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需要取决于根据生物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和形态数据集，鸟类生命树的基础仍然没有得到解决。这个问题的原因是，在K/T灭绝事件65Mya之后的一段时间里，主要支系经历了快速的辐射，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方式、历史生物地理学、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关系，并创建一个稳定的分类，其中可以将进化的基本单位(物种)置于比较框架中并进行研究。事实证明，逆转录酶插入在解决哺乳动物生命树中备受争议的更深层次分支方面取得了惊人的成功，这主要是因为可以扫描大量完整的基因组序列，以寻找具有系统发育信息的插入。只有鸡的基因组序列在鸟类中是可用的，这严重限制了逆转录病毒在鸟类系统发育中的应用。使用我的实验室首创的一种创新的逆转录病毒浓缩和基因组行走的新技术，我们已经在鸟类身上克服了这一困难，而不必求助于昂贵得令人望而却步的基因组测序。在过去的18个月里，我们检测到并使用了独特的后位基因插入来解决基础古纳特鸟(有性关系和有性关系)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整个鸟类生命树底部的有问题的分枝模式，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，而且将使对与鸟类保护高度相关的鸟类的比较进化研究成为可能。

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.