Large effects and the infinitesimal model.

The infinitesimal model of quantitative genetics relies on the Central Limit Theorem to stipulate that under additive models of quantitative traits determined by many loci having similar effect size, the difference between an offspring's genetic trait component and the average of their two parents' genetic trait components is Normally distributed and independent of the parents' values. Here, we investigate how the assumption of similar effect sizes affects the model: if, alternatively, the tail of the effect size distribution is polynomial with exponent α<2, then a different Central Limit Theorem implies that sums of effects should be well-approximated by a "stable distribution", for which single large effects are often still important. Empirically, we first find tail exponents between 1 and 2 in effect sizes estimated by genome-wide association studies of many human disease-related traits.

The probability of epidemic burnout in the stochastic SIR model with vital dynamics.

We present an approach to computing the probability of epidemic "burnout," i.e., the probability that a newly emergent pathogen will go extinct after a major epidemic.

Rates of SARS-CoV-2 transmission between and into California state prisons.

Correctional institutions are a crucial hotspot amplifying SARS-CoV-2 spread and disease disparity in the U.S. In the California state prison system, multiple massive outbreaks have been caused by transmission between prisons.

Assessing the risk of cascading COVID-19 outbreaks from prison-to-prison transfers.

COVID-19 transmission has been widespread across the California prison system, and at least two of these outbreaks were caused by transfer of infected individuals between prisons. Risks of individual prison outbreaks due to introduction of the virus and of widespread transmission within prisons due to poor conditions have been documented. We examine the additional risk potentially posed by transfer between prisons that can lead to large-scale spread of outbreaks across the prison system if the rate of transfer is sufficiently high.

Assessing the Risk of Cascading COVID-19 Outbreaks from Prison-to-Prison Transfers.

COVID-19 transmission has been widespread across the California prison system, and at least two of these outbreaks were caused by transfer of infected individuals between prisons. Risks of individual prison outbreaks due to introduction of the virus and of widespread transmission within prisons due to poor conditions have been documented. We examine the additional risk potentially posed by transfer between prisons that can lead to large-scale spread of outbreaks across the prison system if the rate of transfer is sufficiently high.

The Price equation and evolutionary epidemiology.

The Price equation has found widespread application in many areas of evolutionary biology, including the evolutionary epidemiology of infectious diseases. In this paper, we illustrate the utility of this approach to modelling disease evolution by first deriving a version of Price's equation that can be applied in continuous time and to populations with overlapping generations. We then show how this version of Price's equation provides an alternative perspective on pathogen evolution by considering the epidemiological meaning of each of its terms.

Pathogen evolution in finite populations: slow and steady spreads the best.

The theory of life-history evolution provides a powerful framework to understand the evolutionary dynamics of pathogens. It assumes, however, that host populations are large and that one can neglect the effects of demographic stochasticity. Here, we expand the theory to account for the effects of finite population size on the evolution of pathogen virulence.

Adaptation reveals sensory and decision components in the visual estimation of locomotion speed.

Locomotion speed provides important social information about an individual's fitness, mood and intent. Visual estimation of locomotion speed is a complex task for the visual system because viewing distance must be taken into account, and the estimate has to be calibrated by recent experience of typical speeds. Little is known about how locomotion speed judgements are made.

Invasion probabilities, hitting times, and some fluctuation theory for the stochastic logistic process.

We consider excursions for a class of stochastic processes describing a population of discrete individuals experiencing density-limited growth, such that the population has a finite carrying capacity and behaves qualitatively like the classical logistic model Verhulst (Corresp Math Phys 10:113-121, 1838) when the carrying capacity is large. Being discrete and stochastic, however, our population nonetheless goes extinct in finite time. We present results concerning the maximum of the population prior to extinction in the large population limit, from which we obtain establishment probabilities and upper bounds for the process, as well as estimates for the waiting time to establishment and extinction.

An active and selective molecular mechanism mediating the uptake of sex steroids by prostate cancer cells.

Steroid hormones play important roles in normal physiological functions and diseases. Sex steroids hormones are important in the biology and treatment of sex hormone-related cancer such as prostate cancer and breast cancer. Cells may take up steroids using multiple mechanisms.

Visual adaptation alters the apparent speed of real-world actions.

The apparent physical speed of an object in the field of view remains constant despite variations in retinal velocity due to viewing conditions (velocity constancy). For example, people and cars appear to move across the field of view at the same objective speed regardless of distance. In this study a series of experiments investigated the visual processes underpinning judgements of objective speed using an adaptation paradigm and video recordings of natural human locomotion.

Evolutionary consequences of behavioral diversity.

Iterated games provide a framework to describe social interactions among groups of individuals. This body of work has focused primarily on individuals who face a simple binary choice, such as "cooperate" or "defect." Real individuals, however, can exhibit behavioral diversity, varying their input to a social interaction both qualitatively and quantitatively.

Environmental robustness and the adaptability of populations.

Recent work has shown that genetic robustness can either facilitate or impede adaptation. But the impact of environmental robustness on adaptation remains unclear. Environmental robustness helps ensure that organisms consistently develop the same phenotype in the face of "environmental noise" during development.

Reconciling molecular phylogenies with the fossil record.

Historical patterns of species diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record. According to the fossil record, species frequently go extinct, and many clades experience periods of dramatic diversity loss. However, most analyses of molecular phylogenies fail to identify any periods of declining diversity, and they typically infer low levels of extinction.

Epistasis increases the rate of conditionally neutral substitution in an adapting population.

Kimura observed that the rate of neutral substitution should equal the neutral mutation rate. This classic result is central to our understanding of molecular evolution, and it continues to influence phylogenetics, genomics, and the interpretation of evolution experiments. By demonstrating that neutral mutations substitute at a rate independent of population size and selection at linked sites, Kimura provided an influential justification for the idea of a molecular clock and emphasized the importance of genetic drift in shaping molecular evolution.

Some consequences of demographic stochasticity in population genetics.

Much of population genetics is based on the diffusion limit of the Wright-Fisher model, which assumes a fixed population size. This assumption is violated in most natural populations, particularly for microbes. Here we study a more realistic model that decouples birth and death events and allows for a stochastically varying population size.

Mutational robustness can facilitate adaptation.

Robustness seems to be the opposite of evolvability. If phenotypes are robust against mutation, we might expect that a population will have difficulty adapting to an environmental change, as several studies have suggested. However, other studies contend that robust organisms are more adaptable.

Absorption and fixation times for neutral and quasi-neutral populations with density dependence.

We study a generalisation of Moran's population-genetic model that incorporates density dependence. Rather than assuming fixed population size, we allow the number of individuals to vary stochastically with the same events that change allele number, according to a logistic growth process with density dependent mortality. We analyse the expected time to absorption and fixation in the 'quasi-neutral' case: both types have the same carrying capacity, achieved through a trade-off of birth and death rates.

Fixation in haploid populations exhibiting density dependence II: the quasi-neutral case.

We determine fixation probabilities in a model of two competing types with density dependence. The model is defined as a two-dimensional birth-and-death process with density-independent death rates, and birth rates that are a linearly decreasing function of total population density. We treat the 'quasi-neutral case' where both types have the same equilibrium population densities.

Fixation in haploid populations exhibiting density dependence I: The non-neutral case.

We extend the one-locus two allele Moran model of fixation in a haploid population to the case where the total size of the population is not fixed. The model is defined as a two-dimensional birth-and-death process for allele number. Changes in allele number occur through density-independent death events and birth events whose per capita rate decreases linearly with the total population density.

Influence of age and run training on cardiac Na+/Ca2+ exchange.

Effects of age and training on myocardial Na+/Ca2+ exchange were examined in young sedentary (YS; 14-15 mo), aged sedentary (AS; 27-31 mo), and aged trained (AT; 8- to 11-wk treadmill run training) male Fischer Brown Norway rats. Whole heart performance and isolated cardiocyte Na+/Ca2+ exchange characteristics were measured. At the whole heart level, a small but significant slowing of late isovolumic left ventricular (LV) relaxation, which may be indicative of altered Na+/Ca2+ exchange activity, was seen in hearts from AS rats.