Berlin Sofia, Quintela Maria, Höglund Jacob
Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
BMC Genet. 2008 Dec 19;9:89. doi: 10.1186/1471-2156-9-89.
There is so far very little data on autosomal nucleotide diversity in birds, except for data from the domesticated chicken and some passerines species. Estimates of nucleotide diversity reported so far in birds have been high (approximately 10(-3)) and a likely explanation for this is the generally higher effective population sizes compared to mammals. In this study, the level of nucleotide diversity has been examined in the willow grouse, a non-domesticated bird species from the order Galliformes, which also holds the chicken. The willow grouse (Lagopus lagopus) has an almost circumpolar distribution but is absent from Greenland and the north Atlantic islands. It primarily inhabits tundra, forest edge habitats and sub-alpine vegetation. Willow grouse are hunted throughout its range, and regionally it is a game bird of great cultural and economical importance.
We sequenced 18 autosomal protein coding loci from approximately 15-18 individuals per population. We found a total of 127 SNP's, which corresponds to 1 SNP every 51 bp. 26 SNP's were amino acid replacement substitutions. Total nucleotide diversity (pit) was between 1.30 x 10(-4) and 7.66 x 10(-3) (average pi(t) = 2.72 x 10(-3) +/- 2.06 x 10(-3)) and silent nucleotide diversity varied between 4.20 x 10(-4) and 2.76 x 10(-2) (average pi(S) = 9.22 x 10(-3) +/- 7.43 x 10(-4)). The synonymous diversity is approximately 20 times higher than in humans and two times higher than in chicken. Non-synonymous diversity was on average 18 times lower than the synonymous diversity and varied between 0 and 4.90 x 10(-3) (average pi(a) = 5.08 x 10(-4) +/- 7.43 x 10(3)), which suggest that purifying selection is strong in these genes. F(ST) values based on synonymous SNP's varied between -5.60 x 10(-4) and 0.20 among loci and revealed low levels of differentiation among the four localities, with an overall value of F(ST) = 0.03 (95% CI: 0.006 - 0.057) over 60 unlinked loci. Non-synonymous SNP's gave similar results. Low levels of linkage disequilibrium were observed within genes, with an average r2 = 0.084 +/- 0.110, which is expected for a large outbred population with no population differentiation. The mean per site per generation recombination parameter (rho) was comparably high (0.028 +/- 0.018), indicating high recombination rates in these genes.
We found unusually high levels of nucleotide diversity in the Scandinavian willow grouse as well as very little population structure among localities with up to 1647 km distance. There are also low levels of linkage disequilibrium within the genes and the population recombination rate is high, which is indicative of an old panmictic population, where recombination has had time to break up any haplotype blocks. The non-synonymous nucleotide diversity is low compared with the silent, which is in agreement with effective purifying selection, possibly due to the large effective population size.
到目前为止，除了来自家鸡和一些雀形目物种的数据外，关于鸟类常染色体核苷酸多样性的数据非常少。迄今为止报道的鸟类核苷酸多样性估计值较高（约为10^(-3)），对此可能的解释是与哺乳动物相比，鸟类的有效种群规模通常更大。在本研究中，对柳雷鸟（一种来自鸡形目的非家养鸟类，鸡也属于该目）的核苷酸多样性水平进行了检测。柳雷鸟（Lagopus lagopus）几乎分布于环北极地区，但在格陵兰岛和北大西洋岛屿没有分布。它主要栖息于苔原、森林边缘栖息地和亚高山植被中。柳雷鸟在其整个分布范围内都被猎杀，在一些地区它是具有重要文化和经济意义的猎禽。
我们对每个种群约15 - 18个个体的18个常染色体蛋白质编码基因座进行了测序。我们总共发现了127个单核苷酸多态性（SNP），即每51个碱基对中有1个SNP。26个SNP是氨基酸替换替换。总核苷酸多样性（πt）在1.30×10^(-4)至7.66×10^(-3)之间（平均πt = 2.72×10^(-3)±2.06×10^(-3)），沉默核苷酸多样性在4.20×10^(-4)至2.76×10^(-2)之间（平均πS = 9.22×10^(-3)±7.43×10^(-4)）。同义多样性比人类高约20倍，比鸡高两倍。非同义多样性平均比同义多样性低18倍，在0至4.90×10^(-3)之间变化（平均πa = 5.08×10^(-4)±7.43×10^(3)），这表明这些基因中纯化选择很强。基于同义SNP的F(ST)值在基因座之间在 - 5.60×10^(-4)至0.20之间变化，显示四个地点之间的分化水平较低，在60个不连锁基因座上的总体F(ST)值为0.03（95%置信区间：0.006 - 0.057）。非同义SNP给出了类似的结果。在基因内观察到低水平的连锁不平衡，平均r2 = 0.084±0.110，这对于一个没有种群分化的大型远交种群来说是预期的。每个位点每代的平均重组参数（ρ）相对较高（0.028±0.018），表明这些基因中的重组率很高。
我们发现斯堪的纳维亚柳雷鸟的核苷酸多样性水平异常高，并且在距离达1647公里的不同地点之间种群结构非常少。基因内也存在低水平的连锁不平衡，种群重组率很高，这表明是一个古老的随机交配种群，在其中重组有时间打破任何单倍型块。与沉默核苷酸多样性相比，非同义核苷酸多样性较低，这与有效的纯化选择一致，可能是由于有效种群规模较大。
