Paleochronobiology circadian rhythms, gauges of adaptive Darwinian evolution; about 7-day (circaseptan) rhythms, gauges of integrative internal evolution.
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Animals↗
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[Evolution of adaptation technics for contact lenses].
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Adaptation, Ocular↗
The evolution and adaptive value of fever.
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Adaptation, Physiological↗
Adaptive mutation: has the unicorn landed?
Reversion of an episomal Lac- allele during lactose selection has been studied as a model for adaptive mutation. Although recent results show that the mutations that arise during selection are not "adaptive" in the original sense, the mutagenic mechanism that produces these mutations may nonetheless be of evolutionary significance. In addition, a transient mutational state induced in a subpopulation of starving cells could provide a species with a mechanism for adaptive evolution.
Adaptation, Biological↗
Barriers to horizontal gene transfer by natural transformation in soil bacteria.
Bacteria can utilize horizontally transferred DNA from other bacterial species to adapt and evolve to their changing environments. Natural transformation is a process that allows bacteria, which are able to express a regulated physiological state of competence, to take up and integrate free DNA from their surroundings. This uptake of DNA does not necessarily depend on DNA sequence, thus, indicating the potential of gene transfer from diverged donor organisms. Barriers active against such interspecies transfer are present at different phases of the transformation process. The functionality of these barriers will be discussed, and seen in relation to mechanisms that may enable bacterial cells to respond to environmental stress by adaptive evolution.
Adaptation, Biological↗
Structural genome variation drives adaptation of the xylose-fermenting yeast Scheffersomyces stipitis to lignocellulosic hydrolysates.
Second-generation (2G) bioethanol from lignocellulosic feedstocks is a sustainable alternative to fossil fuels. However, its production is constrained by the poor performance of industrial microbes in hydrolysates that are generated during biomass pretreatment. Scheffersomyces stipitis is a native xylose fermenting yeast and a promising platform for 2G bioethanol production, and adaptive evolution under hydrolysate stress has yielded strains with enhanced performance. However, the chromosomal basis of this adaptation is unknown. Here, we demonstrate that chromosome scale structural variation, rather than point mutations, underlies the improved phenotype of the evolved strains. By integrating long- and short-read genome sequencing, we identify two major chromosomal rearrangements in the top performing isolate: a reciprocal translocation between chromosomes 1 and 2 that disrupts the NUDIX hydrolase gene YSA1, and the formation of a mitotically stable 175 kb minichromosome derived from chromosome 5. Functional analyses show that disruption of YSA1 enhances xylose utilisation and ethanol yield, while the minichromosome contributes to improved performance in hydrolysate conditions. These findings provide direct evidence that balanced rearrangements and minichromosome formation can be selected during prolonged stress and can generate adaptive phenotypes. Taken together, our study establishes genome reorganisation as a key driver of adaptation in S. stipitis.
Xylose↗
Detection of convergent and parallel evolution at the amino acid sequence level.
Adaptive evolution at the molecular level can be studied by detecting convergent and parallel evolution at the amino acid sequence level. For a set of homologous protein sequences, the ancestral amino acids at all interior nodes of the phylogenetic tree of the proteins can be statistically inferred. The amino acid sites that have experienced convergent or parallel changes on independent evolutionary lineages can then be identified by comparing the amino acids at the beginning and end of each lineage. At present, the efficiency of the methods of ancestral sequence inference in identifying convergent and parallel changes is unknown. More seriously, when we identify convergent or parallel changes, it is unclear whether these changes are attributable to random chance. For these reasons, claims of convergent and parallel evolution at the amino acid sequence level have been disputed. We have conducted computer simulations to assess the efficiencies, of the parsimony and Bayesian methods of ancestral sequence inference in identifying convergent and parallel-change sites. Our results showed that the Bayesian method performs better than the parsimony method in identifying parallel changes, and both methods are inefficient in identifying convergent changes. However, the Bayesian method is recommended for estimating the number of convergent-change sites because it gives a conservative estimate. We have developed statistical tests for examining whether the observed numbers of convergent and parallel changes are due to random chance. As an example, we reanalyzed the stomach lysozyme sequences of foregut fermenters and found that parallel evolution is statistically significant, whereas convergent evolution is not well supported.
Amino Acid Sequence↗
Rapid and repeated evolution of increased competitive ability in a global invader.
Rapid adaptive evolution can increase the competitive ability of invasive species in their non-native ranges. However, whether this increase is a general response and what drives it remain uncertain because the evidence is largely based on studies with limited sampling, inadequate consideration of population co-ancestry, and oversimplified estimates of competitive ability. We conduct a large-scale glasshouse experiment testing the effects of competition and drought on 100 native and 165 non-native populations of Erigeron canadensis, all genotyped to account for co-ancestry. Plants from non-native populations are significantly more competitive against other species than the conspecifics from native populations under both mesic and dry conditions. Genetic clustering indicates that the rapid evolution of competitive ability occurs independently in two out of four clusters in the non-native range. This advantage is present only during interspecific interactions and is absent during intraspecific competition. Repeated evolution of increased competitive ability suggests that adaptation following introduction can reshape species interactions and promote invasion success, even under future drought conditions, highlighting the importance of rapid evolution in determining the ecological impacts of invasive plants.
Biological Evolution↗
Molecular evolution of a duplication: the sex-peptide (Acp70A) gene region of Drosophila subobscura and Drosophila madeirensis.
In Drosophila melanogaster, the Acp70A gene, which is involved in the postmating reactions of the female, is a single-copy gene. However, in Drosophila subobscura, the gene is duplicated and both copies are transcribed. To study the molecular evolution of the duplication, a 2.1-kb fragment encompassing both copies of the duplication was sequenced for 10 lines of D. subobscura and one line of Drosophila madeirensis. Estimates of the divergence between the two copies of the duplicated region and between the two species studied, D. subobscura and D. madeirensis, revealed that both copies of the Acp70a gene had evolved independently since their duplication. The ratio of nonsynonymous to silent divergence between copies was generally higher than one. The McDonald and Kreitman test revealed an excess of nonsynonymous changes fixed since the duplication and before the split of the D. subobscura and D. madeirensis lineages. These results point to natural selection driving protein evolution after the duplication. Specifically, adaptive evolution appears to have caused the initial differentiation between copies of the N-terminal parts of the proteins, while purifying selection could be responsible for the high conservation of the C-terminal parts.
Amino Acid Sequence↗
Vestige: maximum likelihood phylogenetic footprinting.
BACKGROUND: Phylogenetic footprinting is the identification of functional regions of DNA by their evolutionary conservation. This is achieved by comparing orthologous regions from multiple species and identifying the DNA regions that have diverged less than neutral DNA. Vestige is a phylogenetic footprinting package built on the PyEvolve toolkit that uses probabilistic molecular evolutionary modelling to represent aspects of sequence evolution, including the conventional divergence measure employed by other footprinting approaches. In addition to measuring the divergence, Vestige allows the expansion of the definition of a phylogenetic footprint to include variation in the distribution of any molecular evolutionary processes. This is achieved by displaying the distribution of model parameters that represent partitions of molecular evolutionary substitutions. Examination of the spatial incidence of these effects across regions of the genome can identify DNA segments that differ in the nature of the evolutionary process. RESULTS: Vestige was applied to a reference dataset of the SCL locus from four species and provided clear identification of the known conserved regions in this dataset. To demonstrate the flexibility to use diverse models of molecular evolution and dissect the nature of the evolutionary process Vestige was used to footprint the Ka/Ks ratio in primate BRCA1 with a codon model of evolution. Two regions of putative adaptive evolution were identified illustrating the ability of Vestige to represent the spatial distribution of distinct molecular evolutionary processes. CONCLUSION: Vestige provides a flexible, open platform for phylogenetic footprinting. Underpinned by the PyEvolve toolkit, Vestige provides a framework for visualising the signatures of evolutionary processes across the genome of numerous organisms simultaneously. By exploiting the maximum-likelihood statistical framework, the complex interplay between mutational processes, DNA repair and selection can be evaluated both spatially (along a sequence alignment) and temporally (for each branch of the tree) providing visual indicators to the attributes and functions of DNA sequences.
Algorithms↗
Protein evolution and codon usage bias on the neo-sex chromosomes of Drosophila miranda.
The neo-sex chromosomes of Drosophila miranda constitute an ideal system to study the effects of recombination on patterns of genome evolution. Due to a fusion of an autosome with the Y chromosome, one homolog is transmitted clonally. Here, I compare patterns of molecular evolution of 18 protein-coding genes located on the recombining neo-X and their homologs on the nonrecombining neo-Y chromosome. The rate of protein evolution has significantly increased on the neo-Y lineage since its formation. Amino acid substitutions are accumulating uniformly among neo-Y-linked genes, as expected if all loci on the neo-Y chromosome suffer from a reduced effectiveness of natural selection. In contrast, there is significant heterogeneity in the rate of protein evolution among neo-X-linked genes, with most loci being under strong purifying selection and two genes showing evidence for adaptive evolution. This observation agrees with theory predicting that linkage limits adaptive protein evolution. Both the neo-X and the neo-Y chromosome show an excess of unpreferred codon substitutions over preferred ones and no difference in this pattern was observed between the chromosomes. This suggests that there has been little or no selection maintaining codon bias in the D. miranda lineage. A change in mutational bias toward AT substitutions also contributes to the decline in codon bias. The contrast in patterns of molecular evolution between amino acid mutations and synonymous mutations on the neo-sex-linked genes can be understood in terms of chromosome-specific differences in effective population size and the distribution of selective effects of mutations.
Animals↗
Genetic recombination and adaptation to fluctuating environments: selection for geotaxis in Drosophila melanogaster.
Heritable variation in fitness is the fuel of adaptive evolution, and sex can generate new adaptive combinations of alleles. If the generation of beneficial combinations drives the evolution of recombination, then the level of recombination should result in changes in the response to selection. Three types of lines of Drosophila melanogaster varying in their level of genetic recombination were selected over 38 generations for geotaxis. The within-chromosome recombination level of these lines was controlled for 60% of the genome: chromosome X and chromosome II. The full recombination lines had normal, unmanipulated levels of recombination on these two chromosomes. Conversely, nonrecombination lines had recombination effectively eliminated within the X and second chromosomes. Finally, partial recombination lines had the effective rate of within-chromosome recombination lowered to 10% of natural levels for these two chromosomes. The rate of response to selection was measured for continuous negative geotaxis and for a fluctuating environment (alternating selection for negative and positive geotaxis). All selected Drosophila lines responded to selection and approximately 36% of the response to selection was because of the X and second chromosomes. However, recombination did not accelerate adaptation during either directional or fluctuating selection for geotaxis.
Adaptation, Physiological↗
Local adaptation in the monocarpic perennial Carlina vulgaris at different spatial scales across Europe.
Spatial variation in environmental conditions can lead to local adaptation of plant populations, particularly if gene flow among populations is low. Many studies have investigated adaptation to contrasting environmental conditions, but little is known about the spatial scale of adaptive evolution. We studied population differentiation and local adaptation at two spatial scales in the monocarpic grassland perennial Carlina vulgaris. We reciprocally transplanted seedlings among five European regions (northwestern Czech Republic, central Germany, Luxembourg, southern Sweden and northwestern Switzerland) and among populations of different sizes within three of the regions. We recorded survival, growth and reproduction over three growing periods. At the regional scale, several performance traits and the individual fitness of C. vulgaris were highest if the plants were grown in their home region and they decreased with increasing transplant distance. The effects are likely due to climatic differences that increased with the geographical distance between regions. At the local scale, there were significant interactions between the effects of the population of origin and the transplant site, but these were not due to an enhanced performance of plants at their home site and they were not related to the geographical or environmental distance between the site of origin and the transplant site. The size of the population of origin did not influence the strength of local adaptation. The results of our study suggest that C. vulgaris consists of regionally adapted genotypes, and that distance is a good predictor of the extent of adaptive differentiation at large scales ( > 200 km) but not at small scales. We conclude that patterns of local adaptation should be taken into account for the efficient preservation of genetic resources, when assessing the status of a plant species and during conservation planning.
Adaptation, Biological↗
Genomic Insights Into Local Adaptation Across Heterogeneous Understory Habitats and Climate Change Vulnerability.
Understanding adaptive evolution and survival risks in understory herbs is crucial for the effective conservation of biodiversity. How environmental gradients shape species local adaptation patterns is not well understood, nor is how populations of understory herbs respond to a changing climate. In this study, we conducted population genomic analyses of Adenocaulon himalaicum (Asteraceae) with a pan-East Asian distribution, representing a good model for dominant understory herbs to elucidate adaptation mechanisms in heterogeneous forest ecosystems. Based on 34,398 putatively neutral single nucleotide polymorphisms (SNPs) across 27 populations, we identified three genetic lineages accompanied by high levels of genetic differentiation between populations. Our isolation by environment results (IBE) indicated a significant effect of environmental gradients on genomic variation of A. himalaicum (r = 0.18, p = 0.03). To decompose the relative contributions of climate, geography and population structure in explaining genetic variance, our partial RDA found that the prominent contribution of environmental effects (climatic and soil variables) explained 29% and 36% of the neutral and adaptive genetic variation, respectively. Using two genotype-environment association (GEA) methods, we identified 13 SNPs as candidates for core climate-related adaptation loci, with two of these loci further validated by qRT-PCR experiments. Projections of spatiotemporal genomic vulnerability under different future climate scenarios revealed that populations in the southeastern edge of the Himalayas, near the Sichuan Basin, the southernmost region of Northeast China and the northern Korean Peninsula, as well as northern Japan, were identified as the most vulnerable and should be prioritised for conservation. Therefore, our current study provides the genomic foundations for conservation and management strategies to elucidate how these understory herbs cope with future climate changes.
Climate Change↗
Comparative analysis of olfactory receptor repertoires reveals evolutionary dynamics and high-altitude adaptation in Schizopygopsis younghusbandi based on the chromosome-level genomes.
The olfactory receptor (OR) gene represent a significant multigene family in vertebrates, forming the core molecular basis of olfactory perception and playing a crucial role in the environmental adaptation of species. High-altitude ecosystems represent extreme habitats characterized by specific abiotic stresses, including low oxygen levels, low temperatures, and intense ultraviolet radiation. These environments also exhibit low aquatic biodiversity and a limited variety of odor molecules, factors that have influenced the adaptive evolution of the sensory systems in endemic species. However, the genetic mechanisms underlying olfactory adaptation in high-altitude freshwater fish remained inadequately understood. In this study, we performed comparative genomics analyses to reveal the evolutionary processes underlying the adaptive and functional evolution of OR genes in S. younghusbandi, a cyprinid fish endemic to the Qinghai-Xizang Plateau. The results indicated that, compared to their low-altitude relatives, S. younghusbandi possessed a significantly smaller number of OR genes, with only 98 genes, which revealed the contraction of the gene family. Phylogenetic analysis revealed that the OR genes of cyprinid fish could be categorized into two major lineages: type I and type II. The η and δ families, which perceive water-soluble odors, in S. younghusbandi underwent significant and specific expansion, while the ε family was completely absent. This pattern reflected adaptive changes in olfactory recognition to accommodate the simplified odor spectrum of high-altitude water bodies. Chromosomal localization analysis demonstrated that OR genes were clustered, and collinearity analysis confirmed the presence of conserved genomic fragments among species. Selection pressure analysis revealed that the Ka/Ks values of all homologous gene pairs were less than 1, indicating that the OR genes of S. younghusbandi underwent strong purifying selection as a group to preserve core olfactory function. A few genes exhibited relaxed selection characteristics, which may have facilitated the fine-tuning of adaptability to high-altitude environments. In conclusion, this study elucidated the evolutionary dynamics and adaptive characteristics of the OR gene in S. younghusbandi, offering a new perspective on the molecular mechanisms underlying olfactory adaptation at high altitudes and enriching the research on sensory evolution in vertebrates.
Schizopygopsis younghusbandi↗
Maternal inheritance and rapid evolution of sexual size dimorphism: passive effects or active strategies?
Adaptive evolution is often strongly influenced by maternal inheritance that transfers the parental strategies across generations. The consequences of maternal effects for the offspring generation depend on the between-generation similarity in environments and on the evolved sensitivity of the offspring's ontogeny to maternal effects. When these factors differ between sons and daughters, maternal effects can influence the evolution of sexual dimorphism. The establishment of house finch populations across western Montana during the last 30 years was accompanied by rapid evolutionary change in sexual size dimorphism. Here I show that traits that changed the most across generations were most influenced by maternal effects in males but not females. Maternal effects differentially affected sons' and daughters' survival; greater maternal effects were commonly associated with higher survival of sons, especially when maternal and offspring environments were similar. Stronger maternal effects extended preselection phenotypic variance in morphological traits of males, thereby producing some locally adaptive phenotypes and lessening juvenile mortality. Thus, the observed sex-specific maternal effects and their contribution to the evolution of sexual size dimorphism are likely a passive consequence of the distinct sensitivity of sons and daughters to maternal adaptations to breeding in ecologically distinct parts of the house finch's expanding range.
Animals↗
Effects of linkage on rates of molecular evolution.
When an advantageous mutation is fixed in a population by selection, a closely linked selectively neutral or mildly detrimental mutation may "hitchhike" to fixation along with it. It has been suggested that hitchhiking might increase the rate of molecular evolution. Computer simulations and a mathematical argument show that complete linkage to either advantageous or deleterious mutations does not affect the substitution of selectively neutral mutations. However, the simulations show that linkage to selected background mutations decreases the rate of fixation of advantageous mutations and increases the rate of fixation of detrimental mutations. This is true whether the linked background mutations are advantageous or detrimental, and it verifies and extends previous observations that linkage tends to reduce the effects of selection on evolution. These results can be interpreted in terms of the Hill-Robertson effect: a locus linked to another locus under selection experiences a reduction in effective population size. The interpretation of differences in evolutionary rates between different genomes or different regions of a genome may be confounded by the effects of strong linkage and selection. Recombination is expected to reduce the overall rate of molecular evolution while enhancing the rate of adaptive evolution.
Biological Evolution↗
Wright's shifting balance theory: an experimental study.
Experimental confirmation of Wright's shifting balance theory of evolution, one of the most comprehensive theories of adaptive evolution, is presented. The theory is regarded by many as a cornerstone of modern evolutionary thought, but there has been little direct empirical evidence supporting it. Some of its underlying assumptions are viewed as contradictory, and the existence and efficacy of the theory's fundamental adaptive process, interdemic selection, is the focus of controversy. Interdemic selection was imposed on large arrays of laboratory populations of the flour beetle Tribolium castaneum in the manner described by Wright: the differential dispersion of individuals from demes of high fitness into demes of low fitness. A significant increase in average fitness was observed in the experimental arrays when compared to control populations with equivalent but random migration rates. The response was not proportional to the selection differential: The largest response occurred with interdemic selection every two generations rather than every generation or every three generations. The results indicate that the interdemic phase of Wright's shifting balance theory can increase average fitness and suggest that gene interactions are involved in the observed response.
Adaptation, Physiological↗