, 1966; balwin and Ingram, 1967).

Adaptation, Physiological

A low temperature investigation of the intermediates of the photocycle of light-adapted bacteriorhodopsin. Optical absorption and fluorescence measurements.

Optical absorption and emission measurements have been made on samples of light-adapted purple membrane of Halobacterium halobium at temperatures ranging from 77 K to room temperature. As a result of these experiments a set of equations is given which described thermal and photochemical reactions interrelating various intermediates of the reaction cycle of the chromophore of light-adapted bacteriorhodopsin (BR). Further some specific problems connected to these intermediates have been investigated. Thus the room temperature emission spectrum of bacteriorhodopsin has been found to exhibit a Stokes shift of 3430 cm-1 only, if low excitation intensities are used. The recently detected intermiediate P-BR can be shown to convert thermally into bacteriorhodopsin following a first-order decay with the activation energy delta E = 2.4 +/- 0.2 kcal/mol. The thermal decay of K-BR consists of two exponentials if measured on purple membrane suspensions in a mixture of H2O and glycerol (1 : 1, v/v). A simple procedure is given for trapping the intermediate L-BR at 170 K in a very pure form. M-BR is shown to consist of two species, MI-BR and MII-BR. They are characterized by similar optical absorption spectra but different thermal stability. Further the oscillator strengths corresponding to the long wavelength absorption bands of the intermediates bacteriorhodopsin, K-, L, MI- and MII-BR have been calculated. They have been discussed with respect to the question which of the corresponding absorption spectra show the characteristics of isomerism of the chromophore or simply solvatochromism.

Bacteriorhodopsins

Adaptation of biological membranes to temperature. The lack of homeoviscous adaptation in the sarcoplasmic reticulum.

Temperature adaptation of biological membranes was examined by comparing the fragmented sarcoplasmic reticulum preparation of goldfish acclimated to different temperatures. Membrane fluidity was estimated using the fluorescence polarization technique. There was considerable variation between preparations, but no consistent differences in fluidity were observed between 5- and 25 degrees C-acclimated goldfish, fish species adapted over an evolutionary period to arctic or desert temperatures, and rat. The fatty acid composition of the sarcoplamic reticulum preparations of differently acclimated goldfish showed differences in the proportion of mono- and polyunsaturated fatty acids while the proportion of saturated fatty acids remained relatively constant. However, the fatty acid composition of sarcoplasmic reticulum phosphoglycerides became more unsaturated in the order rat, desert pupfish, arctic sculpin, which correlates with their respective environmental or body temperature. It is concluded that differences in membrane components other than fatty acids are important in determining membrane dynamic structure. The inability to demonstrate homeoviscous adaptation in sarcoplasmic reticulum is supported by other evidence suggesting that functions of the sarcoplasmic reticulum that are measured in vitro are not affected by such modifications of their phosphoglyceride fatty acid composition as occur during thermal acclimation.

Adaptation, Biological