Early Metazoan Evolution: Reconciling Paleontology and Molecular Biology

SYNOPSIS. Molecular "clocks" are now widely accepted as pointingto a protracted, but cryptic, history of pre-Ediacaran metazoanevolution. The inhabitants of this interval (ca. 1300–600Myr ago) are usually envisaged as equivalent to either planktotrophiclarvae or the meiofauna. Reassessment of the evidence, however,suggests that this pre-Ediacaran history was neither deep norwas represented by analogues of microscopic living metazoans.The origination of this Kingdom may have been no earlier thanca. 650 Myr, and the earliest forms emerged from the Metazoa-Fungi-Mycetozoastem-group. Accordingly the time-frame and search image needto be reset with this hypothesis in mind.     

Cooperative Equilibrium in Biosphere Evolution: Reconciling Competition and Cooperation in Evolutionary Ecology

Acta Biotheoretica - As our understanding of biological evolution continues to deepen, tension still surrounds the relationship between competition and cooperation in the evolution of the...     

Note on The Stability Problem for Mammillary Matrices

The importance of the stability problem for matrices of the special form called mammillary matrices has been noted by Hearon (1). The stability problem may be formulated in terms of the Liapounov matrix equation. A constructive procedure, dependent upon the particular structure of mammillary matrices, for the solution of the Liapounov equation and the subsequent solution of the stability problem is described in this note. For an n × n matrix the principal computational steps are the solution of an n × n linear system and the determination of the rank and signature of an n × n symmetric matrix.     

Function and the Evolution of Phenotypic Stability: Connecting Pattern to Process

Phenotypes manifest a balance between the inherited tendencyto remain the same (phenotypic stability) and the tendency tochange in response to current environmental conditions (adaptation).This paper explores the role of functional integration and functionaltrade-offs in generating phenotypic stability by limiting theresponses of individual characters to environmental selection.Evolutionarily stable configurations (ESCs) are systems of functionallyinteracting characters within which characters are "judged"by their contribution to system-level functionality. This "internal"component of selection differs from traditional "external" selectionin that it travels with the organism wherever it goes and ismaintained across a wide range of environments. External selection,in contrast, is by definition environment-dependent. The temporaland geographic constancy of internal selection therefore actsto maintain phenotypic stability even as environments change.Functional trade-offs occur when one character participatesin more than one function, but can only be optimized for one.Participation of certain ("keystone") characters in a trade-offpotentially causes stabilization of an entire system owing toa cascade of functional dependencies on that character. Phylogeneticcharacter analysis is an essential part of elucidating theseprocesses, but patterns cannot be used as prima facie evidenceof particular processes.     

The Development of the Sauropsid Integument: A Contribution to the Problem of the Origin and Evolution of Feathers

Developmental anatomical data are insufficient to discuss plausibleintermediates between an ancestral, scaled, reptilian skin andappendage-bearing, avian skin. We also review adult tissue replacementand ubiquitous mechanisms underlying skin morphogenesis. Combiningdevelopmental data sensu lato with consideration of necessarybiological roles permits evaluation of major form/function trendsin skin evolution. New data on feathers reveal retention ofthe sauropsid synapomorphy of vertical alteration of - and ß-keratogenesis.By identifying roles that were obligatorily maintained throughoutevolution, we demonstrate constraints on hypothetical skin morphologiesin preavian taxa. We analyze feather origins as a problem ofemergence of complex form via modulations of morphogenesis.While existing data do not permit presentation of sequential,hypothetical, intermediates culminating in a plumage, the analysis:(1) implies that a protofeather and its follicle are most easilyderived from isolated, flattened, elongate, reptilian scales;(2) explains diversification of feather morphs from a contour-like"basic" feather and the similarity between feather and hairfollicles; and thus (3) reveals several developmental constraintson structures proposed as antecedent to avian feathers, whetherhypothetical constructs or palaeontological interpretations.Although these conclusions do not depend on any previous scenario,they are consistent with Regal's (1975) model and the limited,fossil evidence, especially that of the "basal archosaur" Longisquama.     

Reconciling the omnivory-stability debate

Despite attempts at reconciliation, the role of omnivory in food web stability remains unclear. Here we develop a novel community matrix approach that is analogous to the bifurcation method of modular food web theory to show that the stability of omnivorous food chains depends critically on interaction strength. We find that there are only six possible ways that omnivorous interaction strengths can influence the stability of linear food chains. The results from these six cases suggest that: (1) strong omnivory is always destabilizing, (2) stabilization by weak to intermediate omnivorous interaction strengths dominates the set of possible stability responses, and, (3) omnivory can be occasionally strictly destabilizing or intermittently destabilizing. We then revisit the classical results of Pimm and Lawton to show that although their parameterization tends to produce a low percentage of stable omnivorous webs, the same parameterization shows strong theoretical support for the weak interaction effect. Finally, we end by arguing that our current empirical knowledge of omnivory resonates with this general theory.     

森林发展系统强解的存在唯一性及稳定性分析

对森林发展系统的动态数学模型,运用泛函分析和积分方程的理论,证明了系统强解的存在性和唯一性,并对系统的稳定性进行了讨论．     

Problem Concepts in Evolution Part I: Purpose and Design

In 1999, Scott suggested that evolution has existential repercussions for some students because they confuse methodological naturalism with philosophical naturalism: conflating the incapacity of scientific explanations to appeal to the supernatural with the idea that God must not exist. Unfortunately, part of the reason for the confusion involves terms that are used in a technical sense by evolutionary biologists but that also convey existential meanings to the general public. Such terms therefore should be used carefully by teachers, and their scientific meanings distinguished from their common meanings. We revisit these problem concepts, particularly in light of recent papers in cognitive psychology as they relate to understanding evolution, in a two-part series of articles. Here, in part I, we address design and purpose.     

Problem Concepts in Evolution Part II: Cause and Chance

In a previous article, we suggested that differences in how the general public and scientists use terms such as purpose and design can lead to confusion, particularly around understanding evolution and mechanisms of evolutionary change. Here, we present two additional problem concepts, cause and chance, and discuss how these concepts lead to confusion, suggesting how to address these specific challenges to understanding evolution in light of recent research in cognitive psychology and biological concept inventories.     

Adaptive Evolution of p53 Thermodynamic Stability

The thermodynamic stability of a protein plays an important role during evolution and adaptation in order to maintain a folded and active conformation. p53 is a tumour suppressor involved in the regulation of numerous genes. Human p53 has an unusually low thermodynamic stability and is frequently inactivated by oncogenic missense mutations. Here, we examined the thermodynamic and kinetic stability of p53 DNA binding domains from selected invertebrate and vertebrate species by differential scanning calorimetry and equilibrium urea denaturation. There is a correlation in the apparent melting temperature of p53 with the body temperature of homeotherm vertebrates. We found that p53 from these organisms has a half-life for spontaneous unfolding at organismal body temperature of 10-20 min. We also found that p53 from invertebrates has higher stability, bearing more resemblance towards p63 and p73 from humans. Using structure-guided mutagenesis on the human p53 scaffold, we demonstrated that the amino acid changes on the protein surface and in the protein interior lead to the elevated stability of p53 orthologs. We propose a model in which the p53 DNA binding domain has been shaped by the complex interplay of different selective pressures and underwent adaptive evolution leading to pronounced effects on its stability. p53 from vertebrates has evolved to have a low thermodynamic stability and similarly short spontaneous half-life at organismal body temperature, which is related to function.     

改进酶稳定性的定向进化技术

酶作为一种生物催化剂,以其独特的优良特性,在绿色化学和清洁生产中得到了广泛的应用。随着酶定向进化技术的建立和发展,通过定向进化改进酶稳定性的研究越来越多。详细综述了各种定向进化方法的特点及在提高酶稳定性方面的应用,并从结构和功能的角度进一步解释了相关机理。     

Reconciling the Structural Attributes of Avian Antibodies

Antibodies are high value therapeutic, diagnostic, biotechnological, and research tools. Combinatorial approaches to antibody discovery have facilitated access to unique antibodies by surpassing the diversity limitations of the natural repertoire, exploitation of immune repertoires from multiple species, and tailoring selections to isolate antibodies with desirable biophysical attributes. The V-gene repertoire of the chicken does not utilize highly diverse sequence and structures, which is in stark contrast to the mechanism employed by humans, mice, and primates. Recent exploitation of the avian immune system has generated high quality, high affinity antibodies to a wide range of antigens for a number of therapeutic, diagnostic and biotechnological applications. Furthermore, extensive examination of the amino acid characteristics of the chicken repertoire has provided significant insight into mechanisms employed by the avian immune system. A paucity of avian antibody crystal structures has limited our understanding of the structural consequences of these uniquely chicken features. This paper presents the crystal structure of two chicken single chain fragment variable (scFv) antibodies generated from large libraries by phage display against important human antigen targets, which capture two unique CDRL1 canonical classes in the presence and absence of a non-canonical disulfide constrained CDRH3. These structures cast light on the unique structural features of chicken antibodies and contribute further to our collective understanding of the unique mechanisms of diversity and biochemical attributes that render the chicken repertoire of particular value for antibody generation.     

Evolution of Diversity, Efficiency, and Community Stability

The response in species diversity associated with successionalchange in vegetation, or in a more general sense, species diversityas a function of time in any system of primary producers, hasbeen the subject of much speculation but little direct study.All evidence available shows that pioneer communities are lowin diversity, that in mesic environments the peak in diversityin forest communities can be expected 100-200 years after theinitiation of a secondary successional sequence (when elementsof both the pioneer and the stable communities are present),and that a downturn in both diversity and primary productiontakes place when the entire community is made up of the shade-tolerantclimax species. The natural tendency in forest systems toward periodic perturbation(at intervals of 50-200 years) recycles the system and maintainsa periodic wave of peak diversity. This wave is associated witha corresponding wave in peak primary production. Specializationfor the habitats in the early, middle, and later phases of thecycle has figured prominently in species-isolating mechanisms,giving rise to the diversity in each stage of the forest succession.It is concluded that any modifications of the system that precludeperiodic, random perturbation and recycling would be detrimentalto the system in the long run.