Mathematics,genetics and evolution

The importance of mathematics and statistics in genetics is well known. Perhaps less well known is the importance of these subjects in evolution. The main problem that Darwin saw in his theory of evolution by natural selection was solved by some simple mathematics. It is also not a coincidence that the re-writing of the Darwinian theory in Mendelian terms was carried largely by mathematical methods. In this article I discuss these historical matters and then consider more recent work showing how mathematical and statistical methods have been central to current genetical and evolutionary research.     

Evolutionary genetics: evolution with foresight

Evolution has no foresight, but produces ad hoc solutions by tinkering with available variation. A new study demonstrates how evolution nevertheless prepares organisms for the future by increasing their evolvability.     

Multilocus genetics to reconstruct aeromonad evolution

ABSTRACT: BACKGROUND: Aeromonas spp. are versatile bacteria that exhibit a wide variety of lifestyles. In an attempt to improve the understanding of human aeromonosis, we investigated whether clinical isolates displayed specific characteristics in terms of genetic diversity, population structure and mode of evolution among Aeromonas spp. A collection of 195 Aeromonas isolates from human, animal and environmental sources was therefore genotyped using multilocus sequence analysis (MLSA) based on the dnaK, gltA, gyrB, radA, rpoB, tsf and zipA genes. RESULTS: The MLSA showed a high level of genetic diversity among the population, and multilocus-based phylogenetic analysis (MLPA) revealed 3 major clades: the A. veronii, A. hydrophila and A. caviae clades, among the eleven clades detected. Lower genetic diversity was observed within the A. caviae clade as well as among clinical isolates compared to environmental isolates. Clonal complexes, each of which included a limited number of strains, mainly corresponded to host-associated subsclusters of strains, i.e., a fish-associated subset within A. salmonicida and 11 human-associated subsets, 9 of which included only disease-associated strains. The population structure was shown to be clonal, with modes of evolution that involved mutations in general and recombination events locally. Recombination was detected in 5 genes in the MLSA scheme and concerned approximately 50% of the STs. Therefore, these recombination events could explain the observed phylogenetic incongruities and low robustness. However, the MLPA globally confirmed the current systematics of the genus Aeromonas. CONCLUSIONS: Evolution in the genus Aeromonas has resulted in exceptionally high genetic diversity. Emerging from this diversity, subsets of strains appeared to be host adapted and/or "disease specialized" while the A. caviae clade displayed an atypical tempo of evolution among aeromonads. Considering that A. salmonicida has been described as a genetically uniform pathogen that has adapted to fish through evolution from a variable ancestral population, we hypothesize that the population structure of aeromonads described herein suggested an ongoing process of adaptation to specialized niches associated with different degrees of advancement according to clades and clusters.     

The evolution and genetics of innate immunity

The immune system provides protection from a wide range of pathogens. One component of immunity, the phylogenetically ancient innate immune response, fights infections from the moment of first contact and is the fundamental defensive weapon of multicellular organisms. The Toll family of receptors has a crucial role in immune defence. Studies in fruitflies and in mammals reveal that the defensive strategies of invertebrates and vertebrates are highly conserved at the molecular level, which raises the exciting prospects of an increased understanding of innate immunity.     

The genetics and evolution of female choice

Darwin based his theory of evolution on the central theme of 'the struggle for existence', 'the preservation of favoured races', 'the survival of the fittest'. In addition to this 'natural selection', he proposed a second type of selection, sexual selection. 'This depends, not on a struggle for existence, but on a struggle between males for possession of the females; the result is not death to the unsuccessful competitor, but few or no offspring. Males would compete for females, and females would choose between males. Since Darwin's work, many examples of natural selection have been observed in nature and in laboratory experiments, and knowledge of genetics has given natural selective theory a sound basis. The theory of sexual selection through male competition has also been widely accepted. However, the theory of sexual selection through female choice has had a much more chequered passage.     

The genetics of plant morphological evolution.

Considerable progress has been made in identifying genes that are involved in the evolution of plant morphologies. Elements of the ABC model of flower development are conserved throughout angiosperms, and homologous MADS-box genes function in gymnosperm reproduction. Candidate gene and mapping analyses of floral symmetry, sex determination, inflorescence architecture, and compound leaves provide intriguing glimpses into the evolution of morphological adaptations.     

Studying phenotypic evolution using multivariate quantitative genetics

Quantitative genetics provides a powerful framework for studying phenotypic evolution and the evolution of adaptive genetic variation. Central to the approach is G, the matrix of additive genetic variances and covariances. G summarizes the genetic basis of the traits and can be used to predict the phenotypic response to multivariate selection or to drift. Recent analytical and computational advances have improved both the power and the accessibility of the necessary multivariate statistics. It is now possible to study the relationships between G and other evolutionary parameters, such as those describing the mutational input, the shape and orientation of the adaptive landscape, and the phenotypic divergence among populations. At the same time, we are moving towards a greater understanding of how the genetic variation summarized by G evolves. Computer simulations of the evolution of G, innovations in matrix comparison methods, and rapid development of powerful molecular genetic tools have all opened the way for dissecting the interaction between allelic variation and evolutionary process. Here I discuss some current uses of G, problems with the application of these approaches, and identify avenues for future research.     

Crop evolution: from genetics to genomics

The advent of the genomics age has greatly facilitated the study of crop evolution. While full-scale genome sequencing projects are underway for just a handful of crop plants, recent years have witnessed a tremendous increase in the availability of DNA sequence data for virtually all major crops. Such resources have bolstered 'traditional' genetic approaches such as QTL mapping and candidate gene-based association studies. They have also allowed us to undertake genome-wide analyses in which we simultaneously consider the importance of a large and essentially random collection of genes. These sorts of analyses promise a more or less unbiased view of the genetic basis of crop evolution and will probably result in the identification of agronomically important genes that would have otherwise been overlooked.     

Developmental genetics and early hominid craniodental evolution

Although features of the dentition figure prominently in discussions of early hominid phylogeny, remarkably little is known of the developmental basis of the variations in occlusal morphology and dental proportions that are observed among taxa. Recent experiments on tooth development in mice have identified some of the genes involved in dental patterning and the control of tooth specification. These findings provide valuable new insight into dental evolution and underscore the strong developmental links that exist among the teeth and the jaws and cranium. The latter has important implications for cladistic studies that traditionally consider features of the skull independently from the dentition.     

Evolutionary genetics: the evolution of plumage patterns

The identification and sequencing of a gene affecting melanin production in the bananaquit, a bird species notable for its polymorphic plumage colour, paves the way for much greater understanding of the evolution of plumage patterns in birds, and the developmental modulations involved in producing new patterns.     

The (r)evolution of cancer genetics

The identification of an increasing number of cancer genes is opening up unexpected scenarios in cancer genetics. When analyzed for their systemic properties, these genes show a general fragility towards perturbation. A recent paper published in BMC Biology shows how the founder domains of known cancer genes emerged at two macroevolutionary transitions - the advent of the first cell and the transition to metazoan multicellularity.     

Bacterial population genetics, evolution and epidemiology.

Asexual bacterial populations inevitably consist of an assemblage of distinct clonal lineages. However, bacterial populations are not entirely asexual since recombinational exchanges occur, mobilizing small genome segments among lineages and species. The relative contribution of recombination, as opposed to de novo mutation, in the generation of new bacterial genotypes varies among bacterial populations and, as this contribution increases, the clonality of a given population decreases. In consequence, a spectrum of possible population structures exists, with few bacterial species occupying the extremes of highly clonal and completely non-clonal, most containing both clonal and non-clonal elements. The analysis of collections of bacterial isolates, which accurately represent the natural population, by nucleotide sequence determination of multiple housekeeping loci provides data that can be used both to investigate the population structure of bacterial pathogens and for the molecular characterization of bacterial isolates. Understanding the population structure of a given pathogen is important since it impacts on the questions that can be addressed by, and the methods and samples required for, effective molecular epidemiological studies.