Standardized nuclear markers improve and homogenize species delimitation in Metazoa

Species are the fundamental units of life and evolution. Their recognition
is essential for science and society. Molecular methods have been
increasingly employed for the identification of animal species, despite
several challenges.  Here, we explore with genomic data from nine
animal lineages a set of nuclear markers, namely metazoan-level
universal single-copy orthologs (metazoan USCOs), for their use in species
delimitation. Our data sets include arthropods and vertebrates. We use
various data assembly strategies and employ coalescent-based species
inference as well as population admixture analyses and phenetic methods.
We demonstrate that metazoan USCOs well distinguish closely related
morphospecies and consistently outperform classical mitochondrial DNA
barcoding in discriminating closely related species in different animal
taxa. USCOs overcome the general shortcomings of mitochondrial DNA
barcodes, and due to standardization across Metazoa, also those of other
approaches. They accurately assign samples not only to lower but also to
higher taxonomic levels.  Metazoan USCOs provide a powerful and
unifying framework for DNA-based species delimitation and taxonomy in
animals and their employment could result in a more efficient use of
research data and resources.