A Critique of R.D. Alexander's Views on Group Selection

Group selection is increasingly being viewed as an important force in human evolution. This paper examines the views of R.D. Alexander, one of the most influential thinkers about human behavior from an evolutionary perspective, on the subject of group selection. Alexander's general conception of evolution is based on the gene-centered approach of G.C. Williams, but he has also emphasized a potential role for group selection in the evolution of individual genomes and in human evolution. Alexander's views are internally inconsistent and underestimate the importance of group selection. Specific themes that Alexander has developed in his account of human evolution are important but are best understood within the framework of multilevel selection theory. From this perspective, Alexander's views on moral systems are not the radical departure from conventional views that he claims, but remain radical in another way more compatible with conventional views.     

The evolution of plant development

There has been much recent interest in the evolution of plant development and especially in trying to understand the developmental genetic basis of morphological evolution. Significant progress has been made in understanding the evolution of floral organization and the mechanisms that might underlie the evolution of compound leaves and inflorescence morphology. These advances are reinforcing the idea that phenotypic evolution can proceed via changes at few loci of large effect and that promoter evolution may be an important and frequent mechanism.     

Niche evolution and diversification in a Neotropical radiation of birds (Aves: Furnariidae)

Rapid diversification may be caused by ecological adaptive radiation via niche divergence. In this model, speciation is coupled with niche divergence and lineage diversification is predicted to be correlated with rates of niche evolution. Studies of the role of niche evolution in diversification have generally focused on ecomorphological diversification but climatic‐niche evolution may also be important. We tested these alternatives using a phylogeny of 298 species of ovenbirds (Aves: Furnariidae). We found that within Furnariidae, variation in species richness and diversification rates of subclades were best predicted by rate of climatic‐niche evolution than ecomorphological evolution. Although both are clearly important, univariate regression and multivariate model averaging more consistently supported the climatic‐niche as the best predictor of lineage diversification. Our study adds to the growing body of evidence, suggesting that climatic‐niche divergence may be an important driver of rapid diversification in addition to ecomorphological evolution. However, this pattern may depend on the phylogenetic scale at which rate heterogeneity is examined.     

<Emphasis Type="Italic">Motilin</Emphasis> and <Emphasis Type="Italic">ghrelin</Emphasis> gene experienced episodic evolution during primitive placental mammal evolution

Motilin and ghrelin, members of a structure-function-related hormone family, play important roles in gastrointestinal function, regulation of energy homeostasis and growth hormone secretion. We observed episodic evolution in both of their prehormone gene sequences during primitive placental mammal evolution, during which most of the nonsynonymous changes result in radical substitution. Of note, a functional obestatin hormone might have only originated after this episodic evolution event. Early in placental mammal evolution, a series of biology complexities evolved. At the same time the motilin and ghrelin prehormone genes, which play important roles in several of these processes, experienced episodic evolution with dramatic changes in their coding sequences. These observations suggest that some of the lineage-specific physiological adaptations are due to episodic evolution of the motilin and ghrelin genes.     

Degeneration and domestication of a selfish gene in yeast: molecular evolution versus site-directed mutagenesis

VDE is a homing endonuclease gene in yeasts with an unusual evolutionary history including horizontal transmission, degeneration, and domestication into the mating-type switching locus HO. We investigate here the effects of these features on its molecular evolution. In addition, we correlate rates of evolution with results from site-directed mutagenesis studies. Functional elements have lower rates of evolution than degenerate ones and higher conservation at functionally important sites. However, functionally important and unimportant sites are equally likely to have been involved in the evolution of new function during the domestication of VDE into HO. The domestication event also indicates that VDE has been lost in some species and that VDE has been present in yeasts for more than 50 Myr.     

Molecular bases of evolution

The general notions of the theory of evolution are listed. The unity of the "engineering principles" of the living nature is emphasized. The generalists and specialists species are discussed. The estimation of their evolution rates must be different if it is expressed by the number of species or by the morphological changes. The principles of "protein engineering" of the organisms and the role of metals in protein evolution are discussed. It is suggested that in the presence of ions of transition metals and zinc the Fox's proteinoids can possess more specific forms of enzymatic activity. In the evolution of language the horizontal transfer plays a much more important role than in the biological evolution. However in this case also the initial basis of the language remains. The random drift is considered and it is shown that in concordance with the neutralist theory there are no grounds to replace the calculation of the rates of mutational changes per time unity by the calculation per generation. The molecular drive is the main source of the evolutionary novelties. The drive is connected with drift. The synonymic mutations and the mutations in non-functional DNA are evolutionary important. The future mathematical theory of evolution must be based on the theory of Markov's chains with the stochastic matrix changing along the chain and containing the set of the non-diagonal members equal to zero. The results obtained in the theory of ontogeny are presented. The evolution of species is the evolution of ontogenies, the formation of the molecular theory of evolution can be possible only on the basis of the molecular theory of ontogeny. The internal causes of extinction of species reduce the accumulation of neutral and pseudo-neutral mutations.     

Motilin and ghrelin gene experienced episodic evolution during primitive placental mammal evolution

Motilin and ghrelin,members of a structure-function-related hormone family,play important roles in gastrointestinal function,regulation of energy homeostasis and growth hormone secretion.We observed episodic evolution in both of their prehormone gene sequences during primitive placental mammal evolution,during which most of the nonsynonymous changes result in radical substitution.Of note,a functional obestatin hormone might have only originated after this episodic evolution event.Early in placental mammal evolution,a series of biology complexities evolved.At the same time the motilin and ghrelin prehormone genes,which play important roles in several of these processes,experienced episodic evolution with dramatic changes in their coding sequences.These observations suggest that some of the lineage-specific physiological adaptations are due to episodic evolution of the motilin and ghrelin genes.     

Selectionism and neutralism in molecular evolution

Charles Darwin proposed that evolution occurs primarily by natural selection, but this view has been controversial from the beginning. Two of the major opposing views have been mutationism and neutralism. Early molecular studies suggested that most amino acid substitutions in proteins are neutral or nearly neutral and the functional change of proteins occurs by a few key amino acid substitutions. This suggestion generated an intense controversy over selectionism and neutralism. This controversy is partially caused by Kimura's definition of neutrality, which was too strict (|2Ns|< or =1). If we define neutral mutations as the mutations that do not change the function of gene products appreciably, many controversies disappear because slightly deleterious and slightly advantageous mutations are engulfed by neutral mutations. The ratio of the rate of nonsynonymous nucleotide substitution to that of synonymous substitution is a useful quantity to study positive Darwinian selection operating at highly variable genetic loci, but it does not necessarily detect adaptively important codons. Previously, multigene families were thought to evolve following the model of concerted evolution, but new evidence indicates that most of them evolve by a birth-and-death process of duplicate genes. It is now clear that most phenotypic characters or genetic systems such as the adaptive immune system in vertebrates are controlled by the interaction of a number of multigene families, which are often evolutionarily related and are subject to birth-and-death evolution. Therefore, it is important to study the mechanisms of gene family interaction for understanding phenotypic evolution. Because gene duplication occurs more or less at random, phenotypic evolution contains some fortuitous elements, though the environmental factors also play an important role. The randomness of phenotypic evolution is qualitatively different from allele frequency changes by random genetic drift. However, there is some similarity between phenotypic and molecular evolution with respect to functional or environmental constraints and evolutionary rate. It appears that mutation (including gene duplication and other DNA changes) is the driving force of evolution at both the genic and the phenotypic levels.     

Covarion structure in plastid genome evolution: a new statistical test

Covarion models of molecular evolution allow the rate of evolution of a site to vary through time. There are few simple and effective tests for covarion evolution, and consequently, little is known about the presence of covarion processes in molecular evolution. We describe two new tests for covarion evolution and demonstrate with simulations that they perform well under a wide range of conditions. A survey of covarion evolution in sequenced plastid genomes found evidence of covarion drift in at least 26 out of 57 genes. Covarion evolution is most evident in first and second codon positions of the plastid genes, and there is no evidence of covarion evolution in third codon positions. Therefore, the significant covarion tests are likely due to changes in the selective constraints of amino acids. The frequency of covarion evolution within the plastid genome suggests that covarion processes of evolution were important in generating the observed patterns of sequence variation among plastid genomes.     

Evolutionary genomics of pathogenic bacteria

Complete genome sequences are now available for multiple strains of several bacterial pathogens and comparative analysis of these sequences is providing important insights into the evolution of bacterial virulence. Recently, DNA microarray analysis of many strains of several pathogenic species has contributed to our understanding of bacterial diversity, evolution and pathogenesis. Comparative genomics has shown that pathogens such as Escherichia coli, Helicobacter pylori and Staphylococcus aureus contain extensive variation in gene content whereas Mycobacterium tuberculosis nucleotide divergence is very limited. Overall, these approaches are proving to be a powerful means of exploring bacterial diversity, and are providing an important framework for the analysis of the evolution of pathogenesis and the development of novel antimicrobial agents.     

Multiple convergent evolution of arboreal life in oribatid mites indicates the primacy of ecology

Frequent convergent evolution in phylogenetically unrelated taxa points to the importance of ecological factors during evolution, whereas convergent evolution in closely related taxa indicates the importance of favourable pre-existing characters (pre-adaptations). We investigated the transitions to arboreal life in oribatid mites (Oribatida, Acari), a group of mostly soil-living arthropods. We evaluated which general force—ecological factors, historical constraints or chance—was dominant in the evolution of arboreal life in oribatid mites. A phylogenetic study of 51 oribatid mite species and four outgroup taxa, using the ribosomal 18S rDNA region, indicates that arboreal life evolved at least 15 times independently. Arboreal oribatid mite species are not randomly distributed in the phylogenetic tree, but are concentrated among strongly sclerotized, sexual and evolutionary younger taxa. They convergently evolved a capitate sensillus, an anemoreceptor that either precludes overstimulation in the exposed bark habitat or functions as a gravity receptor. Sexual reproduction and strong sclerotization were important pre-adaptations for colonizing the bark of trees that facilitated the exploitation of living resources (e.g. lichens) and served as predator defence, respectively. Overall, our results indicate that ecological factors are most important for the observed pattern of convergent evolution of arboreal life in oribatid mites, supporting an adaptationist view of evolution.     

Does nothing in evolution make sense except in the light of population genetics?

“The Origins of Genome Architecture” by Michael Lynch (2007) may not immediately sound like a book that someone interested in the philosophy of biology would grab off the shelf. But there are three important reasons why you should read this book. Firstly, if you want to understand biological evolution, you should have at least a passing familiarity with evolutionary change at the level of the genome. This is not to say that everyone interested in evolution should be a geneticist or a bioinformatician, but that a working knowledge of genetic change is an essential part of the intellectual toolkit of modern evolutionary biology, even if your primary focus is the evolution of behaviour or the diversity of communities. Secondly, this book provides excellent examples of another important tool in the biologist’s intellectual toolkit, but one that is rarely explained or illustrated to such an extent: null (or neutral) models. The role null models play in testing hypotheses in evolution is a central focus of this book. Thirdly, as an accomplished work of advocacy for a strictly microevolutionary view of evolution, this book provides grist for the mill for the important debate about whether population genetic processes are the sine qua non of evolutionary explanations.     

Lipid metabolism, human evolution and schizophrenia.

There are only small genetic differences between humans and the great apes. Yet these differences must be very important. Major known differences include the accumulation of subcutaneous fat, the expansion of breasts and buttocks, the growth of the brain and the connectivity of neurons. All these involve lipid metabolism yet, because fat leaves no fossils, lipids are rarely mentioned in discussions of human evolution. This paper attempts to identify some candidate areas of lipid metabolism which may be important in human evolution. It draws attention to abnormalities in phospholipid metabolism in schizophrenia and suggests that these may have proved important in enhancing brain connectivity in the later stages of evolution of modern humans.     

Does rapid evolution matter? Measuring the rate of contemporary evolution and its impacts on ecological dynamics

Rapid contemporary evolution due to natural selection is common in the wild, but it remains uncertain whether its effects are an essential component of community and ecosystem structure and function. Previously we showed how to partition change in a population, community or ecosystem property into contributions from environmental and trait change, when trait change is entirely caused by evolution (Hairston et al. 2005). However, when substantial non-heritable trait change occurs (e.g. due to phenotypic plasticity or change in population structure) that approach can mis-estimate both contributions. Here, we demonstrate how to disentangle ecological impacts of evolution vs. non-heritable trait change by combining our previous approach with the Price Equation. This yields a three-way partitioning into effects of evolution, non-heritable phenotypic change and environment. We extend the approach to cases where ecological consequences of trait change are mediated through interspecific interactions. We analyse empirical examples involving fish, birds and zooplankton, finding that the proportional contribution of rapid evolution varies widely (even among different ecological properties affected by the same trait), and that rapid evolution can be important when it acts to oppose and mitigate phenotypic effects of environmental change. Paradoxically, rapid evolution may be most important when it is least evident.     

Superinfection and the evolution of resistance to antimalarial drugs

A major issue in the control of malaria is the evolution of drug resistance. Ecological theory has demonstrated that pathogen superinfection and the resulting within-host competition influences the evolution of specific traits. Individuals infected with Plasmodium falciparum are consistently infected by multiple parasites; however, while this probably alters the dynamics of resistance evolution, there are few robust mathematical models examining this issue. We developed a general theory for modelling the evolution of resistance with host superinfection and examine: (i) the effect of transmission intensity on the rate of resistance evolution; (ii) the importance of different biological costs of resistance; and (iii) the best measure of the frequency of resistance. We find that within-host competition retards the ability and slows the rate at which drug-resistant parasites invade, particularly as the transmission rate increases. We also find that biological costs of resistance that reduce transmission are less important than reductions in the duration of drug-resistant infections. Lastly, we find that random sampling of the population for resistant parasites is likely to significantly underestimate the frequency of resistance. Considering superinfection in mathematical models of antimalarial drug resistance may thus be important for generating accurate predictions of interventions to contain resistance.     

HOW IS THE RATE OF CLIMATIC‐NICHE EVOLUTION RELATED TO CLIMATIC‐NICHE BREADTH?

The rate of climatic‐niche evolution is important to many research areas in ecology, evolution, and conservation biology, including responses of species to global climate change, spread of invasive species, speciation, biogeography, and patterns of species richness. Previous studies have implied that clades with higher rates of climatic‐niche evolution among species should have species with narrower niche breadths, but there is also evidence suggesting the opposite pattern. However, the relationships between rate and breadth have not been explicitly analyzed. Here, we examine the relationships between the rate of climatic‐niche evolution and climatic‐niche breadth using phylogenetic and climatic data for 250 species in the salamander family Plethodontidae, a group showing considerable variation in both rates of climatic‐niche evolution and climatic‐niche breadths. Contrary to some expectations, we find no general relationship between climatic‐niche breadth and the rate of climatic‐niche evolution. Climatic‐niche breadths for some ecologically important climatic variables considered separately (temperature seasonality and annual precipitation) do show significant relationships with the rate of climatic‐niche evolution, but rates are faster in clades in which species have broader (not narrower) niche breadths. In summary, our results show that narrower niche breadths are not necessarily associated with faster rates of niche evolution.     

Functional evolution of Hox proteins in arthropods

It is presumed that the evolution of morphological diversity in animals and plants is driven by changes in the developmental processes that govern morphology, hence basically by changes in the function and/or expression of a defined set of genes that control these processes. A large body of evidence has suggested that changes in developmental gene regulation are the predominant mechanisms that sustain morphological evolution, being much more important than the evolution of the primary sequences and functions of proteins. Recent reports challenge this idea by highlighting functional evolution of Hox proteins during the evolutionary history of arthropods.     

Biopolymers and evolution

Biopolymers are usually studied being extracted from the whole system of a cell or of an organism. Some important features are lost during such a procedure. It is necessary to take into account the behavior of proteins and nucleic acids in metabolic networks and to investigate their evolution. The substitutions of amino-acids metabolic networks residues are biologically possible in the polypeptides and proteins if they do not influence their spatial structure and function. The correlations of the primary structure with these properties are degenerate. The protein can be treated as "an edited statistical copolymer" (Ptitsyn). In the process of "edition" an important role is played by the ions of transient metals. Nucleic acids possess similar properties. It can be shown that the deleterious mutations of proteins can be compensated by the changes of their amount, spatial and temporal characteristics of the synthesis. Not only the structure of the protein is important but also the exact answers of the questions: how much, when and where? The contemporary theory of evolution unites phylogeny and onthogeny. The directionality of evolution is determined both by natural selection and by the already existing structure of an organism. Hence many characters are not adaptive. This is valid also for the molecular level of the structure. Thus three independent groups of facts and suggestions are presented, which confirm the neutral theory of evolution (Kimura) and elucidate its physical meaning. The molecular evolution does not coincide with the biological evolution.     

Comparative genomic analysis reveals evolutionary characteristics and patterns of microRNA clusters in vertebrates

MicroRNAs (miRNAs) are a class of small non-coding RNAs that can play important regulatory roles in many important biological processes. Although clustering patterns of miRNA clusters have been uncovered in animals, the origin and evolution of miRNA clusters in vertebrates are still poorly understood. Here, we performed comparative genomic analyses to construct 51 sets of orthologous miRNA clusters (SOMCs) across seven test vertebrate species, a collection of miRNA clusters from two or more species that are likely to have evolved from a common ancestral miRNA cluster, and used these to systematically examine the evolutionary characteristics and patterns of miRNA clusters in vertebrates. We found that miRNA clusters are continuously generated, and most of them tend to be conserved and maintained in vertebrate genomes, although some adaptive gains and losses of miRNA cluster have occurred during evolution. Furthermore, miRNA clusters appeared relatively early in the evolutionary history might suffer from more complicated adaptive gain-and-loss than those young miRNA clusters. Detailed analysis showed that genomic duplication events of ancestral miRNAs or miRNA clusters are likely to be major driving force and apparently contribute to origin and evolution of miRNA clusters. Comparison of conserved with lineage-specific miRNA clusters revealed that the contribution of duplication events for the formation of miRNA cluster appears to be more important for conserved miRNA clusters than lineage-specific. Our study provides novel insights for further exploring the origins and evolution of miRNA clusters in vertebrates at a genome scale.