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

目前地球上生物多样性的丧失和保护生命形式的必要性取决于根据生物体的进化关系对其进行稳定的分类。 虽然鸟类被认为是很好的分类学研究，鸟类生命树的基础仍然没有解决，尽管尝试与大的DNA和形态数据集。这个问题的原因是，在K/T灭绝事件65 Mya之后的一段时间，主要的分支经历了快速的辐射，这使得重建它们的分支顺序变得非常困难，以及它们如何通过共享共同祖先而联系起来。因此，不可能阐明鸟类的基本进化特性，如时间进化速率、谱系多样化和物种形成的克里思和模式、历史地理学、基因组大小的进化以及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更高层次的关系，并建立一个稳定的分类，其中进化的基本单位（物种）可以放在比较框架中进行研究。逆转录酶插入在解决哺乳动物生命树中激烈争论的更深层次分支方面已经证明是非常成功的，主要是因为可以扫描的完整基因组序列的数量，以获得遗传学信息插入。鸟类中只有鸡的基因组序列，这严重限制了逆转录酶在鸟类遗传学中的应用。利用我的实验室开创的逆转录酶富集和基因组行走的创新新技术，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，我们已经检测到并使用独特的逆转录酶插入来解决基底古颚鸟类（平胸和tinamous）中的困难关系，从而提供了概念验证。因此，我们建议使用独特的插入来解决在整个鸟类生命树的基础上有问题的分支模式，因为它们几乎是系统发育关系的无错误标记。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.