Kumar S, Gadagkar S R, Filipski A, Gu X
Department of Biology, Arizona State University, Tempe, Arizona 85287-1501, USA.
Genetics. 2001 Mar;157(3):1387-95. doi: 10.1093/genetics/157.3.1387.
Genomic divergence between species can be quantified in terms of the number of chromosomal rearrangements that have occurred in the respective genomes following their divergence from a common ancestor. These rearrangements disrupt the structural similarity between genomes, with each rearrangement producing additional, albeit shorter, conserved segments. Here we propose a simple statistical approach on the basis of the distribution of the number of markers in contiguous sets of autosomal markers (CSAMs) to estimate the number of conserved segments. CSAM identification requires information on the relative locations of orthologous markers in one genome and only the chromosome number on which each marker resides in the other genome. We propose a simple mathematical model that can account for the effect of the nonuniformity of the breakpoints and markers on the observed distribution of the number of markers in different conserved segments. Computer simulations show that the number of CSAMs increases linearly with the number of chromosomal rearrangements under a variety of conditions. Using the CSAM approach, the estimate of the number of conserved segments between human and mouse genomes is 529 +/- 84, with a mean conserved segment length of 2.8 cM. This length is <40% of that currently accepted for human and mouse genomes. This means that the mouse and human genomes have diverged at a rate of approximately 1.15 rearrangements per million years. By contrast, mouse and rat are diverging at a rate of only approximately 0.74 rearrangements per million years.
物种之间的基因组差异可以根据自它们从共同祖先分化以来各自基因组中发生的染色体重排数量来量化。这些重排破坏了基因组之间的结构相似性，每次重排都会产生额外的（尽管较短）保守片段。在此，我们基于常染色体标记连续集（CSAM）中标记数量的分布提出一种简单的统计方法，以估计保守片段的数量。CSAM识别需要一个基因组中直系同源标记的相对位置信息，以及另一个基因组中每个标记所在的染色体编号信息。我们提出一个简单的数学模型，该模型可以解释断点和标记的不均匀性对不同保守片段中标记数量的观察分布的影响。计算机模拟表明，在各种条件下，CSAM的数量随染色体重排数量呈线性增加。使用CSAM方法，人类和小鼠基因组之间保守片段数量的估计值为529±84，平均保守片段长度为2.8厘摩。这个长度不到目前人类和小鼠基因组公认长度的40%。这意味着小鼠和人类基因组的分化速率约为每百万年1.15次重排。相比之下，小鼠和大鼠的分化速率仅约为每百万年0.74次重排。
