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

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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.