Phylogenomics: the beginning of incongruence?

@article{citeulike:532511, abstract = {Until recently, molecular phylogenies based on a single or few orthologous genes often yielded contradictory results. Using multiple genes in a large concatenation was proposed to end these incongruences. Here we show that single-gene phylogenies often produce incongruences, albeit ones lacking statistically significant support. By contrast, the use of different tree reconstruction methods on different partitions of the concatenated supergene leads to well-resolved, but real (i.e. statistically significant) incongruences. Gathering a large amount of data is not sufficient to produce reliable trees, given the current limitation of tree reconstruction methods, especially when the quality of data is poor. We propose that selecting only data that contain minimal nonphylogenetic signals takes full advantage of phylogenomics and markedly reduces incongruence.}, address = {Canadian Institute for Advanced Research, Centre Robert-Cedergren, D\'{e}partement de Biochimie, Universit\'{e} de Montr\'{e}al, Succursale Centre-Ville, Montr\'{e}al, Qu\'{e}bec, Canada, H3C3J7.}, author = {Jeffroy, Olivier and Brinkmann, Henner and Delsuc, Fr\'{e}d\'{e}ric and Philippe, Herv\'{e} }, citeulike-article-id = {532511}, doi = {http://dx.doi.org/10.1016/j.tig.2006.02.003}, issn = {0168-9525}, journal = {Trends Genet}, keywords = {genome, molecular-evolution, phylogenomics, phylogeny, review}, month = {February}, posted-at = {2007-05-26 14:26:56}, priority = {3}, title = {Phylogenomics: the beginning of incongruence?}, url = {http://dx.doi.org/10.1016/j.tig.2006.02.003}, year = {2006} }

TY - JOUR ID - citeulike:532511 L3 - citeulike-article-id:532511 N2 - Until recently, molecular phylogenies based on a single or few orthologous genes often yielded contradictory results. Using multiple genes in a large concatenation was proposed to end these incongruences. Here we show that single-gene phylogenies often produce incongruences, albeit ones lacking statistically significant support. By contrast, the use of different tree reconstruction methods on different partitions of the concatenated supergene leads to well-resolved, but real (i.e. statistically significant) incongruences. Gathering a large amount of data is not sufficient to produce reliable trees, given the current limitation of tree reconstruction methods, especially when the quality of data is poor. We propose that selecting only data that contain minimal nonphylogenetic signals takes full advantage of phylogenomics and markedly reduces incongruence. JF - Trends Genet SN - 0168-9525 AD - Canadian Institute for Advanced Research, Centre Robert-Cedergren, Département de Biochimie, Université de Montréal, Succursale Centre-Ville, Montréal, Québec, Canada, H3C3J7. TI - Phylogenomics: the beginning of incongruence? KW - genome KW - molecular-evolution KW - phylogenomics KW - phylogeny KW - review AU - Jeffroy, Olivier AU - Brinkmann, Henner AU - Delsuc, Frédéric AU - Philippe, Hervé PY - 2006/02/18/ UR - http://dx.doi.org/10.1016/j.tig.2006.02.003 ER -