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

Rota, Jadranka LU orcid ; Twort, Victoria LU ; Chiocchio, Andrea LU ; Peña, Carlos ; Wheat, Christopher W. ; Kaila, Lauri and Wahlberg, Niklas LU (2022) In Systematic Entomology 47(4). p.531-550
Abstract

The field of molecular phylogenetics is being revolutionized 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. Here, we focus on one of the largest animal groups on the planet – butterflies and moths (order Lepidoptera), whose phylogeny remains unresolved despite several recent phylogenomic studies. In this study, we assess the potential causes and consequences of the conflicting phylogenetic hypotheses. With a dataset consisting of 331 protein-coding genes and the... (More)

The field of molecular phylogenetics is being revolutionized 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. Here, we focus on one of the largest animal groups on the planet – butterflies and moths (order Lepidoptera), whose phylogeny remains unresolved despite several recent phylogenomic studies. In this study, 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 83% 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 and possible other model violations. Furthermore, we employed a series of analyses to dissect our dataset and demonstrate that there is sufficient phylogenetic signal to resolve much – but not all – of the lepidopteran tree of life. The relationships among superfamilies within Ditrysia, the most species rich lepidopteran clade containing 98% of the extant species, remain poorly resolved. 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.

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author
; ; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
amino acids, Ditrysia, Lepidoptera, model violation, nucleotides, phylogenetic inference, phylogenomics
in
Systematic Entomology
volume
47
issue
4
pages
20 pages
publisher
Wiley-Blackwell
external identifiers
  • scopus:85126453662
ISSN
0307-6970
DOI
10.1111/syen.12545
language
English
LU publication?
yes
additional info
Funding Information: We are grateful to Maria Heikkilä for reading the manuscript and providing valuable insight. We thank Christoffer Fägerström for photographs of several specimens included in Figure 1 and the graphical abstract. AC was funded by a Crafoord Foundation (Sweden) grant awarded to JR (grant no. 20180794). NW acknowledges funding from the Swedish Research Council (grant no. 2015‐0444). We thank anonymous reviewers and Thomas Simonsen for their helpful reviews. Publisher Copyright: © 2022 The Authors. Systematic Entomology published by John Wiley & Sons Ltd on behalf of Royal Entomological Society.
id
48816aba-07b9-437b-87be-9cd87ab2d169
date added to LUP
2022-03-31 08:09:45
date last changed
2023-05-10 11:47:53
@article{48816aba-07b9-437b-87be-9cd87ab2d169,
  abstract     = {{<p>The field of molecular phylogenetics is being revolutionized 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. Here, we focus on one of the largest animal groups on the planet – butterflies and moths (order Lepidoptera), whose phylogeny remains unresolved despite several recent phylogenomic studies. In this study, 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 83% 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 and possible other model violations. Furthermore, we employed a series of analyses to dissect our dataset and demonstrate that there is sufficient phylogenetic signal to resolve much – but not all – of the lepidopteran tree of life. The relationships among superfamilies within Ditrysia, the most species rich lepidopteran clade containing 98% of the extant species, remain poorly resolved. 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.</p>}},
  author       = {{Rota, Jadranka and Twort, Victoria and Chiocchio, Andrea and Peña, Carlos and Wheat, Christopher W. and Kaila, Lauri and Wahlberg, Niklas}},
  issn         = {{0307-6970}},
  keywords     = {{amino acids; Ditrysia; Lepidoptera; model violation; nucleotides; phylogenetic inference; phylogenomics}},
  language     = {{eng}},
  month        = {{03}},
  number       = {{4}},
  pages        = {{531--550}},
  publisher    = {{Wiley-Blackwell}},
  series       = {{Systematic Entomology}},
  title        = {{The unresolved phylogenomic tree of butterflies and moths (Lepidoptera) : Assessing the potential causes and consequences}},
  url          = {{http://dx.doi.org/10.1111/syen.12545}},
  doi          = {{10.1111/syen.12545}},
  volume       = {{47}},
  year         = {{2022}},
}