Population genetics from 1966 to 2016.

We describe the astonishing changes and progress that have occurred in the field of population genetics over the past 50 years, slightly longer than the time since the first Population Genetics Group (PGG) meeting in January 1968. We review the major questions and controversies that have preoccupied population geneticists during this time (and were often hotly debated at PGG meetings). We show how theoretical and empirical work has combined to generate a highly productive interaction involving successive developments in the ability to characterise variability at the molecular level, to apply mathematical models to the interpretation of the data and to use the results to answer biologically important questions, even in nonmodel organisms. We also describe the changes from a field that was largely dominated by UK and North American biologists to a much more international one (with the PGG meetings having made important contributions to the increased number of population geneticists in several European countries). Although we concentrate on the earlier history of the field, because developments in recent years are more familiar to most contemporary researchers, we end with a brief outline of topics in which new understanding is still actively developing.

Use of high-density SNP data to identify patterns of diversity and signatures of selection in broiler chickens.

The development of broiler chickens over the last 70 years has been accompanied by large phenotypic changes, so that the resulting genomic signatures of selection should be detectable by current statistical techniques with sufficiently dense genetic markers. Using two approaches, this study analysed high-density SNP data from a broiler chicken line to detect low-diversity genomic regions characteristic of past selection. Seven regions with zero diversity were identified across the genome. Most of these were very small and did not contain many genes. In addition, fifteen regions were identified with diversity increasing asymptotically from a low level. These regions were larger and thus generally included more genes. Several candidate genes for broiler traits were found within these 'regression regions', including IGF1, GPD2 and MTNR1AI. The results suggest that the identification of zero-diversity regions is too restrictive for characterizing regions under selection, but that regions showing patterns of diversity along the chromosome that are consistent with selective sweeps contain a number of genes that are functional candidates for involvement in broiler development. Many regions identified in this study overlap or are close to regions identified in layer chicken populations, possibly due to their shared precommercialization history or to shared selection pressures between broilers and layers.

The evolution of sex chromosomes.

Structurally distinct sex chromosomes (X and Y) are the most familiar mode of genetic sex determination and have evolved independently in many different taxa. The evolutionary paths by which their characteristic properties may have evolved are reviewed. These properties include the failure of X and Y to recombine through much or all of their length, the genetic inertness of much of the Y chromosome, dosage compensation of the activity of X chromosomal loci, and the accumulation of repeated DNA sequences on the Y chromosome.

Why sex and recombination?

REVIEW Most higher organisms reproduce sexually, despite the automatic reproductive advantage experienced by asexual variants. This implies the operation of selective forces that confer an advantage to sexuality and genetic recombination, at either the population or individual level. The effect of sex and recombination in breaking down negative correlations between favorable variants at different genetic loci, which increases the efficiency of natural selection, is likely to be a major factor favoring their evolution and maintenance. Various processes that can cause such an effect have been studied theoretically. It has, however, so far proved hard to discriminate among them empirically.

Adaptive evolution: the struggle for dominance.

Although wild-type alleles are generally dominant over mutant alleles, recently established alleles for pesticide resistance are rarely recessive in combination with their progenitors. This seems to be caused by a combination of a 'selective sieve' favouring non-recessive mutations, and the biochemical basis of resistance.

Sex chromosomes: evolving dosage compensation.

Dosage compensation of some X-linked genes varies among mammals. Inactivation of an X-linked copy of a gene in females appears to correlate with lack of an active homologue on the Y chromosome, implying that dosage compensation evolves in response to the loss of function of genes on the Y.

Evolution of senescence: Alzheimer's disease and evolution.

The genetic basis of Alzheimer's disease is becoming clear; it appears to fit the postulates of the two main theories of the evolution of senescence, with both polymorphic alleles and rare mutations involved.

The evolution of chromosomal sex determination and dosage compensation.

In many species, sex is determined by a system based on X and Y chromosomes, the latter having lost much of their genetic activity. Y chromosomes have evolved independently many times, and the associated change in gene dosage in the heterogametic (XY) sex is often compensated for by regulatory mechanisms which ensure equal amounts of gene products of X-linked loci in males and females. There have recently been substantial advances in our knowledge of the molecular biology and genetics of sex chromosomes and dosage compensation, and in our understanding of the population genetic processes which are involved in their evolution.

Genome analysis: More Drosophila Y chromosome genes.

The Drosophila melanogaster Y chromosome has long been known to contain few functional genes other than several required for male fertility. The D. melanogaster genome sequence has now allowed characterization of two more male fertility genes, shedding light on the function and evolution of Y chromosomes.

Evolution. How does increased fitness evolve?

Populations of bacteria exposed to a new environment have undergone adaptive evolutionary change over 10,000 generations. These populations provide a testing ground for alternative models of long-term evolution.

Speciation. Down the bottleneck?

Experiments in which laboratory populations of fruitflies have been repeatedly passed through bottlenecks fail to support 'founder-effect' models of speciation.

Genetic recombination. Patterns in the genome.

Recent analyses suggest that the GC content of gene sequences is related to the local frequency of genetic recombination; this may reflect the greater efficacy of natural selection when recombination is frequent.

Evolutionary genetics. The nature and origin of mating types.

Specialized genes in lower eukaryotes prevent fusion between gametes of identical mating type; their molecular characterization has revealed features that may shed light on the evolutionary origin of mating types.

Ageing: levelling of the grim reaper.

Recent observations of a levelling of the death rate in extreme old age, in both experimental species and humans, are posing difficult problems for evolutionary biologists, in particular about the evolution of the post-reproductive period.

Sequence variation: looking for effects of genetic linkage.

Selection at linked loci probably reduces the variability of genes in regions of infrequent recombination. Detailed sequence information is needed to test possible causes of this effect; such information is now becoming available, but its interpretation can be difficult.

Reduced levels of microsatellite variability on the neo-Y chromosome of Drosophila miranda.

BACKGROUND: In many species, sex is determined by a system involving X and Y chromosomes, the latter having lost much of their genetic activity. Sex chromosomes have evolved independently many times, and several different mechanisms responsible for the degeneration of the Y chromosome have been proposed. Here, we have taken advantage of the secondary sex chromosome pair in Drosophila miranda to test for the effects of evolutionary forces involved in the early stages of Y-chromosome degeneration. Because of a fusion of one of the autosomes to the Y chromosome, a neo-Y chromosome and a neo-X chromosome have been formed, resulting in the transmission of formerly autosomal genes in association with the sex chromosomes. RESULTS: We found a 25-fold lower level of variation at microsatellites located on the neo-Y chromosome compared with homologous loci on the neo-X chromosome, or with autosomal and X-linked microsatellites. Sequence analyses of the region flanking the microsatellites suggested that the neo-sex chromosomes originated about 1 million years ago. CONCLUSIONS: Variability of the neo-Y chromosome of D. miranda is substantially reduced below expectations at mutation-drift equilibrium. Such a reduction is predicted by theories of the degeneration of the Y chromosome. Another possibility is that there is little or no mutation at microsatellite loci on a non-recombining chromosome such as the neo-Y, but this seems inconsistent with other data.

Natural selection at work.

Although much is known about the genetic basis of reproductive isolation between species, little is understood about its underlying evolutionary causes. A study of two very closely related, but reproductively isolated, plant species has provided some valuable insights.

Recombination modification in a flucturating environment.

This paper examines the theory of the evolution of increased recombination between two loci subjected to interactive selection in a temporally fluctuating environment. Both cyclical and stochastic environments are considered. It is shown that temporal variation in the linkage disequilibrium coefficient for the pair of selected loci, due to fluctuations in the selective values of the genotypes at these loci, can give rise to selection in favor of modifier genes increasing recombination. The equilibrium level of recombination established in a given population depends on several factors; it is highest for intermediate values of the environmental periodicity or autocorrelation, for cases when the modifier genes are themselves linked to the selected loci, and for high levels of environmental variation. In general, it seems that the rate of modification of recombination values by this process will be low except when the modifiers are tightly linked to the selected loci. The possible evolutionary significance of this process is discussed in relation to observations on genetic systems of plants and animals.

Selection on recombination in clines.

Computer runs have been done to examine Slatkin's (1975) model for selection on recombination rates in linear sets of populations with environmental changes affecting two loci. In order to determine whether the suggested selection pressures on recombination do, in fact, exist, we follow the changes in frequency at a third locus that is polymorphic for alleles affecting the recombination rate between the two selected loci. With haploid or diploid selection models, there can be selection for increased recombination if the parameter values are chosen suitably, but changes in parameter values often lead to changes in the direction of selection, so that decreased recombination is favored. The selection for increased recombination is usually weak, while that for decreased recombination is frequently much stronger. Weaker selection on the selected loci often leads to increasing selection for decreased recombination.

Selection on recombination in a multi-locus system.

The model of Wills and Miller (1976) for selection on recombination rates in finite populations was studied by means of a computer model involving 80 selected loci and a linked or unlinked modifier gene affecting the map length occupied by the selected loci. The selected loci were subject to heterozygote advantage, and multiplicative fitness interactions between loci were assumed. In all cases studied, selection for reduction in recombination out-weighed any selection for increased recombination that may have been present.