ArticleSystematic biology2013
When outgroups fail; phylogenomics of rooting the emerging pathogen, Coxiella burnetii.
Article in Systematic biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 49 citations in OpenAlex.
- Genome characteristics and type IV effector protein repertoire of Coxiella burnetii depend rather on Genomic Groups than on host species.BMC microbiology · 2026Article
- Reliable estimation of tree branch lengths using deep neural networks.PLoS computational biology · 2024Article
- Community ecology and functional potential of bacteria, archaea, eukarya and viruses in Guerrero Negro microbial mat.Scientific reports · 2024Article
- Genetic characterization and description of Leishmania (Leishmania) ellisi sp. nov.: a new human-infecting species from the USA.Parasitology research · 2023Article
- DISCO+QR: rooting species trees in the presence of GDL and ILS.Bioinformatics advances · 2023Article
- A critical analysis of the current state of virus taxonomy.Frontiers in microbiology · 2023Review
- Characterization and Identification of Probiotic Features in Lacticaseibacillus Paracasei Using a Comparative Genomic Analysis Approach.Probiotics and antimicrobial proteins · 2022Article
- nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.Systematic biology · 2022Article
- Correlating Genotyping Data ofPathogens (Basel, Switzerland) · 2021Article
- Pathogen to commensal? Longitudinal within-host population dynamics, evolution, and adaptation during a chronic >16-year Burkholderia pseudomallei infection.PLoS pathogens · 2020Article
- Selective whole genome amplification and sequencing of Coxiella burnetii directly from environmental samples.Genomics · 2020Article
- Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups.BMC genomics · 2019Article
- Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity.Microbial genomics · 2018Article
- Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions.Evolutionary bioinformatics online · 2018Review
- Draft Genome Sequences of the AvirulentGenome announcements · 2017Article
- Genome-wide characterization of cellulases from the hemi-biotrophic plant pathogen,Biotechnology for biofuels · 2017Article
- Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction.PloS one · 2017Article
- Article
- Genotyping and Axenic Growth of Coxiella burnetii Isolates Found in the United States Environment.Vector borne and zoonotic diseases (Larchmont, N.Y.) · 2016Article
- Massive dispersal ofMicrobial genomics · 2016Article
Corrections and comments
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Authors and funding
14 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rooting phylogenies is critical for understanding evolution, yet the importance, intricacies and difficulties of rooting are often overlooked. For rooting, polymorphic characters among the group of interest (ingroup) must be compared to those of a relative (outgroup) that diverged before the last common ancestor (LCA) of the ingroup. Problems arise if an outgroup does not exist, is unknown, or is so distant that few characters are shared, in which case duplicated genes originating before the LCA can be used as proxy outgroups to root diverse phylogenies. Here, we describe a genome-wide expansion of this technique that can be used to solve problems at the other end of the evolutionary scale: where ingroup individuals are all very closely related to each other, but the next closest relative is very distant. We used shared orthologous single nucleotide polymorphisms (SNPs) from 10 whole genome sequences of Coxiella burnetii, the causative agent of Q fever in humans, to create a robust, but unrooted phylogeny. To maximize the number of characters informative about the rooting, we searched entire genomes for polymorphic duplicated regions where orthologs of each paralog could be identified so that the paralogs could be used to root the tree. Recent radiations, such as those of emerging pathogens, often pose rooting challenges due to a lack of ingroup variation and large genomic differences with known outgroups. Using a phylogenomic approach, we created a robust, rooted phylogeny for C. burnetii. [Coxiella burnetii; paralog SNPs; pathogen evolution; phylogeny; recent radiation; root; rooting using duplicated genes.].
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