Base-substitution rates of nuclear and mitochondrial genes for polyclad flatworms

Daniel Cuadrado*, Jorge Rodríguez, Annie Machordom, Carolina Noreña, Fernando Fernández-Álvarez, Pat A. Hutchings, Jane E. Williamson

*Corresponding author for this work

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Abstract

The increase in the use of molecular methodologies in systematics has driven the necessity for a comprehensive understanding of the limitations of different genetic markers. Not every marker is optimal for all species, which has led to multiple approaches in the study of the taxonomy and phylogeny of polyclad flatworms. The present study evaluates base-substitution rates of nuclear ribosomal (18S rDNA and 28S rDNA), mitochondrial ribosomal (16S rDNA), and protein-codifying (cytb, cox1) markers for this taxonomic group, with the main objective of assessing the robustness of these different markers for phylogenetic studies. Mutation rates and Ti/Tv ratios of the other markers were assessed for the first time. We estimated substitution rates and found cytb to be the most variable, while 18S rDNA was the least variable among them. On the other hand, the transition to transversion (Ti/Tv) ratio of the different genes revealed differences between the markers, with a higher number of transitions in the nuclear gene 28S and a higher number of transversions in the mitochondrial genes. Lastly, we identified that the third codon position of the studied protein-codifying genes was highly variable and that this position was saturated in the cox1 marker but not in cytb. We conclude that it is important to assess the markers employed for different phylogenetic levels for future studies, particularly in the order Polycladida. We encourage the use of mitochondrial genes cytb and 16S for phylogenetic studies at suborder, superfamily, and family levels and species delimitation in polyclads, in addition to the well-known 28S and cox1.

Original languageEnglish
Pages (from-to)863-876
Number of pages14
JournalZoosystematics and Evolution
Volume100
Issue number3
Early online date1 Jul 2024
DOIs
Publication statusPublished - 2024

Bibliographical note

Copyright the Author(s) 2024. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Keywords

  • Acotylea
  • codon
  • Cotylea
  • entropy
  • flatworm
  • molecular
  • purines
  • pyrimidines
  • saturation

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