@ARTICLE{TreeBASE2Ref26331, author = {David M. Spooner and Holly M Ruess and Massimo Iorizzo and Douglas Senalik and Philipp W. Simon}, title = {Entire Plastid Phylogeny of the Carrot Genus (Daucus, Apiaceae); Concordance to Nuclear Data and Mitochondrial and Nuclear DNA Transfer to the Plastid}, year = {2017}, keywords = {}, doi = {}, url = {http://www.amjbot.org/content/104/2/296.full}, pmid = {}, journal = {American Journal of Botany}, volume = {104}, number = {2}, pages = {296--312}, abstract = {Premise of the study: We explored (1) the phylogenetic utility of entire plastid DNA sequence data in Daucus, (2) the concordance among various subsets of the plastid data, (3) the concordance to nuclear DNA sequence data, and (4) the concordance to currently known mitochondrial DNA transfer to the plastid (DcMP), in wild and cultivated carrot, Daucus species. Methods: We studied the phylogeny of 36 accessions of 20 Daucus and Daucus ingroup (Pseudorlaya pumila and Rouya polygama) taxa and two outgroups (Caucalis platycarpos and Oenanthe virgata) (38 accessions in total) with entire plastid DNA sequences. We compared these results to various subsets of the entire plastid data, including those traditionally used for phylogeny reconstruction, to a well-resolved nuclear phylogeny using 94 nuclear orthologs (Arbizu et al., 1994. Amer. J. Bot. 101: 1666-1685), and to other phylogenies of Daucus using nuclear and/or plastid markers; and expanded knowledge of the mitochondrial DNA transfer to the plastid data (DcMP). Key results: Our maximum parsimony and maximum likelihood trees of the entire dataset of about 155,000 aligned bases (excluding one of the two inverted repeat regions) were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. Various subsets of the data, including regions traditionally used as phylogenetically informative regions, however, provide support and congruence to the entire dataset ranging from high to low; however, there was only incongruence. Discussion of mitochondrial results (short). Conclusions: Resequencing data of Daucus and generic ingroups, and two outgroups, analyzed with the benefit of a well-resolved de-novo sequence of D. carota, and with a previously well-resolved nuclear phylogeny of the same dataset, have allowed us to (1) produce a well-resolved plastid phylogeny of Daucus, (2) allow us to compare subsets of the entire plastid data for phylogeny, (3) allow us to examine plastid and nuclear DNA phylogenetic incongruence, and (4) allow us to examine mitochondrial and nuclear DNA transfer into the plastid. However, this is just one of many applications that await the mining of these resequencing datasets. The tremendous power of this approach suggests that as more de-novo sequences become available such a strategy will become more common in phylogenetic and genetic studies. } }

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