A simple and direct method to define clonal selection in somatic mosaicism

Dividing somatic stem cells acquire DNA changes marking different clones. With time, clones can become large, either stochastically through neutral drift, or increased fitness and consequent selection. We present a simple, direct, and general approach that distinguishes between these two processes in normal somatic tissue in individuals. The method relies on single time point whole genome sequencing to study somatic mosaicism as tissues age. Using this method, we show that in human clonal hemopoiesis (CH), clones with CH driver mutations, that comprise a median of 24% of hematopoiesis originate decades before they are detected. They expand, through selection by a median of 26% per year. Overall, there is a 3-fold increased rate of stem cell division and an 8.6-fold increase in active long-term stem cells.

The network structure affects the fixation probability when it couples to the birth-death dynamics in finite population

The study of evolutionary dynamics on graphs is an interesting topic for researchers in various fields of science and mathematics. In systems with finite population, different model dynamics are distinguished by their effects on two important quantities: fixation probability and fixation time. The isothermal theorem declares that the fixation probability is the same for a wide range of graphs and it only depends on the population size. This has also been proved for more complex graphs that are called complex networks. In this work, we propose a model that couples the population dynamics to the network structure and show that in this case, the isothermal theorem is being violated. In our model the death rate of a mutant depends on its number of neighbors, and neutral drift holds only in the average. We investigate the fixation probability behavior in terms of the complexity parameter, such as the scale-free exponent for the scale-free network and the rewiring probability for the small-world network.

Graph representations in genetic programming

Graph representations promise several desirable properties for genetic programming (GP); multiple-output programs, natural representations of code reuse and, in many cases, an innate mechanism for neutral drift. Each graph GP technique provides a program representation, genetic operators and overarching evolutionary algorithm. This makes it difficult to identify the individual causes of empirical differences, both between these methods and in comparison to traditional GP. In this work, we empirically study the behaviour of Cartesian genetic programming (CGP), linear genetic programming (LGP), evolving graphs by graph programming and traditional GP. By fixing some aspects of the configurations, we study the performance of each graph GP method and GP in combination with three different EAs: generational, steady-state and $$(1+\lambda )$$ ( 1 + λ ) . In general, we find that the best choice of representation, genetic operator and evolutionary algorithm depends on the problem domain. Further, we find that graph GP methods can increase search performance on complex real-world regression problems and, particularly in combination with the ($$1 + \lambda$$ 1 + λ ) EA, are significantly better on digital circuit synthesis tasks. We further show that the reuse of intermediate results by tuning LGP’s number of registers and CGP’s levels back parameter is of utmost importance and contributes significantly to better convergence of an optimization algorithm when solving complex problems that benefit from code reuse.

Niche partitioning among dead wood-dependent beetles

Niche partitioning among species with virtually the same requirements is a fundamental concept in ecology. Nevertheless, some authors suggest that niches have little involvement in structuring communities. This study was done in the Pardubice Region (Czech Republic) on saproxylic beetles with morphologically similar larvae and very specific requirements, which are related to their obligatory dependence on dead wood material: Cucujus cinnaberinus, Pyrochroa coccinea, and Schizotus pectinicornis. This work was performed on 232 dead wood pieces at the landscape scale over six years. Based on the factors studied, the relationships among these species indicated that their co-occurrence based on species presence and absence was low, which indicated niche partitioning. However, based on analyses of habitat requirements and species composition using observed species abundances, there was no strong evidence for niche partitioning at either studied habitat levels, the tree and the microhabitat. The most likely reasons for the lack of strong niche partitioning were that dead wood is a rich resource and co-occurrence of saproxylic community was not driven by resource competition. This might be consistent with the theory that biodiversity could be controlled by the neutral drift of species abundance. Nevertheless, niche partitioning could be ongoing, meaning that the expanding C. cinnaberinus may have an advantage over the pyrochroids and could dominate in the long term.

Correlated and geographically predictable Neanderthal and Denisovan legacies are difficult to reconcile with a simple model based on inter-breeding

Although the presence of archaic hominin legacies in humans is taken for granted, little attention has been given as to how the data fit with how humans colonized the world. Here, I show that Neanderthal and Denisovan legacies are strongly correlated and that inferred legacy size, like heterozygosity, exhibits a strong correlation with distance from Africa. Simulations confirm that, once created, legacy size is extremely stable: it may reduce through admixture with lower legacy populations but cannot increase significantly through neutral drift. Consequently, populations carrying the highest legacies are likely to be those whose ancestors inter-bred most with archaics. However, the populations with the highest legacies are globally scattered and are unified, not by having origins within the known Neanderthal range, but instead by living in locations that lie furthest from Africa. Furthermore, the Simons Genome Diversity Project data reveal two distinct correlations between Neanderthal and Denisovan legacies, one that starts in North Africa and increases west to east across Eurasia and into some parts of Oceania, and a second, much steeper trend that starts in Africa, peaking with the San and Ju/’hoansi and which, if extrapolated, predicts the large inferred legacies of both archaics found in Oceania/Australia. Similar ‘double’ trends are observed for the introgression statistic f 4 in a second large dataset published by Qin and Stoneking (Qin & Stoneking 2015 Mol. Biol. Evol. 32 , 2665–2674 ( doi:10.1093/molbev/msv141 )). These trends appear at odds with simple models of how introgression occurred though more complicated patterns of introgression could potentially generate better fits. Moreover, substituting archaic genomes with those of great apes yields similar but biologically impossible signals of introgression, suggesting that the signals these metrics capture arise within humans and are largely independent of the test group. Interestingly, the data do appear to fit a speculative model in which the loss of diversity that occurred when humans moved further from Africa created a gradient in heterozygosity that in turn progressively reduced mutation rate such that populations furthest from Africa have diverged less from our common ancestor and hence from the archaics. In this light, the two distinct trends could be interpreted in terms of two ‘out of Africa’ events, an early one ending in Oceania and Australia and a later one that colonized Eurasia and the Americas.

Plants Are the Drivers of Geographic Variation of Floral Scents in a Highly Specialized Pollination Mutualism: a Study of Ficus Hirta in China

BackgroundFloral volatiles play an important role in pollinator attraction. This is particularly true in obligate brood site pollination mutualisms. The plants generally produce inconspicuous flowers and depend on odours to attract to their inflorescences specialised pollinators that breed in their floral structures. Little is known about the processes shaping the micro-evolution of these floral odours. Here, we investigate geographic variation of floral odour in an obligate host-specific brood site pollination mutualism where plant and pollinator genetic structures are different, Ficus hirta and its specialised pollinators.ResultsWe evidence progressive geographic divergence of floral odours. The pattern of variation fits plant genetic structure but differs from pollinating insect structuring into species and populations. In our study system, the evolution of receptive floral odour presents a pattern that is not distinguishable from neutral drift that is not canalised by the insects.ConclusionWe propose that this pattern characterises obligate brood site pollination mutualisms in which pollinators are host specific and dispersal is limited. Insects with their short generation times and large population sizes track variation in host receptive inflorescence odours. Plants are the drivers and insects the followers. Strict sense plant-insect co-evolution is not involved. In contrast, stabilizing selection may be at work in more dispersive brood site pollination mutualisms, while pollinators may mediate local interspecific plant floral odour convergence when plant species share local pollinators.

Convergence rate of Euler–Maruyama scheme for SDDEs of neutral type

In this paper, we are concerned with the convergence rate of Euler–Maruyama (EM) scheme for stochastic differential delay equations (SDDEs) of neutral type, where the neutral, drift, and diffusion terms are allowed to be of polynomial growth. More precisely, for SDDEs of neutral type driven by Brownian motions, we reveal that the convergence rate of the corresponding EM scheme is one-half; Whereas for SDDEs of neutral type driven by pure jump processes, we show that the best convergence rate of the associated EM scheme is slower than one-half. As a result, the convergence rate of general SDDEs of neutral type, which is dominated by pure jump process, is slower than one-half.

Мощные диоды Шоттки с участком отрицательного дифференциального сопротивления на вольт-амперной характеристике

It is shown that at high current densities the carrier transport in base layer of Schottky diodes in addition to commonly accepted diffusive and drift currents is defined by recently discovered diffusion stimulated by quasi-neutral drift (DSQD). The influence of this recently discovered component of current on current-voltage characteristics of Schottky diode has been investigated. It was shown that in case if the ratio of base width $W$ to ambipolar diffusive length $L$ is higher than 1 ($W/L>1$) a part with negative differential resistance appears on the current-voltage characteristics of Schottky diode. The results of analytical investigation are confirmed by numerical calculation using INVESTIGATION program.

From the field into the lab: Causal approaches to the evolution of spatial language

There is striking variation in preferences for specific spatial linguistic strategies among different speech communities. Increasing evidence now suggests that this might not simply be a result of neutral drift, but rather a form of linguistic adaptation to the local social, cultural, or physical environment. Recent studies indicate that different factors like, e.g., topography, subsistence style, or bilingualism successfully predict the choice of spatial Frames of Reference (FoR) on linguistic and non-linguistic tasks. However, the exact causal relationships between these variables and the cultural evolutionary mechanisms that lead to selection of one FoR strategy over another are still not fully understood. In this paper, we argue that in order to arrive at a more mechanistic and causal understanding of the cultural evolution of spatial language, observations from descriptive fieldwork should be combined with experimental and computational methods. In such a framework, causal relationships between linguistic and non-linguistic variables (such as topography and FoR choice) can be isolated and empirically tested in order to shed light on how sociotopographic factors motivate the variation in spatial language we observe cross-linguistically.

Turbulent dissipation, CH+ abundance, H2 line luminosities, and polarization in the cold neutral medium

ABSTRACT In the cold neutral medium, high out-of-equilibrium temperatures are created by intermittent dissipation processes, including shocks, viscous heating, and ambipolar diffusion. The high-temperature excursions are thought to explain the enhanced abundance of CH+ observed along diffuse molecular sightlines. Intermittent high temperatures should also have an impact on H2 line luminosities. We carry out simulations of magnetohydrodynamic (MHD) turbulence in molecular clouds including heating and cooling, and post-process them to study H2 line emission and hot-gas chemistry, particularly the formation of CH+. We explore multiple magnetic field strengths and equations of state. We use a new H2 cooling function for $n_{\text{H}}\le 10^5\, {\text{cm}}^{-3}$, $T\le 5000\, {\text{K}}$, and variable H2 fraction. We make two important simplifying assumptions: (i) the H2/H fraction is fixed everywhere and (ii) we exclude from our analysis regions where the ion–neutral drift velocity is calculated to be greater than 5 km s−1. Our models produce H2 emission lines in accord with many observations, although extra excitation mechanisms are required in some clouds. For realistic root-mean-square (rms) magnetic field strengths (≈10 μG) and velocity dispersions, we reproduce observed CH+ abundances. These findings contrast with those of Valdivia et al. (2017) Comparison of predicted dust polarization with observations by Planck suggests that the mean field is ≳5 µG, so that the turbulence is sub-Alfvénic. We recommend future work treating ions and neutrals as separate fluids to more accurately capture the effects of ambipolar diffusion on CH+ abundance.