Reconstructing phylogenetic relationships based on repeat sequence similarities

Daniel Vitales*, Sònia Garcia, Steven Dodsworth

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


A recent phylogenetic method based on genome-wide abundance of different repeat types proved to be useful in reconstructing the evolutionary history of several plant and animal groups. Here, we demonstrate that an alternative information source from the repeatome can also be employed to infer phylogenetic relationships among taxa. Specifically, this novel approach makes use of the repeat sequence similarity matrices obtained from the comparative clustering analyses of RepeatExplorer 2, which are subsequently transformed to between-taxa distance matrices. These pairwise matrices are used to construct neighbour-joining trees for each of the top most-abundant clusters and they are finally summarized in a consensus network. This methodology was tested on three groups of angiosperms and one group of insects, resulting in congruent evolutionary hypotheses compared to more standard systematic analyses based on commonly used DNA markers. We propose that the combined application of these phylogenetic approaches based on repeat abundances and repeat sequence similarities could be helpful to understand mechanisms governing genome and repeatome evolution.

Original languageEnglish
Article number106766
Number of pages10
JournalMolecular Phylogenetics and Evolution
Early online date28 Feb 2020
Publication statusPublished - 1 Jun 2020


  • genomics
  • graph-based clustering
  • high-throughput sequencing
  • next-generation sequencing
  • phylogenetics
  • repetitive DNA


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