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Results for “Evolutionary adaptability”

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PubMed1998

Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins.

3-Isopropylmalate dehydrogenase (IPMDH, E.C. 1.1.1.85) from the thermophilic bacterium Thermus thermophilus HB8 is homologous to IPMDH from the mesophilic Escherichia coli, but has an approximately 17 degreesC higher melting temperature. Its temperature optimum is 22-25 degreesC higher than that of the E. coli enzyme; however, it is hardly active at room temperature. The increased conformational rigidity required to stabilize the thermophilic enzyme against heat denaturation might explain its different temperature-activity profile. Hydrogen/deuterium exchange studies were performed on this thermophilic-mesophilic enzyme pair to compare their conformational flexibilities. It was found that Th. thermophilus IPMDH is significantly more rigid at room temperature than E. coli IPMDH, whereas the enzymes have nearly identical flexibilities under their respective optimal working conditions, suggesting that evolutionary adaptation tends to maintain a "corresponding state" regarding conformational flexibility. These observations confirm that conformational fluctuations necessary for catalytic function are restricted at room temperature in the thermophilic enzyme, suggesting a close relationship between conformational flexibility and enzyme function.

3-Isopropylmalate Dehydrogenase↗

PubMed2025

Genetic and phenotypic diversity of wine-associated Hanseniaspora species.

The genus Hanseniaspora includes apiculate yeasts commonly found in fruit- and fermentation-associated environments. Their genetic diversity and evolutionary adaptations remain largely unexplored despite their ecological and oenological significance. This study investigated the phylogenetic relationships, genome structure, selection patterns, and phenotypic diversity of Hanseniaspora species isolated primarily from Australian wine environments, focusing on Hanseniaspora uvarum, the most abundant non-Saccharomyces yeast in wine fermentation. A total of 151 isolates were sequenced, including long-read genomes for representatives of the main phylogenetic clades. Comparative genomics revealed ancestral chromosomal rearrangements between the slow-evolving lineage (SEL) and fast-evolving lineage (FEL) that could have contributed to their evolutionary split, as well as significant loss of genes associated with mRNA splicing, chromatid segregation and signal recognition particle protein targeting in the FEL. Pangenome analysis within H. uvarum identified extensive copy number variation, particularly in genes related to xenobiotic tolerance and nutrient transport. Investigation into the selective landscape following the FEL/SEL divergence identified diversifying selection in 229 genes in the FEL, with significant enrichment in genes within the lysine biosynthetic pathway. Furthermore, phenotypic screening of 116 isolates revealed substantial intraspecific diversity, with specific species exhibiting enhanced ethanol, osmotic, copper, SO₂, and cold tolerance.

Wine↗

PubMed1983

On a functional-morphological approach to phylogenetic reconstruction: a critique.

A method of phylogenetic reconstruction as proposed by a number of scientists of the Senckenberg Research Institute is discussed. The method is based on functional-morphological studies, the evolutionary adaptation principle of Bock and Von Wahlert (1965) and so-called model reconstruction. It is argued in this paper that direction of the adaptation process cannot be determined because of lack of knowledge about particular selective forces and that theories of model reconstruction are not open to contradiction in the sense of Popperian falsification. Although it has been claimed that the method provides the only valid directional argument for morphoclines in cladistic studies, it remains unclear how to proceed when morphoclines show contradictory polarities. Moreover, it is doubtful whether polarities of morphoclines can be determined independently of phylogenetic hypotheses, and also whether the use of multistate morphoclines is methodologically valid. By relying on a particular evolutionary theory, i.e. the neo-Darwinian theory, and consequently assigning natural selection as the major agent of directional progress, the Senckenburg method of phylogenetic reconstruction restricts itself to microevolutionary change and, therefore, cannot be used when other hypotheses on the evolutionary process appear to explain the speciation process more plausibly, i.e. hypotheses on macroevolution. Furthermore, it is an unproved statement that evolution always proceeds according to the principle of economy.

Animals↗

PubMed2002

Endothelial response to hypoxia: physiologic adaptation and pathologic dysfunction.

When subjected to a period of oxygen deprivation, endothelial cells exhibit a characteristic pattern of responses that can be considered either adaptive or pathologic, depending on the circumstances. In this review, the molecular basis for these responses is detailed. Hypoxia shifts the endothelial phenotype towards one in which anticoagulant properties are diminished, permeability and leukoadhesivity are increased, and proinflammatory features dominate the endovascular milieu. Of all the different points of intersection between the coagulation and inflammatory axes in the vasculature, perhaps most fundamentally, hypoxia alters several key transcriptional factors, including early growth response gene 1 (Egr1) and hypoxia-inducible factor (HIF) 1, which coordinate separate programs of gene activation. The preponderance of forces in the hypoxic endovascular environment, perhaps designed as an evolutionary adaptation to oxygen deprivation, can trigger severe, pathologic, clinical consequences in the setting of tissue ischemia.

Adaptation, Physiological↗

PubMed2004

Changes in gene expression as biochemical adaptations to environmental change: a tribute to Peter Hochachka.

Changes in gene expression are likely to play a critical role in both acclimation and adaptation to a changing environment. There is a rapidly growing body of literature implicating quantitative changes in gene expression during acclimation to environmental change, but less is known about the role of qualitative changes in gene expression, such as switching between alternative isoforms. Alternative isoforms can arise via gene duplication, alternative splicing, or alternative promoter usage. Organisms that have undergone recent genome duplication events may make use of environment-specific isoforms coded by multiple genes, but their role in other organisms is less well known. However, recent data suggest that isoforms arising from alternative splicing may be an under-appreciated source of physiological variation. The role of changes in gene expression during evolutionary adaptation has received comparatively limited attention, but novel approaches to addressing the adaptive significance of changes in gene expression have been applied to a few cases of differences in gene expression among taxa. Recent advances in genomics, including microarray technology, knock-out and knock-down approaches, and the wealth of data coming from large-scale sequencing projects have provided (and will continue to provide at ever increasing rates) new insights into these classic questions in comparative biochemistry.

Adaptation, Physiological↗

PubMed2000

Phototropism: a "simple" physiological response modulated by multiple interacting photosensory-response pathways.

Phototropism is the process by which plants reorient growth of various organs, most notably stems, in response to lateral differences in light quantity and/or quality. The ubiquitous nature of the phototropic response in the plant kingdom implies that it provides some adaptive evolutionary advantage. Upon visual inspection it is tempting to surmise that phototropic curvatures result from a relatively simple growth response to a directional stimulus. However, detailed photophysiological, and more recently genetic and molecular, studies have demonstrated that phototropism is in fact regulated by complex interactions among several photosensory systems. At least two receptors, phototropin and a presently unidentified receptor, appear to mediate the primary photoreception of directional blue light cues in dark-grown plants. PhyB may also function as a primary receptor to detect lateral increases in far-red light in neighbor-avoidance responses of light-grown plants. Phytochromes (phyA and phyB at a minimum) also appear to function as secondary receptors to regulate adaptation processes that ultimately modulate the magnitude of curvature induced by primary photoperception. As a result of the interactions of these multiple photosensory systems plants are able to maximize the adaptive advantage of the phototropic response in ever changing light environments.

Adaptation, Physiological↗

PubMed2002

Evolution of the visual cycle: the role of retinoid-binding proteins.

The trafficking of retinoids in the retina represents a model to study soluble hormone-binding proteins in a complex system subject to profound evolutionary adaptations. Although a remarkable illustration of convergent evolution, all visual systems detect light in the same way, that is through the photoisomerization of an 11-cis retinoid to a corresponding trans isomer. What is strikingly different between the systems, is the mechanism by which the 11-cis chromophore is reformed and visual pigment regenerated in a process known as the visual cycle. The variations of the cycle address a problem inherent to retinoids themselves. That is, the properties that make these molecules suited for light detection also account for their susceptibility to oxidative and isomeric degradation, and cellular toxicity. The cycle therefore provides an opportunity to examine the role of soluble hormone-binding proteins within an integrative and evolutionary context. The present review focuses on interphotoreceptor retinoid-binding protein (IRBP), a controversial glycolipoprotein that recruits a protein fold common to Cterminal-processing proteases and the crotonase family. This unorthodox retinoid-binding protein is entrapped in the subretinal compartment of those eyes that translocate visual cycle retinoids between the photoreceptors and the retinal pigment epithelium. Recent studies suggest that we should look beyond a strictly carrier function if we are to appreciate the role of IRBP in the visual cycle. Here we draw lessons from other soluble hormone-binding proteins to anticipate avenues of future research likely to provide insight into the structure and function of IRBP in vision.

Amino Acid Sequence↗

PubMed2005

Mongoose rabies in southern Africa: a re-evaluation based on molecular epidemiology.

Relative to the developed world, rabies has been poorly studied in the vast African continent. The southern African countries of Zimbabwe and South Africa, however, are known to sustain a great diversity of lyssaviruses, with large biological variations amongst genotype 1 (rabies viruses) at present more apparent here than elsewhere on the continent. One recognized biotype of rabies virus in the subcontinent appears to be specifically adapted to a variety of mongooses, belonging to the Viverrinae subfamily (family Herpestidae) and are commonly referred to as viverrid viruses, although the term mongoose rabies would be more correct, considering the taxonomic status of the host species involved. It was our objective to study the genetic relationships of 77 rabies virus isolates of this mongoose biotype, isolated in South Africa and Zimbabwe, towards elucidation of the molecular epidemiology of this interesting group of African viruses. In our study of a 592 nucleotide sequence encompassing the cytoplasmic domain of the glycoprotein and the G-L intergenic region of the viral genomes, we provide the first comprehensive data on the molecular epidemiology of these viruses and indicate a history of extended evolutionary adaptation in this geographical domain. The molecular epidemiological observations reported here are highly unlikely to be limited to the small geographical areas of South Africa and Zimbabwe and illustrate the need for lyssavirus surveillance in the rest of sub-Saharan Africa and throughout the entire continent.

Adaptation, Biological↗

PubMed2025

Large future genetic diversity losses are predicted even with habitat protection.

Genetic diversity within species is the basis for evolutionary adaptive capacity and has recently been included as a target for protection in the United Nations' Global Biodiversity Framework (GBF). However, we lack large-scale mathematical frameworks to quantify how much genetic diversity has already been lost, let alone to predict future losses under 21st century conservation scenarios. To fill this gap, we developed an area-based spatio-temporal predictive framework of genetic diversity calibrated with population-scale genomic data of 29 plant and animal species. To estimate present genetic diversity loss with our framework, we used species' habitat area and population sizes losses reported in the Living Planet Index, the Red List, and new GBF indicators across 13,808 species for the last 5 decades. Applying our evolutionary framework across these species, we estimate genetic diversity loss lags behind population and habitat area declines, with an estimated current 13-22% π genetic diversity loss. However, we forecast future genetic diversity losses will reach 41-76% even if populations are not further contracted. These results highlight that safeguarding existing habitats is insufficient to maintain the genetic health of species and relying solely on continuous genetic monitoring underestimates lagging long term impacts.

Genetic diversity↗

PubMed2005

Eucalyptus foliar chemistry explains selective feeding by koalas.

The koala is the quintessential specialist herbivore, feeding almost exclusively on Eucalyptus foliage. Consequently, the limitations imposed on the koala's diet by plant defences indicate the extent to which evolutionary adaptations allow mammalian herbivores to circumvent such defences. We tested whether a recently discovered group of plant secondary metabolites, the formylated phloroglucinol compounds (FPCs), deters koalas from feeding on some eucalypt foliage. We found that captive koalas ate less foliage in a single night from trees with high FPC concentrations. Individual trees also differ in the types of FPC they possess, but for a given eucalypt species, most FPCs were similarly effective deterrents. Two closely related and sympatric eucalypt species could be clearly separated by the amounts that koalas ate from each; however, this difference could not be explained by total FPC concentrations alone. We suggest, that in this case, the presence of a distinct type of FPC deters koala herbivory on the less palatable species, and may have facilitated the evolutionary divergence of these species. We conclude that plant defences probably play an important role in determining the distribution and abundance of koalas.

Animals↗

PubMed2003

Evolutionary convergence in adaptation of proteins to temperature: A4-lactate dehydrogenases of Pacific damselfishes (Chromis spp.).

We have compared the kinetic properties (Michaelis-Menten constant [K(m)] and catalytic rate constant [k(cat)]) and amino acid sequences of orthologs of lactate dehydrogenase-A (A(4)-LDH) from congeners of Pacific damselfishes (genus Chromis) native to cold-temperate and tropical habitats to elucidate mechanisms of enzymatic adaptation to temperature. Specifically, we determined whether the sites of adaptive variation and the types of amino acids involved in substitutions at these sites were similar in the Chromis orthologs and other orthologs of warm-adapted and cold-adapted A(4)-LDH previously studied. We report striking evolutionary convergence in temperature adaptation of this protein and present further support for the hypothesis that enzyme adaptation to temperature involves subtle amino acid changes at a few sites that affect the mobility of the portions of the enzyme that are involved in rate-determining catalytic conformational changes. We tested the predicted effects of differences in sequence using site-directed mutagenesis. A single amino acid substitution in a key hinge region of the A(4)-LDH molecule is sufficient to change the kinetic characteristics of a temperate A(4)-LDH to that of a tropical ortholog. This substitution is at the same location that was identified in previous studies of adaptive variation in A(4)-LDH and was hypothesized to be important in adjusting K(m) and k(cat). Our results suggest that certain sites within an enzyme, notably those that establish the energy changes associated with rate-limiting movements of protein structure during catalysis, are "hot spots" of adaptation and that common types of amino acid substitutions occur at these sites to adapt structural "flexibility" and kinetic properties. Thus, despite the wide array of options that proteins have to adjust their structural stabilities in the face of thermal stress, the adaptive changes that couple "flexibility" to alterations of function may be limited in their diversity.

Adaptation, Physiological↗

PubMed2004

Mammalian microevolution in action: adaptive edaphic genomic divergence in blind subterranean mole-rats.

Genomic diversity of anonymous regions across the genome, most probably including coding and noncoding amplified fragment length polymorphisms (AFLPs), was examined in 20 individuals of the blind mole-rat, Spalax galili, one of four allospecies of the Spalax ehrenbergi superspecies of blind subterranean mole-rats in Israel. We compared 10 individuals from two nearby populations in Upper Galilee, separated by only a few dozen to hundreds of metres and living in two sharply contrasting ecologies: white chalk and rendzina soil with Sarcopterium spinosum and Majorana syriaca versus black volcanic basalt soil with Carlina hispanica-Psorelea bitominosa and Alhagi graecorum plant formations. The microsite tested ranged in an area of less than 10000 m2. Out of 729 AFLP loci, 433 (59.4%) were polymorphic, with 211 soil unique alleles. Genetic polymorphism was significantly higher on the ecologically more xeric and stressful chalky rendzina soil than on the neighbouring mesic basalt soil. This is a remarkable pattern for a mammal that can disperse each generation between tens to hundreds of metres. These results cannot be explained by migration (which causes homogenization) or by chance (which will exclude sharp genomic soil divergence). Natural selection is the only evolutionary adaptive force that can cause genetic divergence across the genome matching the sharp microscale ecological contrast.

Animals↗

PubMed2026

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. Using a pedigree and whole genome sequencing data, we characterized the genetic basis of CTMax (as a metric of upper thermal tolerance) across control and elevated rearing temperatures, alongside covarying traits (body size and degree of hatchery ancestry). Warmer rearing temperatures increased CTMax through acclimation but also resulted in reduced additive genetic variation for the trait. 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 (i.e., many loci detected with a GxE effect). This temperature-dependent genomic architecture is consistent with our finding that additive genetic variation for CTMax was reduced under warmer rearing conditions, indicating a potential constraint on adaptive evolutionary change. 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 captive management and may inform supplementation of fish to the wild in an ever-warming environment.

conservation physiology↗

PubMed2005

The photoactivation energy of the visual pigment in two spectrally different populations of Mysis relicta (Crustacea, Mysida).

We report the first study of the relation between the wavelength of maximum absorbance (lambdamax) and the photoactivation energy (Ea) in invertebrate visual pigments. Two populations of the opossum shrimp Mysis relicta were compared. The two have been separated for 9,000 years and have adapted to different spectral environments ("Sea" and "Lake") with porphyropsins peaking at lambdamax=529 nm and 554 nm, respectively. The estimation of Ea was based on measurement of temperature effects on the spectral sensitivity of the eye. In accordance with theory (Stiles in Transactions of the optical convention of the worshipful company of spectacle makers. Spectacle Makers' Co., London, 1948), relative sensitivity to long wavelengths increased with rising temperature. The estimates calculated from this effect are Ea,529=47.8+/-1.8 kcal/mol and Ea,554=41.5+/-0.7 kcal/mol (different at P<0.01). Thus the red-shift of lambdamax in the "Lake" population, correlating with the long-wavelength dominated light environment, is achieved by changes in the opsin that decrease the energy gap between the ground state and the first excited state of the chromophore. We propose that this will carry a cost in terms of increased thermal noise, and that evolutionary adaptation of the visual pigment to the light environment is directed towards maximizing the signal-to-noise ratio rather than the quantum catch.

Animals↗

PubMed2006

Evolutionary origin of Venturia canescens virus-like particles.

Insect host-parasitoid interactions provide fascinating examples of evolutionary adaptations in which the parasitoid employs a variety of measures and countermeasures to overcome the immune responses of its host. Maternal factors introduced by the female wasps during egg deposition play an important role in interfering with cellular and humoral components of the host's immune defence. Some of these components actively suppress host immune components and some are believed to confer protection for the developing endoparasitoid by rather passive means. The Venturia canescens/Ephestia kuehniella parasitoid-host system is unique among other systems in that the cellular defence capacity of the host remains virtually intact after parasitization. This system raises some important questions that are discussed in this mini-review: If immune protection of the egg and the emerging larva is achieved by surface properties comprising glycoproteins and virus-like particles (VLPs) produced by the female wasp, why is the prophenoloxidase activating cascade blocked in parasitized caterpillars? Another question is the evolutionary origin of these particles, given that the functional role and structural features of V. canescens VLP proteins are more related to cellular proteins than to viruses.

Animals↗

PubMed2002

Adaptation of protein secretion to extremely high-salt conditions by extensive use of the twin-arginine translocation pathway.

Halophilic archaea thrive in environments with salt concentrations approaching saturation. However, little is known about the way in which these organisms stabilize their secreted proteins in such 'hostile' conditions. Here, we present data suggesting that the utilization of protein translocation pathways for protein secretion by the Halobacteriaceae differs significantly from that of non-haloarchaea, and most probably represents an adaptation to the high-salt environment. Although most proteins are secreted via the general secretion (Sec) machinery, the twin-arginine translocation (Tat) pathway is mainly used for the secretion of redox proteins and is distinct from the Sec pathway, in that it allows cytoplasmic folding of secreted proteins. tatfind (developed in this study) was used for systematic whole-genome analysis of Halobacterium sp. NRC-1 and several other prokaryotes to identify putative Tat substrates. Our analyses revealed that the vast majority of haloarchaeal secreted proteins were predicted substrates of the Tat pathway. Strikingly, most of these putative Tat substrates were non-redox proteins, the homologues of which in non-haloarchaea were identified as putative Sec substrates. We confirmed experimentally that the secretion of one such putative Tat substrate depended on the twin-arginine motif in its signal sequence. This extensive utilization of the Tat pathway in haloarchaea suggests an evolutionary adaptation to high-salt conditions by allowing cytoplasmic folding of secreted proteins before their secretion.

Adaptation, Physiological↗

PubMed1996

Long-term experimental evolution in Escherichia coli. IV. Targets of selection and the specificity of adaptation.

This study investigates the physiological manifestation of adaptive evolutionary change in 12 replicate populations of Escherichia coli that were propagated for 2000 generations in a glucose-limited environment. Representative genotypes from each population were assayed for fitness relative to their common ancestor in the experimental glucose environment and in 11 novel single-nutrient environments. After 2000 generations, the 12 derived genotypes had diverged into at least six distinct phenotypic classes. The nutrients were classified into four groups based upon their uptake physiology. All 12 derived genotypes improved in fitness by similar amounts in the glucose environment, and this pattern of parallel fitness gains was also seen in those novel environments where the limiting nutrient shared uptake mechanisms with glucose. Fitness showed little or no consistent improvement, but much greater genetic variation, in novel environments where the limiting nutrient differed from glucose in its uptake mechanisms. This pattern of fitness variation in the novel nutrient environments suggests that the independently derived genotypes adapted to the glucose environment by similar, but not identical, changes in the physiological mechanisms for moving glucose across both the inner and outer membranes.

Adaptation, Physiological↗

PubMed2001

Limits to human locomotor performance: phylogenetic origins and comparative perspectives.

Studies of human exercise physiology have been conducted from a largely ahistorical perspective. This approach usefully elucidates proximate limits to locomotor performance, but ignores potential sources of biomechanical and physiological variation that derive from adaptation to ancestral environments. Phylogenetic reconstruction suggests that multiple hominoid lineages, including that leading to Homo sapiens, evolved in African highlands at altitudes of 1000-2000 m. The evolution of human locomotor physiology therefore occurred under conditions of hypobaric hypoxia. In contrast to present-day humans running on treadmills or exercising in otherwise rectilinear trajectories, ancestral patterns of hominid locomotion probably involved intermittent knuckle-walking over variable terrain, occasional bouts of arboreality and an evolving capacity for bipedalism. All such factors represent potential axes of locomotor variation at present unstudied in extant hominoid taxa. As with humans, hummingbirds evolved in mid-montane contexts but pose an extreme contrast with respect to body size, locomotor mode and metabolic capacity. Substantial biomechanical and physiological challenges are associated with flight in hypobaria. Nonetheless, hummingbird lineages demonstrate a progressive invasion of higher elevations and a remarkable tolerance to hypoxia during hovering. Upregulation of aerobic capacity and parallel resistance to hypoxia may represent coupled evolutionary adaptations to flight under high-altitude conditions.

Altitude↗