“Actually, the orgy of fact extraction in which everybody is currently engaged has, like most consumer economies, accumulated a vast debt. This is a debt of theory, and some of us are soon going to have an exciting time paying it back—with interest, I hope.” —Sydney Brenner, In Theory ,

species, but rather affects concrete groups of interbreeding individuals, termed populations. The size and structure of the evolving population largely determines the trajectory and outcome of evolution. In particular, Fisher formulated and proved the fundamental theorem of natural selection (commonly known as Fisher’s theorem), which states that the intensity of selection (and, hence, the rate of evolution due to selection) is proportional to the magnitude of the standing genetic variation in an evolving population, which, in turn, is proportional to the effective population size. Box 1-1 gives the basic definitions and equations that determine the effects of mutation and selection on the elimination or fixation of 8 the logic of chance mutant alleles, depending on the effective population size. The qualitative bottom line is that, given the same mutation rate, in a population with a large effective size, selection is intense. In this case, even mutations with a small positive selection coefficient (“slightly” beneficial mutations) quickly come to fixation. On the other hand, mutations with even a small negative selection coefficient (slightly deleterious mutations) are rapidly eliminated. This effect found its rigorous realization in Fisher’s theorem. Box 1-1: The fundamental relationships defining the roles of selection and drift in the evolution of populations Nearly neutral evolution dominated by drift

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Y chromosomes are genetically degenerate, having lost most of the active genes that were present in their ancestors. The causes of this degeneration have attracted much attention from evolutionary theorists. Four major theories are reviewed here: Muller's ratchet, background selection, the Hill Robertson effect with weak selection, and the 'hitchhiking' of deleterious alleles by favourable mutations. All of these involve a reduction in effective population size as a result of selective events occurring in a non-recombining genome, and the consequent weakening of the efficacy of selection. We review the consequences of these processes for patterns of molecular evolution and variation at loci on Y chromosomes, and discuss the results of empirical studies of these patterns for some evolving Y-chromosome and neo-Y-chromosome systems. These results suggest that the effective population sizes of evolving Y or neo-Y chromosomes are severely reduced, as expected if some or all of the hypothesized processes leading to degeneration are operative. It is, however, currently unclear which of the various processes is most important; some directions for future work to help to resolve this question are discussed.

While seed-propagated crops have contributed many evolutionary insights, evolutionary biologists have often neglected clonally propagated crops. We argue that widespread notions about their evolution under domestication are oversimplified, and that they offer rich material for evolutionary studies. The diversity of their wild ancestors, the diverse ecologies of the crop populations themselves, and the intricate mix of selection pressures, acting not only on the parts harvested but also on the parts used by humans to make clonal propagules, result in complex and diverse evolutionary trajectories under domestication. We examine why farmers propagate some plants clonally, and discuss the evolutionary dynamics of sexual reproduction in clonal crops. We explore how their mixed clonal/sexual reproductive systems function, based on the sole example studied in detail, cassava (Manihot esculenta). Biotechnology is now expanding the number of clonal crops, continuing the 10 000-yr-old trend to increase crop yields by propagating elite genotypes. In an era of rapid global change, it is more important than ever to understand how the adaptive potential of clonal crops can be maintained. A key component of strategies for preserving this adaptive potential is the maintenance of mixed clonal/sexual systems, which can be achieved by encouraging and valuing farmer knowledge about the sexual reproductive biology of their clonal crops.

We investigate the relationship between the average fitness decay due to single mutations and the strength of epistatic interactions in genetic sequences. We observe that epistatic interactions between mutations are correlated to the average fitness decay, both in RNA secondary structure prediction as well as in digital organisms replicating in silico. This correlation implies that, during adaptation, epistasis and average mutational effect cannot be optimized independently. In experiments with RNA sequences evolving on a neutral network, the selective pressure to decrease the mutational load then leads to a reduction in the amount of sequences with strong antagonistic interactions between deleterious mutations in the population.

We investigate the evolutionary dynamics of a finite population of sequences adapting to NK fitness landscapes. We find that, unlike in the case of an infinite population, the average fitness in a finite population is maximized at a small but finite, rather than vanishing, mutation rate. The highest local maxima in the landscape are visited for even larger mutation rates, close to a transition point at which the population delocalizes (i.e., leaves the fitness peak at which it was localized) and starts traversing the sequence space. If the mutation rate is increased even further, the population undergoes a second transition and loses all sensitivity to fitness peaks. This second transition corresponds to the standard error threshold transition first described by Eigen. We discuss the implications of our results for biological evolution and for evolutionary optimization techniques.

We investigate a population-genetic model with a temporally-fluctuating sawtooth fitness landscape. We numerically show that a counter-intuitive behavior occurs where the rate of evolution of the system decreases as selection pressure increases from zero. This phenomenon is understood by analogy with absolute negative mobility in particle flow. A phenomenological explanation about the direction of evolution is also provided.

We have sequenced the entire exon (∼1,180 bp) encoding the zinc finger domain of the X-linked and Y-linked zinc finger genes (ZFX and ZFY, respectively) in the orangutan, the baboon, the squirrel monkey, and the rat; a total of 9,442 by were sequenced. The ratio of the rates of synonymous substitution in the ZFY and ZFX genes is estimated to be 2.1 in primates. This is close to the ratio of 2.3 estimated from primate ZFY and ZFX intron sequences and supports the view that the male-to-female ratio of mutation rate in humans is considerably higher than 1 but not extremely large. The ratio of synonymous substitution rates in ZFY and ZFX is estimated to be 1.3 in the rat lineage but 4.2 in the mouse lineage. The former is close to the estimate (1.4) from introns. The much higher ratio in the mouse lineage (not statistically significant) might have arisen from relaxation of selective constraints. The synonymous divergence between mouse and rat ZFX is considerably lower than that between mouse and rat autosomal genes, agreeing with previous observations and providing some evidence for stronger selective constraints on synonymous changes in X-linked genes than in autosomal genes. At the protein level ZFX has been highly conserved in all placental mammals studied while ZFY has been well conserved in primates and foxes but has evolved rapidly in mice and rats, possibly due to relaxation of functional constraints as a result of the development of X-inactivation of ZFX in rodents. The long persistence of the ZFY-ZFX gene pair in mammals provides some insight into the process of degeneration of Y-linked genes.

We discuss the self-deprecating strategy introduced by Peter Blau as one of stages of the process of social integration. Recently we have introduced a two-dimensional space of status, real and surface one ($A$ and $B$), and we have demonstrated that with this setup, the self-deprecating strategy efficiently prevents the rejection [K. Malarz and K. Kulakowski, International Journal of Modern Physics C 30, 1950040 (2019)]. There, the process of reducing the conflict was described by master equations, i.e. a set of differential equations describing evolution of density $v(A,B)$ of actors of status $(A,B)$. Here we reformulate the problem in terms of probabilistic cellular automata. The obtained results for number $n(A,B)$ of actors of status $(A,B)$ are qualitatively the same as in the previous approach, both for synchronous and asynchronous version of the automaton. Namely, an enhancement of the surface status compensates a deficiency of the real one.

We develop a formal framework for the optimal allocation of limited resources that includes and clarifies the interplay between individual optimization and the resulting effects at the population level. As an example, in regard to the evolution of sexual recombination, the paradox of the twofold cost of sex is avoided by distinguishing between the evolution of recombination and the subsequent emergence and stability of different mating types as a result of individual optimization within a population that benefits from recombination.

We describe the initial phase of a research project to develop an artificial life framework designed to extract knowledge from large data sets with minimal preparation or ramp-up time. In this phase, we evolved an artificial life population with a new brain architecture. The agents have sufficient intelligence to discover patterns in data and to make survival decisions based on those patterns. The species uses diploid reproduction, Hebbian learning, and Kohonen self-organizing maps, in combination with novel techniques such as using pattern-rich data as the environment and framing the data analysis as a survival problem for artificial life. The first generation of agents mastered the pattern discovery task well enough to thrive. Evolution further adapted the agents to their environment by making them a little more pessimistic, and also by making their brains more efficient.

We describe a stochastic birth-and-death model of evolution of horizontally transferred genes in microbial populations. The model is a generalization of the stochastic model described by Berg and Kurland and includes five parameters: the rate of mutational inactivation, selection coefficient, invasion rate (i.e., rate of arrival of a novel sequence from outside of the recipient population), within-population horizontal transmission ("infection") rate, and population size. The model of Berg and Kurland included four parameters, namely, mutational inactivation, selection coefficient, population size, and "infection." However, the effect of "infection" was disregarded in the interpretation of the results, and the overall conclusion was that horizontally acquired sequences can be fixed in a population only when they confer a substantial selective advantage onto the recipient and therefore are subject to strong positive selection. Analysis of the present model in different domains of parameter values shows that, as long as the rate of within-population horizontal transmission is comparable to the mutational inactivation rate and there is even a low rate of invasion, horizontally acquired sequences can be fixed in the population or at least persist for a long time in a substantial fraction of individuals in the population even when they are neutral or slightly deleterious. The available biological data strongly suggest that intense within-population and even between-populations gene flows are realistic for at least some prokaryotic species and environments. Therefore, our modeling results are compatible with the notion of a pivotal role of horizontal gene transfer in the evolution of prokaryotes.

We consider a class of nonlocal reaction-diffusion problems, referred to as replicator-mutator equations in evolutionary genetics. By using explicit changes of unknown function, we show that they are equivalent to the heat equation and, therefore, compute their solution explicitly. Based on this, we then prove that, in the case of beneficial mutations in asexual populations, solutions dramatically depend on the tails of the initial data: they can be global, become extinct in finite time or, even, be defined for no positive time. In the former case, we prove that solutions are accelerating, and in many cases converge for large time to some universal Gaussian profile. This sheds light on the biological relevance of such models.

University of Minnesota Ph.D. dissertation. May 2011. Major: Physics. Advisor: Alex Kamenev. 1 computer file (PDF); vi, 74 pages, appendices A-B.

Understanding why some organisms reproduce by sexual reproduction while others can reproduce asexually remains an important unsolved problem in evolutionary biology. Simple demography suggests that asexuals should outcompete sexually reproducing organisms, because of their higher intrinsic rate of increase. However, the majority of multicellular organisms have sexual reproduction. The widely accepted explanation for this apparent contradiction is that asexual lineages have a higher extinction rate. A number of models have indicated that population size might play a crucial role in the evolution of asexuality. The strength of processes that lead to extinction of asexual species is reduced when population sizes get very large, so that the long‐term advantage of sexual over asexual reproduction may become negligible. Here, we use a comparative approach using scale insects (Coccoidea, Hemiptera) to show that asexuality is indeed more common in species with larger population density and geographic distribution and we also show that asexual species tend to be more polyphagous. We discuss the implication of our findings for previously observed patterns of asexuality in agricultural pests.

Understanding the rates, spectra, and fitness effects of spontaneous mutations is fundamental to answering key questions in evolution, molecular biology, disease genetics, and conservation biology. To estimate mutation rates and evaluate the effect of selection on new mutations, we propagated mutation accumulation (MA) lines of Daphnia pulex for more than 82 generations and maintained a non-MA population under conditions where selection could act. Both experiments were started with the same obligate asexual progenitor clone. By sequencing 30 genomes and implementing a series of validation steps that informed the bioinformatic analyses, we identified a total of 477 single nucleotide mutations (SNMs) in the MA lines, corresponding to a mutation rate of 2.30 × 10−9 (95% CI 1.90–2.70 × 10−9) per nucleotide per generation. The high overall rate of loss of heterozygosity (LOH) of 4.82 × 10−5 per site per generation was due to a large ameiotic recombination event spanning an entire arm of a chromosome (∼6 Mb) and several hemizygous deletion events spanning ∼2 kb each. In the non-MA population, we found significantly fewer mutations than expected based on the rate derived from the MA experiment, indicating purifying selection was likely acting to remove new deleterious mutations. We observed a surprisingly high level of genetic variability in the non-MA population, which we propose to be driven by balancing selection. Our findings suggest that both positive and negative selection on new mutations is powerful and effective in a strictly clonal population.

Understanding the purpose of sex remains one of the most important unresolved problems in evolutionary biology (Otto and Lenormand, 2002; Rice, 2002). Two leading theories of sex are the mutational deterministic hypothesis that sex reduces mutational load, and the Red Queen hypothesis that sex permits a host organism to maintain parity in a never-ending con‡ict with parasites. These theories have similar predictions and have been di¢ cult to distinguish. We propose to distinguish between them by asking if either is consistent with the fact that sexually produced o¤spring have only two parents, not three or more. It is shown that the mutational deterministic hypothesis implies that a suitable triparental system dominates biparental sex, so the latter should never be observed, contrary to fact. In contrast, it is shown that the Red Queen hypothesis can explain biparental sex without conferring an additional advantage to triparental sex. Keywords: Biparental sex; Triparental sex; Purpose of sex; Twofold cost of sex; Deleterious mutations; Red queen. 1. Introduction The breadth and variety of methods by which di¤erent species reproduce through sex is stunning. Yet, sexual reproduction displays a remarkable regularity. Each sexually produced o¤spring of any known species is produced 1The Hebrew University of Jerusalem, Jerusalem, 91904 Israel, University of Essex. The University of Chicago, Chicago, IL 60637 USA. Simon Fraser University, Burnaby, BC, Canada V5A 1S6. All authors contributed equally to this work. from the genetic material of precisely two individuals. That is, sex is always biparental. Curiously, this fact has not been exploited to distinguish between competing theories of sex. Indeed, the main objective of the maintenance of sex literature is to explain why genetic mixing is su¢ ciently bene…cial so that biparental sex overcomes the twofold cost of males it su¤ers because an equally-sized asexual population would grow twice as fast (Maynard Smith, 1978). But the fact that sex is always biparental implies that genetic mixing must not be so bene…cial that a further increase in …tness would be obtained from even more of it through triparental sex or quadriparental sex, etc. A theory of sex, therefore, must strike a delicate balance –genetic mixing must be advantageous, but not too advantageous. Whether any current theory of sex strikes this balance has never been considered despite the potential power such consideration holds for distinguishing between theories. Indeed, little or no attention has previously been paid to whether a theory of biparental sex inadvertently confers an advantage to, say, triparental sex. Perhaps this is because one is tempted to dismiss triparental sex on the grounds that the associated costs — be they the cost of unproductive males, mating coordination costs, or the cost of developing the requisite genetic machinery — are prohibitive. But, insofar as such arguments have been provided at all, they are unpersuasive. For example, they fail to take into account the key point that any argument against the transition from biparental sex to triparental sex may be even more persuasive for ruling out the transition from asexual reproduction

This study develops a simplified model describing the evolutionary dynamics of a population composed of obligate sexually and asexually reproducing, unicellular organisms. The model assumes that the organisms have diploid genomes consisting of two chromosomes, and that the sexual organisms replicate by first dividing into haploid intermediates, which then combine with other haploids, followed by the normal mitotic division of the resulting diploid into two new daughter cells. We assume that the fitness landscape of the diploids is analogous to the single-fitness-peak approach often used in single-chromosome studies. That is, we assume a master chromosome that becomes defective with just one point mutation. The diploid fitness then depends on whether the genome has zero, one, or two copies of the master chromosome. We also assume that only pairs of haploids with a master chromosome are capable of combining so as to produce sexual diploid cells, and that this process is described by second-order kinetics. We find that, in a range of intermediate values of the replication fidelity, sexually reproducing cells can outcompete asexual ones, provided the initial abundance of sexual cells is above some threshold value. The range of values where sexual reproduction outcompetes asexual reproduction increases with decreasing replication rate and increasing population density. We critically evaluate a common approach, based on a group selection perspective, used to study the competition between populations and show its flaws in addressing the evolution of sex problem.

This review offers a personal perspective on historical developments related to our current understanding of DNA repair, recombination, and homologous integration in Neurospora crassa. Previous reviews have summarized and analyzed the characteristics of Neurospora DNA repair mutants. The early history is reviewed again here as a prelude to a discussion of the molecular cloning, annotation, gene disruption and reverse genetics of Neurospora DNA repair genes. The classical studies and molecular analysis are then linked in a perspective on new directions in research on mutagen-sensitive mutants.