Addressing the problem of deep coalescence in ancient radiations: Resolving the explosive radiation of the Lophotrochozoa.

25年来，使用分子数据(基因和蛋白质序列)来解决生物之间的关系一直是一个主要的国际研究目标。我们对物种之间关系的了解的提高，已经从根本上影响了我们对生命多样性如何进化的理解。最近，由于来自所谓的下一代测序的大量分子数据，完成这个项目似乎是遥不可及的。尽管有现成的数据，但生命树的一些主要部分仍然被证明是不可能解决的。虽然这是一个影响许多不同生物群体的一般性问题，但我们将专注于解决动物王国中重要部分之间的关系。动物树最显著的特征之一是，在5亿多年前，组成主要类群(脊索动物、环节动物、节肢动物和软体动物等门)的主要类群在所谓的快速甚至爆炸性辐射中彼此分化的时间很短。快速辐射可能会导致两个问题。首先是缺乏系统发育信号，因为积累识别个体群体的基因变化的机会有限。第二个问题是不完全世系排序(ILS)或深层融合的潜伏问题。由于祖先物种的多态，基因序列可能不会在每个物种内全部结合，而是更早地导致基因树与实际物种树相分离。简而言之，ILS导致不同的基因告诉我们关于有机体关系的不同事情。最近解决这些问题的努力集中在汇编非常大的基因组数据集，这些数据集被连接成单个数据集，并作为单个超基因进行分析。这种方法掩盖了我们预期存在的基因之间的不一致性，并可能导致积极的误导性估计。为了解决动物系统发育的最后和最顽固的方面，我们必须使用设计来处理数据不一致的方法。在动物内部，我们将专门专注于解决Lophotrochozoa内的门之间的关系。这是三种古老的两侧对称的动物之一。Lophotrochozoa包含大约一半的动物门，包括扁虫、环节动物和软体动物。我们的最终目标是I。以Lophotrochozoa为例，更好地了解快速辐射所涉及的过程以及如何最好地解决这些过程。2.利用我们的认识重建钩虫动物门之间的系统发育关系。这些实际目标将导致系统发育框架，这是理解动物多样性的这一主要部分的进化的重要基础。我们的工作应该让我们深入了解在古老的爆炸性辐射期间的工作过程。这种辐射事件一再对生命的进化产生重大影响，这意味着开发解决这些问题的方法将具有广泛的用途。简单的问题已经解决，生命之树上的许多剩余的系统发育问题将涉及类似的快速辐射。

Using molecular data (sequences of genes and proteins) to resolve the relationships between living organisms has been a major international research goal for over 25 years. Our improved knowledge of the relationships between species has already radically affected our understanding of how the great diversity of life evolved. Recently, completing this project seemed in reach, thanks to plentiful molecular data from the so called next generation sequencing. Despite the ready availability of data, some major parts of the tree of life have nevertheless proved impossible to resolve.While this is a general problem affecting many different groups of organisms we will focus on resolving the relationships between a significant part portion of the animal kingdom. One of the most striking features of the animal tree is the short time frame over which the constituent major groups (phyla such as chordates, annelids, arthropods and molluscs) diverged from one another over half a billion years ago in so-called rapid, or even explosive radiations. Rapid radiations can cause two problems. First is a lack of phylogenetic signal due to the limited opportunity to accumulate genetic changes that identify individual groups. Second is the insidious problem of Incomplete Lineage Sorting (ILS) or deep coalescence. Due to polymorphism in the ancestral species, gene sequences may not all coalesce within each species but earlier causing gene-trees to diverge from the actual species-trees. Put more simply, ILS results in different genes telling us different things about the relationships of the organisms.Recent efforts to solve these problems focussed on compiling very large genomic datasets that were concatenated into a single data set and analysed as single supergenes. This approach masks the incongruence between genes we expect to exist and may lead to positively misleading estimates. To solve this final and most recalcitrant aspects of the animal phylogeny we must use methods designed to deal with data incongruence.Within the animals we will focus specifically on resolving the relationships between the phyla within the Lophotrochozoa. This is one of three ancient groups of bilaterally symmetrical animals. Lophotrochozoa contains approximately half of animal phyla including flatworms, annelids, and molluscs.Our ultimate goals are I. to use the example of the Lophotrochozoa to better understand the processes involved in rapid radiations and how best to resolve them. II. to use our understanding to reconstruct the phylogenetic relationships between the animal phyla in the Lophotrochozoa. These practical goals will result in the phylogenetic framework that is the essential foundation for understanding the evolution of this major portion of animal diversity. Our work should give us insight into the processes at work during an ancient, explosive radiation. Such radiation events have repeatedly had a major impact on the evolution of life meaning that developing methods to address such questions will be of broad use. The easy problems having been solved, many remaining phylogenetic questions across the tree of life will involve similar rapid radiations.