An introduction to the concepts and methods required to successfully apply genome ecology to real genome data
This thesis is an investigation of the concepts and tools required for the successful application of genome ecology on real genomic transposable element (TE) data. Beginning with the formation of an interdisciplinary working group to examine the distinction between ecology and evolution within genome ecology. By establishing these definitions it was possible to account for the relative effect of proxies for these processes in explaining the variation with the TE communities in a group of genomes. This resulted in the finding that ecological processes were could only explain variation in closely related groups of genomes. Thus ecological methods, developed for examining species distributions along a linear transect, were used to analyze the 30 B.taurus chromosomes. This resulted in the identification of 8 TE species responsible for explaining the spatial distribution in the B.taurus chromosomes. This successful application of ecological methods on TE data promises to inspire many other promising interdisciplinary studies.