Year: 2024
Type: article
Abstract: Ancient divergences within Opisthokonta-a major lineage that includes organisms in the kingdoms Animalia, Fungi, and their unicellular relatives-remain contentious. To assess progress toward a genome-scale Opisthokonta phylogeny, we conducted the most taxon rich phylogenomic analysis using sets of genes inferred with different orthology inference methods and established the geological timeline of Opisthokonta diversification. We also conducted sensitivity analysis by subsampling genes or taxa from the full data matrix based on filtering criteria previously shown to improve phylogenomic inference. We found that approximately 85% of internal branches were congruent across data matrices and the approaches used. Notably, the use of different orthology inference methods was a substantial contributor to the observed incongruence: analyses using the same set of orthologs showed high congruence of 97% to 98%, whereas different sets of orthologs resulted in somewhat lower congruence (87% to 91%). Examination of unicellular Holozoa relationships suggests that the instability observed across varying gene sets may stem from weak phylogenetic signals. Our results provide a comprehensive Opisthokonta phylogenomic framework that will be useful for illuminating ancient evolutionary episodes concerning the origin and diversification of the 2 major eukaryotic kingdoms and emphasize the importance of investigating effects of orthology inference on phylogenetic analyses to resolve ancient divergences.
Source: PLoS Biology
Institutions: Shandong University, Qingdao National Laboratory for Marine Science and Technology, Howard Hughes Medical Institute, University of California, Berkeley, South China Agricultural University, University of Vienna, Monterey Bay Aquarium Research Institute, University of California, Santa Cruz, University of Alabama, Zhejiang University, Vanderbilt University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $5,500
Funders: National Science Foundation, Shandong University, Life Sciences Research Foundation, European Commission, National Natural Science Foundation of China, National Institutes of Health, Key Technologies Research and Development Program, National Key Research and Development Program of China, Fundamental Research Funds for the Central Universities, National Science Fund for Distinguished Young Scholars, National Institute of Allergy and Infectious Diseases, H2020 European Research Council, Science Fund for Distinguished Young Scholars of Zhejiang Province
Awards: G1134414688, G1571511110, G1593943370, Collaborative Research: RoL: The Evolution of the Genotype-Phenotype Map across Budding Yeasts, G2007698898, Modes of genome evolution during major metazoan transitions, G4192505449, G434337789, CAREER: Revolutionizing Biodiversity and Systematics Research on Aplacophora (Mollusca) and Training the Next Generation of Invertebrate Systematists, G4822304152, G8796181593, G8985330327, Deciphering the phenotypic and genomic traits that underlie the evolution of pathogenicity differences among Aspergillus fumigatus and its close relatives
OpenAlex ID: W4402581633