B Charlesworth

..Evidence is discussed that is consistent with the action of these processes in shaping genome-wide patterns of variation and evolution...

..No consistent patterns have emerged from studies that have investigated general levels of evolutionary constraint in introns...

..In freely recombining regions of the genome, selection should more effectively incorporate new beneficial mutations, and eliminate deleterious ones, than in regions with low rates of genetic recombination...

..Several studies have investigated levels of evolutionary constraint along introns and across classes of introns of different length and location within genes. However, thus far these studies have yielded contradictory results...

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..The evolutionary significance of sexual reproduction and genetic recombination is a long-standing puzzle. Some recent experiments on Drosophila show that a lack of recombination can impede adaptive evolution...

..The results should be useful for tests of selection based on the levels of expected and observed ancestral polymorphisms...

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..It is, however, currently unclear which of the various processes is most important; some directions for future work to help to resolve this question are discussed...

..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...

..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...

..Predictions concerning the additive genetic correlations in mortality rates between different ages are also developed. The predictions of the models are compared with data on humans and Drosophila...

..The recent sequencing of a large chunk of euchromatin from the human Y chromosome is a technical tour de force. It answers some evolutionary questions about this unusual chromosome while raising others...

..Under some conditions, however, the enhanced reproductive value of males, caused by the production of inviable Y0 embryos in X0 x X'Y matings, can outweigh any advantage to X'. Inbreeding also reduces any advantage to X'...

..These effects need to be accounted for when trying to understand data on patterns of sequence variation for genes with different transmission modes...

..Possible experimental approaches to resolving outstanding questions are discussed...

..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...

..We also show that HR effects of this type can produce an individual selection advantage to recombination, as well as greatly reduce the mean fitness of nonrecombining genomes and genomic regions...

..Overall, the Symposium portrayed evolution as a field that, while retaining its Darwinian roots, is exploring ever-wider areas of biology as new techniques and ideas emerge...

..In particular, the action of selection means that N(e) varies across the genome, and advances in genomic techniques are giving new insights into how selection shapes N(e)...

..Males of S. papillosus have now been shown to be produced by elimination of chromosomal material that constitutes the X chromosome in its close relatives...

..We discuss how these theoretical results can be related to data on genetic diversity within and between local populations of a species...

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..Finally, the effects of deleterious mutations on population fitness and the possible role of Hill-Robertson interference in shaping patterns of sequence variability are discussed...

..This model is used to show that deleterious mutations could account for the Drosophila data on the effects of inbreeding on components of fitness such as viability...

..The present experiment fails to support this prediction, suggesting that intermediate-frequency alleles contribute substantially to genetic variation in early fecundity...

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..This explanation is supported by the pattern of within-species sequence variation at exu1 and the nearby exu2 locus. The implications of this phenomenon for genome evolution are discussed...

..pseudoobscura C chromosome, which are different from those in the current literature. We also describe a new method for correcting for rearrangements that are not detected with a limited set of markers...

..miranda. However, data on an additional region of period confirm population subdivision for this gene, suggesting that local selection is operating at or near period to promote differentiation between populations...

..Our results suggest that the fused alanine haplotypes have recently increased in frequency in the D. virilis population...

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..Together, these and other characteristics of the exu2 locus suggest the action of selection on the pattern of SNP variation, consistent with a partial selective sweep associated with the newly derived haplotype...

..There is no reduction in variation at two loci close to the centromeric heterochromatin, in contrast to Drosophila melanogaster...

..This is consistent with the recent origin of the neo-Y and neo-X chromosomes, and the slow rates at which the forces that cause Y chromosome degeneration are likely to work...

..Large overall effects are less likely in species with higher levels of genetic recombination, such as mammals, although local reductions in regions of reduced recombination might be detectable...

..On this view, the increased complexity of biological functions associated with large genomes partly reflects evolutionary degeneration...

..However, our tests show that none of the hypotheses we consider seem to explain the data fully...

..These patterns of variation are best explained as a result of selection acting on amino acid substitutions, with geographic variation in selection pressures...

..We discuss how selection during the period when a chromosome is adapting to its role as a Y chromosome might drive such a process...

..Our in situ data are consistent with previous studies, and suggest that selection is the main force controlling element spread by transposition...

..These results show that using inadequate selection (or demographic) models can result in incorrect estimates of demographic (or selection) parameters...

..We show that, when the rate of nonsynonymous evolution is normalized by the rate of neutral evolution, a sex difference in mutation rate has no influence on the conditions for faster-X evolution...

..melanogaster...

..Our results suggest that the majority of non-synonymous mutations in Drosophila are under effective purifying selection...

..Phenotypic assays of the same lines detected only a small proportion of mutations that were predicted to have evolutionarily significant fitness effects...

..Demographic departures from equilibrium expectations in both ancestral and derived populations thus represent a serious challenge to detecting positive selection in genome-wide scans using current methodologies...

..We therefore conclude that coincident patterns of current and ancient selection are responsible for shaping biased codon usage in the C. remanei genome...

..Various processes that can cause such an effect have been studied theoretically. It has, however, so far proved hard to discriminate among them empirically...

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..The simulation results and their implications are discussed in the context of biological conservation and tests for purging...

..This is not expected under a model where the faster evolution of the X chromosome is postulated to be the main force driving the degeneration of the Y chromosome...

..Recombination is selectively disadvantageous when there is diminishing returns epistasis. These results are compared with the results of previous theoretical studies of this problem, and with experimental data...

..Its possible role in causing the degeneration of Y and neo-Y chromosomes is discussed in the light of our present knowledge of deleterious mutation rates and selection coefficients...

..Further experiments are needed to determine whether the selection against recombination due to the immediate load is outweighed by the increased additive variance in fitness produced by recombination...

..We find evidence for recombinational exchange at this locus, and both species appear to be fixed for an insertion of the transposable element HB in an intron of ankyrin...

..The method is also applied to polymorphism data in maize, providing support for the hypothesis of directional selection on genes in the starch pathway...

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..We show that selection at nonsynonymous coding sites can accelerate the process of gene loss and that this effect varies with the number of genes still present on the degenerating neo-Y chromosome...

..Our estimates suggest that there is a small region of very low recombination surrounding the S-locus region...

..The relevance of this process for the degeneration of Y or neo-Y chromosomes is discussed...

..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...

..These results are consistent with those of many other studies that suggest that both unselected mutations and those found segregating in natural populations are partially recessive...

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..Evidence is accumulating that in the green algae the evolution of female and male gametes differing in size--anisogamy--involves genes linked to the mating-type locus, as was predicted theoretically...

..The model overpredicts the effects of background selection with large groups of nonrecombining genes, because it ignores Hill-Robertson interference among the mutations involved...

..2 per diploid genome. This high rate suggests that selection against deleterious mutations may have a key role in explaining patterns of genetic variation in the genome, and help to maintain recombination and sexual reproduction...

..Thus, the X(D) in D. recens appears to be in chromosome-wide linkage disequilibrium and in the early stages of mutational degradation...

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..Overall, the results show that both purifying selection and positive selection on nonsynonymous mutations are pervasive...

..elegans, but subject to purifying selection in C. remanei. These results are consistent with a reduced efficacy of natural selection against TEs in selfing populations, but may in part be explained by non-equilibrium TE dynamics...

..elegans performed better than crosses between strains, indicating outbreeding depression. The results are discussed in relation to the evolution of androdioecy and the effect of mating system on the level of inbreeding depression...

..Mutual interference among linked genetic sites subject to selection may reduce the level of adaptation. A recent study detected this effect using data on protein sequence evolution and codon usage in Drosophila...

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..Alternatively, higher gene expression may be evolving to compensate for defective protein products or reduced translational efficiency...

..melanogaster and to measure their expression levels. This is consistent with the idea that limitations in transcription rates may prevent male-biased genes from accumulating on the X chromosome...

..These results have important implications for differentiating between the leading models of how selection acts on TEs and should help to interpret emerging population genetic and genomic data...

..The proportion of GC-->AT versus AT-->GC polymorphic mutations in a locus is correlated with its GC content. This implies the action of forces that favour GC over AT base pairs, which are apparently strongest in GC-rich sequences...

..They also suggest that genes that have become X-linked have higher levels of codon bias and slower synonymous site evolution, consistent with more effective selection on codon usage at X-linked sites...

..americana lineage are in approximate equilibrium. Biased gene conversion may also contribute to the observed patterns...

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..The results show that mortality levelling is strongly affected by the Gompertz initial mortality rate and exponential rate of increase parameters, probably through the effects of heterogeneity in mortality risks...

..This was particularly strong for the S-element inverted repeats (IRs) and suggests that these are of functional significance for the host...

..The joint intensity of selection and biased gene conversion, in terms of the product of effective population size and the sum of the selection and conversion coefficients, was estimated to be approximately 0.65...

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..Based on these results, a possible explanation for the seasonal fluctuations in resistance to the three organophosphates observed in the natural population was proposed...

..This suggests that flanking DNA should be used to confirm the positions of members of gene families...

..Data on DNA sequence variability in human and plant populations are discussed in the light of the results...

..The level of divergence between these clusters suggests that the S elements invaded the genome of the ancestor of D. melanogaster before the speciation of the D. melanogaster complex. However, other relevant scenarios are also discussed...

..These results may have important consequences for newly arisen asexual lineages and may account for the lack of deleterious retrotransposons in the putatively ancient asexual bdelloid rotifers...

..This finding suggests that genetic exchanges between maternal and paternal mitochondrial DNAs may have contributed to the lack of association we observe between phenotype and genotype...

..Our results provide evidence for the importance of sexual recombination for increasing and maintaining the level of adaptation of a population...

..We caution, however, that the effect of weak selection on the genealogy is specific to the model; a (more realistic) model of multiple linked sites could lead to a more distorted genealogy than is observed for a single site...

..It remains to be decided whether background selection is sufficient to explain the observed extent of reduction in diversity in regions of restricted recombination...

..A few dozen genes are known on the human Y chromosome. The completion of the human genome sequence will allow identification of the remaining loci, which should shed further light on the function and evolution of this peculiar chromosome...

..Finally, we review current understanding of the effect of metapopulation dynamics on the effective population size...

..We argue that inbreeding should be considered when interpreting patterns of molecular evolution...