Standardized nuclear markers improve and homogenize species delimitation in Metazoa

Abstract

Species are the fundamental units of life and evolution. Their recognition is essential for science and society. Molecular methods have been increasingly used 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 use coalescent‐based species inference as well as population admixture analyses and phenetic methods. We demonstrate that metazoan USCOs distinguish well closely related morphospecies and consistently outperform classical mitochondrial DNA barcoding in discriminating closely related species in different animal taxa, as judged by comparison with morphospecies delimitations. 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.

Species Delimitation Under Allopatry: Genomic Divergences Within and Across Continents in Lepidoptera

“…As the delimitation of allopatric populations is bound to be based on arbitrary criteria, applying the same principles throughout taxa, or at least very broadly, would be an optimal solution. We further find that using a large set of universal genetic markers, such as the USCO markers as proposed by Eberle et al (2020), and implemented by Dietz et al (2022) would provide the best means for that. The benefits of this approach would be multiple, but at its best we hope that it would reduce the subjectivity of types of traits used and hence critically improve the scalability and quantifiability of the taxonomic judgement.…”

“…Sequence capture methods such as target enrichment can be useful in bringing stability and even common standards for species delimitation if based on a fixed set of loci that are found across a large diversity of taxa. This idea was recently put forth by Eberle et al (2020) and tested in a selection of metazoan taxa by Dietz et al (2022).…”

Ancistroceruswasps (Hymenoptera, Vespidae) from the Centre of Europe: Phylogeny, cryptic species, neutral and non‐neutral markers

“…For instance, Wiens et al (2010) have documented extensive discordance between phylogenies from mtDNA and nuDNA loci, suggesting that the mitochondrial data alone may be misleading about the rate of speciation. Therefore, the use of solely mitochondrial DNA data in phylogenetics has been considered as controversial (Cong et al, 2017; Dietz et al, 2022; Lin & Danforth, 2004). The most frequent explanations of discordance between mtDNA and nuDNA data are: incomplete lineage sorting, adaptive introgression of mtDNA, demographic disparities and sex‐biased asymmetries, hybrid zone movements, and Wolbachia infections (Platt II et al, 2018; Toews & Brelsford, 2012).…”

Review of the Australian butterfly genus Cyprotides Tite, 1963 (Lepidoptera: Lycaenidae), with descriptions of three new taxa

“…Preliminary mitogenomic sequence data (~15 000 bp) suggest that C. maculosus and C. cyprotus are not well differentiated phylogenetically (A. Zwick, unpublished data). However, further genetic work is required to determine if C. maculosus is reproductively isolated and if some of its component genes (e.g., mitochondrial and/or some of the faster evolving nuclear genes, Dietz et al 2022) are reciprocally monophyletic under neutral divergence according to phylogeographic structure. The phenotype of the 29 adults that were reared under warm temperate conditions and subsequently emerged in captivity after a pupal duration of 8–25 months (i.e., room temperature), rather than cold temperate conditions (i.e., montane/subalpine temperatures), was identical or very similar to wild caught specimens, indicating that the divergent adult pattern observed in C. maculosus is under genetic control and not due to environmental factors, such as temperature or host plant.…”