Faster-X effects in two Drosophila lineages.

Under certain circumstances, X-linked loci are expected to experience more adaptive substitutions than similar autosomal loci. To look for evidence of faster-X evolution, we analyzed the evolutionary rates of coding sequences in two sets of Drosophila species, the melanogaster and pseudoobscura clades, using whole-genome sequences. One of these, the pseudoobscura clade, contains a centric fusion between the ancestral X chromosome and the autosomal arm homologous to 3L in D. melanogaster. This offers an opportunity to study the same loci in both an X-linked and an autosomal context, and to compare these loci with those that are only X-linked or only autosomal. We therefore investigated these clades for evidence of faster-X evolution with respect to nonsynonymous substitutions, finding mixed results. Overall, there was consistent evidence for a faster-X effect in the melanogaster clade, but not in the pseudoobscura clade, except for the comparison between D. pseudoobscura and its close relative, Drosophila persimilis. An analysis of polymorphism data on a set of genes from D. pseudoobscura that evolve rapidly with respect to their protein sequences revealed no evidence for a faster-X effect with respect to adaptive protein sequence evolution; their rapid evolution is instead largely attributable to lower selective constraints. Faster-X evolution in the melanogaster clade was not related to male-biased gene expression; surprisingly, however, female-biased genes showed evidence for faster-X effects, perhaps due to their sexually antagonistic effects in males.

Expansion of the pseudo-autosomal region and ongoing recombination suppression in the Silene latifolia sex chromosomes.

There are two very interesting aspects to the evolution of sex chromosomes: what happens after recombination between these chromosome pairs stops and why suppressed recombination evolves. The former question has been intensively studied in a diversity of organisms, but the latter has been studied largely theoretically. To obtain empirical data, we used codominant genic markers in genetic mapping of the dioecious plant Silene latifolia, together with comparative mapping of S. latifolia sex-linked genes in S. vulgaris (a related hermaphrodite species without sex chromosomes). We mapped 29 S. latifolia fully sex-linked genes (including 21 newly discovered from transcriptome sequencing), plus 6 genes in a recombining pseudo-autosomal region (PAR) whose genetic map length is ∼25 cM in both male and female meiosis, suggesting that the PAR may contain many genes. Our comparative mapping shows that most fully sex-linked genes in S. latifolia are located on a single S. vulgaris linkage group and were probably inherited from a single autosome of an ancestor. However, unexpectedly, our maps suggest that the S. latifolia PAR region expanded through translocation events. Some genes in these regions still recombine in S. latifolia, but some genes from both addition events are now fully sex-linked. Recombination suppression is therefore still ongoing in S. latifolia, and multiple recombination suppression events have occurred in a timescale of few million years, much shorter than the timescale of formation of the most recent evolutionary strata of mammal and bird sex chromosomes.

Selection responses of means and inbreeding depression for female fecundity in Drosophila melanogaster suggest contributions from intermediate-frequency alleles to quantitative trait variation.

The extent to which quantitative trait variability is caused by rare alleles maintained by mutation, versus intermediate-frequency alleles maintained by balancing selection, is an unsolved problem of evolutionary genetics. We describe the results of an experiment to examine the effects of selection on the mean and extent of inbreeding depression for early female fecundity in Drosophila melanogaster. Theory predicts that rare, partially recessive deleterious alleles should cause a much larger change in the effect of inbreeding than in the mean of the outbred population, with the change in inbreeding effect having an opposite sign to the change in mean. The present experiment fails to support this prediction, suggesting that intermediate-frequency alleles contribute substantially to genetic variation in early fecundity.

Estimates of the genomic mutation rate for detrimental alleles in Drosophila melanogaster.

The net rate of mutation to deleterious but nonlethal alleles and the sizes of effects of these mutations are of great significance for many evolutionary questions. Here we describe three replicate experiments in which mutations have been accumulated on chromosome 3 of Drosophila melanogaster by means of single-male backcrosses of heterozygotes for a wild-type third chromosome. Egg-to-adult viability was assayed for nonlethal homozygous chromosomes. The rates of decline in mean and increase in variance (DM and DV, respectively) were estimated. Scaled up to the diploid whole genome, the mean DM for homozygous detrimental mutations over the three experiments was between 0.8 and 1.8%. The corresponding DV estimate was approximately 0.11%. Overall, the results suggest a lower bound estimate of at least 12% for the diploid per genome mutation rate for detrimentals. The upper bound estimates for the mean selection coefficient were between 2 and 10%, depending on the method used. Mutations with selection coefficients of at least a few percent must be the major contributors to the effects detected here and are likely to be caused mostly by transposable element insertions or indels.