Standardized nuclear markers improve and homogenize species delimitation in Metazoa
Creators
- 1. Zoological Research Museum Alexander Koenig
- 2. University of Salzburg
- 3. Natural History Museum of Bern
- 4. Louisiana State University
- 5. Technische Universität Braunschweig
- 6. University of Florida
- 7. University of Freiburg
Description
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.
Notes
All alignments, including SNP datasets, are in FASTA format and can be opened with standard alignment viewers. In alignments for approaches A1 and A2, ambiguity codes (R, Y, W, S, M, K) stand for positions inferred to be heterozygous.
Phylogenetic trees are in NEWICK format, files including multiple named trees are in NEXUS format. Both can be opened in a standard phylogenetic tree viewer such as FigTree. Individual gene trees are unrooted, trees based on whole USCO datasets are rooted.
SNP datasets recoded for NMDS analysis are tab-delimited text and numbers have the following meaning: 0: homozygous for more common allele, 1: heterozygous, 2: homozygous for less common allele. Unknown positions are represented by empty cells.
Funding provided by: Deutsche Forschungsgemeinschaft
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001659
Award Number: AH175/3-1
Funding provided by: Deutsche Forschungsgemeinschaft
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001659
Award Number: AH175/6-1
Funding provided by: Deutsche Forschungsgemeinschaft
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001659
Award Number: AH175/6-2
Funding provided by: Deutsche Forschungsgemeinschaft
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001659
Award Number: MI649/18-1
Funding provided by: Deutsche Forschungsgemeinschaft
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001659
Award Number: MI649/18-1
Funding provided by: Deutsche Forschungsgemeinschaft
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001659
Award Number: NI1387/6-1
Funding provided by: Deutsche Forschungsgemeinschaft
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001659
Award Number: NI1387/6-1
Funding provided by: Deutsche Forschungsgemeinschaft
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001659
Award Number: NI1387/7-1
Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: DEB-1256742
Files
usco-scripts-readme.txt
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Additional details
Related works
- Is derived from
- 10.5281/zenodo.4598814 (DOI)
- Is source of
- 10.5061/dryad.hhmgqnkg5 (DOI)