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The unresolved phylogenomic tree of butterflies and moths (Lepidoptera): assessing the potential causes and consequences

View ORCID ProfileJadranka Rota, View ORCID ProfileVictoria Twort, View ORCID ProfileAndrea Chiocchio, Carlos Peña, View ORCID ProfileChristopher W. Wheat, Lauri Kaila, Niklas Wahlberg
doi: https://doi.org/10.1101/2021.04.09.439156
Jadranka Rota
1Biological Museum, Lund University
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Victoria Twort
2Finnish Museum of Natural History, University of Helsinki
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Andrea Chiocchio
3Department of Ecological and Biological Science, Universita degli Studi della Tuscia
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Carlos Peña
4Private person
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Christopher W. Wheat
5Stockholm University
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Lauri Kaila
2Finnish Museum of Natural History, University of Helsinki
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Niklas Wahlberg
6Department of Biology, Lund University
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Abstract

The field of molecular phylogenetics is being revolutionised with next-generation sequencing technologies making it possible to sequence large numbers of genomes for non-model organisms ushering us into the era of phylogenomics. The current challenge is no longer how to get enough data, but rather how to analyse the data and how to assess the support for the inferred phylogeny. We focus on one of the largest animal groups on the planet – butterflies and moths (order Lepidoptera). We clearly demonstrate that there are unresolved issues in the inferred phylogenetic relationships of the major lineages, despite several recent phylogenomic studies of the group. We assess the potential causes and consequences of the conflicting phylogenetic hypotheses. With a dataset consisting of 331 protein-coding genes and the alignment length over 290 000 base pairs, including 200 taxa representing 81% of lepidopteran superfamilies, we compare phylogenetic hypotheses inferred from amino acid and nucleotide alignments. The resulting two phylogenies are discordant, especially with respect to the placement of the superfamily Gelechioidea, which is likely due to compositional bias of both the nucleotide and amino acid sequences. With a series of analyses, we dissect our dataset and demonstrate that there is sufficient phylogenetic signal to resolve much of the lepidopteran tree of life. Overall, the results from the nucleotide alignment are more robust to the various perturbations of the data that we carried out. However, the lack of support for much of the backbone within Ditrysia makes the current butterfly and moth tree of life still unresolved. We conclude that taxon sampling remains an issue even in phylogenomic analyses, and recommend that poorly sampled highly diverse groups, such as Gelechioidea in Lepidoptera, should receive extra attention in the future.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 11, 2021.
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The unresolved phylogenomic tree of butterflies and moths (Lepidoptera): assessing the potential causes and consequences
Jadranka Rota, Victoria Twort, Andrea Chiocchio, Carlos Peña, Christopher W. Wheat, Lauri Kaila, Niklas Wahlberg
bioRxiv 2021.04.09.439156; doi: https://doi.org/10.1101/2021.04.09.439156
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The unresolved phylogenomic tree of butterflies and moths (Lepidoptera): assessing the potential causes and consequences
Jadranka Rota, Victoria Twort, Andrea Chiocchio, Carlos Peña, Christopher W. Wheat, Lauri Kaila, Niklas Wahlberg
bioRxiv 2021.04.09.439156; doi: https://doi.org/10.1101/2021.04.09.439156

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