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.}

Phylogenetic Analysis May be Misleading Due to Compositional Bias

Phylogenetic Analysis May be Misleading Due to Compositional Bias

In this paper, Foster et al* looked at DNA composition bias and how it adversely affects phylogenetic analysis. That is, phylogenetic analysis produces false results by grouping unrelated taxa. This has been shown to be the result of compositional bias i.e. AT/GC-rich components of the genome. With these biases, it is clear how errors would occur in phylogenetic analysis—they are being grouped together based on biased areas of the genome. For example, the nematode and honeybee were grouped together even though they are obviously biologically unrelated. They also mention how bias in the DNA can affect protein bias.

In their experiment, Foster et al performed phylogenetic analyses of the protein coding sequences from the mitochondria. The specie’s genes selected for analysis were known to have varying amounts of both DNA and amino acid composition bias and therefore, they are ideal for observation of the effect(s) of compositional bias.

Results revealed incorrect grouping of taxa with large compositional bias. Compositional bias couldn’t be the only factor, however, as the fruit fly is biologically more closely related to the honeybee than is the nematode and is slightly more AT-rich than the nematode. Foster et al speculate that this is due to strong amino acid bias—these are elements, which evolved independently and in a similar position in the genome.

In conclusion, Foster et al have shown that compositional bias can take away from the integrity of phylogenetic analysis. With this, we should keep in mind that we should be cautious when interpreting phylogenetic results. It is important to predetermine any compositional biases in your samples.

*^{Foster PG, Hickey DA (1999) Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. Journal of Molecular Evolution 48: 283–290. doi: 10.1007/pl00006471.}