Transposable Elements May Be Extremely Helpful in Phylogenetics—But They’re Not Perfect

Transposable Elements May Be Extremely Helpful in Phylogenetics—But They’re Not Perfect

In the world of phylogenetics, where one is attempting to build an evolutionary tree for a set of species, there are certain elements in analysis that are considered “perfect”. These perfect elements are considered to be homoplasy free. That is, these elements have not evolved analogously. This is obviously helpful to phylogeneticists because it removes any unambiguity between species.

With that said, are transposable elements “perfect”? Han et al*. analyze the characteristics of transposable elements (TE) in avian genomes in order to find out. These TE are very rare yet accumulate rapidly enough for easy distinction between closely related species. In addition, the TE can have different orientations and types. For the most part, retrotransposons are the most common for TE analysis in phylogenetics.

Han et al. later go on to talk about how TE are, in fact, not completely free of homoplasy. There are two types of TEs: retrotransposons, which use a “copy-and-paste” mechanism, the second type uses “cut-and-paste”. And so they found there to be “hotspots” for transposable elements. These hotspots were found to be mutual through several avian genomes. Therefore, although, TE are distinct, they still lend themselves to homoplasy.

And so Han et al. found TE to be very useful as they are extremely prevalent in avian genomes and are distinct. However, they may not be the magical element that every phylogeneticist had hoped for. Still, further research into hotspots of TE may help us overcome the problem of homoplasy.  

_{*Han, et al. (2011) Are Transposable Element Insertions Homoplasy Free? An Examination Using the Avian Tree of Life. Systematic Biology 60: 1-12. doi: 10.1093/sysbio/sysq100.}