Evolutionists use transposable elements to infer common ancestry. Not so fast.


Bard summary:

The paper "Are Transposable Element Insertions Homoplasy Free?: An Examination Using the Avian Tree of Life" by Han et al. (2011) examines the hypothesis that transposable element (TE) insertions are homoplasy-free characters. Homoplasy is the independent evolution of similar traits in two or more lineages. TEs are mobile genetic elements that can insert themselves into the genome at random. They are thought to be a major source of genetic variation in organisms.

The authors of the paper analyzed the TE insertion patterns in 64 bird genomes. They found that TE insertions were not homoplasy-free. In fact, they found that TE insertions were more likely to be homoplastic than other types of genetic changes, such as single-nucleotide substitutions.

The authors of the paper suggest that the high rate of homoplasy in TE insertions is due to the fact that TEs are mobile genetic elements. They can move from one genome to another, which can lead to the independent evolution of similar TE insertion patterns in different lineages.

The findings of the paper have implications for the use of TE insertions in phylogenetics. TE insertions have been used in the past as a source of "perfect" characters, that is, characters that are not homoplastic. However, the findings of the paper suggest that TE insertions should not be used as a source of perfect characters.

The paper also has implications for our understanding of the evolution of birds. The high rate of homoplasy in TE insertions suggests that TEs have played a major role in the evolution of birds. TEs may have contributed to the diversification of birds by providing a source of genetic variation.

In conclusion, the paper "Are Transposable Element Insertions Homoplasy Free?: An Examination Using the Avian Tree of Life" by Han et al. (2011) provides evidence that TE insertions are not homoplasy-free characters. This finding has implications for the use of TE insertions in phylogenetics and our understanding of the evolution of birds.

Article snippets:

https://doi.org/10.1093/sysbio/syq100

In an attempt to find the true evolutionary tree of life, phylogeneticists have searched for “perfect” characters—those free of homoplasy

Rare genomic changes (RGCs) are infrequent mutations such as transposable element (TE) insertions

RGCs are candidates for perfect characters, as they are believed to exhibit little or no homoplasy for two reasons. First, they typically accumulate slowly, with some types of RGCs accumulating so slowly that they are useful for defining the deepest branches in the tree of life (

Despite the reasons to expect RGCs to be perfect homoplasy-free characters, many different RGCs can exhibit homoplasy

Even phylogenetic hypotheses based upon more than one TE insertion (e.g., Kriegs et al. 2006) can show conflict with large-scale studies of nucleotides or other RGCs

It is unclear how much of the conflict observed in published studies can be explained by conflicts among gene trees (hemiplasy) rather than homoplasy.

The argument that TE insertions exhibit little or no homoplasy is ultimately based upon assumptions about their biology

This mechanism has the potential to result in a bias toward specific insertion sites depending on the degree of endonuclease specificity, which appears to range from very strong (

Thus, predicting the probability that specific TE types will exhibit homplasy remains difficult, making it critical to evaluate this empirically.

Our results also suggest that TEs should not be viewed as perfect characters exempt from homoplasy

TE insertions present many of the same challenges for phylogenetic analyses as other types of data, such as nucleotide sequences.

Available statistical methods for the analysis of TEs assume that any apparent homoplasy is due to differences between gene trees and species trees

However, hemiplasy due to gene tree–species tree conflicts were not consistent with the homoplasy evident in our study


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