A Machine-Learning Approach Reveals That Alignment Properties Alone Can Accurately Predict Inference of Lateral Gene Transfer from Discordant Phylogenies Export

@article{citeulike:5433504, abstract = {Among the methods currently used in phylogenomic practice to detect the presence of lateral gene transfer (LGT), one of the most frequently employed is the comparison of gene tree topologies for different genes. In cases where the phylogenies for different genes are incompatible, or discordant, for well-supported branches there are three simple interpretations for the result: 1) gene duplications (paralogy) followed by many independent gene losses have occurred, 2) LGT has occurred, or 3) the phylogeny is well supported but for reasons unknown is nonetheless incorrect. Here, we focus on the third possibility by examining the properties of 22,437 published multiple sequence alignments, the Bayesian maximum likelihood trees for which either do or do not suggest the occurrence of LGT by the criterion of discordant branches. The alignments that produce discordant phylogenies differ significantly in several salient alignment properties from those that do not. Using a support vector machine, we were able to predict the inference of discordant tree topologies with up to 80\% accuracy from alignment properties alone. 10.1093/molbev/msp105}, author = {Roettger, Mayo and Martin, William and Dagan, Tal}, citeulike-article-id = {5433504}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/molbev/msp105}, citeulike-linkout-1 = {http://mbe.oxfordjournals.org/content/26/9/1931.abstract}, citeulike-linkout-2 = {http://mbe.oxfordjournals.org/content/26/9/1931.full.pdf}, citeulike-linkout-3 = {http://mbe.oxfordjournals.org/cgi/content/abstract/26/9/1931}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19443855}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19443855}, day = {1}, doi = {10.1093/molbev/msp105}, journal = {Mol Biol Evol}, keywords = {alignment, computational\_biology, horizontal\_gene\_transfer, methods}, month = {September}, number = {9}, pages = {1931--1939}, posted-at = {2009-08-21 20:55:09}, priority = {2}, title = {A Machine-Learning Approach Reveals That Alignment Properties Alone Can Accurately Predict Inference of Lateral Gene Transfer from Discordant Phylogenies}, url = {http://dx.doi.org/10.1093/molbev/msp105}, volume = {26}, year = {2009} }

TY - JOUR ID - citeulike:5433504 L3 - citeulike-article-id:5433504 N2 - Among the methods currently used in phylogenomic practice to detect the presence of lateral gene transfer (LGT), one of the most frequently employed is the comparison of gene tree topologies for different genes. In cases where the phylogenies for different genes are incompatible, or discordant, for well-supported branches there are three simple interpretations for the result: 1) gene duplications (paralogy) followed by many independent gene losses have occurred, 2) LGT has occurred, or 3) the phylogeny is well supported but for reasons unknown is nonetheless incorrect. Here, we focus on the third possibility by examining the properties of 22,437 published multiple sequence alignments, the Bayesian maximum likelihood trees for which either do or do not suggest the occurrence of LGT by the criterion of discordant branches. The alignments that produce discordant phylogenies differ significantly in several salient alignment properties from those that do not. Using a support vector machine, we were able to predict the inference of discordant tree topologies with up to 80% accuracy from alignment properties alone. 10.1093/molbev/msp105 IS - 9 JF - Mol Biol Evol EP - 1939 TI - A Machine-Learning Approach Reveals That Alignment Properties Alone Can Accurately Predict Inference of Lateral Gene Transfer from Discordant Phylogenies VL - 26 SP - 1931 KW - alignment KW - computational_biology KW - horizontal_gene_transfer KW - methods AU - Roettger, Mayo AU - Martin, William AU - Dagan, Tal PY - 2009/09/01/ UR - http://dx.doi.org/10.1093/molbev/msp105 ER -