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

点击翻译按钮获取中文摘要

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.