Phylogenomic approaches to inferring ancient relationships amongst eukaryotes

In a letter to T.H. Huxley, Charles Darwin famously commented that: "The time will come, I believe, though I will not live to see it, when we shall have very nearly true genealogical trees of each great kingdom of nature...". It now seems possible that we will realize Darwin's dream within our lifetimes. Indeed, one of the most exciting long-standing problems in evolutionary biology has been to determine what exactly are the 'great kingdoms of nature'. In the last few decades, by applying molecular biology and genomic techniques to understanding the tree of Life we have found that kingdoms such as the animals, fungi and plants represent only a small corner of the diversity of Life. The deepest evolutionary divergences amongst nucleus-containing organisms (eukaryotes) involve a wide array of single-celled organismal lineages called 'protists'. However, the relationships amongst these ancient evolutionary lineages have, until recently, remained elusive. In this proposal we will use high-throughput DNA sequencing technology to characterize the expressed portion of the genomes of ten newly-described single celled organisms. By comparing these data to similar data from dozens of better characterized organisms representing the full breadth of biological diversity using sophisticated computational methods, we can delineate the super-kingdoms of Life. In so doing, we will clarify how and when some of the major 'transitions' in evolutionary history of Life took place on the ancient Earth.