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.