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1.
  • Hans, Ellegren, et al. (författare)
  • Molecular evolutionary genomics of birds
  • 2007
  • Ingår i: Cytogenetic and Genome Research. - 1424-8581 .- 1424-859X. ; 117:1-4, s. 120-130
  • Forskningsöversikt (refereegranskat)abstract
    • Insight into the molecular evolution of birds has been offered by the steady accumulation of avian DNA sequence data, recently culminating in the first draft sequence of an avian genome, that of chicken. By studying avian molecular evolution we can learn about adaptations and phenotypic evolution in birds, and also gain an understanding of the similarities and differences between mammalian and avian genomes. In both these lineages, there is pronounced isochore structure with highly variable GC content. However, while mammalian isochores are decaying, they are maintained in the chicken lineage, which is consistent with a biased gene conversion model where the high and variable recombination rate of birds reinforces heterogeneity in GC. In Galliformes, GC is positively correlated with the rate of nucleotide substitution; the mean neutral mutation rate is 0.12-0.15% at each site per million years but this estimate comes with significant local variation in the rate of mutation. Comparative genomics reveals lower dN/dS ratios on micro- compared to macrochromosomes, possibly due to population genetic effects or a non-random distribution of genes with respect to chromosome size. A non-random genomic distribution is shown by genes with sex-biased expression, with male-biased genes over-represented and female-biased genes under-represented on the Z chromosome. A strong effect of selection is evident on the non-recombining W chromosome with high dN/dS ratios and limited polymorphism. Nucleotide diversity in chicken is estimated at 4-5 × 10-3 which might be seen as surprisingly high given presumed bottlenecks during domestication, but is lower than that recently observed in several natural populations of other species. Several important aspects of the molecular evolutionary process of birds remain to be understood and it can be anticipated that the upcoming genome sequence of a second bird species, the zebra finch, as well as the integration of data on gene expression, shall further advance our knowledge of avian evolution.
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4.
  • Backström, Niclas, et al. (författare)
  • Genetic mapping in a natural population of collared flycatchers (Ficedula albicollis) : Conserved synteny but gene order rearrangements on the avian Z chromosome
  • 2006
  • Ingår i: Genetics. - 0016-6731 .- 1943-2631. ; 174:1, s. 377-386
  • Tidskriftsartikel (refereegranskat)abstract
    • Data from completely sequenced genomes are likely to open the way for novel studies of the genetics of nonmodel organisms, in particular when it comes to the identification and analysis of genes responsible for traits that are under selection in natural populations. Here we use the draft sequence of the chicken genome as a starting point for linkage mapping in a wild bird species, the collared flycatcher-one of the most well-studied avian species in ecological and evolutionary research. A pedigree of 365 flycatchers was established and genotyped for single nucleotide polymorphisms in 23 genes selected from (and spread over most of) the chicken Z chromosome. All genes were also found to be located on the Z chromosome in the collared flycatcher, confirming conserved synteny at the level of gene content across distantly related avian lineages. This high degree of conservation mimics the situation seen for the mammalian X chromosome and may thus be a general feature in sex chromosome evolution, irrespective of whether there is male or female heterogamety. Alternatively, such unprecedented chromosomal conservation may be characteristic of most chromosomes in avian genome evolution. However, several internal rearrangements were observed, meaning that the transfer of map information from chicken to nonmodel bird species cannot always assume conserved gene orders. Interestingly, the rate of recombination on the Z chromosome of collared flycatchers was only similar to 50% that of chicken, challenging the widely held view that birds generally have high recombination rates.
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5.
  • Hansson, B, et al. (författare)
  • Avian genome evolution : insights from a linkage map of the blue tit (Cyanistes caeruleus)
  • 2010
  • Ingår i: Heredity. - : Macmillan. - 0018-067X .- 1365-2540. ; 104:1, s. 67-78
  • Tidskriftsartikel (refereegranskat)abstract
    • We provide a first-generation linkage map of the blue tit (Cyanistes caeruleus), a passerine within the previously genetically uncharacterized family Paridae, which includes 91 orthologous loci with a single anchored position in the chicken (Gallus gallus) sequence assembly. The map consists of 18 linkage groups and covers 935 cM. There was highly conserved synteny between blue tit and chicken with the exception of a split on chromosome 1, potential splits on chromosome 4 and the translocation of two markers from chromosome 2 and 3, respectively, to chromosome 5. Gene order was very well conserved for the majority of chromosomes, an exception being chromosome 1 where multiple rearrangements were detected. Similar results were obtained in a comparison to the zebra finch (Taeniopygia guttata) genome assembly. The recombination rate in females was slightly higher than in males, implying a moderate degree of heterochiasmy in the blue tit. The map distance of the blue tit was similar to 78% of that of the Wageningen chicken broiler population, and very similar to the Uppsala chicken mapping population, over homologous genome regions. Apart from providing insights into avian recombination and genome evolution, our blue tit linkage map forms a valuable genetic resource for ecological and evolutionary research in Paridae. Heredity (2010) 104, 67-78; doi:10.1038/hdy.2009.107; published online 26 August 2009
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