Phylogenomics and the Avian Tree of Life

地球上生物多样性的加速丧失和对生物多样性的保护需要依赖于根据生物的进化关系对生物进行稳定的分类。尽管鸟类是生态系统中引人注目的组成部分，在美学和经济上都有价值，但鸟类生命之树的基础仍未得到解决。这个问题的主要原因是，在6500万年前（Mya）的K/Pg灭绝事件发生后的一段时间里，主要群体经历了快速的辐射，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。我课题组计划利用逆转录子标记和低成本的下一代测序技术，快速组装27目鸟类135种100个基因的序列，解决鸟类目的分支顺序问题。这个前沿的研究项目也将使我们能够测试进化生物学中的以下主要假设：冠类鸟类的许多谱系是起源于白垩纪还是在K-Pg灭绝事件之后辐射出来的？现代鸟类的分布是由于大陆漂移还是大陆破碎后的分散？大型不会飞的扁齿鸟的惊人形态变化是由在飞禽中起作用的选择约束的放松引起的吗？形态表型的变异是否与蛋白质编码基因的突变或基因组中调控元件的增殖有关？不同鸟类群体的进化率差异是否与世代时间、代谢率或体型的差异有关？通过在高度确定的鸟类系统发育上绘制特征并使用比较方法，我们可以区分这些选择，并显着推进鸟类进化生物学的知识。该方案将为能够在大学或应用基因组中心或生物技术企业工作的高素质人员提供基因组应用于生态学和进化生物学方面的培训。这项研究在鸟类繁殖计划和保护方面有应用。

The accelerating loss of biodiversity on the planet and the need for the conservation depends on having a stable classification of living organisms based on their evolutionary relationships. Although birds are conspicuous components of ecosystems and are valued aesthetically and economically, the base of the avian tree of life remains unresolved. The major cause of this problem is that some time after the K/Pg extinction event 65million years ago (Mya) the major groups underwent rapid radiations that make it extremely difficult to reconstruct their branching order, and how they are related by shared common ancestry. My research group plans to use retroposon markers and cost-effective next generation sequencing to rapidly assemble sequences of 100 genes for 135 species in all 27 orders of birds to resolve the branching order of bird orders. This cutting edge research program will also allow us to test the following major hypotheses in evolutionary biology: did many lineages of crown-group birds originate in the Cretaceous or radiated after the K-Pg extinction event? Is the distribution of modern birds due to continental drift or dispersal well after continental fragmentation? Are the amazing morphological changes in the large flightless ratite birds caused by relaxation of selective constraints that operate in flying birds? Is variation in morphological phenotypes associated with mutations in protein-coding genes or proliferation of regulatory elements in genomes? Is variation in rates of evolution in different groups of birds associated with variation in generation time, metabolic rate or body size? By mapping characters on a highly resolved bird phylogeny and using comparative methods we can discriminate among these alternatives, and significantly advance knowledge of the evolutionary biology of birds. This programme will provide training in genomic applications to ecology and evolutionary biology for highly qualified personnel that can work in Universities or applied genome centres or biotechnology businesses. This research has applications in breeding programmes of birds and in conservation.