Are transposon insertions really homoplasy-free phylogenetic markers? Pretty much

Retrotransposons are highly abundant mobile genetic elements that can copy and insert themselves randomly (more or less) across the genome. Because it’s very unlikely that a transposon would insert itself into the same exact position independently in multiple lineages, TE insertions have long been considered to be “homoplasy-free” markers that can be reliably used to identify monophyletic groups.

But is this really true?

A new study in Systematic Biology looks at millions of primate TE insertions and finds that, technically speaking, transpososons are not completely free of homoplasy. However, the incidence of homoplasy is so low that TEs are still highly reliable markers.

I don’t have access to the full paper at the moment, but here’s the abstract:

How reliable are the presence/absence insertion patterns of the supposedly homoplasy-free retrotransposons, which were randomly inserted in the quasi infinite genomic space? To systematically examine this question in an up-to-date, multigenome comparison, we screened millions of primate transposed Alu SINE elements for incidences of homoplasious precise insertions and deletions. In genome-wide analyses, we identified and manually verified nine cases of precise parallel Alu insertions of apparently identical elements at orthologous positions in two ape lineages and twelve incidences of precise deletions of previously established SINEs. Correspondingly, eight precise parallel insertions and no exact deletions were detected in a comparison of lemuriform primate and human insertions spanning the range of primate diversity. With an overall frequency of homoplasious Alu insertions of only 0.01% (for human–chimpanzee–rhesus macaque) and 0.02–0.04% (for human–bushbaby–lemurs) and precise Alu deletions of 0.001–0.002% (for human–chimpanzee–rhesus macaque), real homoplasy is not considered to be a quantitatively relevant source of evolutionary noise. Thus, presence/absence patterns of Alu retrotransposons and, presumably, all LINE1-mobilized elements represent indeed the virtually homoplasy-free markers they are considered to be. Therefore, ancestral incomplete lineage sorting and hybridization remain the only serious sources of conflicting presence/absence patterns of retrotransposon insertions, and as such are detectable and quantifiable.

This means that retrotransposon insertions can be used to independently validate existing phylogenetic hypotheses. That’s not exactly news, but it’s good to have this kind of large-scale confirmation.


Here’s a link to the paper:


Hah, thanks. Knew I forgot something! :smile:

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How can it be homeplasy free? What about ILS?

That was my first thought too, but I’ve having issues getting the full text of the paper, so I may have to read it tomorrow when I’m connected to the university network.


That’s still an issue, but it’s one that can be modeled.

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Therefore, ancestral incomplete lineage sorting and hybridization remain the only serious sources of conflicting presence/absence patterns of retrotransposon insertions, and as such are detectable and quantifiable.

I’d be curious to see the homoplasy between humans and the great apes as a control. I note that they did not do, for example, human-chimp-gorilla or human-chip-orangotan.

Possibly it’s already been done before? Like @evograd, I won’t have access to the paper until tomorrow. I’ll read it then.

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ILS is not homoplasy. The character is still shared because of shared inheritance from a single ancestor; it’s just that the pattern of inheritance for the trait doesn’t match that of the organism. It has been proposed that “hemiplasy” be used to describe ILS.


I got access to the full text. Really nice paper, I found this part especially interesting:

Interestingly, in the human-bushbaby-lemur comparison no clear cases of precise
deletions were detected. There might be two explanations that are not mutually exclusive.
One, the time between HBL speciation events was long enough (~12 myr, dos Reis et al. 2018) to accumulate mutations in TSD sequences, making them unsuitable for illegitimate
recombination. Two, because there was only a relatively short internode before the first
primate diversification (~8 myr, dos Reis et al. 2018), the number of Alu insertions was too
low for the occurrence of such rare events as precise deletions.


Also try Han, K.-L., E.L. Braun, R.T. Kimball, S. Reddy, R.C.K. Bowie, M.J. Braun, J.L. Chojnowski, S.J. Hackett, J. Harshman, C.J. Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore, F.H. Sheldon, D.W. Steadman, C.C. Witt, and T. Yuri. 2011. Are transposable element insertions homoplasy free?: An examination using the avian tree of life. Systematic Biology , 60: 375-386.

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The authors mention that paper in this paper:

During past usage of retrotransposons as phylogenetic markers, they acquired a gradient
of assessments, including “SINEs of the perfect character” (Hillis et al. 1999), “SINEs of a
nearly perfect character” (Ray et al. 2006), and “Are transposable element insertions
homoplasy free?” (Han et al. 2011). In the last study, the authors concluded that “no” they are
not. However, it should be mentioned that they examined an inadequate test group, notorious
for its impenetrable jungle of ILS-infiltrated short internodes, namely birds. It was shown in
neoavian birds that the polymorphic hemiplasious state of characters persists over extremely
long evolutionary periods (Suh et al. 2015) and renders this group unsuitable as an ILS-free
reference group to access potential homoplasy. Furthermore, the authors examined precise
deletions of CR1 elements, which lack the minimal criteria for the described mechanism of
illegitimate recombination via 10-20-nt TSDs. CR1 elements are known to have no or only
very short 4-6-nt TSDs (Ichiyanagi and Okada 2008) that are too short for recombination (van
de Lagemaat et al. 2005).

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It’s funny how many things in biology can be described in the same way. Biology certainly lacks the hard boundaries found in much of physics.

Does homologous recombination between insertions also pose a problem, or is it more of a problem when basing phylogenies on sequence divergence between orthologous TE’s?