In this article, a method is proposed for detecting recombination in the sequences of a gene from a set of closely related organisms. The method, the Homoplasy Test, is appropriate when the sequences are rather similar, differing by 1%-5% of nucleotides. It is effective in detecting relatively frequent recombination between a set of rather similar strains, in contrast to previous methods which detect rare or unique transfers between more distant strains. It is based on the fact that, if there is no recombination and if no repeated mutations have occurred (homoplasy), then the number of polymorphic sites, v, is equal to the number of steps, t, in a most-parsimonious tree. If the number of "apparent homoplasies" in the most-parsimonious tree, h = t-v, is greater than zero, then either homoplasies have occurred by mutation or there has been recombination. An estimate of the distribution of h expected on the null hypothesis of no recombination depends on Se, the "effective site number," defined as follows: if ps is the probability that two independent substitutions in the gene occur at the same site, then Se = 1/ps. Se can be estimated if a suitable outgroup is available. The Homoplasy Test is applied to three bacterial genes and to simulated gene trees with varying amounts of recombination. Methods of estimating the rate, as opposed to the occurrence, of recombination are discussed.

Borrelia↗

PubMed1998

The units of selection.

Darwin's idea of evolution by natural selection is almost universally accepted by biologists, but debate continues about the units of selection. The history of this debate starts with Wynne-Edwards' arguments for group selection, and Hamilton's explantation of social behaviour in terms of the inclusive fitness of individuals. Hamilton's approach differs from the gene-centred approach pioneered by Williams and Dawkins, although both the problem and its solution are essentially the same. The choice of approach depends on conceptual and mathematical simplicity, and on one's attitude to the causal efficacy of genes. The problem of selection on units above the species level is discussed. Today, we are in the main concerned with cases in which selection acts simultaneously at two levels. This is true of current research on intragenomic conflict and of the suggestion by Maynard Smith and Szathmáry that in the major transitions in evolution, entities that were capable of independent replication before the transition can only replicate as part of a larger whole after it.

Animals↗

PubMed1997

From replicators to reproducers: the first major transitions leading to life.

A classification of replicators is proposed: life depends on replicators that can exist in an indefinitely large number of forms (unlimited heredity), and whose replication is modular rather than processive. The first template replicators would have increased at a rate less than exponential, because of self-inhibition arising from molecular complementarity. The result would be the survival of a varied population of replicators, rather than the victory of one type. This variability was important, because inaccurate copying meant that individual replicators were small (Eigen's paradox). The origin of cooperation between replicators, and the problem of molecular parasites, are discussed. Today, cooperation depends on cellular compartments, and on the linkage of genes on chromosomes, but we argue that at an earlier stage surface metabolism, in which replicators react only with neighbours, was important. The origin of translation and the genetic code is discussed. The essential step is the binding of amino acids to specific oligonucleotides. We suggest that this binding originated, not as a step in protein synthesis, but in the formation of coenzymes in a metabolically complex RNA world. Existing organisms are not replicators (that is, new individuals do not arise by copying), but reproducers that contain replicators. We outline Griesemer's concept of a reproducer, which brings out the essential role of development in evolution.

Animals↗

PubMed1996

A comparison of the nucleotide sequences of the adk and recA genes of pathogenic and commensal Neisseria species: evidence for extensive interspecies recombination within adk.

The sequences of the adenylate kinase gene (adk) and the RecA gene (recA) were determined from the same isolates of Neisseria gonorrhoeae, N. meningitidis, N. lactamica, N. polysaccharea, N. cinerea, N. mucosa, N. pharyngis var. flava, N. flavescens, and N. animalis. The patterns of sequence divergence observed at adk and recA were very different. Dendrograms constructed from the recA data using two different algorithms were statistically robust and were congruent with each other and with the relationships between the species previously proposed using other data. In contrast, the dendrograms derived from the adk data were noncogruent with each other, and with those from the recA data, and were statistically poorly supported. These results, along with the uniform distribution of pairwise sequence divergences between the species at adk, suggest there has been a history of interspecies recombination within the adk gene of the human Neisseria species which has obscured the phylogenetic relationships between the species. This view was supported by Sawyer's runs test, and the Index of Association (IA) between codons, which provided significant evidence for interspecies recombination between the adk genes from the human Neisseria species, but no evidence of interspecies recombination between the recA sequences.

Adenylate Kinase↗

PubMed1995

Sequence evolution of the porB gene of Neisseria gonorrhoeae and Neisseria meningitidis: evidence of positive Darwinian selection.

Protein 1 (PI) is a major porin of Neisseria gonorrhoeae and Neisseria meningitidis and is encoded by a single locus, porB. Alleles of the porB locus of N. gonorrhoeae are assigned to two homology groups, PI(A) and PI(B), on the basis of immunological and structural similarity. In a like manner, alleles of the porB locus of the closely related bacterium, N. meningitidis, are allocated into class 2 and class 3 homology groups. An individual strain of N. gonorrhoeae or N. meningitidis expresses either one or other of these porin homology groups but never both, and the antigenic reactions of these highly diverse outer membrane proteins form part of the N. gonorrhoeae and N. meningitidis serotyping schemes. A comparison of the number of synonymous and nonsynonymous substitutions per site between the two most divergent alleles of each of these four groups of porB alleles shows that PI(A) alleles have accumulated significantly more nonsynonymous substitutions per site than synonymous substitutions. In contrast the distribution of synonymous and nonsynonymous substitutions between alleles of class 2 and class 3 porins are not significantly different from random. We localize the regions of the PI(A) alleles with an excess of amino acid changes to the surface-exposed loops of these outer membrane proteins and suggest that positive Darwinian selection for diversity, driven by the human immune system, can most easily explain the allelic polymorphism and the pattern of synonymous and nonsynonymous substitutions.

Alleles↗

PubMed1990

Models of a dual inheritance system.

In higher plants, animals and fungi, there are two inheritance systems: the familiar system, depending on DNA sequence, used in transmitting information between sexual generations, and an epigenetic inheritance system, depending on gene activation, responsible for the transmission of states of differentiation during development. Occasionally, epigenetic changes are transmitted in sexual reproduction. A formal model of such a dual inheritance system is presented, and it is shown how the separation between the two systems can sometimes break down. The evolutionary significance of such breakdowns is discussed.

Animals↗

PubMed1988

The evolution of aggression: can selection generate variability?

Three models--the war of attrition, the size game and the badges of dominance game--are described, in which natural selection can maintain genetic variability for aggression. The models differ in whether or not the traits that settle contests are costly in contexts other than fighting, and also in whether signals are used. It is concluded that contests will be settled by non-costly traits only if the value of the contested resource is small relative to the cost of fighting, and that 'honest' signalling of aggressiveness is stable only if individuals giving signals that are inconsistent with their behaviour suffer costs. The literature on 'badges of dominance' in birds is reviewed. New data on great tits, greenfinches and corn buntings show that there is plumage variability within age and sex that sometimes serves to settle contests, and that, in the first two species but not the third, the badges are uncorrelated with size, and settle contests only over trivial resources.

Aggression↗

PubMed1987

On the equality of origin and fixation times in genetics.

For any sexually reproducing entity (e.g. asexual organism, mitochondrion or gene), the fixation time is the number of generations in the future before all entities are descended from a single one in the present. The origin time is the number of generations in the past when a single entity was ancestral to all entities in the present. It is proved that, over a sufficiently long time, the means and distributions of the fixation and origin times are identical. The proof holds even if population size varies, selection is acting, or conditions change with time.

Biological Evolution↗