Spatial dynamics of adaptive sex ratios

According to Fisherian sex allocation theory, parents that can adjust their offspring sex ratio in response to skews in population sex ratio will maximize their fitness over parents lacking this ability. There is good evidence that adaptive sex ratio adjustment occurs in many natural populations, but deviations from theoretical predictions have also been observed. These anomalies may be more apparent than real. When the spatial dimension of sex ratio variation is ignored, then a mismatch between empirical data and theoretical predictions based on panmictic mating is to be expected. We illustrate this with data on human sex ratio variation in 21 preindustrial populations, and with a cellular automaton model built to obey Fisherian sex allocation rules. The results from the model generally match with the data. When information about the ambient sex ratio is limited, then the sex allocation decisions may appear locally maladaptive. In general, the results indicate that Fisher's sex-ratio theory may have greater explanatory power than previously thought.     

麦蚜自然种群的空间动态

一、引言在生态学中研究种群动态有两个分支,一是追踪数量随时间变化,既所谓数量动态的问题,另一是考查种群个体在空间散布状态的变化,即所谓空间动态的问题。关于空间动态中分布型的研究过去多采用传统的块面调查,用     

Prebiotic Methylation and the Evolution of Methyl Transfer Reactions in Living Cells

An hypothesis is presented for theprebiotic origin of methyl groups and the evolution ofmethyl transfer reactions in living cells. This hypothesis,described in terms of prebiotic and early biotic chemicalevolution, is based on experimental observations in our laband in those of others, and on the mechanisms of enzymaticmethyl transfer reactions that occur in living cells. Ofparticular interest is our demonstration of the reductivemethylation of ethanolamine and glycine in aqueous solutionby excess formaldehyde. These reactions, involving prebioticcompounds and conditions, are mechanistically analogous tothe de novo origin of methyl groups in modern cellsby reduction of methylene tetrahydrofolate. Furthermore,modern cellular methyl transfers from S-adenosylmethionineto amine nitrogen may involve formaldehyde as anintermediate and subsequent reductive methylation, analogousto the prebiotic chemistry observed herein.     

人口动力学中非线性发展方程解的爆破现象

讨论描述人口发展规律的一类非线性发展方程具有第三类非线性边界条件的混合问题．在已知函数满足某些假设条件下,证明了其解在有限时间内爆破．     

Multilevel Selection in Models of Prebiotic Evolution: Compartments and Spatial Self-organization

In this paper we explore the impact of new levels ofselection in models of early evolution.We contrast two types of higher levels of selection. On the one hand we look at spatially explicitmodels of replicators in which, by a process of self-organization, new levels of selection ariseas large scale spatial patterns with a dynamics of their own. Alternatively externally imposedlevels of selection above the basic replicators are created by enclosing the replicators in vesicles.In this paper we first review some results on the impact of emerging higher levels of selection onthe evolutionary persistence of interacting co-evolvingreplicator systems. Moreover, we presenta vesicle model, which can potentially integrate emerging and imposed levels of selection. We use the models to examinethe classical problem information integration in early evolution.Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1023/A:1025754907141     

枇杷园蜘蛛混合种群空间分布型的动态分析

枇杷园蜘蛛混合种群的空间分布型在不同季节存在差异,其空间分布型主要由枇杷园蜘蛛本身的生殖水平、游猎型和定居型数量的多寡,主要目标害虫的数量及分布,气候环境的变化及其越冬生态习性,枇杷园蜘蛛的种群密度及其种间竞争程度决定。     

Evolution of cell motility in an individual-based model of tumour growth

Tumour invasion is driven by proliferation and importantly migration into the surrounding tissue. Cancer cell motility is also critical in the formation of metastases and is therefore a fundamental issue in cancer research. In this paper we investigate the emergence of cancer cell motility in an evolving tumour population using an individual-based modelling approach. In this model of tumour growth each cell is equipped with a micro-environment response network that determines the behaviour or phenotype of the cell based on the local environment. The response network is modelled using a feed-forward neural network, which is subject to mutations when the cells divide. With this model we have investigated the impact of the micro-environment on the emergence of a motile invasive phenotype. The results show that when a motile phenotype emerges the dynamics of the model are radically changed and we observe faster growing tumours exhibiting diffuse morphologies. Further we observe that the emergence of a motile subclone can occur in a wide range of micro-environmental growth conditions. Iterated simulations showed that in identical growth conditions the evolutionary dynamics either converge to a proliferating or migratory phenotype, which suggests that the introduction of cell motility into the model changes the shape of fitness landscape on which the cancer cell population evolves and that it now contains several local maxima. This could have important implications for cancer treatments which focus on the gene level, as our results show that several distinct genotypes and critically distinct phenotypes can emerge and become dominant in the same micro-environment.     

西南地区生态系统服务价值时空演变及模拟预测

生态系统服务价值(ESV)分析对构建生态安全格局和实现区域可持续发展具有决定作用,为揭示西南地区ESV过去-现在-未来时空演变规律,运用ESV计算体系对西南地区2005—2015ESV动态演变进行定量分析,采用Logistic-CA-Markov耦合模型预测2025年ESV格局。结果表明:(1)2005—2015年西南地区总体呈现增长的趋势,其值达到20.85亿元,主要受青海、西藏水域ESV增加所致,青海、西藏ESV增长率占绝对优势。(2)空间上呈现西北和东南部ESV高、北部ESV低的分布格局;不同类型和不同等级的ESV在空间上相互转换,低等级向高等级转化明显,其他生态景观向建设用地亏损流动减少的价值不足以抵消向水域流动增加的价值,盈利大于亏损,生态环境明显好转。(3)Logistic回归分析各生态景观的ROC值均大于0.87,拟合结果能够满足预测要求;CA-Markov模拟ESV空间布局,Kappa系数为0.86,可以在整体上较准确的反映其空间演变格局。(4)2015—2025年ESV空间演化表明西南地区各区域生态环境总体趋于良好,但建设用地增加的生态负效应不可忽视,还需合理进行用地布局。研究揭示了西南地区过去-现在-未来ESV时空演化规律,提供了长时间序列的时空演化图谱,对该地区实施卓有成效的生态规划及可持续发展提供了科技支撑和重要参考。     

Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily

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Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn-Glycerol-1-phosphate Dehydrogenase

One of the most critical events in the origins of cellular life was the development of lipid membranes. Archaea use isoprenoid chains linked via ether bonds to sn-glycerol 1-phosphate (G1P), whereas bacteria and eukaryotes use fatty acids attached via ester bonds to enantiomeric sn-glycerol 3-phosphate. NAD(P)H-dependent G1P dehydrogenase (G1PDH) forms G1P and has been proposed to have played a crucial role in the speciation of the Archaea. We present here, to our knowledge, the first structures of archaeal G1PDH from the hyperthermophilic methanogen Methanocaldococcus jannaschii with bound substrate dihydroxyacetone phosphate, product G1P, NADPH, and Zn²⁺ cofactor. We also biochemically characterized the enzyme with respect to pH optimum, cation specificity, and kinetic parameters for dihydroxyacetone phosphate and NAD(P)H. The structures provide key evidence for the reaction mechanism in the stereospecific addition for the NAD(P)H-based pro-R hydrogen transfer and the coordination of the Zn²⁺ cofactor during catalysis. Structure-based phylogenetic analyses also provide insight into the origins of G1PDH.     

Molecular Evolution in Static and Dynamical Landscapes

In an attempt to understand protein evolution, we address the issues ofhow much variety in the sequences is needed to prompt the evolution ofan enzyme from random polypeptides and how does cellular interactionaffect the dynamics of molecular evolution to allow genetic diversity inpopulation. The experimental evolution of phage-displayed randompolypeptides of about 140 amino acid residues panned with transition stateanalogue for an esterase reaction showed that even with a population sizeas small as ten, not only could significant varieties be found but also therandom polypeptides in each of the generation had great promise towardsdeveloping into functional proteins. Hence, it is evident that the enzymeevolution is prompted even within a small local area of the static landscapeof the sequence space. Considering that interaction among living cells is aninevitable event in natural evolution, its role was investigated through threeconsecutive rounds of random mutagenesis on the glutamine synthetasegene and chemostat culture of the transformed Escherichia colicellscontaining the mutated genes. The molecular phylogeny and populationdynamics show the coexistence of some mutants having different level ofglutamine synthetase at each generation. In addition, it was confirmed thatcellular interaction via the medium influences the stability of the coexistenceand bring forth fitness change to the coexisting members of the population,thereby, leading to a dynamical landscape. Based on experimental resultsreflecting the extent of interaction among members in population, here, Iproposed that protein evolution could change its mode from theoptimization on static landscape to diversification on dynamicallandscape.     

Dynamics of induced CAT expression in E. coli

The dynamics of chemically induced chloramphenicolaceyl-transferase (CAT) expression are determined in batch cultures of Escherichia coli DH5alphaF'IQ [pKK262-1]. This article is directed towards understanding the coupling of induced cloned-protein synthesis and reduced cell growth which are balanced in the optimal system. Experimental results indicate that the best inducer (IPTG) concentration is near 1.0 mM when added during midexponential growth. Lower concentrations cause only weak induction, whereas higher concentrations cause sufficiently strong induction that cell growth is suppressed. Induction at the onset of the stationary phase results in high expression but is accompanied by stimulated protease activity. Also, cell mass yield is adversely affected by enhanced protein synthesis. A structured metabolic model is shown to predict the responses of instantaneous growth rate and productivity which result from protein overexpression. This model can be employed to predict alternative reactor strategies and operating conditions necessary for the design of efficient bioprocess.     

On the theoretical and experimental modeling of initial stages of metabolism formation in prebiotic systems

A concept of the initial stages of chemical prebiotic evolution, which eliminates a number of difficulties in the problem of the origin of life and permits experimental verification, is proposed. According to this concept, a predecessor of living beings has to be sufficiently simple to allow its self-assembly during a geologically short time period. In addition, the predecessor has to possess autocatalytic properties, and an ability for further complication (evolution). A possible scenario of the initial steps of the origin of life in nature and inside an experimental facility is considered. In the scope of the scenario the model of a multivariant oligomeric autocatalyst coupled with phase-separated particles is described. Results of computational simulations of possible initial steps in chemical evolution are presented. The estimates obtained show that the emergence of autocatalytic oligomeric phase-separated systems is possible at reasonable values of kinetics parameters of involved chemical reactions in a small-scale flow reactor.     

酶的分子定向进化及其应用

酶的分子定向进化是20世纪90年代初兴起的一种蛋白质工程的新策略,是一种在生物体外模拟自然进化过程的、具有一定目的性的快速改造蛋A质的方法.该方法引起了生物催化技术领域的又一次革命.目前分子定向进化技术已被广泛应用于工业、农业及制药业等的相关领域.本文详细综述了酶的分子定向进化的概念、过程、基本策略及其核心技术,并着重介绍了酶的分子定向进化技术在提高酶的活力、稳定性、底物特异性和对映体选择性等几方面的应用及取得的相关成果.     

Evolutionary stability under the replicator and the gradient dynamics

We unite two general models for evolutionary change under the forces of selection, mutation and reproduction, a genetic model (replicator dynamics) and a cultural model (gradient dynamics). Under the assumption of normality, we find that the mean and variance dynamics are essentially identical under the two models and we relate these to the ESS and convergence stability conditions.     

Spatial Dynamics of Lyme Disease: A Review

Lyme disease (LD), the most frequently reported vector-borne disease in the United States, requires that humans, infected vector ticks, and infected hosts all occur in close spatial proximity. Understanding the spatial dynamics of LD requires an understanding of the spatial determinants of each of these organisms. We review the literature on spatial patterns and environmental correlates of human cases of LD and the vector ticks, Ixodes scapularis in the northeastern and midwestern United States and Ixodes pacificus in the western United States. The results of this review highlight a need for a more standardized and comprehensive approach to studying the spatial dynamics of the LD system. Specifically, we found that the only environmental variable consistently associated with increased LD risk and incidence was the presence of forests. However, the reasons why some forests are associated with higher risk and incidence than others are still poorly understood. We suspect that the discordance among studies is due, in part, to the rapid developments in both conceptual and technological aspects of spatial ecology hastening the obsolescence of earlier approaches. Significant progress in identifying the determinants of spatial variation in LD risk and incidence requires that: (1) existing knowledge of the biology of the individual components of each LD system is utilized in the development of spatial models; (2) spatial data are collected over longer periods of time; (3) data collection and analysis among regions are more standardized; and (4) the effect of the same environmental variables is tested at multiple spatial scales.     

Evolution of reproductive effort in viscous populations: the importance of population dynamics

I present two ecological models for the evolution of reproductive effort in viscous populations with empty sites. In contrast with previous studies, I show that limited dispersal needs not have a positive effect on the evolutionarily stable allocation of resources to fecundity versus survival. Rather, depending on the feedback between the trait and the population dynamics, population viscosity may have no effect or even lead to a decrease in the evolutionarily stable reproductive effort when individuals can degrade their environment during their lifetime. I show that the different evolutionary outcomes can be explained by the asymmetry in the level of kin competition resulting from investing into juveniles or into adults.     

The Early Phases of Genetic Code Origin: Conjectures on the Evolution of Coded Catalysis

A review of the most significant contributions on the early phases of genetic code origin is presented. After stressing the importance of the key intermediary role played in protein synthesis, by peptidyl-tRNA, which is attributed with a primary function in ancestral catalysis, the general lines leading to the codification of the first amino acids in the genetic code are discussed. This is achieved by means of a model of protoribosome evolution which sees protoribosome as the central organiser of ancestral biosynthesis and the mediator of the encounter between compounds (metabolite-pre-tRNAs) and catalysts (peptidyl-pre-tRNAs). The encounter between peptidyl-pre-tRNA catalysts in protoribosome is favoured by metabolic pre-mRNAs and later resulted (given the high temperature at which this evolution is supposed to have taken place) in the evolution of mRNAs with codons of the type GNS. These mRNAs codified only for those amino acids that the coevolution theory of genetic code origin sees as the precursors of all other amino acids. Some aspects of the model here discussed might be rendered real by the transfer-messenger RNA molecule (tmRNA) which is here considered a molecular fossil of ancestral protein synthesis.     

The Sugar Model: Catalytic Flow Reactor Dynamics of Pyruvaldehyde Synthesis from Triose Catalyzed by Poly-L-Lysine Contained in a Dialyzer

The formation of pyruvaldehyde from triose sugars was catalyzedby poly-L-lysine contained in a small dialyzer with a 100molecular weight cut off (100 MWCO) suspended in a much largertriose substrate reservoir at pH 5.5 and 40 °C. Thepolylysine confined in the dialyzer functioned as a catalyticflow reactor that constantly brought in triose from thesubstrate reservoir by diffusion to offset the drop in trioseconcentration within the reactor caused by its conversion topyruvaldehyde. The catalytic polylysine solution (400 mM, 0.35mL) within the dialyzer generated pyruvaldehyde with a syntheticintensity (rate/volume) that was 3400 times greater than that ofthe triose substrate solution (12 mM, 120 mL) outside thedialyzer. Under the given conditions the final yield ofpyruvaldehyde was greater than twice the weight of thepolylysine catalyst. During the reaction the polylysine catalystwas poisoned presumably by reaction of its amino groups withaldehyde reactants and products. Similar results were obtainedusing a dialyzer with a 500 MWCO. The dialyzer method ofcatalyst containment was selected because it provides a simpleand easily manipulated experimental system forstudying the dynamics and evolutionary development of confinedautocatalytic processes related to the origin of life underanaerobic conditions.     

The Evolution of a Kleptoparasitic System under Adaptive Dynamics

Kleptoparasitism, the stealing of food items, is a common biological phenomenon which has been modelled mathematically in a series of recent papers. A common assumption, following early work, was that mixed strategy solutions were not possible. In this paper we consider the evolution of mixed strategies under adaptive dynamics and show that such mixed strategies can be stable solutions under certain assumptions. In particular we revisit the recent paper of Broom et al. (Bull math Biol 66, 1645–1658, 2004) which assumed pure solutions only, and reanalyze the model under this new formulation. The second author was supported by the UNCG New Faculty Grant.