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PubMed1997

Escape from evolutionary stasis by transposon-mediated deleterious mutations.

Evolution within a rugged fitness landscape is limited by the tendency for organisms to become trapped on local optima resulting in evolutionary stasis. It is presently unclear how founder populations escape from an adaptive peak to found a new species. Insertion sequences, transposons and other mobile DNA elements are found in all species of eukaryotes, bacteria and archaebacteria, where they have been sought and are usually considered to be genomic parasites or selfish genes. However, many transposons and other mobile repetitive DNA are remarkably species or phyla-specific, indicating that infection with transposable elements coincides with speciation events and is involved in promoting evolutionary change. We propose here a model in which transposable elements are involved in speciation events by their ability to produce irreversible deleterious mutations that promote escape from evolutionary stasis. We have constructed a genetic algorithm designed to model both spontaneous and transposon-mediated mutations in populations of asexual digital organisms. We use this model to investigate the effect of transposon-mediated mutations on the rate of evolution of digital organisms as they compete for resources within an artificial adaptive landscape. In the absence of transposon mutations the seed organisms quickly evolve to occupy the nearest adaptive peak but thereafter evolutionary stasis ensues and adjacent empty peaks are left unoccupied. In the presence of transposon mutations, evolution is again dominated by stasis but is punctuated by bursts of rapid evolution in with consecutive unoccupied adaptive peaks are filled with organisms derived from single transposition events. Rapid evolutionary events leading to founding of new biological species, may be similarly initiated by irreversible deleterious mutations induced by transposition.

Adaptation, Physiological↗
PubMed2003

On the evolutionary advantage of fitness-associated recombination.

The adaptive value of recombination remains something of a puzzle. One of the basic problems is that recombination not only creates new and advantageous genetic combinations, but also breaks down existing good ones. A negative correlation between the fitness of an individual and its recombination rate would result in prolonged integrity of fitter genetic combinations while enabling less fit ones to produce new combinations. Such a correlation could be mediated by various factors, including stress responses, age, or direct DNA damage. For haploid population models, we show that an allele for such fitness-associated recombination (FAR) can spread both in asexual populations and in populations reproducing sexually at any uniform recombination rate. FAR also carries an advantage for the population as a whole, resulting in a higher average fitness at mutation-selection balance. These results are demonstrated in populations adapting to new environments as well as in well-adapted populations coping with deleterious mutations. Current experimental results providing evidence for the existence of FAR in nature are discussed.

Adaptation, Physiological↗
PubMed2003

Temporal oscillations and phase transitions in the evolutionary minority game.

The study of societies of adaptive agents seeking minority status is an active area of research. Recently, it has been demonstrated that such systems display an intriguing phase transition: agents tend to self-segregate or to cluster according to the value of the prize-to-fine ratio R. We show that such systems do not establish a true stationary distribution. The winning probabilities of the agents display temporal oscillations. The amplitude and frequency of the oscillations depend on the value of R. The temporal oscillations that characterize the system explain the transition in the global behavior from self-segregation to clustering in the R<1 case.

Journal Article↗
PubMed2000

Autonomy and process closure as the basis for functionality

Most accounts of functionality are based in etiology, either design or selection. In this paper I give an account of function as serving autonomy, which is the closure of self-maintaining processes, including those interacting with the environment. Autonomy is inherently dynamic, being based entirely on interacting processes, whose organization constitutes the integrity of the autonomous system. The etiological account focuses on external factors, either intentions in design or outcomes in selection. It ignores any but idiosyncratic organizational requirements within the biological entity and in its interactions with its environment, even though these may play a central role in the functionality of the trait in question. In particular, there is no simple relation between adaptation on the etiological account and adaptability, a higher order emergent trait that plays a central role in behavior and the evolutionary and developmental genesis of intelligence. I propose redefining adaptiveness in terms of autonomy. The definition naturally extends to adaptability and focuses on the organizational character of adaptiveness, forcing attention on this central biological characteristic, which is easily ignored in the etiological account. The result is a much richer account of both adaptation and selection.

Journal Article↗
PubMed2000

In vivo selection of functional ribosomes with variations in the rRNA-binding site of Escherichia coli ribosomal protein S8: evolutionary implications.

The highly conserved nature of rRNA sequences throughout evolution allows these molecules to be used to build philogenic trees of different species. It is unknown whether the stability of specific interactions and structural features of rRNA reflects an optimal adaptation to a functional task or an evolutionary trap. In the work reported here, we have applied an in vivo selection strategy to demonstrate that unnatural sequences do work as a functional replacement of the highly conserved binding site of ribosomal protein S8. However, growth competition experiments performed between Escherichia coli isolates containing natural and unnatural S8-binding sites showed that the fate of each isolate depended on the growth condition. In exponentially growing cells, one unnatural variant was found to be equivalent to wild type in competition experiments performed in rich media. In culture conditions leading to slow growth, however, cells containing the wild-type sequence were the ultimate winner of the competition, emphasizing that the wild-type sequence is, in fact, the most fit solution for the S8-binding site.

Base Sequence↗
PubMed2004

Experimental evidence for sympatric ecological diversification due to frequency-dependent competition in Escherichia coli.

We investigate adaptive diversification in experimental Escherichia coli populations grown in serial batch cultures on a mixture of glucose and acetate. All 12 experimental lines were started from the same genetically uniform ancestral strain but became highly polymorphic for colony size after 1000 generations. Five populations were clearly dimorphic and thus serve as a model for an adaptive lineage split. We analyzed the ecological basis for this dimorphism by studying bacterial growth curves. All strains exhibit diauxie, that is, sequential growth on the two resources. Thus, they exhibit phenotypic plasticity, using mostly glucose when glucose is abundant, then switching to acetate when glucose concentration is low. However, the coexisting strains differ in their diauxie pattern, with one cluster in the dimorphic populations growing better in the glucose phase, and the other cluster having a much shorter lag when switching to the acetate phase. Using invasion experiments, we show that the dimorphism of these two ecological types is maintained by frequency-dependent selection. Using a mathematical model for the adaptive dynamics of diauxie behavior, we show that evolutionary branching in diauxie behavior is a plausible theoretical scenario. Our results support the hypothesis that, in our experiments, adaptive diversification from a genetically uniform ancestor occurred due to frequency-dependent ecological interactions. Our results have implications for understanding the evolution of cross-feeding polymorphism in microorganisms, as well as adaptive speciation due to frequency-dependent selection on phenotypic plasticity.

Adaptation, Physiological↗
PubMed2004

Adaptive evolution of centromere proteins in plants and animals.

BACKGROUND: Centromeres represent the last frontiers of plant and animal genomics. Although they perform a conserved function in chromosome segregation, centromeres are typically composed of repetitive satellite sequences that are rapidly evolving. The nucleosomes of centromeres are characterized by a special H3-like histone (CenH3), which evolves rapidly and adaptively in Drosophila and Arabidopsis. Most plant, animal and fungal centromeres also bind a large protein, centromere protein C (CENP-C), that is characterized by a single 24 amino-acid motif (CENPC motif). RESULTS: Whereas we find no evidence that mammalian CenH3 (CENP-A) has been evolving adaptively, mammalian CENP-C proteins contain adaptively evolving regions that overlap with regions of DNA-binding activity. In plants we find that CENP-C proteins have complex duplicated regions, with conserved amino and carboxyl termini that are dissimilar in sequence to their counterparts in animals and fungi. Comparisons of Cenpc genes from Arabidopsis species and from grasses revealed multiple regions that are under positive selection, including duplicated exons in some grasses. In contrast to plants and animals, yeast CENP-C (Mif2p) is under negative selection. CONCLUSIONS: CENP-Cs in all plant and animal lineages examined have regions that are rapidly and adaptively evolving. To explain these remarkable evolutionary features for a single-copy gene that is needed at every mitosis, we propose that CENP-Cs, like some CenH3s, suppress meiotic drive of centromeres during female meiosis. This process can account for the rapid evolution and the complexity of centromeric DNA in plants and animals as compared to fungi.

Adaptation, Physiological↗
PubMed2006

Evolutionary explanations of the "actuarial senescence in the wild" and of the "state of senility".

A large set of data suggests that progressive reduction of fitness and senile decay in vertebrates are in correlation with the decline of cell replication capacities. However, the limits in such capacities are hardly explained in evolutionarily terms by current gerontological theories that rule out fitness decline as something genetically determined and regulated, and therefore somehow favored by natural selection. Four theories are tested as possible explanations of the "increasing mortality with increasing chronological age in populations in the wild" ("IMICAW"[1]), alias "actuarial senescence in the wild"[2], and of the observed negative correlation between extrinsic mortality and the ratio between deaths due to intrinsic mortality and deaths due to extrinsic mortality. Only the theory attributing an adaptive value to IMICAW allows an evolutionary explanation for it and for the aforesaid inverse correlation, while the other three theories ("mutation accumulation", "antagonistic pleiotropy", and "disposable soma" th.) even predict a positive correlation. Afterwards, the same theories are tested as possible explanations for the "state of senility"[3], namely the deteriorated state of individuals in artificially protected conditions (captivity, civilization, etc.) at ages rarely or never observable in the wild. With the distinction between "damage resulting from intrinsic living processes"[4], alias "age changes"[5], and "age-associated diseases"[4,5], the same theory explaining IMICAW allows a rational interpretation of the first category of phenomena while another theory, the "mutation accumulation" hypothesis, gives an immediate interpretation for the second category. The current gerontological paradigm explaining the increasing mortality with increasing chronological age as consequence of insufficient selection should be restricted to the "age-associated diseases". For IMICAW, it should be substituted with the concept of a physiologic phenomenon genetically determined by a balance of opposite selective pressures--strictly in terms of kin selection--and, for "age changes", with the action of the same IMICAW-causing mechanisms at ages when selection becomes ineffective.

Aging↗
PubMed1988

The sociobiology of bereavement: a reply to Littlefield and Rushton.

This article offers a critique of Littlefield and Rushton's (1986) application of sociobiological principles to bereavement following the death of a child. The following general issues are considered: (a) whether behavior is always adaptive and (b) the distinction between proximate and ultimate explanations. It is argued that grief is a maladaptive by-product of another, adaptive feature and that hypotheses about the severity of grief are best derived from proximate considerations rather than genetic relatedness. The use of a single-item rating scale to measure grief is questioned, and it is noted that interspouse reliabilities reported in the article were low, a problem not solved (as claimed) by aggregation. Criticisms are made of the specific hypotheses, notably in terms of their origins in sociobiological theory. It is argued that functional hypotheses are not alternatives to proximate mechanisms, but enable some proximate mechanisms to be viewed from the perspective of evolutionary biology.

Adaptation, Biological↗
PubMed2006

Historical evolution of the concept environment proposed in the Roy Adaptation Model.

The concern for the development of concepts becomes even more important when we report to its use in Nursing theories, in which some concepts are considered central, such as person, environment, health and nursing. This study aims to discuss the historical evolution of the environment concept used in the Roy Adaptation Model. The method of analysis the study was based on is the evolutionary conceptual analysis of the concept Environment of the Roy Adaptation Model. According to the research results, Environment is introduced as the second major concept in the Roy Adaptation Model. In this theorist's interpretation of the environment, we notice her interest in surpassing the mechanistic point of view upon which the first version of the model was based. The approach of the concept of interaction between people and groups seems to represent an improvement, influenced by the current thoughts that are preeminent in nursing.

Adaptation, Psychological↗
PubMed1997

Molecular evolution and host adaptation of Bordetella spp.: phylogenetic analysis using multilocus enzyme electrophoresis and typing with three insertion sequences.

A total of 188 Bordetella strains were characterized by the electrophoretic mobilities of 15 metabolic enzymes and the distribution and variation in positions and copy numbers of three insertion sequences (IS). The presence or absence of IS elements within certain lineages was congruent with estimates of overall genetic relationships as revealed by multilocus enzyme electrophoresis. Bordetella pertussis and ovine B. parapertussis each formed separate clusters, while human B. parapertussis was most closely related to IS1001-containing B. bronchiseptica isolates. The results of the analysis provide support for the hypothesis that the population structure of Bordetella is predominantly clonal, with relatively little effective horizontal gene flow. Only a few examples of putative recombinational exchange of an IS element were detected. Based on the results of this study, we tried to reconstruct the evolutionary history of different host-adapted lineages.

Adaptation, Biological↗
PubMed2005

Testing for adaptive evolution of the female reproductive protein ZPC in mammals, birds and fishes reveals problems with the M7-M8 likelihood ratio test.

BACKGROUND: Adaptive evolution appears to be a common feature of reproductive proteins across a very wide range of organisms. A promising way of addressing the evolutionary forces responsible for this general phenomenon is to test for adaptive evolution in the same gene but among groups of species, which differ in their reproductive biology. One can then test evolutionary hypotheses by asking whether the variation in adaptive evolution is consistent with the variation in reproductive biology. We have attempted to apply this approach to the study of a female reproductive protein, zona pellucida C (ZPC), which has been previously shown by the use of likelihood ratio tests (LRTs) to be under positive selection in mammals. RESULTS: We tested for evidence of adaptive evolution of ZPC in 15 mammalian species, in 11 avian species and in six fish species using three different LRTs (M1a-M2a, M7-M8, and M8a-M8). The only significant findings of adaptive evolution came from the M7-M8 test in mammals and fishes. Since LRTs of adaptive evolution may yield false positives in some situations, we examined the properties of the LRTs by several different simulation methods. When we simulated data to test the robustness of the LRTs, we found that the pattern of evolution in ZPC generates an excess of false positives for the M7-M8 LRT but not for the M1a-M2a or M8a-M8 LRTs. This bias is strong enough to have generated the significant M7-M8 results for mammals and fishes. CONCLUSION: We conclude that there is no strong evidence for adaptive evolution of ZPC in any of the vertebrate groups we studied, and that the M7-M8 LRT can be biased towards false inference of adaptive evolution by certain patterns of non-adaptive evolution.

Adaptation, Biological↗
PubMed2026

Matching genomic evidence to claims about Mycobacterium avium subsp. paratuberculosis: Host association, host adaptation, mechanism, and virulence.

Whole-genome sequencing (WGS) permits high-resolution comparison of Mycobacterium avium subsp. paratuberculosis (MAP) isolates and pangenome analysis. Combined with animal-movement data, WGS can support transmission inference, but resolution alone does not establish the biological meaning of genomic variation. This focused narrative review applies a two-dimensional framework to purposively selected MAP studies, separating claim targets from support profiles. Claim targets include lineage identity, host-source or lineage characterization, host association, transmission, candidate genomic features, measured bacterial or host-cell phenotypes, natural-host infection fitness, disease or damage, shedding, and control outcomes. Depending on the claim, evidence operations may include characterization, context-aware comparative inference, direct endpoint ascertainment, and controlled feature perturbation; these are non-ordinal and may co-occur. On-target attribution, independent replication, and transportability are reported separately. The claim, not the study, is the unit of assessment. Typing markers support isolate or lineage discrimination, whereas phylogenomics supports evolutionary inference; neither alone establishes host adaptation. Pangenome comparisons and microbial genome-wide association studies nominate candidate features rather than establish adaptation. Cell-envelope and iron-associated studies support specified biochemical, transcriptional, or physiological phenotypes under defined conditions, while macrophage and calf models support only the endpoints measured. Annotated sequence variation alone nominates pathogenicity hypotheses. Across the illustrative studies selected here, MAP genomics most directly supported lineage classification, candidate discovery, measured bacterial phenotypes, bounded transmission inference, and natural-host infection-fitness claims. Claims about adaptation, mechanism, virulence, or control require endpoints and comparisons matched to the stated claim and model; feature-specific causal claims additionally require evidence linking the bacterial feature to the measured endpoint.

Claim boundaries↗
PubMed1987

[Adaptive significance of the limited gene expression of the immune system].

Evolutionary development of immunity multigene systems seems to involve host-parasite molecular coevolution, as evidenced by comparison of metasoans and unicellular organisms in fixation rates of neutral and adaptive point mutations per one pair of corresponding genes. The estimations we attempted revealed that organisms with maximal restriction of Ig-like gene repertoire expression by an individual immune cell are more adaptive in formation of competent antigen-induced immune response, provided that the magnitude of potential repertoire of functional Ig-like receptors exceeds lymphoid cell population size. In contrast, when phage and bacteria populations are in coevolution, there is no need to limit the repertoire of expressive genes encoding bacteria surface receptor proteins which are recognized by a phage adsorption system. Other hypotheses of evolutionary premises and stimulus of immune genes expression limitation (allelic, isotypic etc.) are critically discussed.

Adaptation, Physiological↗
PubMed2006

Tempo and mode of early gene loss in endosymbiotic bacteria from insects.

BACKGROUND: Understanding evolutionary processes that drive genome reduction requires determining the tempo (rate) and the mode (size and types of deletions) of gene losses. In this study, we analysed five endosymbiotic genome sequences of the gamma-proteobacteria (three different Buchnera aphidicola strains, Wigglesworthia glossinidia, Blochmannia floridanus) to test if gene loss could be driven by the selective importance of genes. We used a parsimony method to reconstruct a minimal ancestral genome of insect endosymbionts and quantified gene loss along the branches of the phylogenetic tree. To evaluate the selective or functional importance of genes, we used a parameter that measures the level of adaptive codon bias in E. coli (i.e. codon adaptive index, or CAI), and also estimates of evolutionary rates (Ka) between pairs of orthologs either in free-living bacteria or in pairs of symbionts. RESULTS: Our results demonstrate that genes lost in the early stages of symbiosis were on average less selectively constrained than genes conserved in any of the extant symbiotic strains studied. These results also extend to more recent events of gene losses (i.e. among Buchnera strains) that still tend to concentrate on genes with low adaptive bias in E. coli and high evolutionary rates both in free-living and in symbiotic lineages. In addition, we analyzed the physical organization of gene losses for early steps of symbiosis acquisition under the hypothesis of a common origin of different symbioses. In contrast with previous findings we show that gene losses mostly occurred through loss of rather small blocks and mostly in syntenic regions between at least one of the symbionts and present-day E. coli. CONCLUSION: At both ancient and recent stages of symbiosis evolution, gene loss was at least partially influenced by selection, highly conserved genes being retained more readily than lowly conserved genes: although losses might result from drift due to the bottlenecking of endosymbiontic populations, we demonstrated that purifying selection also acted by retaining genes of greater selective importance.

Animals↗
PubMed2004

Molecular, morphological and behavioural data reveal the presence of a cryptic species in the widely studied Drosophila serrata species complex.

The Drosophila serrata species complex from Australia and New Guinea has been widely used in evolutionary studies of speciation and climatic adaptation. It is believed to consist of D. serrata, D. birchii and D. dominicana, although knowledge of the latter is limited. Here we present evidence for a previously undescribed cryptic member of the D. serrata species complex. This new cryptic species is widespread in far north Queensland, Australia and is likely to have been previously mistaken for D. serrata. It shows complete reproductive isolation when crossed with both D. serrata and D. birchii. The cryptic species can be easily distinguished from D. serrata and D. birchii using either microsatellite loci or visual techniques. Although it occurs sympatrically with both D. serrata and D. birchii, it differs from these species in development time, viability, wing size and wing morphology. Its discovery explains patterns of recently described mitochondrial DNA divergence within D. serrata, and may also help to clarify some ambiguities evident in early evolutionary literature on reproductive incompatibility within the D. serrata species complex.

Analysis of Variance↗
PubMed2001

Chromosomal effects of rapid gene evolution in Drosophila melanogaster.

Rapid adaptive fixation of a new favorable mutation is expected to affect neighboring genes along the chromosome. Evolutionary theory predicts that the chromosomal region would show a reduced level of genetic variation and an excess of rare alleles. We have confirmed these predictions in a region of the X chromosome of Drosophila melanogaster that contains a newly evolved gene for a component of the sperm axoneme. In D. simulans, where the novel gene does not exist, the pattern of genetic variation is consistent with selection against recurrent deleterious mutations. These findings imply that the pattern of genetic variation along a chromosome may be useful for inferring its evolutionary history and for revealing regions in which recent adaptive fixations have taken place.

Alleles↗