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Reconstructing phylogenetic relationships based on repeat sequence similarities

  • Daniel Vitales
    ,
  • Sonia Garcia
    ,
  • Steven Dodsworth
  • University of Barcelona
    ,
  • Institut Botànic de Barcelona (IBB CSIC-Ajuntament de Barcelona)
Research Output: Contribution to journal Article Peer-review

Abstract

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.

Publication Information

Output type

Research Output: Contribution to journal Article Peer-review

Original language

English

Pages from-to (Number of pages)

Pages 106766

Journal (Volume, Issue Number)

Molecular Phylogenetics and Evolution (Volume 147)

Publication milestones

  • Accepted/In press - 12/02/2020
  • Published - 28/02/2020

Publication status

Published - 28/02/2020

ISSN

1055-7903

External Publication IDs

  • handle.net: 10547/624050
  • Scopus: 85081218787

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