This theory seeks to define species and to explore evolutionary forces and genetic elements in speciation and species maintenance. The theory explains how speciation and species maintenance are caused by natural selection acting on non-Mendelian and Mendelian variation, respectively. The emergence and maintenance of species as groups of populations are balanced by evolutionary forces including complementary mechanisms of gene flow within and between populations at population-specific rates: sexual and asexual reproduction, recombining and nonrecombining genome regions, vertical and horizontal DNA transfer, and transposon proliferation and control. While recombining genome regions carry conserved genes and are subjected to meiotic recombination, nonrecombining genome regions carry accessory genes and are not subjected to such structural restrain. Sexual reproduction, vertical DNA transfer, recombining genome regions and transposon control keep species in existence by maintaining recombining chromosome number and structure, while asexual reproduction, horizontal DNA transfer, nonrecombining genome regions and transposon proliferation help species emerge by promoting reproductive isolation and changes in chromosome number and structure. The theory is based on the analysis of the genome sequences of isolates in the Fusarium oxysporum complex. The rate of horizontal supernumerary chromosome transfer in this complex was estimated to be 0.1 per genome per year.
We present an approximate analytic study of our previously introduced model of evolution including the effects of genetic exchange. This model is motivated by the process of bacterial transformation. We solve for the velocity, the rate of increase of fitness, as a function of the fixed population size, $N$. We find the velocity increases with $\ln N$, eventually saturated at an $N$ which depends on the strength of the recombination process. The analytical treatment is seen to agree well with direct numerical simulations of our model equations.
Molecular traits, such as gene expression levels or protein binding affinities, are increasingly accessible to quantitative measurement by modern high-throughput techniques. Such traits measure molecular functions and, from an evolutionary point of view, are important as targets of natural selection. We review recent developments in evolutionary theory and experiments that are expected to become building blocks of a quantitative genetics of molecular traits. We focus on universal evolutionary characteristics: these are largely independent of a trait's genetic basis, which is often at least par…
The Wright-Fisher model is the most popular population model for describing the behaviour of evolutionary systems with a finite population size. Approximations to the model have commonly been used for the analysis of time-resolved genome sequence data, but the model itself has rarely been tested against genomic data. Here, we evaluate the extent to which it can be inferred as the correct model given experimental data. Given genome-wide data from an evolutionary experiment, we validate the Wright-Fisher model as the better model for variance in a finite population in contrast to a Gaussian mode…
The Indo-Pacific region contains a unique mix of opportunities for the development and use of genetic-pest-management, gene-drive, and gene-drive-like technologies. Here I collectively refer to these technologies as Evolutionary Genetic Engineering (EGE). Indo-Pacific Islands have some of the world's highest rates of endemism and extinction---species and entire ecosystems are at risk. This threat to the natural world is coupled with the burden of human diseases, many of which are new and emerging or neglected tropical diseases. The same factors which have led to high rates of endemism also, in…
Over the last fifty years, geneticists have made great strides in understanding how our species' evolutionary history gave rise to current patterns of human genetic diversity classically summarized by Lewontin in his 1972 paper, 'The Apportionment of Human Diversity'. One evolutionary process that requires special attention in both population genetics and statistical genetics is admixture: gene flow between two or more previously separated source populations to form a new admixed population. The admixture process introduces unique patterns of genetic variation within and between populations, w…
There is an urgent and well-recognized need to extend genetic studies to diverse populations, but several obstacles continue to be prohibitive, including (but not limited to) the difficulty of recruiting individuals from diverse populations in large numbers and the lack of representation in available genomic references. These obstacles notwithstanding, studying multiple diverse populations would provide informative, population-specific insights. Using Native Hawaiians as an example of an understudied population with a unique evolutionary history, I will argue that by developing key genomic res…
Non-genetic perturbations, such as environmental change or developmental noise, can induce novel phenotypes. If an induced phenotype confers a fitness advantage, selection may promote its genetic stabilization. Non-genetic perturbations can thus initiate evolutionary innovation. Genetic variation that is not usually phenotypically visible may play an important role in this process. Populations under stabilizing selection on a phenotype that is robust to mutations can accumulate such variation. After non-genetic perturbations, this variation can become a source of new phenotypes. We here study …
1) Micro-evolutionary predictions are complicated by ecological feedbacks like density dependence, while ecological predictions can be complicated by evolutionary change. A widely used approach in micro-evolution, quantitative genetics, struggles to incorporate ecological processes into predictive models, while structured population modelling, a tool widely used in ecology, rarely incorporates evolution explicitly. 2) In this paper we develop a flexible, general framework that links quantitative genetics and structured population models. We use the quantitative genetic approach to write down t…
I review the evolutionary history of human populations in Europe with an emphasis on what has been learned in recent years through the study of ancient DNA. Human populations in Europe ~430-39kya (archaic Europeans) included Neandertals and their ancestors, who were genetically differentiated from other archaic Eurasians (such as the Denisovans of Siberia), as well as modern humans. Modern humans arrived to Europe by ~45kya, and are first genetically attested by ~39kya when they were still mixing with Neandertals. The first Europeans who were recognizably genetically related to modern ones app…
After an introduction to the general topic of models for a given locus of a diploid population whose quadratic dynamics is determined by a fitness landscape, we consider more specifically the models that can be treated using genetic (or train) algebras. In this setup, any quadratic offspring interaction can produce any type of offspring and after the use of specific changes of basis, we study the evolution and possible stability of some examples. We also consider some examples that cannot be treated using the framework of genetic algebras. Among these are bistochastic matrices.
The question of what determines genetic diversity both between and within species has long remained unsolved by the modern evolutionary theory (MET). However, it has not deterred researchers from producing interpretations of genetic diversity by using MET. We here examine the two key experimental observations of genetic diversity made in the 1960s, one between species and the other within a population of a species, that directly contributed to the development of MET. The interpretations of these observations as well as the assumptions by MET are widely known to be inadequate. We review the rec…
The evolution of genetic systems has been analyzed through the use of modifier gene models, in which a neutral gene is posited to control the transmission of other genes under selection. Analysis of modifier gene models has found the manifestations of an "evolutionary reduction principle": in a population near equilibrium, a new modifier allele that scales equally all transition probabilities between different genotypes under selection can invade if and only if it reduces the transition probabilities. Analytical results on the reduction principle have always required some set of constraints fo…
The accumulation of beneficial mutations on many competing genetic backgrounds in rapidly adapting populations has a striking impact on evolutionary dynamics. This effect, known as clonal interference, causes erratic fluctuations in the frequencies of observed mutations, randomizes the fixation times of successful mutations, and leaves distinct signatures on patterns of genetic variation. Here, we show how this form of `genetic draft' affects the forward-time dynamics of site frequencies in rapidly adapting asexual populations. We calculate the probability that mutations at individual sites sh…
A conflict exists between field biologists and physiologists ("functional biologists" or "evolutionary ecologists") on the one hand and those working in molecular evolution ("evolutionary biologists" or "population geneticists") on the other concerns the relative importance of natural selection and genetic drift. This paper is concerned with this issue in the case of vertebrates such as birds, fishes, mammals, and specifically humans, and views the issue in that context from a multilevel perspective. It proposes that the resolution is that adaptive selection outcomes occurring at the organism …
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a simplified form, these basic principles were transferred from the genetics of populations to the field of evolutionary computations, in order to solve applied optimization problems. Over almost half a century of development in this field of computer science, considerable practical experience has been gained and interesting theoretical results have been obtai…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution? Are there quantitative laws that govern and constrain evolution? Is evolution repeatable or predictable? Historically, the study of evolution involved classifying and comparing species, typically based on morphology. In addition to phenotypes on the organismal and molecular scales, we now use whole-genome sequencing to uncover not only the differences betwee…
Whether or not biodiversity dynamics tend toward stable equilibria remains an unsolved question in ecology and evolution with important implications for our understanding of diversity and its conservation. Phylo/population genetic models and macroecological theory represent two primary lenses through which we view biodiversity. While phylo/population genetics provide an averaged view of changes in demography and diversity over timescales of generations to geological epochs, macroecology provides an ahistorical description of commonness and rarity across contemporary co-occurring species. Our g…
We represent a process of learning by using bit strings, where 1-bits represent the knowledge acquired by individuals. Two ways of learning are considered: individual learning by trial-and-error; and social learning by copying knowledge from other individuals, or from parents in the case of species with parental care. The age-structured bit string allows us to study how knowledge is accumulated during life and its influence over the genetic pool of a population after many generations. We use the Penna model to represent the genetic inheritance of each individual. In order to study how the accu…
Population genetics struggles to model extinction; standard models track the relative rather than absolute fitness of genotypes, while the exceptions describe only the short-term transition from imminent doom to evolutionary rescue. But extinction can result from failure to adapt not only to catastrophes, but also to a backlog of environmental challenges. We model long-term evolution to long series of small challenges, where fitter populations reach higher population sizes. The population's long-term fitness dynamic is well approximated by a simple stochastic Markov chain model. Long-term pers…
Empirical evidence is presented which contradicts the established interpretation of the intraspecific genetic variability as the adaptive potential of the species: the uniform evolutionary tempo across the life kingdom, species discreteness, and absence of correlation between genetic variability and prosperity of extant species testify against the ruling paradigm. Consistent interpretation of the nature of intraspecific genetic variability is based on recognizing the limited sensitivity of stabilising selection, which allows for accumulation and persistence in the population of a considerable …
The origin of diversification and coexistence of genes and species have been traditionally studied in isolated biological levels. Ecological and evolutionary views have focused on the mechanisms that enable or constrain species coexistence, genetic variation and the genetics of speciation, but a unified theory linking those approaches is still missing. Here we introduce evolutionary graphs in the context of neutral theories of molecular evolution and biodiversity to provide a framework that simultaneously addresses speciation rate and joint genetic and species diversities. To illuminate this q…
Genetic interactions pervade every aspect of biology, from evolutionary theory where they determine the accessibility of evolutionary paths, to medicine where they contribute to complex genetic diseases. Until very recently, studies on epistatic interactions have been based on a handful of mutations, providing at best anecdotal evidence about the frequency and the typical strength of genetic interactions. In this study we analyze the publicly available Data Repository of Yeast Genetic INteractions (DRYGIN), which contains the growth rates of over five million double gene knockout mutants. We d…
Discrete dynamical systems defined by the iteration of a polynomial map of the unit simplex to itself appear in the context of population genetic systems evolving under mutation, recombination and weak selection. Although exceptional progress has been made in finding particular solutions to these systems, our knowledge of the general properties of the space of all possible dynamical systems of this kind is still limited. We prove that the space of bounded-degree polynomial maps of the unit simplex to itself is a compact and convex subset of a Euclidean space. We provide an explicit characteriz…
Robustness to genetic or environmental disturbances is often considered as a key property of living systems. Yet, in spite of being discussed since the 1950s, how robustness emerges from the complexity of genetic architectures and how it evolves still remains unclear. In particular, whether or not robustness is independent to various sources of perturbations conditions the range of adaptive scenarios that can be considered. For instance, selection for robustness to heritable mutations is likely to be modest and indirect, and its evolution might result from indirect selection on a pleiotropical…
Integrating population genetics into community ecology theory is a major goal in ecology and evolution, but analyzing the resulting models is computationally daunting. Here we describe sPEGG ($\underline{\textrm{s}}\textrm{imulating}$ $\underline{\textrm{P}}\textrm{henotypic}$ $\underline{\textrm{E}}\textrm{volution}$ on $\underline{\textrm{G}}\textrm{eneral Purpose}$ $\underline{\textrm{G}}\textrm{raphics Processing Units}$ (GPGPUs)), an open-source, multi-species forward-time population genetics simulator. Using a single commodity GPGPU instead of a single central processor, we find sPEGG ca…
We review and extend results for mutation, selection, genetic drift, and migration in a one-dimensional continuous population. The population is described by a continuous limit of the stepping stone model, which leads to the stochastic Fisher-Kolmogorov-Petrovsky-Piscounov equation with additional terms describing mutations. Although the stepping stone model was first proposed for population genetics, it is closely related to "voter models" of interest in nonequilibrium statistical mechanics. The stepping stone model can also be regarded as an approximation to the dynamics of a thin layer of a…
The equations of evolutionary change by natural selection are commonly expressed in statistical terms. Fisher's fundamental theorem emphasizes the variance in fitness. Quantitative genetics expresses selection with covariances and regressions. Population genetic equations depend on genetic variances. How can we read those statistical expressions with respect to the meaning of natural selection? One possibility is to relate the statistical expressions to the amount of information that populations accumulate by selection. However, the connection between selection and information theory has never…
We propose that genetic encoding of self-assembling components greatly enhances the evolution of complex systems and provides an efficient platform for inductive generalization, i.e. the inductive derivation of a solution to a problem with a potentially infinite number of instances from a limited set of test examples. We exemplify this in simulations by evolving scalable circuitry for several problems. One of them, digital multiplication, has been intensively studied in recent years, where hitherto the evolutionary design of only specific small multipliers was achieved. The fact that this and …
Globally, we are witnessing the rise of complex, non-communicable diseases (NCDs) related to changes in our daily environments. Obesity, asthma, cardiovascular disease, and type 2 diabetes are part of a long list of "lifestyle" diseases that were rare throughout human history but are now common. A key idea from anthropology and evolutionary biology--the evolutionary mismatch hypothesis--seeks to explain this phenomenon. It posits that humans evolved in environments that radically differ from the ones experienced by most people today, and thus traits that were advantageous in past environments …
We propose that the evolutionary purpose of junk DNA is to protect the gene. Mutation agents, such as retro-viruses, hit ``decoy'' DNA most of the time. Although the argument is far from general, we propose that the percentage of junk DNA should correlate with the number of retroviruses attacking a given species. It should also anti-correlate with the ideal mutation rates (higher in insects than in mammals).
University of Birmingham（伯明翰大学）；University of Maryland School of Medicine（马里兰大学医学院）；Baltimore VA Medical Center（巴尔的摩退伍军人事务医疗中心）
Adaptation to changing environments is a hallmark of biological systems. Diversity in traits is necessary for adaptation and can influence the survival of a population faced with novelty. In habitats that remain stable over many generations, stabilizing selection reduces trait differences within populations, thereby appearing to remove the diversity needed for heritable adaptive responses in new environments. Paradoxically, field studies have documented numerous populations under long periods of stabilizing selection and evolutionary stasis that have rapidly evolved under changed environmental…
Here, we investigate how competition in the Eden model is affected by short range dispersal and the requirement that site updates occur only after several updates of the same site have been attempted previously. The latter models the effect of tissue or media resistance to invasion. We found that the existence of tissue intensifies 'Natural Selection' and de-accelerating 'Genetic Drift', both to a limited extent. More interestingly, our results show that short-range migration can eliminate Genetic demixing and conceal Natural Selection.
Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent development, as with stochastic methods in population genetics. We discuss aspects of population genetics that have embraced methods from physics: amongst others, non-equilibrium statistical mechanics, travelling waves, and Monte-Carlo methods have been used to study polygenic evolution, rates of adaptation, and range expansions. These applicati…
A topological approach to the study of genetic recombination, based on persistent homology, was introduced by Chan, Carlsson, and Rabadán in 2013. This associates a sequence of signatures called barcodes to genomic data sampled from an evolutionary history. In this paper, we develop theoretical foundations for this approach. First, we present a novel formulation of the underlying inference problem. Specifically, we introduce and study the novelty profile, a simple, stable statistic of an evolutionary history which not only counts recombination events but also quantifies how recombination creat…
Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are a type of networks. The terminal nodes of these trees represent species, which are made of individuals and populations among which gene flow occurs. This flow can also be represented as a network. In this paper we briefly show some properties of these complex networks of evolutionary and ecological relationships. First, we characterize large scale evolutionary relationships in the Tree of Life by a degree distribution. Second, we represent genetic relationships between individu…
Modeling Protein Evolution via Generative Inference From Monte Carlo Chains to Population Genetics
Politecnico di Torino（都灵理工大学）；Sorbonne Université（索邦大学）；CNRS（法国国家科学研究中心）；Laboratory of Computational and Quantitative Biology（计算与定量生物学实验室）；École Normale Supérieure（巴黎高等师范学院）；PSL Université（巴黎文理研究大学）；Université de Paris（巴黎大学）；The James Franck Institute（詹姆斯·弗兰克研究所）；The University of Chicago（芝加哥大学）；Department of Physics, The University of Chicago（芝加哥大学物理系）；INFN, Sezione di Torino（意大利国家核物理研究所都灵分部）；Italian Institute for Genomic Medicine, IRCCS Candiolo（意大利基因组医学研究所坎迪奥洛医院）；Dipartimento di Fisica, Sapienza Università di Roma（罗马大学物理系）
We analyse a large data set of genetic markers obtained from populations of Cymodocea nodosa, a marine plant occurring from the East Mediterranean to the Iberian-African coasts in the Atlantic Ocean. We fully develop and test a recently introduced methodology to infer the directionality of gene flow based on the concept of geographical segregation. Using the Jensen-Shannon divergence, we are able to extract a directed network of gene flow describing the evolutionary patterns of Cymodocea nodosa. In particular we recover the genetic segregation that the marine plant underwent during its evoluti…
We present a model for evolving agents using both genetic and cultural inheritance mechanisms. Within each agent our model maintains two distinct information stores we call the genome and the memome. Processes of adaptation are modeled as evolutionary processes at each level of adaptation (phylogenetic, ontogenetic, sociogenetic). We review relevant competing models and we show how our model improves on previous attempts to model genetic and cultural evolutionary processes. In particular we argue our model can achieve divergent gene-culture co-evolution.
We introduce and analyse an individual-based evolutionary model, in which a population of genetically diverse organisms compete with each other for limited resources. Through theoretical analysis and stochastic simulations, we show that the model exhibits a pattern-forming instability which is highly amplified by the effects of demographic noise, leading to the spontaneous formation of genotypic clusters. This mechanism supports the thesis that stochasticity has a central role in the formation and coherence of species.
Emergent frequency-dependent selection predicts mutation outcomes in complex ecological communities
MIT Center for Theoretical Physics - a Leinweber Institute（麻省理工学院理论物理中心（莱因韦伯研究所））；Department of Physics, Boston University（波士顿大学物理系）；International Centre for Theoretical Sciences, Tata Institute of Fundamental Research（塔塔基础研究院国际理论科学中心）；Faculty of Computing and Data Sciences, Boston University（波士顿大学计算与数据科学学院）
