Metazoa-level USCOs as markers in species delimitation and classification

Metazoa-level Universal Single-Copy Orthologs (USCOs) are universally applicable markers for DNA taxonomy in animals which can replace or supplement single-gene barcoding. While Metazoa-level USCOs from target enrichment data were shown to reliably distinguish species, it remains to be tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome, and hence can facilitate detection of past hybridization events. Besides, unlinked loci are a principal assumption in coalescent-based species delimitation approaches. 239 chromosome-level genomes were analyzed to show that Metazoa-level USCOs are a representative sample of a genome: in terms of distances to each other on a chromosome, but also over the chromosomes, they are almost as evenly distributed as protein-coding genes in general are. We tested the suitability of Metazoa-level USCOs extracted from genomes for species delimitation and phylogeny in four case studies: Anopheles mosquitos, Drosophila frui..., , , Supplementary files for study \"From benchmarking to systematics: exploiting metazoan USCOs from whole genome data\", L. Dietz et al., submitted
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Each of these ZIP files contains a folder with several files containing alignments, phylogenetic trees, or other data. For more information on these files, please consult the accompanying description files.
All alignments, including SNP datasets, are in FASTA format and can be opened with standard alignment viewers. Except in the metazoan alignments, ambiguity codes (R, Y, W, S, M, K) stand for positions inferred to be heterozygous.
Phylogenetic trees are in NEWICK format and can be opened in a standard phylogenetic tree viewer such as FigTree. All trees are unrooted. Partition files for concatenated alignments are in NEXUS format for use in IQ-TREE.
SNP datasets recoded for NMDS analysis are tab-delimited text and numbers have the following meaning: 0: homozygous for more common allele, 1: ...