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PubMed2005

Adaptive speciation when assortative mating is based on female preference for male marker traits.

Adaptive speciation occurs when frequency-dependent ecological interactions generate conditions of disruptive selection to which lineage splitting is an adaptive response. Under such selective conditions, evolution of assortative mating mechanisms enables the break-up of the ancestral lineage into diverging and reproductively isolated descendent species. Extending previous studies, I investigate models of adaptive speciation due to the evolution of indirect assortative mating that is based on three different mating traits: the degree of assortativity, a female preference trait and a male marker trait. For speciation to occur, linkage disequilibria between different mating traits, e.g. between female preference and male marker traits, as well as between mating traits and the ecological trait, must evolve. This can lead to novel speciation scenarios, e.g. when reproductive isolation is generated by a splitting in the degree of assortativeness, with one of the emerging lineages mating assortatively, and the other one disassortatively. I investigate the effects of variation in various model parameters on the likelihood of speciation, as well as robustness of speciation to introducing costs of assortative mating. Even though in the models presented speciation requires the genetic potential for strong assortment as well as rather restrictive ecological conditions, the results show that adaptive speciation due to the evolution of assortative mating when mate choice is based on separate female preference and male marker traits is a theoretically plausible evolutionary scenario.

Adaptation, Biological↗
PubMed2026

From colonization to infection: Genomic evolution of Clostridioides difficile pathogenesis.

Clostridioides difficile is a spore-forming, toxin-producing anaerobe that is a leading cause of healthcare-associated infections. Its success as a pathogen reflects a complex interplay between bacterial evolution, virulence regulation, ecological adaptation, environmental selection, and host susceptibility. Comparative genomics has revealed deep C. difficile lineage diversification, driven by mobile genetic elements and selective pressures from antibiotics and host environments. These events affect strain-specific virulence by shaping the organization and regulation of the pathogenicity toxin loci, metabolic adaptations for nutrient utilization, and enhanced spore resilience. This review integrates evolutionary and genomic perspectives to illustrate how adaptive diversification has sculpted C. difficile pathogenesis and epidemic success.

CP: microbiology↗
PubMed2002

Anti-aging effects of caloric restriction: Involvement of neuroendocrine adaptation by peripheral signaling.

Many hormonal signals from peripheral tissues contribute to the regulation of energy homeostasis and food intake. These regulators including leptin, insulin, and ghrelin, modulate the orexigenic and anorexigenic neuropeptide expression in hypothalamic nuclei. The anti-aging effects of caloric restriction have been explained from an evolutional viewpoint of the adaptive response of the neuroendocrine and metabolic response systems to maximize survival during periods of food shortage. In organisms, excess energy is stored in adipose tissues as a triglyceride preparation for such survival situations. Adipose tissue has recently been recognized as an endocrine organ, and leptin, as secreted by adipocyte, seems to be an especially important factor for the adaptive response to fasting and neuroendocrine alterations under caloric restriction. In this review, we discuss the potential involvement of neuroendocrine modulators in longevity and the anti-aging effects of caloric restriction.

Adaptation, Physiological↗
PubMed1990

The Spalacidae: evolutionary history, speciation and population biology.

The evolutionary history of Spalacidae is reviewed taxonomically, paleontologically and neontologically. We focused selectively on taxonomy, biogeography, paleontology and evolutionary origins, chromosomal evolution, population biology and the species concept in Spalacidae. We concluded that the taxonomy of Spalacidae needs a modern revision based on chromosome and molecular-genetic data, beside that of morphology, physiology and behavior. The subterranean Spalacidae originated probably from a muroid-cricetoid stock in Asia Minor or vicinity, in Upper Oligocene times and adaptively radiated underground in the Balkans, steppic Russia and Middle East, extending into North Africa. The major important evolutionary feature in peripatric or allopatric speciation and adaptive radiation was karyotypic evolution, primarily through Robertsonian changes. More than 30 karyotypes (2n = 38-62; NF = 72-124) earlier represented by 8 classical species, occur primarily allopatrically or parapatrically, with only marginal sympatry, across the Eastern Mediterranean range of the family. Most karyotypes represent biospecies adapted at multiple organizational levels to their different ecologies. A short overview is presented on population biology and life history parameters of the Spalacidae which result in K-selected, "equilibrium species". Speciation in action and adaptive radiation embracing molecular and organismal adptations to the subterranean unique ecotope and to four different climatic regimes, have been multidisciplinarily studied in the Israeli Spalax ehrenbergi superspecies.

Animals↗
PubMed2001

Model of geometrical and smooth muscle tone adaptation of carotid artery subject to step change in pressure.

Recent experimental studies have shown significant alterations of the vascular smooth muscle (VSM) tone when an artery is subjected to an elevation in pressure. Therefore, the VSM participates in the adaptation process not only by means of its synthetic activity (fibronectins and collagen) or proliferative activity (hypertrophy and hyperplasia) but also by adjusting its contractile properties and its tone level. In previous theoretical models describing the time evolution of the arterial wall adaptation in response to induced hypertension, the contribution of VSM tone has been neglected. In this study, we propose a new biomechanical model for the wall adaptation to induced hypertension, including changes in VSM tone. On the basis of Hill's model, total circumferential stress is separated into its passive and active components, the active part being the stress developed by the VSM. Adaptation rate equations describe the geometrical adaptation (wall thickening) and the adaptation of active stress (VSM tone). The evolution curves that are derived from the theoretical model fit well the experimental data describing the adaptation of the rat common carotid subjected to a step increase in pressure. This leads to the identification of the model parameters and time constants by characterizing the rapidity of the adaptation processes. The agreement between the results of this simple theoretical model and the experimental data suggests that the theoretical approach used here may appropriately account for the biomechanics underlying the arterial wall adaptation.

Adaptation, Physiological↗
PubMed2001

The role of selfish genetic elements in eukaryotic evolution.

'Selfish genetic elements', such as transposons, homing endonucleases, meiotic drive chromosomes and heritable microorganisms, are common features of eukaryotes. However, their importance in the evolution of eukaryotic genomes is still controversial. In this review, we discuss these diverse elements and their potential importance in the evolution of genetic systems, adaptation, and the extinction and birth of species.

Animals↗
PubMed2003

Adaptive diversification of bitter taste receptor genes in Mammalian evolution.

The diversity and evolution of bitter taste perception in mammals is not well understood. Recent discoveries of bitter taste receptor (T2R) genes provide an opportunity for a genetic approach to this question. We here report the identification of 10 and 30 putative T2R genes from the draft human and mouse genome sequences, respectively, in addition to the 23 and 6 previously known T2R genes from the two species. A phylogenetic analysis of the T2R genes suggests that they can be classified into three main groups, which are designated A, B, and C. Interestingly, while the one-to-one gene orthology between the human and mouse is common to group B and C genes, group A genes show a pattern of species- or lineage-specific duplication. It is possible that group B and C genes are necessary for detecting bitter tastants common to both humans and mice, whereas group A genes are used for species-specific bitter tastants. The analysis also reveals that phylogenetically closely related T2R genes are close in their chromosomal locations, demonstrating tandem gene duplication as the primary source of new T2Rs. For closely related paralogous genes, a rate of nonsynonymous nucleotide substitution significantly higher than the rate of synonymous substitution was observed in the extracellular regions of T2Rs, which are presumably involved in tastant-binding. This suggests the role of positive selection in the diversification of newly duplicated T2R genes. Because many natural poisonous substances are bitter, we conjecture that the mammalian T2R genes are under diversifying selection for the ability to recognize a diverse array of poisons that the organisms may encounter in exploring new habitats and diets.

Amino Acid Sequence↗
PubMed2001

Perspective: Evolution of flower color in the desert annual Linanthus parryae: Wright revisited.

Linanthus parryae, a diminutive desert annual with white or blue flowers, has been the focus of a long-standing debate among evolutionary biologists. At issue is whether the flower color polymorphism in this species is the product of random genetic drift, as Sewall Wright argued, or of natural selection, as proposed by Carl Epling and his colleagues. Our long-term studies of three polymorphic populations in the Mojave Desert demonstrate that flower color is subject to selection that varies in both time and space in its direction and magnitude. For all sites taken together, blue-flowered plants produced more seeds than white-flowered plants in years of relatively low seed production, whereas white-flowered plants had higher fitness in years of high seed production. Evidence of selection on flower color was found in two of the three study sites. Differences in fitness between the color morphs were sometimes large, with selection coefficients as high as 0.60 in some years. Our longest period of observations was at Pearblossom site 1, where plants reached appreciable densities in seven of the 11 years of study. Here we found significant differences in the seed production of the color morphs in six years, with three years of blue advantage and three years of white advantage. For all sites taken together, total spring precipitation (March and April) was positively correlated with both absolute and relative seed production of the color morphs. At Pearblossom site 1, blue-flowered plants typically had a fitness advantage in years of low spring precipitation, whereas white-flowered plants had a fitness advantage in years of high spring precipitation. This temporal variation in selection may contribute to the maintenance of the flower-color polymorphism at Pearblossom site 1, whereas gene flow from neighboring populations is proposed as the principal factor maintaining the polymorphism at the other study sites. We found no significant differences between the color morphs in pollinator visitation rate or in their carbon isotope ratio, a measure of water-use efficiency. Although the mechanism of selection remains elusive, our results refute Wright's conclusion that the flower color polymorphism in L. parryae is an example of isolation by distance, a key component of his shifting balance theory of evolution.

Adaptation, Physiological↗
PubMed1998

Adaptive Walks by the Fittest among Finite Random Mutants on a Mt. Fuji-type Fitness Landscape.

Based on the theory of fitness distributions on a Mt. Fuji-type fitness landscape in a multivalued sequence space (Aita & Husimi, 1996 J. theor. Biol. 182, 469-485), we investigated the properties of adaptive walks on the ideal landscape in the case of a cloning-screening-type evolution experiment. We modeled that an adaptive walk is performed by repetition of the evolution cycle composed of the mutagenesis process generating random d-fold point mutants of population size N and the selection process looking for the fittest mutant among them. While an adaptive walk is described in a sequence space, we simplified the description as follows. We mapped the landscape in an x-y plane, where x and y represent a normalized Hamming distance from the global peak and a scaled fitness, respectively. An adaptive walk is described as a trajectory in the plane. The most certain step for a walker to move in a single evolution cycle is represented by a vector in the plane. Then, a walker moves along the streams in the vector field determined by d and N. The walker performs fast hill-climbing until a "trap-line", which traverses the plane. Subsequently, the walker is likely to get trapped in an "apparent local optimum". To continue the walk, apparent local optima must be eliminated by resetting d and N larger. Therefore, for the fastest walk, the optimal schedule of the d-values (initially large d, then small d) is effective, although the economical walk with high cost-performance is different. If a real landscape is just of the Mt. Fuji-type, the walk with the highest cost-performance will be performed by scanning site-directed optimization through all sites. However, in the case of the rough Mt. Fuji-type, which seems to be more realistic, the walking method we have examined will be effective for a walker to sidestep true local optima.Copyright 1998 Academic Press

Journal Article↗
PubMed2000

[Comparative study of iodine and thyroid gland in biological processes: development and reproduction].

Iodine is an scarce metalloid, essential for life, more abundant in the aquatic ecosystem than in land. Marine species do not need to store and transform the inorganic iodine into organic iodine through the thyroid gland. Adaptation to terrestrial ecosystem has required phylogenetic processes, and animal species have used different strategies to solve the iodine captation problem according to their needs. Jellyfish lack of thyroid gland while lampery developed the thyroid gland during evolution in order to adapt to the terrestrial ecosystem. This review is a comparative phylogenetic study of thyroid gland development and iodine physiology, includes functional disorders, as well as iodine captation ability and requirements during growth and reproduction in different species.

Animals↗
PubMed2000

Molecular evolution of the chalcone synthase multigene family in the morning glory genome.

Plant genomes appear to exploit the process of gene duplication as a primary means of acquiring biochemical and developmental flexibility. Thus, for example, most of the enzymatic components of plant secondary metabolism are encoded by small families of genes that originated through duplication over evolutionary time. The dynamics of gene family evolution are well illustrated by the genes that encode chalcone synthase (CHS), the first committed step in flavonoid biosynthesis. We review pertinent facts about CHS evolution in flowering plants with special reference to the morning glory genus, Ipomoea. Our review shows that new CHS genes are recruited recurrently in flowering plant evolution. Rates of nucleotide substitution are frequently accelerated in new duplicate genes, and there is clear evidence for repeated shifts in enzymatic function among duplicate copies of CHS genes. In addition, we present new data on expression patterns of CHS genes as a function of tissue and developmental stage in the common morning glory (I. purpurea). These data show extensive differentiation in gene expression among duplicate copies of CHS genes. We also show that a single mutation which blocks anthocyanin biosynthesis in the floral limb is correlated with a loss of expression of one of the six duplicate CHS genes present in the morning glory genome. This suggests that different duplicate copies of CHS have acquired specialized functional roles over the course of evolution. We conclude that recurrent gene duplication and subsequent differentiation is a major adaptive strategy in plant genome evolution.

Acyltransferases↗
PubMed2003

A uniquely human consequence of domain-specific functional adaptation in a sialic acid-binding receptor.

Most mammalian cell surfaces display two major sialic acids (Sias), N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc). Humans lack Neu5Gc due to a mutation in CMP-Neu5Ac hydroxylase, which occurred after evolutionary divergence from great apes. We describe an apparent consequence of human Neu5Gc loss: domain-specific functional adaptation of Siglec-9, a member of the family of sialic acid-binding receptors of innate immune cells designated the CD33-related Siglecs (CD33rSiglecs). Binding studies on recombinant human Siglec-9 show recognition of both Neu5Ac and Neu5Gc. In striking contrast, chimpanzee and gorilla Siglec-9 strongly prefer binding Neu5Gc. Simultaneous probing of multiple endogenous CD33rSiglecs on circulating blood cells of human, chimp, or gorilla suggests that the binding differences observed for Siglec-9 are representative of multiple CD33rSiglecs. We conclude that Neu5Ac-binding ability of at least some human CD33rSiglecs is a derived state selected for following loss of Neu5Gc in the hominid lineage. These data also indicate that endogenous Sias (rather than surface Sias of bacterial pathogens) are the functional ligands of CD33rSiglecs and suggest that the endogenous Sia landscape is the major factor directing evolution of CD33rSiglec binding specificity. Exon-1-encoded Sia-recognizing domains of human and ape Siglec-9 share only approximately 93-95% amino acid identity. In contrast, the immediately adjacent intron and exon 2 have the approximately 98-100% identity typically observed among these species. Together, our findings suggest ongoing adaptive evolution specific to the Sia-binding domain, possibly of an episodic nature. Such domain-specific divergences should also be considered in upcoming comparisons of human and chimpanzee genomes.

Amino Acid Sequence↗
PubMed1997

On the coevolution of cognition and consciousness.

In this article it is argued that an evolutionary perspective leads to the view that adaptation and learning is a widespread and old property of living organisms, even as old as life itself. Cognition, defined as knowledge processing mediated by a centralised nervous system, is suggested mainly to be based on the same principles as non-neural adaptive processes. The emergence of conscious cognition, however, is seen as a major transition in the evolution of life, although it appears in different degrees and at various stages in evolution. Both cognition and consciousness depend on the organisation and complexity of the organism, primarily with regard to the nervous system. Computational and neurophysiological approaches are discussed, in particular some experimental attempts to determine anatomical, physiological and physical correlates to consciousness. It is argued that an evolutionary perspective suggests an interactionistic solution to the mind-brain problem, i.e. the question of subjective experience. In an interactionistic perspective consciousness can be understandable as a biological phenomenon. It can be regarded as a driving force in evolution, amplifying and improving the adaptive and cognitive processes of an organism.

Biological Evolution↗
PubMed2025

Comparative Analysis of Mammalian Adaptive Immune Loci Revealed Spectacular Divergence and Common Genetic Patterns.

Adaptive immune responses are mediated by the production of adaptive immune receptors, antibodies, and T-cell receptors, which bind antigens, thus causing their neutralization. Unlike other proteins, adaptive immune receptors are not fully encoded in the germline genome and result from a complex of somatic processes collectively called V(D)J recombination affecting germline immunoglobulin (IG) and T-cell receptor (TR) loci consisting of template genes. While various existing studies report extreme diversity of antibodies and T-cell receptors, little is known about the diversity of germline IG and TR loci. To overcome this gap, the first comparative analysis of full-length sequences of IG/TR loci across 46 mammalian species from 13 taxonomic orders was performed. First, germline gene counts were shown to correlate in immunoglobulin heavy chain immunoglobulin heavy chain (IGH)/immunoglobulin lambda (IGL) loci and T-cell receptor alpha (TRA)/T-cell receptor beta (TRB) and anticorrelate in immunoglobulin kappa (IGK)/IGL, possibly indicating coevolution between corresponding chains. Second, structures of IG/TR loci were analyzed, and it was shown that IG/TR loci formed by long arrays of high multiplicity repeats are more common for species that have experienced population bottlenecks. Finally, haplotypes of IG/TR loci with little or no sequence similarity within a species were found, suggesting that they may have a limited potential for homologous recombination. These results demonstrate that IG/TR loci are rapidly evolving genomic regions whose structural variation is shaped by the population history of the species and open new perspectives for immunogenomics studies.

Animals↗
PubMed2004

Natural selection and evolution of streptococcal virulence genes involved in tissue-specific adaptations.

The molecular mechanisms underlying niche adaptation in bacteria are not fully understood. Primary infection by the pathogen group A streptococcus (GAS) takes place at either the throat or the skin of its human host, and GAS strains differ in tissue site preference. Many skin-tropic strains bind host plasminogen via the plasminogen-binding group A streptococcal M protein (PAM) present on the cell surface; inactivation of genes encoding either PAM or streptokinase (a plasminogen activator) leads to loss of virulence at the skin. Unlike PAM, which is present in only a subset of GAS strains, the gene encoding streptokinase (ska) is present in all GAS isolates. In this study, the evolution of the virulence genes known to be involved in skin infection was examined. Most genetic diversity within ska genes was localized to a region encoding the plasminogen-docking domain (beta-domain). The gene encoding PAM displayed strong linkage disequilibrium (P << 0.01) with a distinct phylogenetic cluster of the ska beta-domain-encoding region. Yet, ska alleles of distant taxa showed a history of intragenic recombination, and high intrinsic levels of recombination were found among GAS strains having different tissue tropisms. The data suggest that tissue-specific adaptations arise from epistatic coselection of bacterial virulence genes. Additional analysis of ska genes showed that approximately 4% of the codons underwent strong diversifying selection. Horizontal acquisition of one ska lineage from a commensal Streptococcus donor species was also evident. Together, the data suggest that new phenotypes can be acquired through interspecies recombination between orthologous genes, while constrained functions can be preserved; in this way, orthologous genes may provide a rich and ready source for new phenotypes and thereby play a facilitating role in the emergence of new niche adaptations in bacteria.

Bacterial Proteins↗
PubMed2006

Strong assortative mating between allopatric sticklebacks as a by-product of adaptation to different environments.

Speciation involves the evolution of reproductive isolation between populations. One potentially important mechanism is the evolution of pre- or postzygotic isolation between populations as a by-product of adaptation to different environments. In this paper, we tested for assortative mating between allopatric stickleback populations adapted to different ecological niches. Our experimental design controlled for interpopulation interactions and non-adaptive explanations for assortative mating. We found that prezygotic isolation was surprisingly strong: when given a choice, the majority of matings occurred between individuals from similar environments. Our results indicate that the by-product mechanism is a potent source of reproductive isolation, and likely contributed to the origin of sympatric species of sticklebacks.

Adaptation, Physiological↗
PubMed2006

Tests of parallel molecular evolution in a long-term experiment with Escherichia coli.

The repeatability of evolutionary change is difficult to quantify because only a single outcome can usually be observed for any precise set of circumstances. In this study, however, we have quantified the frequency of parallel and divergent genetic changes in 12 initially identical populations of Escherichia coli that evolved in identical environments for 20,000 cell generations. Unlike previous analyses in which candidate genes were identified based on parallel phenotypic changes, here we sequenced four loci (pykF, nadR, pbpA-rodA, and hokB/sokB) in which mutations of unknown effect had been discovered in one population, and then we compared the substitution pattern in these "blind" candidate genes with the pattern found in 36 randomly chosen genes. Two candidate genes, pykF and nadR, had substitutions in all 11 other populations, and the other 2 in several populations. There were very few cases, however, in which the exact same mutations were substituted, in contrast to the findings from conceptually related work performed with evolving virus populations. No random genes had any substitutions except in four populations that evolved defects in DNA repair. Tests of four different statistical aspects of the pattern of molecular evolution all indicate that adaptation by natural selection drove the parallel changes in these candidate genes.

Animals↗