ArticleNature ecology & evolution2022
Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria.
Article in Nature ecology & evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed, 111 citations in OpenAlex.
- Inheritance and selection of the mitochondrial genome.Nature reviews. Genetics · 2026Review
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- Phylogenomic mixture models outperform homogeneous and partitioned models.Molecular biology and evolution · 2026Article
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- Energetics and evolution: Response to Martin.Biochimica et biophysica acta. Bioenergetics · 2026Article
- The archaeal roots of eukaryotic life.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Toward a genomic understanding of the tree of life.Molecular biology and evolution · 2026Article
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- Comparative mitogenomics of kingdom Fungi - evolutionary insights and metagenomic applications.Nucleic acids research · 2026Article
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- Identification of a deep-branching lineage of algae using environmental plastid genomes.Nature communications · 2025Article
- New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the Pelagibacterales.Nature communications · 2025Article
- Dating the Bacterial Tree of Life Based on Ancient Symbiosis.Systematic biology · 2025Article
- A timetree of Fungi dated with fossils and horizontal gene transfers.Nature ecology & evolution · 2025Article
- Phylogenomic Analyses Reveal that Panguiarchaeum Is a Clade of Genome-Reduced Asgard Archaea Within the Njordarchaeia.Molecular biology and evolution · 2025Article
- Hidden Markov Model-Based Prokaryotic Genome Space Mining Reveals the Widespread Pervasiveness of Complex I and Its Potential Evolutionary Scheme.Genome biology and evolution · 2025Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Determining the phylogenetic origin of mitochondria is key to understanding the ancestral mitochondrial symbiosis and its role in eukaryogenesis. However, the precise evolutionary relationship between mitochondria and their closest bacterial relatives remains hotly debated. The reasons include pervasive phylogenetic artefacts as well as limited protein and taxon sampling. Here we developed a new model of protein evolution that accommodates both across-site and across-branch compositional heterogeneity. We applied this site-and-branch-heterogeneous model (MAM60 + GFmix) to a considerably expanded dataset that comprises 108 mitochondrial proteins of alphaproteobacterial origin, and novel metagenome-assembled genomes from microbial mats, microbialites and sediments. The MAM60 + GFmix model fits the data much better and agrees with analyses of compositionally homogenized datasets with conventional site-heterogenous models. The consilience of evidence thus suggests that mitochondria are sister to the Alphaproteobacteria to the exclusion of MarineProteo1 and Magnetococcia. We also show that the ancestral presence of the crista-developing mitochondrial contact site and cristae organizing system (a mitofilin-domain-containing Mic60 protein) in mitochondria and the Alphaproteobacteria only supports their close relationship.
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