Ellegren H
Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
Cytogenet Genome Res. 2007;117(1-4):120-30. doi: 10.1159/000103172.
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 d(N)/d(S) 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 d(N)/d(S) ratios and limited polymorphism. Nucleotide diversity in chicken is estimated at 4-5 x 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.
鸟类DNA序列数据的不断积累为洞察鸟类的分子进化提供了依据，最近这一积累 culminating（可能是“达到高潮”之意，此处可根据上下文再确认准确意思）在鸟类基因组的首个草图序列，即鸡的基因组序列上。通过研究鸟类分子进化，我们可以了解鸟类的适应性和表型进化，还能理解哺乳动物和鸟类基因组之间的异同。在这两个谱系中，都存在明显的等容线结构，GC含量高度可变。然而，虽然哺乳动物的等容线正在衰退，但在鸡的谱系中它们得以维持，这与一个偏向性基因转换模型一致，即鸟类高且可变的重组率增强了GC的异质性。在鸡形目中，GC与核苷酸替换率呈正相关；平均中性突变率为每百万年每个位点0.12 - 0.15%，但这个估计值伴随着突变率显著的局部变化。比较基因组学显示，与宏观染色体相比，微观染色体上的d(N)/d(S)比率更低，这可能是由于群体遗传效应或基因相对于染色体大小的非随机分布。具有性别偏向性表达的基因呈现出非随机的基因组分布，Z染色体上雄性偏向性基因过度代表，而雌性偏向性基因代表不足。在不发生重组的W染色体上，选择的强烈作用很明显，其d(N)/d(S)比率高且多态性有限。鸡的核苷酸多样性估计为4 - 5×10(-3)，考虑到家养过程中可能存在的瓶颈，这一数值可能高得出奇，但低于最近在其他物种的几个自然种群中观察到的数值。鸟类分子进化过程的几个重要方面仍有待理解，可以预期即将公布的第二种鸟类——斑胸草雀的基因组序列，以及基因表达数据的整合，将进一步推动我们对鸟类进化的认识。
