The seven ways eukaryotes produce repeated colour motifs on external tissues

The external tissues of numerous eukaryote species show repeated colour patterns, usually characterized by units that are present at least twice on the body. These dotted, striped or more complex phenotypes carry out crucial biological functions, such as partner recognition, aposematism or camouflage. Very diverse mechanisms explaining the formation of repeated colour patterns in eukaryotes have been identified and described, and it is timely to review this field from an evolutionary and developmental biology perspective. We propose a novel classification consisting of seven families of primary mechanisms: Turing(-like), cellular automaton, multi-induction, physical cracking, random, neuromuscular and printing. In addition, we report six pattern modifiers, acting synergistically with these primary mechanisms to enhance the spectrum of repeated colour patterns. We discuss the limitations of our classification in light of currently unexplored extant diversity. As repeated colour patterns require both the production of a repetitive structure and colouration, we also discuss the nature of the links between these two processes. A more complete understanding of the formation of repeated colour patterns in eukaryotes will require (i) a deeper exploration of biological diversity, tackling the issue of pattern elaboration during the development of non-model taxa, and (ii) exploring some of the most promising ways to discover new families of mechanisms. Good starting points include evaluating the role of mechanisms known to produce non-repeated colour patterns and that of mechanisms responsible for repeated spatial patterns lacking colouration.     

Can Traditions Emerge from the Interaction of Stimulus Enhancement and Reinforcement Learning? An Experimental Model

The study of social learning in captivity and behavioral traditions in the wild are two burgeoning areas of research, but few empirical studies have tested how learning mechanisms produce emergent patterns of tradition. Studies have examined how social learning mechanisms that are cognitively complex and possessed by few species, such as imitation, result in traditional patterns, yet traditional patterns are also exhibited by species that may not possess such mechanisms. We propose an explicit model of how stimulus enhancement and reinforcement learning could interact to produce traditions. We tested the model experimentally with tufted capuchin monkeys (Cebus apella), which exhibit traditions in the wild but have rarely demonstrated imitative abilities in captive experiments. Monkeys showed both stimulus enhancement learning and a habitual bias to perform whichever behavior first obtained them a reward. These results support our model that simple social learning mechanisms combined with reinforcement can result in traditional patterns of behavior.     

A three-dimensional computer model of four hypothetical mechanisms protecting biofilms from antimicrobials

Four hypothetical mechanisms for protection of biofilms against antimicrobials were incorporated into a three-dimensional model of biofilm growth and development. The model integrated processes of substrate utilization, diffusion, growth, cell migration, death, and detachment in a cellular automaton framework. Compared to simulations of unprotected biofilms, each of the protective mechanisms provided some tolerance to antimicrobial action. When the mechanisms were compared to each other, the behaviors of the four protective mechanisms produced distinct shapes of killing curves, nonuniform spatial patterns of survival and cell type distribution, and anticipated susceptibility patterns for dispersed biofilm cells. The differences between the protective mechanisms predicted in these simulations could guide the design of experiments to discriminate antimicrobial tolerance mechanisms in biofilms. Each of the mechanisms could be a plausible avenue of biofilm protection.     

A Three-Dimensional Computer Model of Four Hypothetical Mechanisms Protecting Biofilms from Antimicrobials

Four hypothetical mechanisms for protection of biofilms against antimicrobials were incorporated into a three-dimensional model of biofilm growth and development. The model integrated processes of substrate utilization, diffusion, growth, cell migration, death, and detachment in a cellular automaton framework. Compared to simulations of unprotected biofilms, each of the protective mechanisms provided some tolerance to antimicrobial action. When the mechanisms were compared to each other, the behaviors of the four protective mechanisms produced distinct shapes of killing curves, nonuniform spatial patterns of survival and cell type distribution, and anticipated susceptibility patterns for dispersed biofilm cells. The differences between the protective mechanisms predicted in these simulations could guide the design of experiments to discriminate antimicrobial tolerance mechanisms in biofilms. Each of the mechanisms could be a plausible avenue of biofilm protection.     

A motion illusion reveals mechanisms of perceptual stabilization

Visual illusions are valuable tools for the scientific examination of the mechanisms underlying perception. In the peripheral drift illusion special drift patterns appear to move although they are static. During fixation small involuntary eye movements generate retinal image slips which need to be suppressed for stable perception. Here we show that the peripheral drift illusion reveals the mechanisms of perceptual stabilization associated with these micromovements. In a series of experiments we found that illusory motion was only observed in the peripheral visual field. The strength of illusory motion varied with the degree of micromovements. However, drift patterns presented in the central (but not the peripheral) visual field modulated the strength of illusory peripheral motion. Moreover, although central drift patterns were not perceived as moving, they elicited illusory motion of neutral peripheral patterns. Central drift patterns modulated illusory peripheral motion even when micromovements remained constant. Interestingly, perceptual stabilization was only affected by static drift patterns, but not by real motion signals. Our findings suggest that perceptual instabilities caused by fixational eye movements are corrected by a mechanism that relies on visual rather than extraretinal (proprioceptive or motor) signals, and that drift patterns systematically bias this compensatory mechanism. These mechanisms may be revealed by utilizing static visual patterns that give rise to the peripheral drift illusion, but remain undetected with other patterns. Accordingly, the peripheral drift illusion is of unique value for examining processes of perceptual stabilization.     

Constant-ratio alternative substrate approach for differentiation of enzyme mechanisms

A new kinetic approach using alternative substrates as a tool for studying enzyme mechanisms is described. In this method the substrate to alternative substrate ratio is maintained constant and the common product (or summation of product analogs) is measured. The double-reciprocal plots so obtained at several constant ratios generate different patterns for various mechanisms, thus permitting a choice of kinetic model. In some cases, secondary intercept plots are utilized as a diagnostic aid. Another feature of this approach is that most of the resultant plots are linear. The graphical patterns for four cases of two-substrate, two-product reactions are presented as examples. These patterns allow one to differentiate several mechanisms which are not distinguishable by conventional alternative substrate, competitive inhibitor, or product inhibition studies alone. When used in combination with other methods, various mechanisms involving isomerization and abortive complex formation can be differentiated even if only one alternative substrate is available.     

Distinct mechanisms underlie pattern formation in the skin and skin appendages

Patterns form with the break of homogeneity and lead to the emergence of new structure or arrangement. There are different physiological and pathological mechanisms that lead to the formation of patterns. Here, we first introduce the basics of pattern formation and their possible biological basis. We then discuss different categories of skin patterns and their potential underlying molecular mechanisms. Some patterns, such as the lines of Blaschko and Naevus, are based on cell lineage and genetic mosaicism. Other patterns, such as regionally specific skin appendages, can be set by distinct combinatorial molecular codes, which in turn may be set by morphogenetic gradients. There are also some patterns, such as the arrangement of hair follicles (hair whorls) and fingerprints, which involve genetics as well as stochastic epigenetic events based on physiochemical principles. Many appendage primordia are laid out in developmental waves. In the adult, some patterns, such as those involving cycling hair follicles, may appear as traveling waves in mice. Since skin appendages can renew themselves in regeneration, their size and shape can still change in the adult via regulation by hormones and the environment. Some lesion patterns are based on pathological changes involving the above processes and can be used as diagnostic criteria in medicine. Understanding the different mechanisms that lead to patterns in the skin will help us appreciate their full significance in morphogenesis and medical research. Much remains to be learned about complex pattern formation, if we are to bridge the gap between molecular biology and organism phenotypes.     

Early axon patterns of the spinal cord: experiments with a computer

In the vertebrate central nervous system, most axons appear in one of two elemental patterns--sheets or bundles. Many developmental mechanisms are involved in the formation of the elemental axon patterns, and these mechanisms often act simultaneously. The major axon-patterning mechanisms include differential adhesivity, internal growth constraints on axons, and initial orientation of axonal outgrowth. To evaluate the effects of these mechanisms on the formation of axon patterns, a computer was used to model axonal growth. Experiments with the computer model suggest that axon sheets are produced by the cooperative action of more than one mechanism. Furthermore, in the appropriate combination, these mechanisms produce orderly axon sheets even on patternless substrates. On the other hand, to transform the sheets into axon bundles, the substrate must be patterned.     

Parametric Pattern Selection in a Reaction-Diffusion Model

We compare spot patterns generated by Turing mechanisms with those generated by replication cascades, in a model one-dimensional reaction-diffusion system. We determine the stability region of spot solutions in parameter space as a function of a natural control parameter (feed-rate) where degenerate patterns with different numbers of spots coexist for a fixed feed-rate. While it is possible to generate identical patterns via both mechanisms, we show that replication cascades lead to a wider choice of pattern profiles that can be selected through a tuning of the feed-rate, exploiting hysteresis and directionality effects of the different pattern pathways.     

Number of mating males and mating interval affect last-male sperm precedence in Tenebrio molitor L.

Polyandrous females often mate with more than two males, and yet most studies of postcopulatory sexual selection involve only two males. In insects, second-male sperm precedence is usually taken as evidence of overall last-male sperm precedence despite some studies to the contrary. Furthermore, the processes or mechanisms causing the patterns are often unknown and yet are important when estimating how postcopulatory sexual selection might act on males. Whether the patterns and processes change in normal sperm competitive situations and the effects of other factors besides mating order need to be examined to better assess the evolutionary potential of postcopulatory sexual selection. In this study, I assessed the effects of mating interval and number of mating males on sperm precedence patterns and their causal mechanisms in the mealworm beetle, Tenebrio molitor. Last-male sperm precedence was the same when two or three males mated, but also depended on mating intervals and hence mechanisms of paternity bias. However, when females mated with many males, one of the mechanisms no longer created last-male sperm precedence. This example illustrates the importance of knowing both the patterns and mechanisms of paternity bias and whether they change depending on female mating frequency to make reasonable inferences about the potential for postcopulatory sexual selection on males. Copyright 2003 Published by Elsevier Ltd on behalf of The Association for the Study of Animal Behaviour.      

The value-added genome: building and maintaining genomic cytosine methylation landscapes

Epigenetic marks, such as cytosine methylation and post-translational histone modifications, are important for interpreting and managing eukaryotic genomes. Recent genetic studies in plants have uncovered details on the different interwoven mechanisms that are responsible for specification of genomic cytosine methylation patterns. These mechanisms include targeting cytosine methylation using heterochromatic histone modifications and RNA guides. Genomic cytosine methylation patterns also reflect locus-specific demethylation initiated by specialized DNA glycosylases. While genetics continues to more fully define these mechanisms, genomic studies in Arabidopsis have yielded an unprecedented high-resolution view of how epigenetic marks are layered over a genome.     

Patterns of ribosomal DNA spacer lengths are inherited

The non-transcribed spacer regions in Xenopus laevis ribosomal DNA vary in length, even within a single nucleolar organizer. The pattern of spacer lengths is sufficiently different from one nucleolar organizer to another to allow the pattern to be used as a genetic marker. We have analyzed the spacer patterns of rDNA² from a total of 50 progeny from three separate matings. Spacer patterns were inherited with no detectable change in all but two cases. The reproducibility of the patterns among siblings and their stable inheritance between generations rule out sudden mechanisms for gene evolution, such as the master-slave model, and support more gradual mechanisms.Two animals out of 50 showed marked changes in their rDNA spacer patterns. It is not possible at present to decide which of several possible mechanisms were responsible for the observed changes.     

土壤微生物多样性海拔格局研究进展

生物多样性的海拔分布格局与维持机制是生物多样性与生态系统功能研究的热点领域。相比动植物多样性海拔分布格局,土壤微生物多样性海拔分布格局的研究还处在起步阶段。近年来,随着以罗氏454、Illumina Mi Seq等为代表的高通量测序平台的发展,土壤微生物海拔梯度分布格局的研究进展较快。对土壤微生物多样性海拔分布格局最新研究综述发现,土壤微生物海拔分布模式并不明确,表现为无趋势、下降、单峰或者下凹型等多种海拔分布模式。这与大型动植物并不相同,暗示其驱动机制可能存在一定的差异。微生物由于其个体微小、扩散能力强以及较高的多样性和个体丰度而在局域尺度上可能更易受到气候环境因素的影响。土壤pH、碳、氮等因子是影响微生物多样性和群落组成在海拔梯度上变异的重要因素。此外,温度和降水也具有重要作用。另外,除微生物自身属性以及取样限制外,测序深度可能是影响土壤微生物物种丰富度海拔分布格局的重要因素。目前,对土壤微生物群落的研究在功能基因、群落构建机制以及生态学理论的验证方面还存在着不足。未来的研究应进一步加大测序深度,增加取样密度,着重关注全球气候变化及生物多样性丧失背景下土壤微生物群落的构建和维持机制及其生态系统功能等方面。     

Orientation and Navigation in Elasmobranchs: Which Way Forward?

Elasmobranchs possess a multiplicity of mechanisms controlling posture and short distance orientation. Visual–vestibular contributions to posture and locomotion are well documented. So too, are the contributions of vision, olfaction and the octavolateralis senses to short distance orientation, particularly orientation to specific environmental stimuli such as those generated by prey. Less well understood are the mechanisms guiding orientation over longer distances. Anecdotal and systematic observations of behaviour show tidal, daily, repeat long distance, and even seasonal movement patterns. True navigation has not been demonstrated in elasmobranchs and the sensory mechanisms underlying the above movement patterns remain largely speculative. However, they are likely to include responses to water currents, and physical parameters such as temperature, pressure, and the geomagnetic field. Of particular interest in elasmobranchs is that geomagnetic orientation could be mediated directly via a magnetite based sensory system, or indirectly via the electrosensory system. Systematic studies of movement patterns and experimental studies of the underlying mechanisms of orientation are required to gain an increased understanding of orientation and navigation in this intriguing group.     

A taxonomic and phylogenetic perspective on plant community assembly along an elevational gradient in subtropical forests

亚热带森林植物群落沿海拔梯度的分类与系统发育研究 生物多样性沿海拔梯度的分布格局已受到广泛关注。然而,生物多样性格局沿海拔梯度的变异及其潜在机制尚不清楚。整合生物多样性的多维度信息为理解群落构建机制提供了新思路。本研究在我国东部亚热带森林沿海拔270–1470 m的梯度上设置了17个木本植物固定样地,分析了沿海拔梯度植物群落 构建的生态和进化驱动力。基于样地内物种出现(0–1数据)和多度信息,计算群落内被子植物的物种和系统发育alpha和beta多样性、系统发育结构等,并量化多样性指标与微气候和地形之间的关系。研究发现,不论多度加权与否,物种alpha多样性均沿海拔升高而增加,物种和系统发育的相似性随海拔距离的增加而呈衰减趋势。然而,多度加权与否会形成不同的系统发育alpha多样性格局。对于系统发育结构而言,沿海拔增加并无明显趋势。地形和微气候是多样性格局和系统发育结构的主要驱动力。与未考虑物种多度的多样性指标相比,多度加权的指标与坡度和胸高断面积相关性更高。这些结果表明,由局域物种多度介导的确定性过程对沿海拔梯度的植物群落构建具有一定影响。     

亚高寒草甸不同生境植物群落物种多度分布格局的拟合

物种多度分布是群落生态学研究的核心内容。通过对青藏高原东部亚高寒草甸3种不同生境草本植物群落的抽样调查,结合16个物种多度分布模型的两种曲线拟合优度检验得出如下结果：多种不同模型可以拟合同一生境的物种多度分布。相比于其他可拟合模型,几何级数模型在3种生境中两种拟合优度检验方法下的平均拟合效果是最好的,拟合优度值均在最优拟合优度值10左右波动。次优模型鉴于不同生境不同的检验方法表现不一。除了几何级数模型外,Sugihara分数模型在最小二乘法的拟合方法下,也可以拟合3种生境的物种多度分布。研究结果表明,仅用拟合优度检验区分产生不同物种分布格局的模型和机制是不可靠的,需要做进一步的检验性实验研究。     

Comparative analysis of the mechanisms of attack and defense among higher brain animals

Many studies have investigated different mechanisms of attack and defense in different species of higher brain animals including cats, rats, rodents, mice, and even in some bird species. However, detailed comparative analysis has not been carried out to understand the major similarities in the mechanisms of attack and defense across the different species of vertebrates. Although there are differences, there are also significant similarities as well, which warrant comparative assessment. By considering ethological ideas associated with the motivational defense system, we investigated the motor patterns of attack and defense in cats and rats, using the “resident-intruder” experimental paradigm. Our results reveal specific similarities and differences in the motor patterns of attack and defense in rats and cats. We discuss comparatively the mechanisms of attack and defense across different species of vertebrates, focusing on motor patterns, neuromodulating factors, brains neural substrates, and circuitry.     

The origin and maintenance of montane diversity: integrating evolutionary and ecological processes

Determining how ecological and evolutionary processes produce spatial variation in local species richness remains an unresolved challenge. Using mountains as a model system, we outline an integrative research approach to evaluate the influence of ecological and evolutionary mechanisms on the generation and maintenance of patterns of species richness along and among elevational gradients. Biodiversity scientists interested in patterns of species richness typically start by documenting patterns of species richness at regional and local scales, and based on their knowledge of the taxon, and the environmental and historical characteristics of a mountain region, they then ask whether diversity–environment relationships, if they exist, are explained mostly by ecological or evolutionary hypotheses. The final step, and perhaps most challenging one, is to tease apart the relative influence of ecological and evolutionary mechanisms. We propose that elucidating the relative influence of ecological and evolutionary mechanisms can be achieved by taking advantage of the replicated settings afforded by mountains, combined with targeted experiments along elevational gradients. This approach will not only identify potential mechanisms that drive patterns of species richness, but also allow scientists to generate more robust hypotheses about which factors generate and maintain local diversity.     

Are orientation mechanisms among migratory birds speciesospecific?

The mechanisms by which migratory birds find their way from breeding grounds to winter quarters and back have been the subject of intensive research during the past four decades. Birds are equipped with genetic information about the migratory direction, and they can use the earth's magnetic field, star patterns and the sun and/or skylight polarization patterns as compass references. Studies on a number of North American and European species have suggested possible species-specific differences in the relative role of the compass mechanisms. This may be largely the result of divergent experimental designs, which make results difficult to compare. Comparative studies with identical methods are needed to see how much species-specific variation exists in basic orientation mechanisms.     

Diverse initiation in a conserved left-right pathway?

Preceding stereotypical left-right asymmetric morphogenesis, asymmetric gene expression patterns of nodal and pitx2 are very similar in major groups of vertebrates. I propose that these conserved expression patterns are indicative of 'left-right' phylotypic stages' of development. It is not known whether these patterns are initiated by conserved or divergent developmental mechanisms.