Simultaneous Bayesian gene tree reconstruction and reconciliation analysis Export

@article{citeulike:4204246, abstract = {10.1073/pnas.0806251106 We present GSR, a probabilistic model integrating gene duplication, sequence evolution, and a relaxed molecular clock for substitution rates, that enables genomewide analysis of gene families. The gene duplication and loss process is a major cause for incongruence between gene and species tree, and deterministic methods have been developed to explain such differences through tree reconciliations. Although probabilistic methods for phylogenetic inference have been around for decades, probabilistic reconciliation methods are far less established. Based on our model, we have implemented a Bayesian analysis tool, PrIME-GSR, for gene tree inference that takes a known species tree into account. Our implementation is sound and we demonstrate its utility for genomewide gene-family analysis by applying it to recently presented yeast data. We validate PrIME-GSR by comparing with previous analyses of these data that take advantage of gene order information. In a case study we apply our method to the ADH gene family and are able to draw biologically relevant conclusions concerning gene duplications creating key yeast phenotypes. On a higher level this shows the biological relevance of our method. The obtained results demonstrate the value of a relaxed molecular clock. Our good performance will extend to species where gene order conservation is insufficient.}, author = {\~{A}…kerborg, \~{A}–rjan and Sennblad, Bengt and Arvestad, Lars and Lagergren, Jens}, citeulike-article-id = {4204246}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0806251106}, citeulike-linkout-1 = {http://www.pnas.org/content/106/14/5714.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/106/14/5714.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19299507}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19299507}, day = {7}, doi = {10.1073/pnas.0806251106}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, keywords = {bayesian, duplication, phylogenetics}, month = {April}, number = {14}, pages = {5714--5719}, posted-at = {2009-05-11 17:45:45}, priority = {2}, title = {Simultaneous Bayesian gene tree reconstruction and reconciliation analysis}, url = {http://dx.doi.org/10.1073/pnas.0806251106}, volume = {106}, year = {2009} }

TY - JOUR ID - citeulike:4204246 L3 - citeulike-article-id:4204246 N2 - 10.1073/pnas.0806251106 We present GSR, a probabilistic model integrating gene duplication, sequence evolution, and a relaxed molecular clock for substitution rates, that enables genomewide analysis of gene families. The gene duplication and loss process is a major cause for incongruence between gene and species tree, and deterministic methods have been developed to explain such differences through tree reconciliations. Although probabilistic methods for phylogenetic inference have been around for decades, probabilistic reconciliation methods are far less established. Based on our model, we have implemented a Bayesian analysis tool, PrIME-GSR, for gene tree inference that takes a known species tree into account. Our implementation is sound and we demonstrate its utility for genomewide gene-family analysis by applying it to recently presented yeast data. We validate PrIME-GSR by comparing with previous analyses of these data that take advantage of gene order information. In a case study we apply our method to the ADH gene family and are able to draw biologically relevant conclusions concerning gene duplications creating key yeast phenotypes. On a higher level this shows the biological relevance of our method. The obtained results demonstrate the value of a relaxed molecular clock. Our good performance will extend to species where gene order conservation is insufficient. IS - 14 JF - Proceedings of the National Academy of Sciences SN - 1091-6490 EP - 5719 TI - Simultaneous Bayesian gene tree reconstruction and reconciliation analysis VL - 106 SP - 5714 KW - bayesian KW - duplication KW - phylogenetics AU - Åkerborg, Örjan AU - Sennblad, Bengt AU - Arvestad, Lars AU - Lagergren, Jens PY - 2009/04/07/ UR - http://dx.doi.org/10.1073/pnas.0806251106 ER -