H Ellegren

..Levels of linkage disequilibrium (LD) were significantly higher in regions of low recombination, showing that heterogeneity in recombination rates have left a footprint on the genomic landscape of LD in zebra finch populations...

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..Moreover, recombination might itself be mutagenic and thereby assert a direct effect on diversity levels...

..In order to develop a framework for the analysis of sex-biased genes, we present a characterization of microarray data comparing male and female gene expression in 18 day chicken embryos for brain, gonad, and heart tissue...

..We introduce the use of short insertion-deletion polymorphisms (indels) for genetic analysis of natural populations...

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..Finally, genome sequencing using outbred or multiple individuals has provided a wealth of polymorphism data that gives information on population history, demography and marker evolution...

..These observations suggest that the progressive restriction of recombination is an integral feature of sex chromosome evolution and occurs also in systems of female heterogamety...

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..This would suggest that replication errors play a major role for the generation of new mutations...

..The unusual sex chromosomes of platypus are not homologous to the human X and Y chromosomes, implying that the sex chromosomes of placental mammals evolved after the monotreme and placental mammal lineages split about 165 million years ago...

..This points at a genomic 'large-Z effect', which is widespread and of general significance for adaptive divergence in birds...

..In parallel, an emerging understanding of the quantitative genetics of fitness variation in the wild means that we are poised to see a synthesis of ecological and molecular approaches in evolutionary biology...

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..This suggests that birds' small genomes are not an adaptation to metabolic demands associated with flight...

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..Sex-biased gene expression has implications beyond just evolutionary biology, including for medical genetics...

..While otherwise widespread in systems with heteromorphic sex chromosomes, the case of dosage compensation in birds (males ZZ, females ZW) remains an unsolved enigma...

..Using this new technology, the protein-coding sequences of the Glanville fritillary butterfly genome have now been largely characterized...

..An important aspect for further research in this area is to study whether there is an ultimate evolutionary explanation for mutation rate variation within mammalian genomes...

..Genetically male chicken embryos, which have two Z sex chromosomes, develop female gonads when the Z chromosome-linked gene DMRT1 is knocked out. This suggests that sex is determined by Z chromosome dosage...

..Clearly defining the roles of the DMRT1 and PKC1W genes in gonadal development, and ultimately determining whether avian sex is dependent on Z or W, will require transgenic experiments...

..A recent study in BMC Evolutionary Biology shows that variation in the rate of mutation rather than in population size is the main explanation for variations in mtDNA diversity observed among bird species...

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..Within genomes at equilibrium, the microsatellite-length distribution is a delicate balance between biased mutation processes and point mutations acting towards the decay of repetitive DNA. Indeed, simple repeats do not evolve simply...

..A recently identified hypermethylated region on the Z chromosome, with similarities to the X inactivation centre on the mammalian X chromosome, might play a part in this process or have a role in avian sex determination...

..Therefore, I discuss how patterns and processes associated with sex linkage in male- and female-heterogametic systems offer a useful contrast in the study of sex-chromosome evolution...

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..Our data demonstrate that this process, once initiated, may occur independently in parallel in sister lineages...

..This is consistent with theoretical models on the evolution of sexually antagonistic genes in which new mutations are at least partly dominant...

..However, genetic variation at nuclear markers is partitioned among horse breeds and may reflect sex-biased dispersal and breeding...

..9-6.5. Thus, evolution appears to be male driven in birds--a situation that supports a neutral model of molecular evolution...

..After the last glaciation period, pied and collared flycatchers expanded their breeding ranges and eventually came into secondary contact in Central and Eastern Europe and on the Baltic Isles...

..This demonstrates a lower exchange of males than of females between breeds belonging to different groups, which illustrates how breed founders may have been chosen...

..Our data are compatible with a male-biased mutation rate, manifested by the faster rate of neutral evolution (synonymous substitutions) on the Z chromosome than on the female-specific W chromosome...

..Furthermore, the ability to amplify extremely small fragments makes SNPs of particular use for population monitoring, where faecal and other noninvasive samples are routinely used...

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..Even in these larger populations, bottlenecks and fragmentation with consequent genetic drift are likely to have resulted in few indicators for balancing selection and significant differentiation of populations...

..Our data suggest that progressive and stepwise cessation of recombination is a general feature behind sex chromosome evolution...

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..After 1940, however, there is evidence of several immigration events, coinciding with episodes of marked population increase in Russian Karelia and subsequent westwards migration...

..An excess of paternally transmitted mutations (male-to-female ratio of 4.9) supports a male-biased mutation rate in the human genome...

..The two Scandinavian Y chromosome haplotypes were not found elsewhere in northern Europe, which indicates low male gene flow between Scandinavia and the neighbouring countries...

..The observed subdivision between populations calls for management caution when issuing harvest quotas, especially for the geographically isolated south Norwegian population...

..The assignment of IL1RN permitted analysis of gene order conservation between HSA2 and ECA15, which identified that an event of inversion had occurred during the evolution of these two homologous chromosomes...

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..This suggests that researchers should consider using resequencing-based approaches for assessing genetic diversity when accurate inference is critical, as in many conservation and management contexts...

..This study does therefore not provide support the idea that sex chromosome rearrangements have caused the relatively strong post-zygotic reproductive isolation between these two Ficedula species...

..Natural selection has eliminated about 75% of amino acid changes in coding sequence since the split of the human and chimpanzee genomes...

..The degree of genome stability is likely to have important consequences for general evolutionary patterns and may explain, for example, the comparatively slow rate by which genetic incompatibility among lineages of birds evolves...

..The results suggest that an interaction between increased mutability at CpG motifs and fixation biases due to BGC could explain increased levels of divergence in GC-rich regions...

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..This result suggests that there is a high rate of turnover of functional noncoding elements in the mammalian genome, so measures of functional constraint based on human-mouse comparisons may seriously underestimate the true value...

..Our results indicate that inheritance of mtDNA is free of detectable recombination effects over an evolutionary timescale...

..Instead, they may provide a common mechanism for rapid adaptive changes during speciation, particularly in cases that present strong selective pressures on behavioral characters...

..Reduced variability in female-specific W chromosomes is not easily explained by sexual selection...

..094) are significantly lower than those of macrochromosomes (average, 0.185; P = 0.025), suggesting that the proteins of genes on microchromosomes are under greater evolutionary constraint...

..The correlation between indel and SNP density indicates common effects of mutation and/or selection on the occurrence of indels and point mutations...

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..5). We also note that sexual selection for a male-biased trait is facilitated by Z-linkage, because sons in organisms with female heterogamety will always inherit a Z chromosome from their fathers...

..Interestingly, the rate of recombination on the Z chromosome of collared flycatchers was only approximately 50% that of chicken, challenging the widely held view that birds generally have high recombination rates...

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..Rather than originating from a few geographical areas only, as indicated by mtDNA, our data suggest that the origin of domestic cattle may be far more complex than previously thought...

..Since inbreeding depression has been documented in a captive grey wolf population of Scandinavian origin, the results point out an additional risk for the small Swedish wild population...

..Together with differences in variability, this suggests that the refugia history and/or expansion patterns of E. concolor and E. europaeus differ...

..68, p = 0.04). Our results suggest the importance of using extensive data sets from several genomic regions to avoid the effects of regional mutation rate variation and to ensure accurate estimates of alpha(m)...

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..However, the absence of a clear male age effect is at odds with the idea of an increasing male mutation rate with age, which is thought to arise from the continuous replication of germline cells throughout adulthood...

..Overall, these results highlight the link between the effective population size and positive as well as negative selection...

..Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms...

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..We also found a wild ox haplotype in the Iberian Bronze Age sample, reflecting local hybridization or backcrossing or that aurochs were hunted by these farming cultures...

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..Furthermore, an extensive region of nucleotide sequence shared between DRB1 and DQB alleles and a shared motif suggests intergenic recombination may have contributed to MHC diversity in the Canidae...

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..These observations have important consequences for understanding the molecular mechanisms of microsatellite mutation and for the development of improved measures of genetic distance...

..We conclude that deleterious mutations are accumulating at a high rate on the avian W chromosome, probably as a result of the lack of recombination in this female-specific chromosome...

..This indicates that in addition to sexual dimorphism in recombination rates, the sexes also differ in the relative rates of crossover and gene conversion...

..We thus conclude that the use of claws from tanned hides offers new possibilities to genetic studies of preserved mammalian specimens, for instance, in the monitoring of illegal trade...

..In one case, a significant difference in alpha(m) between two clades was shown to be due to W-linked rates and not Z-linked rates, a result that suggests that mutation rates are not determined by replication alone...

..We conclude that it is unlikely that mitochondrial recombination has large effects on mitochondrial genetic variability in birds...

..These results support the view that, contrary to common assumption, domestic and wild lineages might not have been clearly separated throughout their history...

..These results suggest that the resolution of sexually antagonistic gene expression is determined by the evolutionary constraints acting on any given antagonistic locus...

..We discuss how identification of the genes underlying the three major sources of reproductive isolation can be used to draw conclusions about links between the processes driving their evolution...

..The microsatellite markers are located on nine different horse chromosomes, four of which (ECA6, ECA25, ECA27 and ECA28) had no previously in situ assigned markers...

..4:1 but this parameter varied between chromosomes as well as between regions within chromosomes. An intriguing finding was that blood group loci were overrepresented at the distal ends of linkage groups...

..This finding confirms that inter-specific hybridization between wolves and dogs can occur in natural wolf populations. A possible correlation between hybridization and wolf population density and disturbance deserves further research...

..In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases...

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..Thus, microsatellite mutation and evolution may be viewed as a dynamic and variable process...

..47 and approximate 95% confidence intervals of 2.27 to 2.68. Our data are broadly consistent with the idea that mutation-rate differences between chromosomal classes can be explained by the male mutation bias alone...

..A significant excess of deletion compared to insertion events is observed on the avian W chromosome, consistent with gradual DNA loss on a nonrecombining chromosome...

..We also show that noncoding substitution rates are significantly affected by G+C base composition, partly because the base composition is not at equilibrium...

..Our results imply that even rare interpopulation migration can lead to the rescue and recovery of isolated and endangered natural populations...

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..The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture...