TreeBASE Search-Trees for study 11390

@ARTICLE{TreeBASE2Ref19614, author = {Norman J Wickett and Laura Lowe Forrest and Jessica M. Budke and Blanka Shaw and Bernard Goffinet}, title = {Frequent pseudogenization and loss of the plastid-encoded, sulfate transport gene cysA throughout the evolution of liverworts.}, year = {2011}, keywords = {cysA; gene loss; liverwort; plastid; pseudogene}, doi = {10.3732/ajb.1100010}, url = {http://}, pmid = {}, journal = {American Journal of Botany}, volume = {98}, number = {8}, pages = {1263--75}, abstract = {Premise of the study: Comparative analyses of liverwort plastid genomes revealed that the sulfate transport gene, cysA, is a pseudogene in some species of the clade Metzgeriidae. We surveyed 63 liverworts from all major clades to determine whether the loss of cysA occurs only in Metzgeriidae and whether the loss is phylogenetically significant. We tested whether intact copies of cysA are evolving under selective constraints and whether rates of nucleotide substitution differ in plastid genes from taxa with and without an intact copy of cysA. Methods: Primers annealing to flanking and internal regions were used to amplify and sequence cysA from 61 liverworts. The ancestral states of cysA were reconstructed on a phylogenetic hypothesis inferred from seven markers. Rates of nucleotide substitutions were estimated for three plastid loci to approximate the rate of substitution of plastid genes. The ratio of nonsynonymous to synonymous substitutions was estimated for intact copies of cysA to infer selective constraints. Key results: Throughout liverworts, cysA has been lost up to 29 times. Intact copies of cysA are evolving under selective constraint, which is relaxed in non-complex thalloids. Gene loss is more frequent in groups with an increased rate of substitution in the plastome. Conclusions: The number of inferred losses of cysA in liverworts exceeds any other reported gene. It appears that cysA is lost from the plastome as the intrinsic rate of nucleotide substitution in the plastid genome increases, suggesting that it is this rate that governs the fate of cysA.} }