ArticleGenetics2005
Stochastic models for horizontal gene transfer: taking a random walk through tree space.
Article in Genetics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- HGTs are not SPRs: In the Presence of Ghost Lineages, Series of Horizontal Gene Transfers do not Result in Series of Subtree Pruning and Regrafting.Molecular biology and evolution · 2025Article
- Improving the performance of Bayesian phylogenetic inference under relaxed clock models.BMC evolutionary biology · 2020Article
- Probabilistic inference of lateral gene transfer events.BMC bioinformatics · 2016Article
- Inferring gene duplications, transfers and losses can be done in a discrete framework.Journal of mathematical biology · 2016Article
- Joint amalgamation of most parsimonious reconciled gene trees.Bioinformatics (Oxford, England) · 2015Article
- The inference of gene trees with species trees.Systematic biology · 2015Review
- Recovering the treelike trend of evolution despite extensive lateral genetic transfer: a probabilistic analysis.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Article
- The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis.BMC evolutionary biology · 2011Article
- The origin of multicellularity in cyanobacteria.BMC evolutionary biology · 2011Article
- Evaluating phylogenetic congruence in the post-genomic era.Genome biology and evolution · 2011Review
- Lateral genetic transfer: open issues.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2009Review
- Matrilocal residence is ancestral in Austronesian societies.Proceedings. Biological sciences · 2009Article
- Dealing with incongruence in phylogenomic analyses.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2008Article
- Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria.BMC evolutionary biology · 2008Article
- Phylogenetic detection of recombination with a Bayesian prior on the distance between trees.PloS one · 2008Article
- Leptospira interrogans endostatin-like outer membrane proteins bind host fibronectin, laminin and regulators of complement.PloS one · 2007Article
Corrections and comments
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Authors and funding
1 author.
Funding
Abstract
Horizontal gene transfer (HGT) plays a critical role in evolution across all domains of life with important biological and medical implications. I propose a simple class of stochastic models to examine HGT using multiple orthologous gene alignments. The models function in a hierarchical phylogenetic framework. The top level of the hierarchy is based on a random walk process in "tree space" that allows for the development of a joint probabilistic distribution over multiple gene trees and an unknown, but estimable species tree. I consider two general forms of random walks. The first form is derived from the subtree prune and regraft (SPR) operator that mirrors the observed effects that HGT has on inferred trees. The second form is based on walks over complete graphs and offers numerically tractable solutions for an increasing number of taxa. The bottom level of the hierarchy utilizes standard phylogenetic models to reconstruct gene trees given multiple gene alignments conditional on the random walk process. I develop a well-mixing Markov chain Monte Carlo algorithm to fit the models in a Bayesian framework. I demonstrate the flexibility of these stochastic models to test competing ideas about HGT by examining the complexity hypothesis. Using 144 orthologous gene alignments from six prokaryotes previously collected and analyzed, Bayesian model selection finds support for (1) the SPR model over the alternative form, (2) the 16S rRNA reconstruction as the most likely species tree, and (3) increased HGT of operational genes compared to informational genes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.