Alternative evolutionary outcomes following endosymbiont-mediated selection on male mating preference alleles.

In many arthropods, intracellular bacteria, such as those of the genus Wolbachia, may spread through host populations as a result of cytoplasmic incompatibility (CI). Here, there is sterility or reduced fertility in crosses between infected males and uninfected females. As the bacterium is maternally inherited, the reduced fertility of uninfected females increases the frequency of the infection. If the transmission fidelity of the bacterium is less than 100%, the bacterium cannot invade from a low frequency, but if its frequency exceeds a threshold, it increases to a high, stable, equilibrium frequency. We explore the expected evolutionary dynamics of mutant alleles that cause their male bearers to avoid mating with uninfected females. For alleles which create this avoidance behaviour conditional upon the male being infected, there is a wide zone of parameter space that allows the preference allele to drive Wolbachia from the population when it would otherwise stably persist. There is also a wide zone of parameter space that allows a joint stable equilibrium for the Wolbachia and a polymorphism for the preference allele. When the male's avoidance of uninfected females is unconditional, the preference allele's effect on Wolbachia frequency is reduced, but there is a narrow range of values for the transmission rate and CI fertility that allow an unconditional preference allele to drive Wolbachia from the population, in a process driven by positive linkage disequilibrium between Wolbachia and the preference allele. The possibility of the evolution of preference could hamper attempts to manipulate wild populations through Wolbachia introductions.

Why are estimates of the strength and direction of natural selection from wild populations not congruent with observed rates of phenotypic change?

Observing adaptive evolution is difficult. In the fossil record, phenotypic evolution happens much more slowly than in artificial selection experiments or in experimental evolution. Yet measures of selection on phenotypic traits, with high heritabilities, suggest that phenotypic evolution should also be rapid in the wild, and this discrepancy often remains even after accounting for correlations between different traits (i.e. making predictions using the multivariate version of the breeder's equation). Are fitness correlations with quantitative traits adequate measures of selection in the wild? We should instead view fitnesses as average properties of genotypes, while acknowledging that they can be environment-dependent. Populations will tend to remain at fitness equilibria, once these are attained, and phenotypes will then be stable. Thus, studying the causes of adaptive change at a genotypic rather than phenotypic level may reveal that, typically, it is occurring too slowly to be easily observed.

Biased image cropping and non-independent samples.

Any figure in a research article will typically represent only a small portion of the total data gained by a researcher for that experiment, and it is therefore key that the figure accurately reflects what was found overall. Furthermore, if individual observations form clusters with differing mean properties, those individual observations would not represent independent samples from the populations being compared. In this example, the question of how to fairly represent and treat image data is addressed.

The diversity of class II transposable elements in mammalian genomes has arisen from ancestral phylogenetic splits during ancient waves of proliferation through the genome.

DNA transposons make up 3% of the human genome, approximately the same percentage as genes. However, because of their inactivity, they are often ignored in favor of the more abundant, active, retroelements. Despite this relative ignominy, there are a number of interesting questions to be asked of these transposon families. One particular question relates to the timing of proliferation and inactivation of elements in a family. Does an ongoing process of turnover occur, or is the process more akin to a life cycle for the family, with elements proliferating rapidly before deactivation at a later date? We answer this question by tracing back to the most recent common ancestor (MRCA) of each modern transposon family, using two different methods. The first method identifies the MRCA of the species in which a family of transposon fossils can still be found, which we assume will have existed soon after the true origin date of the transposon family. The second method uses molecular dating techniques to predict the age of the MRCA element from which all elements found in a modern genome are descended. Independent data from five pairs of species are used in the molecular dating analysis: human-chimpanzee, human-orangutan, dog-panda, dog-cat, and cow-pig. Orthologous pairs of elements from host species pairs are included, and the divergence dates of these species are used to constrain the analysis. We discover that, in general, the times to element common ancestry for a given family are the same for the different species pairs, suggesting that there has been no order-specific process of turnover. Furthermore, for most families, the ages of the common ancestor of the host species and of that of the elements are similar, suggesting a life cycle model for the proliferation of transposons. Where these two ages differ, in families found only in Primates and Rodentia, for example, we find that the host species date is later than that of the common ancestor of the elements, implying that there may be large deletions of elements from host species, examples of which were found in their ancestors.

Behavioral insensitivity to DEET in Aedes aegypti is a genetically determined trait residing in changes in sensillum function.

N,N-Diethyl-m-toluamide (DEET) is one of the most effective and commonly used mosquito repellents. However, during laboratory trials a small proportion of mosquitoes are still attracted by human odors despite the presence of DEET. In this study behavioral assays identified Aedes aegypti females that were insensitive to DEET, and the selection of either sensitive or insensitive groups of females with males of unknown sensitivity over several generations resulted in two populations with different proportions of insensitive females. Crossing experiments showed the "insensitivity" trait to be dominant. Electroantennography showed a reduced response to DEET in the selected insensitive line compared with the selected sensitive line, and single sensillum recordings identified DEET-sensitive sensilla that were nonresponders in the insensitive line. This study suggests that behavioral insensitivity to DEET in A. aegypti is a genetically determined dominant trait and resides in changes in sensillum function.

Host-parasite relationships in the genome.

Transposable elements are best interpreted as genomic parasites, proliferating in genomes through their over-replication relative to the rest of the genome. A new study examining correlations across Drosophila species between transposable element numbers and rates of host evolution has brought into focus one of the most complex questions in transposable element biology-what it is that determines the proportion of the genome that is transposable elements.

Investigation of the origin and spread of a Mammalian transposable element based on current sequence diversity.

Almost half the human genome consists of mobile DNA elements, and their analysis is a vital part of understanding the human genome as a whole. Many of these elements are ancient and have persisted in the genome for tens or hundreds of millions of years, providing a window into the evolution of modern mammals. The Golem family have been used as model transposons to highlight computational analyses which can be used to investigate these elements, particularly the use of molecular dating with large transposon families. Whole-genome searches found Golem sequences in 20 mammalian species. Golem A and B subsequences were only found in primates and squirrel. Interestingly, the full-length Golem, found as a few copies in many mammalian genomes, was found abundantly in horse. A phylogenetic profile suggested that Golem originated after the eutherian-metatherian divergence and that the A and B subfamilies originated at a much later date. Molecular dating based on sequence diversity suggests an early age, of 175 Mya, for the origin of the family and that the A and B lineages originated much earlier than expected from their current taxonomic distribution and have subsequently been lost in some lineages. Using publically available data, it is possible to investigate the evolutionary history of transposon families. Determining in which organisms a transposon can be found is often used to date the origin and expansion of the families. However, in this analysis, molecular dating, commonly used for determining the age of gene sequences, has been used, reducing the likelihood of errors from deleted lineages.

Population Genetics: How Many Variable Genes Affect Variable Traits?

How many genes control a given trait? And are genes with defined knockout phenotypes affecting a given trait the same genes that also underlie population-wide variation in that trait? A new study in Drosophila melanogaster has some surprising answers.

Genetic Variation: Harmful Recessive Mutations Have Unexpected Effects on Variation.

New data are causing the standard model for the effect of selection on linked neutral variation in low recombination regions, combining the effects of background selection and selective sweeps, to be refined to include harmful recessive mutations creating associative overdominance.

Source gene composition and gene conversion of the AluYh and AluYi lineages of retrotransposons.

BACKGROUND: Alu elements are a family of SINE retrotransposons in primates. They are classified into subfamilies according to specific diagnostic mutations from the general Alu consensus. It is now believed that there may be several retrotranspositionally-competent source genes within an Alu subfamily. In this study, subfamilies falling on the AluYi and AluYh lineages, and the AluYg6 subfamily, are assessed for the presence of secondary source genes, and the influence of gene conversion on the AluYh and AluYi lineages is also described. RESULTS: The AluYh7 and AluYi6 subfamilies appear to contain multiple source genes. The novel subfamilies AluYh3a1 and AluYh3a3 are described, for which there is no convincing evidence to suggest the presence of secondary sources. The mutational substructure of AluYh3a3 can be explained completely by inference of single master gene. A complete backwards gene conversion event appears to have inactivated the AluYh3a3 master gene in humans. Polymorphism data suggest a larger number of secondary source elements may be active in the AluYg6 family than previously thought. CONCLUSION: It is clear that there is considerable variation in the number of source genes present in each of the young Alu subfamilies. This can range from a single master source gene, as for AluYh3a3, to as many as 14 source elements in AluYi6.

Evolutionary modelling of feed forward loops in gene regulatory networks.

Feed forward loops (FFLs) are gene regulatory network motifs. They exist in different types, defined by the signs of the effects of genes in the motif on one another. We examine 36 feed forward loops in Escherichia coli, using evolutionary simulations to predict the forms of FFL expected to evolve to generate the pattern of expression of the output gene. These predictions are tested using likelihood ratios, comparing likelihoods of the observed FFL structures with their likelihoods under null models. The very high likelihood ratios generated, of over 10(11), suggest that evolutionary simulation is a valuable component in the explanation of FFL structure.

Mutation Rates: Simpler Than We Thought?

Mutation rate variation is often explained by varying optimal rates, or through effective population sizes determining the effectiveness of selection. But a rate difference between humans and owl monkeys is now explained mechanistically as a consequence of differing reproductive longevities.

Analysis of the features and source gene composition of the AluYg6 subfamily of human retrotransposons.

BACKGROUND: Alu elements are a family of SINE retrotransposons in primates. They are classified into subfamilies according to specific diagnostic mutations from the general Alu consensus. It is now believed that there may be several retrotranspositionally-competent source genes within an Alu subfamily. To investigate the evolution of young Alu elements it is critical to have access to complete subfamilies, which, following the release of the final human genome assembly, can now be obtained using in silico methods. RESULTS: 380 elements belonging to the young AluYg6 subfamily were identified in the human genome, a number significantly exceeding prior expectations. An AluYg6 element was also identified in the chimpanzee genome, indicating that the subfamily is older than previously estimated, and appears to have undergone a period of dormancy before its expansion. The relative contributions of back mutation and gene conversion to variation at the six diagnostic positions are examined, and cases of complete forward gene conversion events are reported. Two small subfamilies derived from AluYg6 have been identified, named AluYg6a2 and AluYg5b3, which contain 40 and 27 members, respectively. These small subfamilies are used to illustrate the ambiguity regarding Alu subfamily definition, and to assess the contribution of secondary source genes to the AluYg6 subfamily. CONCLUSION: The number of elements in the AluYg6 subfamily greatly exceeds prior expectations, indicating that the current knowledge of young Alu subfamilies is incomplete, and that prior analyses that have been carried out using these data may have generated inaccurate results. A definition of primary and secondary source genes has been provided, and it has been shown that several source genes have contributed to the proliferation of the AluYg6 subfamily. Access to the sequence data for the complete AluYg6 subfamily will be invaluable in future computational analyses investigating the evolution of young Alu subfamilies.

Evolutionary genetics: Mobile DNAs as sources of adaptive change?

Mobile DNAs are potent sources of mutation in wild populations, but seem only rarely to have been used in adaptive evolution. A new study has revealed a mobile DNA insertion in Drosophila simulans that is associated with an apparent selective sweep and an elevation in expression level of an adjacent gene which creates insecticide resistance.

Human prehistory: the message from linkage disequilibrium.

The vast amount of information being gathered about human DNA sequence variation raises the question of what these data can tell us about events in our past. A new way has been found by which patterns of linkage disequilibrium can be used to detect the effects of natural selection in human prehistory.

Gene duplications: the gradual evolution of functional divergence.

Budding yeast provides a useful resource for studies of gene function. A new analysis of the fitness effects of deletion mutations in budding yeast reveals that genes that have duplicates create lower fitness losses when inactivated than do genes that are singletons.

Human evolution: a legacy of cannibalism in our genes?

A new study of genetic variation in the human prion protein gene suggests that balancing selection has operated on an amino acid sequence polymorphism in the gene during the last five hundred thousand years. Is this a legacy of widespread cannibalism by our ancestors?

Mobile DNAs: the poacher turned gamekeeper.

The selfish DNA hypothesis imagines the genome as an ecological community, a collection of interacting DNA sequences with differing evolutionary origins and potentially different interests. We are now finding out more about the ways in which host sequences can enlist the help of formerly parasitic DNAs.

A simple method for genome-wide screening for advantageous insertions of mobile DNAs in Escherichia coli.

Laboratory evolution in Escherichia coli has revealed that fitness typically increases in experimental populations. These changes are sometimes associated with changes in insertion sequence positions, some of which may themselves cause advantageous phenotypes. We have a novel and general method for identifying genes in Escherichia coli, whose knockout by mobile DNA insertions is beneficial in experimental evolution. Insertion sites in favored clones can be identified by reference to genomic information. We have implemented the method using modified Tn10 transposons bearing kanamycin and chloramphenicol resistance cassettes. Results are consistent across replicated experiments, demonstrating that the insertions are themselves creating selective advantages, rather than hitch-hiking with favorable base substitutions. The successful clones have subsequently been confirmed to have a fitness advantage relative to the progenitor strain. In experiments in shaking culture, we find that advantageous insertions usually fall in operons required in the pathways creating flagella. The method allows a rapid genome-wide screening for advantageous insertions in arbitrary environmental conditions. It allows investigation of the extent to which transient mutations generating environment-dependent selective advantages may help to explain the persistence of mobile DNAs in primarily clonal organisms, such as E. coli.

The evolution of mobile DNAs: when will transposons create phylogenies that look as if there is a master gene?

Some families of mammalian interspersed repetitive DNA, such as the Alu SINE sequence, appear to have evolved by the serial replacement of one active sequence with another, consistent with there being a single source of transposition: the "master gene." Alternative models, in which multiple source sequences are simultaneously active, have been called "transposon models." Transposon models differ in the proportion of elements that are active and in whether inactivation occurs at the moment of transposition or later. Here we examine the predictions of various types of transposon model regarding the patterns of sequence variation expected at an equilibrium between transposition, inactivation, and deletion. Under the master gene model, all bifurcations in the true tree of elements occur in a single lineage. We show that this property will also hold approximately for transposon models in which most elements are inactive and where at least some of the inactivation events occur after transposition. Such tree shapes are therefore not conclusive evidence for a single source of transposition.