TreeBASE Search-Matrices for study 12348

@ARTICLE{TreeBASE2Ref20409, author = {Ole Seberg and Gitte Petersen and Jerrold I. Davis and J. Chris Pires and Dennis W. Stevenson and Mark W. Chase and M. F. Fay and Tina J?rgensen and Kenneth Jay Sytsma and Yohan Pillon}, title = {Phylogeny of the Asparagales based on three plastid and two mitochondrial genes}, year = {2012}, keywords = {Asparagales, edited sites, incongruence, maximum likelihood, parsimony}, doi = {}, url = {http://}, pmid = {}, journal = {American Journal of Botany}, volume = {99}, number = {5}, pages = {}, abstract = {Premise of the study: The Asparagales, with approximately 40% of all monocotyledons, include a host of commercially important ornamentals in families such as Orchidaceae, Alliaceae, and Iridaceae, and several important crop species in genera such as Allium, Aloe, Asparagus, Crocus, and Vanilla. Though the order is rather well-defined, the number of recognised families, their circumscription, and relationships are somewhat controversial. Methods: Phylogenetic analyses of Asparagales based on parsimony and maximum likelihood were conducted using nucleotide sequence variation in three plastid genes (matK, ndhF, and rbcL) and two mitochondrial genes (atp1 and cob). Branch support was assessed using both jackknife analysis implementing strict-consensus (SC), and bootstrap analysis implementing frequency-within-replicates (FWR). The contribution of edited sites in the mitochondrial genes to topology and branch support is investigated. Key results: The topologies recovered are largely in agreement with previous results, though some clades remain poorly resolved (e.g., Ruscaceae). When the edited sites are included in the analysis the plastid and mitochondrial genes are highly incongruent. However, when removed the two partitions become congruent. Conclusions: Some of the deeper nodes in the Asparagales phylogeny remain poorly or unresolved as do the relationships of certain monogeneric families (e.g., Ixioliriaceae, Doryanthaceae), whereas the support for many families is growing. However, the increased support is dominated by plastid data, and the potential influence of mitochondrial and biparentially inherited single or low-copy nuclear genes should be investigated. } }