Metazoa-level USCOs as markers in species delimitation and classification

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.