Lanfear Robert, Bromham Lindell
Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton, UK.
Syst Biol. 2008 Oct;57(5):708-18. doi: 10.1080/10635150802430079.
The Hox genes encode transcription factors that play vital roles in the anterior-posterior patterning of all bilaterian phyla studied to date. Additionally, the gain of Hox genes by duplication has been widely implicated as a driving force in the evolution of animal body plans. Because of this, reconstructing the evolution of the Hox cluster has been the focus of intense research interest. It has been commonly assumed that an ancestral four-gene ProtoHox cluster was duplicated early in animal evolution to give rise to the Hox and ParaHox clusters. However, this hypothesis has recently been called into question, and a number of alternative hypotheses of Hox and ParaHox gene evolution have been proposed. Here, we present the first statistical comparisons of current hypotheses of Hox and ParaHox gene evolution. We use two statistical methods that represent two different approaches to the treatment of phylogenetic uncertainty. In the first method, we estimate the maximum-likelihood tree for each hypothesis and compare these trees to one another using a parametric bootstrapping approach. In the second method, we use Bayesian phylogenetics to estimate the posterior distribution of trees, then we calculate the support for each hypothesis from this distribution. The results of both methods are largely congruent. We find that we are able to reject five out of the eight current hypotheses of Hox and ParaHox gene evolution that we consider. We conclude that the ProtoHox cluster is likely to have contained either three or four genes but that there is insufficient phylogenetic signal in the homeodomains to distinguish between these alternatives.
Hox基因编码转录因子，在迄今为止研究的所有两侧对称动物门的前后模式形成中发挥着至关重要的作用。此外，通过基因复制产生的Hox基因的增加被广泛认为是动物身体结构进化的驱动力。因此，重建Hox基因簇的进化一直是深入研究的重点。人们通常认为，一个由四个基因组成的原始Hox基因簇在动物进化早期发生了复制，从而产生了Hox基因簇和ParaHox基因簇。然而，这一假设最近受到了质疑，并且已经提出了许多关于Hox和ParaHox基因进化的替代假设。在这里，我们首次对当前关于Hox和ParaHox基因进化的假设进行了统计比较。我们使用两种统计方法，它们代表了处理系统发育不确定性的两种不同方法。在第一种方法中，我们为每个假设估计最大似然树，并使用参数自展方法将这些树相互比较。在第二种方法中，我们使用贝叶斯系统发育学来估计树的后验分布，然后我们从这个分布中计算对每个假设的支持度。两种方法的结果在很大程度上是一致的。我们发现，在所考虑的当前关于Hox和ParaHox基因进化的八个假设中，我们能够否定其中五个。我们得出结论，原始Hox基因簇可能包含三个或四个基因，但同源结构域中的系统发育信号不足以区分这些可能性。
