Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses

By Olga Zhaxybayeva, J. Peter Gogarten. BMC Genomics, 2002

442 citations recorded by the source corpus.

BackgroundHorizontal gene transfer (HGT) played an important role in shaping microbial genomes. In addition to genes under sporadic selection, HGT also affects housekeeping genes and those involved in information processing, even ribosomal RNA encoding genes. Here we describe tools that provide an assessment and graphic illustration of the mosaic nature of microbial genomes.ResultsWe adapted the Maximum Likelihood (ML) mapping to the analyses of all detected quartets of orthologous genes found in four genomes. We have automated the assembly and analyses of these quartets of orthologs given the selection of four genomes. We compared the ML-mapping approach to more rigorous Bayesian probability and Bootstrap mapping techniques. The latter two approaches appear to be more conservative than the ML-mapping approach, but qualitatively all three approaches give equivalent results. All three tools were tested on mitochondrial genomes, which presumably were inherited as a single linkage group.ConclusionsIn some instances of interphylum relationships we find nearly equal numbers of quartets strongly supporting the three possible topologies. In contrast, our analyses of genome quartets containing the cyanobacterium Synechocystis sp. indicate that a large part of the cyanobacterial genome is related to that of low GC Gram positives. Other groups that had been suggested as sister groups to the cyanobacteria contain many fewer genes that group with the Synechocystis orthologs. Interdomain comparisons of genome quartets containing the archaeon Halobacterium sp. revealed that Halobacterium sp. shares more genes with Bacteria that live in the same environment than with Bacteria that are more closely related based on rRNA phylogeny . Many of these genes encode proteins involved in substrate transport and metabolism and in information storage and processing. The performed analyses demonstrate that relationships among prokaryotes cannot be accurately depicted by or inferred from the tree-like evolution of a core of rarely transferred genes; rather prokaryotic genomes are mosaics in which different parts have different evolutionary histories. Probability mapping is a valuable tool to explore the mosaic nature of genomes.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4964a0d38f2c8a7a23a5e7645c23b527cc60465c

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Citations in the corpus

Roussoellaceae , a new pleosporalean family to accommodate the genera Neoroussoella gen. nov., Roussoella and Roussoellopsis (2014, unknown): “Posterior probabilities (PP) (Rannala and Yang 1996, Zhaxybayeva and Gogarten 2002) were determined by Markov Chain Monte Carlo sampling (BMCMC) in MrBayes v. 3.0b4 (Huelsenbeck and Ronquist 2001).”
Morpho-molecular characterization of microfungi associated with marine based habitats (2020, unknown): “1.2 )Huelsenbeck & Ronquist 2001, Zhaxybayeva & Gogarten 2002(.”
Horizontal gene transfer, genome innovation and evolution (2005, background): “Several studies have determined the frequency with which genes belonging to different functional categories are being transferre”
Fungal diversity notes 709–839: taxonomic and phylogenetic contributions to fungal taxa with an emphasis on fungi on Rosaceae (2018, methodology): “Bayesian analysis was performed in MrBayes v. 3.1.2 (Ronquist and Huelsenbeck 2003) to evaluate Posterior probabilities (PP) (Rannala and Yang 1996; Zhaxybayeva and Gogarten 2002) by Markov Chain Monte Carlo sampling (BMCMC).”
Prokaryotic evolution in light of gene transfer. (2002, background): “…its confounding effects in reconstructing the history of organismal evolution (Koonin et al. 1997; Doolittle 1999b; Nelson et al. 1999; Pennisi 1999; Koonin, Aravind, and Kondrashov 2000; Boucher, Nesbo, and Doolittle 2001; Nesbo, Boucher, and Doolittle 2001; Zhaxybayeva and Gogarten 2002).”
Phylogenetic evaluation and taxonomic revision of Schizothecium based on ribosomal DNA and protein coding genes (2005, methodology): “Posterior probabilities (PP) (Rannala and Yang, 1996; Zhaxybayeva and Gogarten, 2002) were determined by Markov Chain Monte Carlo sampling (BMCMC) in MrBayes 3.”
Astrosphaeriella is polyphyletic, with species in Fissuroma gen. nov., and Neoastrosphaeriella gen. nov. (2011, methodology): “Posterior probabilities (PP) (Rannala and Yang 1996; Zhaxybayeva and Gogarten 2002) were determined by Markov Chain Monte Carlo sampling (BMCMC) in MrBayes v.”