Resolving the avian tree of life for comparative studies in ecology and evolution

当前地球上生物多样性的丧失和保护生命形式的需要取决于根据生物的进化关系对生物进行稳定的分类。尽管鸟类被认为在分类学上得到了很好的研究，但尽管尝试了大量的DNA和形态学数据集，鸟类生命树的基础仍然没有得到解决。造成这个问题的原因是，在65亿年前的K/T灭绝事件之后的一段时间里，主要的进化枝经历了快速的辐射，这使得重建它们的分支顺序以及它们是如何通过共同的祖先联系在一起变得极其困难。因此，不可能阐明鸟类的基本进化特性，如随时间的进化速度、谱系多样化和物种形成的速度和模式、历史生物地理学、基因组大小的进化、生态学和进化生物学。需要一种全新的方法来解决鸟类目和科之间的高级关系，并创建一个稳定的分类，在这个分类中，进化的基本单位（物种）可以被放置和研究在一个比较的框架中。反转录子插入在解决哺乳动物生命树中激烈争论的深层分支方面取得了惊人的成功，这主要是因为可以扫描完整基因组序列以获取系统发育信息插入。只有鸡基因组序列在鸟类中可用，严重限制了逆转录子在鸟类系统发育中的应用。利用我实验室首创的逆转录子富集和基因组行走的创新技术，我们已经克服了鸟类的这一困难，而不必求助于昂贵的基因组测序。在过去的18个月里，我们已经检测并使用了独特的逆转录子插入来解决基础古生代鸟类（率鸟和线鸟）的困难关系，从而提供了概念证明。因此，我们建议使用独特的插入来解决整个鸟类生命树基础上的分支模式问题，因为它们几乎是无差错的系统发育关系标记。这不仅将是世界上第一次，而且将使鸟类的比较进化研究与它们的保护高度相关。

The current loss of biodiversity on the planet and the need for conservation of life forms depends on having a stable classification of living organisms based on their evolutionary relationships. Although birds are thought to be well studied taxonomically, the base of the avian tree of life remains unresolved despite attempts with large DNA and morphological data sets. The cause of this problem is that some time after the K/T extinction event 65 Mya the major clades underwent rapid radiations that make it extremely difficult to reconstruct their branching order, and how they are related by shared common ancestry. Thus it is impossible to elucidate fundamental evolutionary properties of birds such as rates of evolution through time, tempo and mode of lineage diversification and speciation, historical biogeography, evolution of genome size, and ecology and evolutionary biology. A completely new approach is called for to resolve higher relationships among orders and families of birds, and create a stable classification in which the basic units of evolution (species) can be placed and studied in a comparative framework. Retroposon insertions have proved spectacularly successful in resolving the hotly debated deeper branches in the mammal tree of life, mostly because of the number of complete genome sequences that can be scanned for phylogenetically informative insertions. Only the chicken genome sequence is available in birds, severely limiting the application of retroposons in bird phylogeny. Using an innovative new technique of retroposon enrichment and genome walking pioneered in my laboratory we have overcome this difficulty in birds without having to resort to prohibitively expensive genome sequencing. In the past 18 months we have detected and used unique retroposon insertions to resolve difficult relationships in the basal paleognath birds (ratites and tinamous) thus providing proof-of-concept. We therefore propose to resolve the problematic branching pattern at the base of the entire bird tree of life using unique insertions because they are almost error-free markers of phylogenetic relationships. Not only will this be a world first but it will enable comparative evolutionary studies of birds highly relevant to their conservation.