D Charlesworth

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

..Theoretical models predict how such populations are expected to differ from outcrossed populations, and DNA sequence data are being collected and used to test the predictions...

..Theories for Y chromosome degeneration are reviewed in the light of recent results from genes on plant sex chromosomes...

..After discussing how the conclusions are affected by some of the many relevant ecological factors, I relate these theoretical ideas to empirical data from some of the many recent breeding system studies in plant populations...

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..DNA sequence data are now starting to become available from suitable plant and animal populations, to measure and compare variability levels and test predictions...

..Patterns of linkage disequilibrium in our SRK sequences do not support the conclusion that recombination occurs, which was suggested from previous analyses based on Brassica SLG sequences...

..This suggests that the high polymorphism in these regions of incompatibility loci is due to balancing selection acting on sites within or near these regions, combined with low selective constraints...

..This suggests maintenance of entire S-haplotypes for long evolutionary times and extreme recombination suppression in the region...

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..thaliana. However, it is difficult to be sure of the time when the selfing habit evolved in the lineage that led to A. thaliana...

..It now seems that this has also happened in honeybees, where the sex-determining gene has now been shown to be a duplicate of another Hymenopteran sex-determining gene...

..Classical genetic studies and modern molecular evolutionary approaches now suggest that inbreeding depression and heterosis are predominantly caused by the presence of recessive deleterious mutations in populations...

..The effect of inbreeding on allozyme diversity is consistently larger than has been estimated from comparisons of unrelated species...

..The results therefore suggest that the Adh-3 locus may have arisen via an mRNA intermediate but, despite loss of the introns, is expressed...

..The results from population 3 are quite similar, though there was no evidence in this population for an unrestored sterility cytoplasm. A similar joint nucleocytoplasmic model with multiple restorers fits data from Thymus vulgaris...

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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...

..Genetic characterisation of a mimicry polymorphism in a butterfly reveals the expected suppression of recombination among its components, preventing the production of unfit character combinations...

..dioica, so it is not simple to test for selective sweeps. We also discuss the possibility that Y-linked diversity is reduced due to highly variable male reproductive success, and we conclude that this explanation is unlikely...

..Thus, all four Y-linked genes that have now been studied in these plants (the two studied here, and two previously studied genes, have low diversity). This supports other evidence for an ongoing degeneration process in these species...

..The homology between the active X-linked locus and the degenerate Y-linked locus supports a common ancestry for these two loci...

..Variability in these sequences follows the pattern of conserved and hypervariable regions seen in other S-RNases, but no regions have higher replacement than silent diversity, unlike the results in some other species...

..thaliana. Our data rule out balancing selection in the pericentromeric regions, suggesting that hitchhiking is more strongly reducing diversity in the chromosome arms than the pericentromere regions...

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

..In contrast, insertions on the Y chromosomes were present at high frequencies. Their potential contribution to Y degeneration is discussed...

..Finally, clusters of linkage disequilibrium within the SLG gene suggest that hypervariable regions are under balancing selection, and are not merely regions of relaxed selective constraint...

..Our estimated recombination in this region, from fitting a model of the effects of S-allele polymorphism on linked neutral sites, supports the hypothesis of locally suppressed recombination around the S-locus...

..Given the two species' large DNA content difference, the similarity of map lengths, particularly for LG1, suggests that crossing-over is more frequent across comparable physical distances in the inbreeder, A. thaliana, as predicted...

..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...

..The age of the haplotypes and the results of Kelly's Z(nS) and Wall's B and Q tests with recombination suggest that the haplotypes are maintained due to balancing selection at or near this locus...

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

..Future deletion mapping work should ensure that markers are studied in the parents of deletion mutants and should probably include additional deletions that were not ascertained by causing mutant sex phenotypes...

..However, SlX9 has higher diversity than other genes on the S. latifolia X chromosome. We evaluate the hypothesis of introgression from the closely related species S. dioica as an explanation for the high sequence diversity observed...

..Using a sample of 52 genes, based on two measures of codon usage (ENC and GC3 content), we show that cyc and fil1 are among the least biased Antirrhinum genes, so that their low diversity is not due to extreme codon bias...

..Repeated gene duplication and loss of elements in the Adh gene family is likely in these lineages, making it impossible to determine orthology of the Adh genes...

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..Overall, the results suggest that recombination rarely occurs in the interval between the S-loci and Aly8 and that linkage to the S-loci can probably account for the observed high Aly8 diversity...

..There were significantly fewer recombination events in the closer than the more distant region, supporting the above prediction, but showing that the low recombination region is very limited in size...

..These results suggest that, as for human XY-linked genes, the sex-linked plant loci ceased recombining at different times and reveal distinct events in the evolutionary history of the sex chromosomes...

..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...

..lyrata endosperm but no evidence for adaptive evolution in the coding region, whereas the 5' flanking region displays high diversity, with distinct haplotypes, suggesting balancing selection in the promoter region...

..Plant self-incompatibility is controlled by different genes for the recognition reactions of pollen and stigmas, yet correct association of the two genes have been maintained in two Brassica species...

..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...

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

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..thaliana chromosomes. However, we cannot tell whether genes were lost along with these centromeres, because such genes are absent from the A. thaliana genome, which is the sole source of markers for our mapping...

..2-0.6 per generation...

..We can now conclude that the divergence value is saturated, confirming the cessation of X-Y recombination in the evolution of the sex chromosomes at approximately 10-20 MYA...

..halleri ssp. halleri. In A. lyrata ssp. lyrata there is some evidence for recent rapid spread of pAge2 variants, suggesting selection favoring these sequences...

..In contrast, HTR12A has low diversity, but many variants are amino acid replacements, possibly due to independent selective sweeps within populations of the species...

..briggsae into northern latitudes. We discuss these findings in relation to their implications for selection, demographic history, and the persistence of self-fertilization...

..diclinis and S. latifolia/S. dioica. Diversity at Slcyt is extremely low (pi(syn) = 0.16%), and we find an excess of high frequency-derived variants and a negative Tajima's D, suggesting that the translocation was driven by selection...

..Complex population histories in both A. thaliana and A. lyrata complicate theoretical predictions and empirical tests of the effects of inbreeding on polymorphism and molecular evolution...

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

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

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..This region is nevertheless a small part of the papaya genome compared with other male-specific genome regions, such as mammalian Y chromosomes...

..This will be especially important if self-fertilization evolved recently in C. elegans history, because most of the evolutionary time separating C. elegans from its known relatives would have occurred in a state of obligate outcrossing...

..In some genera, polyploidy causes failure of self-incompatibility, and dioecy may then evolve...

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..Our results suggest that the acquisition of autosomal genes is an important event in the evolution of plant Y chromosomes...

..thaliana, at least for some period after their split. In addition, the coalescence times of sequences of individual S-haplogroups are expected to be less than those of alleles at non-S-loci...

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..lyrata populations is not related to recombination rate, including genic recombination hotspots, and low gene density in the low recombination rate region...

..We show that among various life-history traits, mating systems have the greatest influence on patterns of polymorphism...

..Cytological analysis of meiotic X-Y pairing in one of the male-sterile mutants indicates that the Y carries sequences or functions specifically affecting sex chromosome pairing...

..Arabidopsis lyrata, a self-incompatible, perennial species with a circumpolar distribution, is an excellent model system in which to study the roles of demographic history and local adaptation in patterning genetic variation...

..We detect signs of degeneration in most of the Y-linked gene sequences analyzed, similar to those of animal Y-linked and neo-Y chromosome genes...

..It is thus probably caused by a difference in per-replication mutation rates between the sex chromosomes. This suggests that the local mutation rate can change in a relatively short evolutionary time...