Conclusions
We demonstrated the usefulness of mzl-USCOs as markers for reliably inferring phylogenies on all systematic levels (species group to phylum) irrespective of the specific taxonomic group under consideration. Our analysis of four different recent radiations using WGS datasets showed that USCO data allow distinguishing between species in almost all tested cases and in most cases allow drawing the same conclusions as corresponding studies that analyzed a more comprehensive amount of genomic data. Mzl-USCOs have been proven to be a useful marker system for DNA taxonomy in diverse animal groups, integrating the overarching issues of marker standardization, data production, data repository, and reuse (Miralles et al., 2020). Mzl-USCOs, like any other marker system, may lack the resolving power of whole genome data, especially when speciation is triggered by a single locus or by a few loci (speciation genes; e.g., Orr et al., 2004; Nosil & Schluter, 2011). However, they have the advantage of being universally applicable and comparable across animals. While their distribution in the genome is not fully random, they are widely spread across the genome rather than being clustered in certain genomic regions or on some specific chromosomes. Mzl-USCOs hence constitute a representative sample of the genome for purposes of phylogeny and taxonomy.