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Metazoa-level USCOs as markers in species delimitation and classification

Dietz, Lars1; Mayer, Christoph1; Stolle, Eckart1; Eberle, Jonas2; Misof, Bernhard1; Podsiadlowski, Lars1; Niehuis, Oliver3; Ahrens, Dirk1

Research facility: Leibniz Institute for the Analysis of Biodiversity Change
Published Dec 26, 2023 on Dryad. https://doi.org/10.5061/dryad.kprr4xhb3

Data files

Dec 26, 2023 version files 689.73 MB

Abstract

Metazoa-level Universal Single-Copy Orthologs (USCOs) are universally applicable markers for DNA taxonomy in animals which can replace or supplement single-gene barcoding. While Metazoa-level USCOs from target enrichment data were shown to reliably distinguish species, it remains to be tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome, and hence can facilitate detection of past hybridization events. Besides, unlinked loci are a principal assumption in coalescent-based species delimitation approaches. 239 chromosome-level genomes were analyzed to show that Metazoa-level USCOs are a representative sample of a genome: in terms of distances to each other on a chromosome, but also over the chromosomes, they are almost as evenly distributed as protein-coding genes in general are. We tested the suitability of Metazoa-level 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 results show that USCO genes can be considered as genetically unlinked for practical purposes and representative for an entire metazoan genome. Our phylogenetic analyses demonstrate that USCOs may complement single-gene barcoding 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 size of genome reference libraries and their sampling of organismic lineages is rapidly increasing.