Who is Who in Phylogenetic Networks

Publication no #2148   Type :   Html | Bib | Both

Created: 2011-10-24 15:13:16     Modified: 2012-01-15 11:13:39

2148 Simon Joly. JML: Testing hybridization from species trees. In Molecular Ecology Ressources, Vol. 12(1):179-184, 2012. Keywords: from species tree, hybridization, lineage sorting, phylogenetic network, phylogeny, Program JML, statistical model. Note: http://www.plantevolution.org/pdf/JMLpaper_accepted.pdf.         Toggle abstract "I introduce the software jml that tests for the presence of hybridization in multispecies sequence data sets by posterior predictive checking following Joly, McLenachan and Lockhart (2009, American Naturalist e54). Although their method could potentially be applied on any data set, the lack of appropriate software made its application difficult. The software jml thus fills a need for an easy application of the method but also includes improvements such as the possibility to incorporate uncertainty in the species tree topology. The jml software uses a posterior distribution of species trees, population sizes and branch lengths to simulate replicate sequence data sets using the coalescent with no migration. A test quantity, defined as the minimum pairwise sequence distance between sequences of two species, is then evaluated on the simulated data sets and compared to the one estimated from the original data. Because the test quantity is a good predictor of hybridization events, departure from the bifurcating species tree model could be interpreted as evidence of hybridization. Software performance in terms of computing time is evaluated for several parameters. I also show an application example of the software for detecting hybridization among native diploid North American roses. © 2011 Blackwell Publishing Ltd." @Article{Joly2012,       AUTHOR = {Joly, Simon},       TITLE = {JML: Testing hybridization from species trees},       YEAR = {2012},       JOURNAL = {Molecular Ecology Ressources},       VOLUME = {12},       NUMBER = {1},       PAGES = {179-184},       URL = {http://dx.doi.org/10.1111/j.1755-0998.2011.03065.x},       NOTE = {http://www.plantevolution.org/pdf/JMLpaper_accepted.pdf},       KEYWORDS = {from species tree, hybridization, lineage sorting, phylogenetic network, phylogeny, Program JML, statistical model} }