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Metazoa-level USCOs as markers in species delimitation and classification
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  • Lars Dietz,
  • Christoph Mayer,
  • Eckart Stolle,
  • Jonas Eberle,
  • Bernhard Misof,
  • Lars Podsiadlowski,
  • Oliver Niehuis,
  • Dirk Ahrens
Lars Dietz
Zoologisches Forschungsinstitut und Museum Alexander Koenig
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Christoph Mayer
Zoologisches Forschungsinstitut und Museum Alexander Koenig
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Eckart Stolle
Zoologisches Forschungsinstitut und Museum Alexander Koenig
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Jonas Eberle
Paris Lodron University of Salzburg
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Bernhard Misof
Zoologisches Forschungsinstitut und Museum Alexander Koenig
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Lars Podsiadlowski
Zoologisches Forschungsinstitut und Museum Alexander Koenig
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Oliver Niehuis
University of Freiburg
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Dirk Ahrens
Zoologisches Forschungsinstitut und Museum Alexander Koenig

Corresponding Author:[email protected]

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Abstract

Metazoa-level Universal Single-Copy Orthologs (mzl-USCOs) are universally applicable markers for DNA taxonomy in animals which can replace or supplement single-gene barcodes. While previously mzl-USCOs from target enrichment data were shown to reliably distinguish species, here we tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome and therefore able to cope with past hybridization events and incomplete lineage sorting. This is relevant for coalescent-based species delimitation approaches, which critically depend on the assumption that the investigated loci do not exhibit autocorrelation due to physical linkage. Based on 239 assessed chromosome-level assembled genomes, we confirmed that mzl-USCOs are genetically unlinked for practical purposes and a representative sample of a genome in terms of reciprocal distances between USCOs on a chromosome and of distribution across chromosomes. We tested the suitability of mzl-USCOs extracted from genomes for species delimitation and phylogeny in four case studies: Anopheles mosquitos, Drosophila fruit flies, Heliconius butterflies, and Darwin’s finches. In almost all instances, USCOs allowed delineating species and yielded phylogenies that correspond to those generated from whole genome data. Our phylogenetic analyses demonstrate that USCOs may complement single-gene DNA barcodes and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and at times impact taxonomic conclusions. However, we expect this problem to become less severe as the rapidly growing number of reference genomes provides a better representation of the number and diversity of organismic lineages.
15 Oct 2023Submitted to Molecular Ecology Resources
16 Oct 2023Submission Checks Completed
16 Oct 2023Assigned to Editor
16 Oct 2023Review(s) Completed, Editorial Evaluation Pending
22 Oct 2023Reviewer(s) Assigned