Species Trees from Highly Incongruent Gene Trees in Rice Export

@article{citeulike:5878782, abstract = {Several methods have recently been developed to infer multilocus phylogenies by incorporating information from topological incongruence of the individual genes. In this study, we investigate 2 such methods, Bayesian concordance analysis and Bayesian estimation of species trees. Our test data are a collection of genes from cultivated rice (genus Oryza) and the most closely related wild species, generated using a high-throughput sequencing protocol and bioinformatics pipeline. Trees inferred from independent genes display levels of topological incongruence that far exceed that seen in previous data sets analyzed with these species tree methods. We identify differences in phylogenetic results between inference methods that incorporate gene tree incongruence. Finally, we discuss the challenges of scaling these analyses for data sets with thousands of gene trees and extensive levels of missing data. 10.1093/sysbio/syp054}, author = {Cranston, Karen A. and Hurwitz, Bonnie and Ware, Doreen and Stein, Lincoln and Wing, Rod A.}, citeulike-article-id = {5878782}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/sysbio/syp054}, citeulike-linkout-1 = {http://sysbio.oxfordjournals.org/content/syp054v1/.abstract}, citeulike-linkout-2 = {http://sysbio.oxfordjournals.org/content/syp054v1/.full.pdf}, citeulike-linkout-3 = {http://sysbio.oxfordjournals.org/cgi/content/abstract/58/5/489}, day = {1}, doi = {10.1093/sysbio/syp054}, journal = {Syst Biol}, keywords = {phylogeny, rice}, month = {October}, number = {5}, pages = {489--500}, posted-at = {2009-10-02 17:49:26}, priority = {2}, title = {Species Trees from Highly Incongruent Gene Trees in Rice}, url = {http://dx.doi.org/10.1093/sysbio/syp054}, volume = {58}, year = {2009} }

TY - JOUR ID - citeulike:5878782 L3 - citeulike-article-id:5878782 N2 - Several methods have recently been developed to infer multilocus phylogenies by incorporating information from topological incongruence of the individual genes. In this study, we investigate 2 such methods, Bayesian concordance analysis and Bayesian estimation of species trees. Our test data are a collection of genes from cultivated rice (genus Oryza) and the most closely related wild species, generated using a high-throughput sequencing protocol and bioinformatics pipeline. Trees inferred from independent genes display levels of topological incongruence that far exceed that seen in previous data sets analyzed with these species tree methods. We identify differences in phylogenetic results between inference methods that incorporate gene tree incongruence. Finally, we discuss the challenges of scaling these analyses for data sets with thousands of gene trees and extensive levels of missing data. 10.1093/sysbio/syp054 IS - 5 JF - Syst Biol EP - 500 TI - Species Trees from Highly Incongruent Gene Trees in Rice VL - 58 SP - 489 KW - phylogeny KW - rice AU - Cranston, Karen AU - Hurwitz, Bonnie AU - Ware, Doreen AU - Stein, Lincoln AU - Wing, Rod PY - 2009/10/01/ UR - http://dx.doi.org/10.1093/sysbio/syp054 ER -