Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany.
Mol Ecol. 2010 Mar;19 Suppl 1(Suppl 1):277-84. doi: 10.1111/j.1365-294X.2009.04482.x.
Improvements in sequencing technology over the past 5 years are leading to routine application of shotgun sequencing in the fields of ecology and evolution. However, the theory to estimate evolutionary parameters from these data is still being worked out. Here we present an extension and implementation of part of this theory, mlRho. This program can efficiently compute the following three maximum likelihood estimators based on shotgun sequence data obtained from single diploid individuals: the population mutation rate (4N(e)mu), the sequencing error rate, and the population recombination rate (4N(e)c). We demonstrate the accuracy of mlRho by applying it to simulated data sets. In addition, we analyse the genomes of the sea squirt Ciona intestinalis and the water flea Daphnia pulex. Ciona intestinalis is an obligate outcrosser, while D. pulex is a cyclic parthenogen, and we discuss how these contrasting life histories are reflected in our parameter estimates. The program mlRho is freely available from http://guanine.evolbio.mpg.de/mlRho.
在过去的 5 年中，测序技术的改进使得鸟枪法测序在生态学和进化领域得到了常规应用。然而，从这些数据中估计进化参数的理论仍在研究中。在这里，我们介绍了该理论的一个扩展和实现，即 mlRho。该程序可以有效地基于从单个二倍体个体获得的鸟枪法序列数据计算以下三个最大似然估计值：种群突变率（4N(e)mu）、测序错误率和种群重组率（4N(e)c）。我们通过将其应用于模拟数据集来证明 mlRho 的准确性。此外，我们还分析了海鞘 Ciona intestinalis 和水蚤 Daphnia pulex 的基因组。Ciona intestinalis 是一种强制性异交者，而 D. pulex 是一种周期性的孤雌生殖者，我们讨论了这些截然不同的生活史如何反映在我们的参数估计中。程序 mlRho 可从 http://guanine.evolbio.mpg.de/mlRho 免费获得。
