Metazoa-level USCOs as markers in species delimitation and classification.
DNA taxonomy
Metazoa
USCOs
WGS
genome assembly
systematics
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
26 Dec 2023
26 Dec 2023
Historique:
revised:
06
12
2023
received:
15
10
2023
accepted:
13
12
2023
medline:
26
12
2023
pubmed:
26
12
2023
entrez:
26
12
2023
Statut:
aheadofprint
Résumé
Metazoa-level universal single-copy orthologs (mzl-USCOs) are universally applicable markers for DNA taxonomy in animals that can replace or supplement single-gene barcodes. Previously, mzl-USCOs from target enrichment data were shown to reliably distinguish species. Here, we tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome and therefore able to cope with past hybridization events and incomplete lineage sorting. This is relevant for coalescent-based species delimitation approaches, which critically depend on the assumption that the investigated loci do not exhibit autocorrelation due to physical linkage. Based on 239 chromosome-level assembled genomes, we confirmed that mzl-USCOs are genetically unlinked for practical purposes and a representative sample of a genome in terms of reciprocal distances between USCOs on a chromosome and of distribution across chromosomes. We tested the suitability of mzl-USCOs extracted from genomes for species delimitation and phylogeny in four case studies: Anopheles mosquitos, Drosophila fruit flies, Heliconius butterflies and Darwin's finches. In almost all instances, USCOs allowed delineating species and yielded phylogenies that corresponded to those generated from whole genome data. Our phylogenetic analyses demonstrate that USCOs may complement single-gene DNA barcodes and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and, at times, impact taxonomic conclusions. However, we expect this problem to become less severe as the rapidly growing number of reference genomes provides a better representation of the number and diversity of organismal lineages.
Identifiants
pubmed: 38146909
doi: 10.1111/1755-0998.13921
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e13921Subventions
Organisme : Deutsche Forschungsgemeinschaft
ID : AH175/6-1, 6-2
Organisme : Deutsche Forschungsgemeinschaft
ID : MA 3684/5-2
Organisme : Deutsche Forschungsgemeinschaft
ID : MI 649/18-2
Organisme : Deutsche Forschungsgemeinschaft
ID : NI1387/6-1, 6-2
Organisme : Deutsche Forschungsgemeinschaft
ID : PO 765/12-2
Informations de copyright
© 2023 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.
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