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Unifying evolutionary dynamics: from individual stochastic processes to macroscopic models.

A distinctive signature of living systems is Darwinian evolution, that is, a propensity to generate as well as self-select individual diversity. To capture this essential feature of life while describing the dynamics of populations, mathematical models must be rooted in the microscopic, stochastic description of discrete individuals characterized by one or several adaptive traits and interacting with each other. The simplest models assume asexual reproduction and haploid genetics: an offspring usually inherits the trait values of her progenitor, except when a mutation causes the offspring to take a mutation step to new trait values; selection follows from ecological interactions among individuals. Here we present a rigorous construction of the microscopic population process that captures the probabilistic dynamics over continuous time of birth, mutation, and death, as influenced by the trait values of each individual, and interactions between individuals. A by-product of this formal construction is a general algorithm for efficient numerical simulation of the individual-level model. Once the microscopic process is in place, we derive different macroscopic models of adaptive evolution. These models differ in the renormalization they assume, i.e. in the limits taken, in specific orders, on population size, mutation rate, mutation step, while rescaling time accordingly. The macroscopic models also differ in their mathematical nature: deterministic, in the form of ordinary, integro-, or partial differential equations, or probabilistic, like stochastic partial differential equations or superprocesses. These models include extensions of Kimura's equation (and of its approximation for small mutation effects) to frequency- and density-dependent selection. A novel class of macroscopic models obtains when assuming that individual birth and death occur on a short timescale compared with the timescale of typical population growth. On a timescale of very rare mutations, we establish rigorously the models of "trait substitution sequences" and their approximation known as the "canonical equation of adaptive dynamics". We extend these models to account for mutation bias and random drift between multiple evolutionary attractors. The renormalization approach used in this study also opens promising avenues to study and predict patterns of life-history allometries, thereby bridging individual physiology, genetic variation, and ecological interactions in a common evolutionary framework.

Algorithms↗

Evolutionary dynamics of biological games.

Darwinian dynamics based on mutation and selection form the core of mathematical models for adaptation and coevolution of biological populations. The evolutionary outcome is often not a fitness-maximizing equilibrium but can include oscillations and chaos. For studying frequency-dependent selection, game-theoretic arguments are more appropriate than optimization algorithms. Replicator and adaptive dynamics describe short- and long-term evolution in phenotype space and have found applications ranging from animal behavior and ecology to speciation, macroevolution, and human language. Evolutionary game theory is an essential component of a mathematical and computational approach to biology.

Adaptation, Biological↗

Unifying the epidemiological and evolutionary dynamics of pathogens.

A key priority for infectious disease research is to clarify how pathogen genetic variation, modulated by host immunity, transmission bottlenecks, and epidemic dynamics, determines the wide variety of pathogen phylogenies observed at scales that range from individual host to population. We call the melding of immunodynamics, epidemiology, and evolutionary biology required to achieve this synthesis pathogen "phylodynamics." We introduce a phylodynamic framework for the dissection of dynamic forces that determine the diversity of epidemiological and phylogenetic patterns observed in RNA viruses of vertebrates. A central pillar of this model is the Evolutionary Infectivity Profile, which captures the relationship between immune selection and pathogen transmission.

Adaptation, Physiological↗

Evolutionary dynamics of HIV-1 and the control of AIDS.

Human immunodeficiency viruses (HIV) have exhibited an extraordinary capacity for genetic change, exploring new evolutionary space after each transmission to a new host. This presents a great challenge to the prevention and management of HIV-1 infection. At the same time, the relentless diversification of HIV-1, developing as it does under the constraints imposed by the human immune system and other selective forces, contains within it information useful for understanding HIV epidemiology and pathogenesis. Comparing the sheer mutational potential of HIV with actual data representing viral lineages that can survive selection suggests that HIV does not have unlimited capacity for change. Rather, clinical and bioinformatic data suggest that, even in the most diverse gene of the most highly variable organism, natural selection places severe limits on the portion of amino acid sequence space that ensures viability. This suggests some optimism for those attempting to identify sets of antigens that can generate effective humoral and cellular immune responses against HIV.

Acquired Immunodeficiency Syndrome↗

Evolutionary dynamics and preferential expression of homeologous 18S-5.8S-26S nuclear ribosomal genes in natural and artificial glycine allopolyploids.

Polyploidy is an important evolutionary process in plants, but much remains to be learned about the evolution of gene expression in polyploids. Evolution and expression of the 18S-5.8S-26S ribosomal gene family was investigated at homeologous loci in the Glycine subgenus Glycine perennial soybean polyploid complex, which consists of several diploid genomes that have formed allopolyploids in various combinations, often recurrently. A semiquantitative PCR method targeting the internal transcribed spacer (ITS) of the 18S-5.8S-26S nuclear ribosomal DNA (nrDNA) was used to survey the ratio between homeologous repeats in polyploid genomes and to test for preferential expression of homeologous nrDNA loci. Most natural polyploids possess one predominant nrDNA homeolog in their genome. Analysis of F2 segregation in an artificial cross suggested that in some plants, most or all repeats at one homeologous locus have been lost, whereas in other plants two loci remain, but both have been homogenized by concerted evolution. In most natural allopolyploids harboring a relatively balanced ratio of homeologs, one homeolog was expressed preferentially, but in the majority of plants, low levels of transcription could be detected from the other homeolog. Individuals within some tetraploid taxa varied as to which homeolog was expressed preferentially. In some plants, the degree of preferential expression also varied among tissues. Preferential expression was absent in synthetic polyploids and in some artificial diploid hybrids, suggesting that nucleolar dominance is not necessarily a direct result of hybridization or polyploidization. The establishment of preferential expression in Glycine allopolyploids appears to be either stochastic within lineages or genotype specific.

DNA, Ribosomal↗

Evolutionary dynamics of transposable elements in prokaryotes and eukaryotes.

This paper summarizes some recent theories about the evolution of transposable genetic elements in outbreeding, sexual eukaryotic organisms. The evolutionary possibilities available to self-replicating transposable elements are shown to vary depending on the reproductive biology of the host genome. This effect can be used to explain, in part, the differences in abundance of transposable elements between prokaryotes and eukaryotes. It is argued that the pattern of sexual outbreeding seen in mammals and plants is especially favorable to the spread of transposons. Moreover, because transposon spread is facilitated by zygote formation, the evolutionary origin of sexual conjugation may have been due to selection on transposon-encoded genes. Finally, evidence is also presented that introns could have originated as transposable genetic elements.

Biological Evolution↗

Evolutionary dynamics of genes controlling floral development.

Advances in the understanding of floral developmental genetics in model species such as Arabidopsis continue to provide an important foundation for comparative studies in other flowering plants. In particular, floral organ identity genes are the focus of many projects that are addressing both ancient and recent evolutionary questions. Expanded analyses of the evolution of these gene lineages have highlighted the dynamic nature of the gene birth-and-death process, and may have significant implications for the evolution of genetic pathways. Crucial functional studies of floral organ identity genes in diverse taxa are allowing the first real insight into the conservation of gene function, while findings on the genetic control of organ elaboration offer to open up new avenues for investigation. Taken together, these trends show that the field of floral developmental evolution continues to make significant progress towards elucidating the processes that have shaped the evolution of flower development and morphology.

Evolution, Molecular↗

The evolutionary dynamics of grammar acquisition.

Grammar is the computational system of language. It is a set of rules that specifies how to construct sentences out of words. Grammar is the basis of the unlimited expressibility of human language. Children acquire the grammar of their native language without formal education simply by hearing a number of sample sentences. Children could not solve this learning task if they did not have some pre-formed expectations. In other words, children have to evaluate the sample sentences and choose one grammar out of a limited set of candidate grammars. The restricted search space and the mechanism which allows to evaluate the sample sentences is called universal grammar. Universal grammar cannot be learned; it must be in place when the learning process starts. In this paper, we design a mathematical theory that places the problem of language acquisition into an evolutionary context. We formulate equations for the population dynamics of communication and grammar learning. We ask how accurate children have to learn the grammar of their parents' language for a population of individuals to evolve and maintain a coherent grammatical system. It turns out that there is a maximum error tolerance for which a predominant grammar is stable. We calculate the maximum size of the search space that is compatible with coherent communication in a population. Thus, we specify the conditions for the evolution of universal grammar.

Algorithms↗

Comprehensive analysis of synonymous codon usage bias and evolutionary dynamics in the chloroplast genomes of eight Coptis species.

Coptis is a medically important genus renowned for producing valuable isoquinoline alkaloids. Although its chloroplast genomes encode key components for photosynthesis and plastid gene expression, the evolutionary constraints acting on their coding sequences and synonymous codon usage remain poorly resolved. Here, we combined a transparent taxon-level sampling strategy with comparative analyses of chloroplast CDSs from eight Coptis taxa. We quantified nucleotide composition, relative synonymous codon usage, effective number of codons, neutrality and PR2 patterns, and correspondence analysis, and then integrated these results with a core-CDS distance analysis and gene-wise pairwise dN/dS estimates. The chloroplast genomes showed a conserved AT-rich composition, especially at the third codon position (GC3 approximately 30.3-30.8%), with a consistent GC1 > GC2 > GC3 trend. Thirty preferred codons were detected, 28 ending in A/T, and eleven optimal codons were shared across the genus. The core-CDS distance analysis recovered a close relationship between C. chinensis and C. chinensis var. brevisepala, whereas most coding genes showed dN/dS values below one, consistent with pervasive purifying constraint. Across 48 consistently filtered CDSs, GC3s was negatively associated with mean dN (Spearman rho = -0.404, P = 0.00439) and CAI was positively associated with mean dN (rho = 0.303, P = 0.0361), whereas the remaining associations were not significant (all P > = 0.0972). These results extend codon-usage analysis by linking synonymous-site composition to coding-sequence evolution within Coptis, while providing a hypothesis-generating resource for future plastid engineering studies.

Genome, Chloroplast↗

Evolutionary dynamics of oncogenes and tumor suppressor genes: higher intensities of purifying selection than other genes.

Oncogenes and tumor suppressor genes (hereafter referred to as "cancer genes") result in cancer when they experience substitutions that prevent or distort their normal function. We examined evolutionary pressures acting on cancer genes and other classes of disease-related genes and compared our results to analyses of genes without known association to disease. We compared synonymous and nonsynonymous substitution rates in 3,035 human genes-approximately 10% of the genome-measuring the intensity of purifying selection on 311 human disease genes, including 122 cancer-related genes. Although the genes examined are similar to nondisease genes in product, expression, function, and pathway affiliation, we found intriguing differences in the selective pressures experienced by cancer genes relative to other (noncancer) disease-related and non-disease-related genes. We found a statistically significant increase in the intensity of purifying selection exerted on cancer genes (the average ratio of nonsynonymous to synonymous substitutions, omega, was 0.079) relative to all other disease-related genes groups (omega = 0.101) and non-disease-related genes (omega = 0.100). This difference indicates a striking increase in selection against nonsynonymous substitutions in oncogenes and tumor suppressor genes. This finding provides insight into the etiology of cancer and the differences between genes involved in cancer and those implicated in other human diseases. Specifically, we found a significant overlap between human oncogenes and tumor suppressor genes and "essential genes," human homologs of mouse lethal genes identified by knockout experiments. This insight may improve our ability to identify cancer-related genes and enhances our understanding of the nature of these genes.

Evolution, Molecular↗

Evolutionary dynamics of insertion sequences in Helicobacter pylori.

Prokaryotic insertion sequence (IS) elements behave like parasites in terms of their ability to invade and proliferate in microbial gene pools and like symbionts when they coevolve with their bacterial hosts. Here we investigated the evolutionary history of IS605 and IS607 of Helicobacter pylori, a genetically diverse gastric pathogen. These elements contain unrelated transposase genes (orfA) and also a homolog of the Salmonella virulence gene gipA (orfB). A total of 488 East Asian, Indian, Peruvian, and Spanish isolates were screened, and 18 and 14% of them harbored IS605 and IS607, respectively. IS605 nucleotide sequence analysis (n = 42) revealed geographic subdivisions similar to those of H. pylori; the geographic subdivision was blurred, however, due in part to homologous recombination, as indicated by split decomposition and homoplasy tests (homoplasy ratio, 0.56). In contrast, the IS607 populations (n = 44) showed strong geographic subdivisions with less homologous recombination (homoplasy ratio, 0.2). Diversifying selection (ratio of nonsynonymous change to synonymous change, >>1) was evident in approximately 15% of the IS605 orfA codons analyzed but not in the IS607 orfA codons. Diversifying selection was also evident in approximately 2% of the IS605 orfB and approximately 10% of the IS607 orfB codons analyzed. We suggest that the evolution of these elements reflects selection for optimal transposition activity in the case of IS605 orfA and for interactions between the OrfB proteins and other cellular constituents that potentially contribute to bacterial fitness. Taken together, similarities in IS elements and H. pylori population genetic structures and evidence of adaptive evolution in IS elements suggest that there is coevolution between these elements and their bacterial hosts.

DNA Transposable Elements↗

The evolutionary dynamics of endogenous retroviruses.

Endogenous retroviruses (ERVs) are vertically transmitted intragenomic elements derived from integrated retroviruses. ERVs can proliferate within the genome of their host until they either acquire inactivating mutations or are lost by recombinational deletion. We present a model that unifies current knowledge of ERV biology into a single evolutionary framework. The model predicts the possible long-term outcomes of retroviral germline infection and can account for the variable patterns of observed ERV genetic diversity. We hope the model will provide a useful framework for understanding ERV evolution, enabling the testing of evolutionary hypotheses and the estimation of parameters governing ERV proliferation.

Endogenous Retroviruses↗

Evolutionary dynamics of pathogen resistance and tolerance.

Host organisms can respond to the threat of disease either through resistance defenses (which inhibit or limit infection) or through tolerance strategies (which do not limit infection, but reduce or offset its fitness consequences). Here we show that resistance and tolerance can have fundamentally different evolutionary outcomes, even when they have equivalent short-term benefit for the host. As a gene conferring disease resistance spreads through a population, the incidence of infection declines, reducing the fitness advantage of carrying the resistance gene. Thus genes conferring complete resistance cannot become fixed (i.e., universal) by selection in a host population, and diseases cannot be eliminated solely by natural selection for host resistance. By contrast, as a gene conferring disease tolerance spreads through a population, disease incidence rises, increasing the evolutionary advantage of carrying the tolerance gene. Therefore, any tolerance gene that can invade a host population will tend to be driven to fixation by selection. As predicted, field studies of diverse plant species infected by rust fungi confirm that resistance traits tend to be polymorphic and tolerance traits tend to be fixed. These observations suggest a new mechanism for the evolution of mutualism from parasitism, and they help to explain the ubiquity of disease.

Animals↗

Colicin diversity: a result of eco-evolutionary dynamics.

Colicins are plasmids that are carried in Escherichia coli. They code for a toxic protein and for proteins that confer on the host immunity against this toxin. When bacteria carry plasmids their growth rate is reduced. At the same time, the production of toxins makes it possible for colicinogenic bacteria to invade bacterium strains that are not immune. In natural bacterium populations there is a high diversity of colicin types. The reason for the maintenance of this diversity has been the subject of much recent debate. We have studied a simple eco-evolutionary model of the interaction of bacteria with colicins and show that high diversity of colicins is to be expected. We find two different dynamical modes each with a high diversity: a hyperimmunity mode and a multitoxicity mode. Bacteria are immune to most toxins in the first mode but in fact produce very few toxins. In the second mode bacteria are immune only to those toxins that they actually produce. In the second mode toxin levels per bacterium are much higher, whereas immunity levels per bacterium are lower.

Bacterial Toxins↗

Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in a evolution reactor, I.

A theory for describing evolution as adaptive walks by a finite population with M walkers (M > or = 1) on an anisotropic Mt. Fuji-type fitness landscape is presented, from a thermodynamical point of view. Introducing the 'free fitness' as the sum of a fitness term and an entropy term and 'evolutionary force' as the gradient of free fitness on a fitness coordinate, we demonstrate that the behavior of these theoretical walkers is almost consistent with the thermodynamical schemes. The major conclusions are as follows: (1) an adaptive walk (=evolution) is driven by an evolutionary force in the direction in which free fitness increases; (2) the expectation of the climbing rate obeys an equation analogous to the Einstein relation in Brownian motion; (3) the standard deviation of the climbing rate is a quantity analogous to the mean thermal energy of a particle, kT (x constant). In addition, on the interpretation that the walkers climb the landscape by absorbing 'fitness information' from the surroundings, we succeeded in quantifying the fitness information and formulating a macroscopic scheme from an informational point of view.

Adaptation, Biological↗

Characterization and evolutionary dynamics of a complex family of satellite DNA in the leaf beetle Chrysolina carnifex (Coleoptera, Chrysomelidae).

The present study characterizes the complex satellite DNA from the specialized phytophagous beetle species Chrysolina carnifex. The satellite DNA is formed by six monomer types, partially homologous but having diverged enough to be separate on the phylogenetic trees, since each monomer type is located on a different branch, having statistically significant bootstrap values. Its analysis suggests a common evolutionary origin of all monomers from the same 211-bp sequence mainly by means of base-substitution mutations evolutionarily fixed to each monomer type and duplications and/or deletions of pre-existing segments in the 211-bp sequence. The analysis of the sequences and Southern hybridizations suggest that the monomers are organized in three types of repeats: monomers (211-bp) and higher-order repeats in the form of dimers (477-bp) or even trimers (633-bp). These repetitive units are not isolated from others, and do not present the pattern characteristic for the regular tandem arrangement of satellite DNA. In-situ hybridization with biotinylated probes corresponding to the three types of repeats showed the pericentromeric location of these sequences in all meiotic bivalents, coinciding with the heterochromatic blocks revealed by C-banding, indicating in addition that each type of repeat is neither isolated from others nor located in specific chromosomes but rather that they are intermixed in the heterochromatic regions. The presence of this repetitive DNA in C. haemoptera, C. bankii and C. americana was also tested by Southern analysis. The results show that this satellite DNA sequence is specific to the C. carnifex genome but has not been found in three other species of Chrysolina occupying similar or different host plants.

Animals↗

The Pleistocene history of the sheepshead minnow (Cyprinodon variegatus): Non-equilibrium evolutionary dynamics within a diversifying species complex.

The sheepshead minnow, Cyprinodon variegatus, is a widespread fish species that typically inhabits coastal tidal marsh and mangrove swamp environments, ranging from Cape Cod, Massaschusetts to northern Mexico and into the Caribbean. This wide range crosses several biogeographic boundaries which are coincident with genetic structuring within numerous species originating in the Pleistocene. In addition, the more northerly reaches of this species range have been further subject to the evolutionary consequences of Pleistocene glaciation due to local extinction and recolonization of formerly glaciated sites. C. variegatus thus provides an excellent vertebrate model system within which to test the extent of genetic differentiation among populations in a dominant coastal ecosystem and examine patterns of historical demography in populations distributed along a latitudinal gradient. Using mitochondrial control region and ND2 sequence data, we discovered monophyletic clades within C. variegatus with divergence times within the Pleistocene, and very low gene flow between most sites. Intraspecific genetic breaks appear to correspond broadly to biogeographic or oceanic boundaries. Pleistocene climate change appears to have had dramatic impacts on the size and distribution of populations within and near the glacial margins, but has also affected populations far from formerly glaciated regions.

Animals↗

The evolutionary dynamics of repetitive DNA in eukaryotes.

Repetitive DNA sequences form a large portion of the genomes of eukaryotes. The 'selfish DNA' hypothesis proposes that they are maintained by their ability to replicate within the genome. The behaviour of repetitive sequences can result in mutations that cause genetic diseases, and confer significant fitness losses on the organism. Features of the organization of repetitive sequences in eukaryotic genomes, and their distribution in natural populations, reflect the evolutionary forces acting on selfish DNA.

Animals↗