Genetic Model For Evolution Research Articles

Bernoulli factories and duality in Wright–Fisher and Allen–Cahn models of population genetics

Mathematical models of genetic evolution often come in pairs, connected by a so-called duality relation. The most seminal example are the Wright–Fisher diffusion and the Kingman coalescent, where the former describes the stochastic evolution of neutral allele frequencies in a large population forwards in time, and the latter describes the genetic ancestry of randomly sampled individuals from the population backwards in time. As well as providing a richer description than either model in isolation, duality often yields equations satisfied by quantities of interest. We employ the so-called Bernoulli factory – a celebrated tool in simulation-based computing – to derive duality relations for broad classes of genetics models. As concrete examples, we present Wright–Fisher diffusions with general drift functions, and Allen–Cahn equations with general, nonlinear forcing terms. The drift and forcing functions can be interpreted as the action of frequency-dependent selection. To our knowledge, this work is the first time a connection has been drawn between Bernoulli factories and duality in models of population genetics.

Characteristics and Genetic Mechanism of Pore Throat Structure of Shale Oil Reservoir in Saline Lake—A Case Study of Shale Oil of the Lucaogou Formation in Jimsar Sag, Junggar Basin

The shale oil reservoir of the Lucaogou Formation in the Jimsar Sag has undergone tectonic movement, regional deposition and complex diagenesis processes. Therefore, various reservoir space types and complex combination patterns of pores have developed, resulting in an intricate pore throat structure. The complex pore throat structure brings great challenges to the classification and evaluation of reservoirs and the efficient development of shale oil. The methods of scanning electron microscopy, high-pressure mercury injection, low-temperature adsorption experiments and thin-slice analysis were used in this study. Mineral, petrology, pore throat structure and evolution process characteristics of the shale oil reservoir were analyzed and discussed qualitatively and quantitatively. Based on these studies, the evolution characteristics and formation mechanisms of different pore throat structures were revealed, and four progressions were made. The reservoir space of the Lucaogou Formation is mainly composed of residual intergranular pores, dissolved pores, intercrystalline pores and fractures. Four types of pore throat structures in the shale oil reservoir of the Lucaogou Formation were quantitatively characterized. Furthermore, the primary pore throat structure was controlled by a sedimentary environment. The pores and throats were reduced and blocked by compaction and cementation, which deteriorates the physical properties of the reservoirs. However, the dissolution of early carbonate, feldspar and tuffaceous minerals and a small amount of carbonate cements by organic acids are the key factors to improve the pore throat structure of the reservoirs. The genetic evolution model of pore throat structures in the shale oil reservoir of the Lucaogou Formation are divided into two types. The large-pore medium-fine throat and medium-pore medium-throat reservoirs are mainly located in the delta front-shallow lake facies and are characterized by the diagenetic assemblage types of weak compaction–weak carbonate cementation–strong dissolution, early medium compaction–medium calcite and dolomite cementation–weak dissolution. The medium-pore fine throats and fine-pore fine throats are mainly developed in shallow lakes and semi-deep lakes. They are characterized by the diagenetic assemblage type of strong compaction–strong calcite cementation–weak dissolution diagenesis. This study provides a comprehensive understanding of the pore throat structure and the genetic mechanism of a complex shale oil reservoir and benefits the exploration and development of shale oil.

Peak shifts and extinction under sex-specific selection

A well-known property of sexual selection combined with a cross-sex genetic correlation (rmf) is that it can facilitate a peak shift on the adaptive landscape. How do these diversifying effects of sexual selection + rmf balance with the constraints imposed by such sexual antagonism, to affect the macroevolution of sexual dimorphism? Here, I extend existing quantitative genetic models of evolution on complex adaptive landscapes. Beyond recovering classical predictions for the conditions promoting a peak shift, I show that when rmf is moderate to strong, relatively weak sexual selection is required to induce a peak shift in males only. Increasing the strength of sexual selection leads to a sexually concordant peak shift, suggesting that macroevolutionary rates of sexual dimorphism may be largely decoupled from the strength of within-population sexual selection. Accounting explicitly for demography further reveals that sex-specific peak shifts may be more likely to be successful than concordant shifts in the face of extinction, especially when natural selection is strong. An overarching conclusion is that macroevolutionary patterns of sexual dimorphism are unlikely to be readily explained by within-population estimates of selection or constraint alone.

Genomic Profiling of Smoldering Multiple Myeloma Identifies Patients at a High Risk of Disease Progression.

Smoldering multiple myeloma (SMM) is a precursor condition of multiple myeloma (MM) with a 10% annual risk of progression. Various prognostic models exist for risk stratification; however, those are based on solely clinical metrics. The discovery of genomic alterations that underlie disease progression to MM could improve current risk models. We used next-generation sequencing to study 214 patients with SMM. We performed whole-exome sequencing on 166 tumors, including 5 with serial samples, and deep targeted sequencing on 48 tumors. We observed that most of the genetic alterations necessary for progression have already been acquired by the diagnosis of SMM. Particularly, we found that alterations of the mitogen-activated protein kinase pathway (KRAS and NRAS single nucleotide variants [SNVs]), the DNA repair pathway (deletion 17p, TP53, and ATM SNVs), and MYC (translocations or copy number variations) were all independent risk factors of progression after accounting for clinical risk staging. We validated these findings in an external SMM cohort by showing that patients who have any of these three features have a higher risk of progressing to MM. Moreover, APOBEC associated mutations were enriched in patients who progressed and were associated with a shorter time to progression in our cohort. SMM is a genetically mature entity whereby most driver genetic alterations have already occurred, which suggests the existence of a right-skewed model of genetic evolution from monoclonal gammopathy of undetermined significance to MM. We identified and externally validated genomic predictors of progression that could distinguish patients at high risk of progression to MM and, thus, improve on the precision of current clinical models.

Outstanding intraindividual genetic diversity in fissiparous planarians (Dugesia, Platyhelminthes) with facultative sex

BackgroundPredicted genetic consequences of asexuality include high intraindividual genetic diversity (i.e., the Meselson effect) and accumulation of deleterious mutations (i.e., Muller’s Ratchet), among others. These consequences have been largely studied in parthenogenetic organisms, but studies on fissiparous species are scarce. Differing from parthenogens, fissiparous organisms inherit part of the soma of the progenitor, including somatic mutations. Thus, in the long term, fissiparous reproduction may also result in genetic mosaicism, besides the presence of the Meselson effect and Muller’s Ratchet. Dugesiidae planarians show outstanding regeneration capabilities, allowing them to naturally reproduce by fission, either strictly or combined with sex (facultative). Therefore, they are an ideal model to analyze the genetic footprint of fissiparous reproduction, both when it is alternated with sex and when it is the only mode of reproduction.ResultsIn the present study, we generate and analyze intraindividual cloned data of a nuclear and a mitochondrial gene of sexual, fissiparous and facultative wild populations of the species Dugesia subtentaculata. We find that most individuals, independently of their reproductive strategy, are mosaics. However, the intraindividual haplotype and nucleotide diversity of fissiparous and facultative individuals is significantly higher than in sexual individuals, with no signs of Muller’s Ratchet. Finally, we also find that this high intraindividual genetic diversity of fissiparous and facultative individuals is composed by different combinations of ancestral and derived haplotypes of the species.ConclusionsThe intraindividual analyses of genetic diversity point out that fissiparous reproduction leaves a very special genetic footprint in individuals, characterized by mosaicism combined with the Meselson effect (named in the present study as the mosaic Meselson effect). Interestingly, the different intraindividual combinations of ancestral and derivate genetic diversity indicate that haplotypes generated during periods of fissiparous reproduction can be also transmitted to the progeny through sexual events, resulting in offspring showing a wide range of genetic diversity and putatively allowing purifying selection to act at both intraindividual and individual level. Further investigations, using Dugesia planarians as model organisms, would be of great value to delve into this new model of genetic evolution by the combination of fission and sex.

Local adaptation stops where ecological gradients steepen or are interrupted.

Population genetic models of evolution along linear environmental gradients cannot explain why adaptation stops at ecological margins. This is because, unless models impose reductions in carrying capacity at species’ edges, the dominant effect of gene flow is to increase genetic variance and adaptive potential rather than swamping local adaptation. This allows the population to match even very steep changes in trait optima. We extend our previous simulations to explore two nonlinear models of ecological gradients: (a) a sigmoid (steepening) gradient and (b) a linear gradient with a flat centre of variable width. We compare the parameter conditions that allow local adaptation and range expansion from the centre, with those that permit the persistence of a perfectly adapted population distributed across the entire range. Along nonlinear gradients, colonization is easier, and extinction rarer, than along a linear gradient. This is because the shallow environmental gradient near the range centre does not cause gene flow to increase genetic variation, and so does not result in reduced population density. However, as gradient steepness increases, gene flow inflates genetic variance and reduces local population density sufficiently that genetic drift overcomes local selection, creating a finite range margin. When a flat centre is superimposed on a linear gradient, gene flow increases genetic variation dramatically at its edges, leading to an abrupt reduction in density that prevents niche expansion. Remarkably local interruptions in a linear ecological gradient (of a width much less than the mean dispersal distance) can prevent local adaptation beyond this flat centre. In contrast to other situations, this effect is stronger and more consistent where carrying capacity is high. Practically speaking, this means that habitat improvement at patch margins will make evolutionary rescue more likely. By contrast, even small improvements in habitat at patch centres may confine populations to limited areas of ecological space.

Asymmetric Evolutionary Games.

Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner’s Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games.

Evolution of phenotypic plasticity and environmental tolerance of a labile quantitative character in a fluctuating environment.

Quantitative genetic models of evolution of phenotypic plasticity are used to derive environmental tolerance curves for a population in a changing environment, providing a theoretical foundation for integrating physiological and community ecology with evolutionary genetics of plasticity and norms of reaction. Plasticity is modelled for a labile quantitative character undergoing continuous reversible development and selection in a fluctuating environment. If there is no cost of plasticity, a labile character evolves expected plasticity equalling the slope of the optimal phenotype as a function of the environment. This contrasts with previous theory for plasticity influenced by the environment at a critical stage of early development determining a constant adult phenotype on which selection acts, for which the expected plasticity is reduced by the environmental predictability over the discrete time lag between development and selection. With a cost of plasticity in a labile character, the expected plasticity depends on the cost and on the environmental variance and predictability averaged over the continuous developmental time lag. Environmental tolerance curves derived from this model confirm traditional assumptions in physiological ecology and provide new insights. Tolerance curve width increases with larger environmental variance, but can only evolve within a limited range. The strength of the trade-off between tolerance curve height and width depends on the cost of plasticity. Asymmetric tolerance curves caused by male sterility at high temperature are illustrated. A simple condition is given for a large transient increase in plasticity and tolerance curve width following a sudden change in average environment.

Practical Comparison Between Genetic Algorithm and Clonal Selection Theory on KDD Dataset

This paper compares between two models: Common Genetic algorithm and the new Clonal selection theory in the field of Intrusion Detection. Genetic algorithms (GA) which is a model of genetic evolution, while Clonal selection theory (CST) is from models of the natural immune system NIS, the two models are from two different fields of Artificial Intelligence AI but they have portion of shared operations and objectives. The comparison to be done by applying the two models on some records of Knowledge Discovery and Data mining tools which is known by the name KDD data sets (its records the data of the interring packets to the computer system from the internet), to produce population ( in case of GA) or antibodies (in case of CST) can recognize these abnormal records.

Gametic conflict versus contact in the evolution of anisogamy

Anisogamy refers to gametes that differ in size, and characterizes the difference between males and females. The evolution of aniosgamy is widely interpreted as involving conflict between gamete producers with small sperm parasitizing on the investment made by the eggs. Using a population genetic model for evolution at a locus that codes jointly for sperm and egg sizes of a hermaphrodite, we show that the origin of anisogamy in an externally spawning population need not involve conflict between gamete producers. Gamete size dimorphism may be an adaptation that increases gamete encounter rates when large zygotes are selected, and we show this in a mechanistically general individual selection model. We use the Vance survival function without specific allometric assumptions to model the zygote fitness dependence on its size, and hence obtain ecological and life-history correlates of isogamy and anisogamy, which we successfully compare with data from Volvocales.

Analysis of genetic abnormalities provides insights into genetic evolution of hyperdiploid myeloma

Aneuploidy is ubiquitous in human cancer and is seen as whole chromosome gains and losses, unbalanced translocations and inversions, duplications, deletions and loss of heterozygosity. Within this complexity, some subgroups of aneuploid tumors emerge as distinct biological and clinical entities. Hyperdiploid myeloma (H-MM), characterized by hyperdiploid chromosome numbers because of nonrandom trisomies, is one such example. We undertook a comprehensive survey of the karyotypes of a large number of H-MM (n = 469) to describe fully genomic instability in these tumors, to dissect pathways of genetic evolution, and identify distinct subgroups based on their genetic changes. While selective pressure apparently favors the emergence of clones with gains of chromosomes 3, 5, 7, 9, 11, 15, 19, and 21, a background of ongoing genomic instability results in gains of other chromosomes, albeit at a much lower prevalence. A deduced temporal analysis of these karyotypes indicates that selected gains are early events. Other events occurring later in the course of the disease include secondary chromosome translocations and monosomies. The development of these genetic aberrations is thus highly ordered and undoubtedly of biological relevance. Within this framework, we propose a model of genetic evolution in H-MM.

Effect of variable surrounding on species creation

We constructed a model of speciation from evolution in an ecosystem consisting of a limited amount of energy recources. The species possesses genetic information, which is inherited according to the rules of the Penna model of genetic evolution. The increase in the number of the individuals of each species depends on the quality of their genotypes and the available energy resources. The decrease in number of the individuals results from genetic death or maximum-age reaching by the individual. The amount of energy resources is represented by a solution of the differential logistic equation, where the growth rate of the amount of the energy resources has been modified to include the number of individuals from all species in the ecosystem under consideration. The fluctuating surrounding is modelled with the help of the function V(x,t)= 1 4 x 4+ 1 2 b(t)x 2 , where x represents phenotype and the coefficient b( t) shows the cos( ωt) time dependence. The closer the value x of an individual to the minimum of V( x, t), the better adapted its genotype to the surrounding. We observed that the life span of the organisms strongly depends on the value of the frequency ω. It becomes shorter the more frequent the changes of the surrounding. However, there is a tendency for the species that have a higher value of the reproduction age a R to win the competition with the other species. Another observation is that small evolutionary changes of the inherited genetic information lead to spontaneous bursts of the evolutionary activity when many new species may appear in a short period. To cite this article: A. Nowicka et al., C. R. Biologies 327 (2004).

EVOLUTION BY IMITATION

Meme theory confronts us with a rather unflattering image of ourselves. In Daniel C. Dennett's words, conscious selves are nothing but the ‘vehicles’ or ‘nests’ of the true heroes of the evolutionary story of culture, the memes. In the memetic view, cultural evolution is not about ‘us’, but about ‘them’: the units of culture such as the ones mentioned by Richard Dawkms: “tunes, ideas, catch-phrases, clothes fashions, ways of making pots or of building arches”. In this paper, I shall take a critical look at some premises of this memetic ‘shift of perspective’, which turn out to be highly problematic. In a first step, the memetic image of the self as a ‘meme nest’ shall be traced back to its neo-Darwinian origins. Meme theory is built directly on the model of genetic evolution (I). As some considerations concerning the ontology of memes shall reveal, there are fundamental differences between genes and memes which cannot be accounted for within the memetic view (II). In a third step, Gabriel Tarde's idea of ‘evolution by association’ shall be introduced as a convincing alternative to the memetic idea of cultural evolution. Writing almost a century before the term ‘meme’ was even coined, Tarde put forth a theory, which already contained much of the insights that make memetics attractive to the social sciences. More than that, Tarde was safe from the fatal memetic tendency to model cultural evolution too closely on genetic evolution (III). In the concluding section (TV), I shall come back to the initial question concerning the place of the self in society: what is our role in cultural evolution in a Tardean view?

Evidence for positive selection on Mycobacterium tuberculosis within patients

BackgroundWhile the pathogenesis and epidemiology of tuberculosis are well studied, relatively little is known about the evolution of the infectious agent Mycobacterium tuberculosis, especially at the within-host level. The insertion sequence IS6110 is a genetic marker that is widely used to track the transmission of tuberculosis between individuals. This and other markers may also facilitate our understanding of the disease within patients.ResultsThis article presents three lines of evidence supporting the action of positive selection on M. tuberculosis within patients. The arguments are based on a comparison between empirical findings from molecular epidemiology, and population genetic models of evolution. Under the hypothesis of neutrality of genotypes, 1) the mutation rate of the marker IS6110 is unusually high, 2) the time it takes for substitutions to occur within patients is too short, and 3) the amount of polymorphism within patients is too low.ConclusionsEmpirical observations are explained by the action of positive selection during infection, or alternatively by very low effective population sizes. I discuss the possible roles of antibiotic treatment, the host immune system and extrapulmonary dissemination in creating opportunities for positive selection.

Genetic variability in MCF-7 sublines: evidence of rapid genomic and RNA expression profile modifications.

BackgroundBoth phenotypic and cytogenetic variability have been reported for clones of breast carcinoma cell lines but have not been comprehensively studied. Despite this, cell lines such as MCF-7 cells are extensively used as model systems.MethodsIn this work we documented, using CGH and RNA expression profiles, the genetic variability at the genomic and RNA expression levels of MCF-7 cells of different origins. Eight MCF-7 sublines collected from different sources were studied as well as 3 subclones isolated from one of the sublines by limit dilution.ResultsMCF-7 sublines showed important differences in copy number alteration (CNA) profiles. Overall numbers of events ranged from 28 to 41. Involved chromosomal regions varied greatly from a subline to another. A total of 62 chromosomal regions were affected by either gains or losses in the 11 sublines studied. We performed a phylogenetic analysis of CGH profiles using maximum parsimony in order to reconstruct the putative filiation of the 11 MCF-7 sublines. The phylogenetic tree obtained showed that the MCF-7 clade was characterized by a restricted set of 8 CNAs and that the most divergent subline occupied the position closest to the common ancestor. Expression profiles of 8 MCF-7 sublines were analyzed along with those of 19 unrelated breast cancer cell lines using home made cDNA arrays comprising 720 genes. Hierarchical clustering analysis of the expression data showed that 7/8 MCF-7 sublines were grouped forming a cluster while the remaining subline clustered with unrelated breast cancer cell lines. These data thus showed that MCF-7 sublines differed at both the genomic and phenotypic levels.ConclusionsThe analysis of CGH profiles of the parent subline and its three subclones supported the heteroclonal nature of MCF-7 cells. This strongly suggested that the genetic plasticity of MCF-7 cells was related to their intrinsic capacity to generate clonal heterogeneity. We propose that MCF-7, and possibly the breast tumor it was derived from, evolved in a node like pattern, rather than according to a linear progression model. Due to their capacity to undergo rapid genetic changes MCF-7 cells could represent an interesting model for genetic evolution of breast tumors.

The application of molecular genetic approaches to the study of human evolution

The past decade of advances in molecular genetic technology has heralded a new era for all evolutionary studies, but especially the science of human evolution. Data on various kinds of DNA variation in human populations have rapidly accumulated. There is increasing recognition of the importance of this variation for medicine and developmental biology and for understanding the history of our species. Haploid markers from mitochondrial DNA and the Y chromosome have proven invaluable for generating a standard model for evolution of modern humans. Conclusions from earlier research on protein polymorphisms have been generally supported by more sophisticated DNA analysis. Co-evolution of genes with language and some slowly evolving cultural traits, together with the genetic evolution of commensals and parasites that have accompanied modern humans in their expansion from Africa to the other continents, supports and supplements the standard model of genetic evolution. The advances in our understanding of the evolutionary history of humans attests to the advantages of multidisciplinary research.

A Model for Evolution of Male Parental Care and Female Multiple Mating

In most animals, males gain a fitness benefit by mating with many females, whereas the number of progeny per female is unlikely to increase as a function of additional mates. Furthermore, males of internally fertilizing species run the risk of investing in offspring of other males if they provide parental care. Nevertheless, males of many avian species and a minority of mammalian species provide parental care, and females of various species mate with multiple males. I investigate a two-locus genetic model for evolution of male parental care and female multiple mating in which females gain a direct benefit by multiple mating from the paternal care they thereby elicit for their offspring. The model suggests that, first, male parental care can evolve when it strongly enhances offspring survival and the direct costs of female multiple mating (e.g., loss of energy, risk of injury, exposure to infectious diseases) are greater than its indirect benefit (e.g., acquisition of good genes, increased genetic diversity among offspring); second, female multiple mating can evolve when paternal care is important for offspring survival or the indirect benefit of multiple mating is larger than its direct cost; and, finally, male parental care and female multiple mating can co-occur.

The Inclusive Fitness Dynamics of Genomic Imprinting

We develop a general inclusive fitness model for genetic evolution at an imprinted locus – one at which selection is allowed to act conditionally upon parental origin of the gene. In many cases of interest, such genes affect the fitness of relatives, particularly sibs. We formulate a matrilineal and patrilineal inclusive fitness and show that these can be used to describe the dynamics of change in mean expression levels. We classify and analyze the stability of equilibrium points and apply our results to some examples that have appeared in the literature, multiple paternity of a female's offspring, the “ovarian time-bomb,” and loss-of-function mutations.

A Model for Evolution of Male Parental Care and Female Multiple Mating

In most animals, males gain a fitness benefit by mating with many females, whereas the number of progeny per female is unlikely to increase as a function of additional mates. Furthermore, males of internally fertilizing species run the risk of investing in offspring of other males if they provide parental care. Nevertheless, males of many avian species and a minority of mammalian species provide parental care, and females of various species mate with multiple males. I investigate a two‐locus genetic model for evolution of male parental care and female multiple mating in which females gain a direct benefit by multiple mating from the paternal care they thereby elicit for their offspring. The model suggests that, first, male parental care can evolve when it strongly enhances offspring survival and the direct costs of female multiple mating (e.g., loss of energy, risk of injury, exposure to infectious diseases) are greater than its indirect benefit (e.g., acquisition of good genes, increased genetic diversity among offspring); second, female multiple mating can evolve when paternal care is important for offspring survival or the indirect benefit of multiple mating is larger than its direct cost; and, finally, male parental care and female multiple mating can co‐occur.

EFFECT OF INHERITED GENETIC INFORMATION ON STOCHASTIC PREDATOR-PREY MODEL

We discuss the Lotka–Volterra dynamics of two populations, preys and predators, in the case when the predators posses a genetic information. The genetic information is inherited according to the rules of the Penna model of genetic evolution. Each individual of the predator population is uniquely determined by sex, genotype and phenotype. In our case, the genes are represented by 8-bit integers and the phenotypes are defined with the help of the 8-state Potts model Hamiltonian. We showed that during time evolution, the population of the predators can experience a series of dynamical phase transitions which are connected with the different types of the dominant phenotypes present in the population.