title: Frequent pseudogenization and loss of the plastid-encoded sulfate-transport gene cysA throughout the evolution of liverworts.
abstract: OBJECTIVE
  The presence or absence of a functional copy of a plastid gene may reflect relaxed selection, and may be phylogenetically significant, reflecting shared ancestry. In some liverworts, the plastid gene cysA is a pseudogene (inferred to be nonfunctional). We surveyed 63 liverworts from all major clades to determine whether the loss of cysA is phylogenetically significant, whether intact copies of cysA are under selective constraints, and whether rates of nucleotide substitution differ in other plastid genes from taxa with and without a functional copy of cysA.
  
  
  METHODS
  Primers annealing to flanking and internal regions were used to amplify and sequence cysA from 61 liverworts. Two additional cysA sequences were downloaded from NCBI. The ancestral states of cysA were reconstructed on a phylogenetic hypothesis inferred from seven markers. Rates of nucleotide substitution were estimated for three plastid loci to reflect the intrinsic mutation rate in the plastid genome. The ratio of nonsynonymous to synonymous substitutions was estimated for intact copies of cysA to infer selective constraints.
  
  
  RESULTS
  Throughout liverworts, cysA has been lost up to 29 times, yet intact copies of cysA are evolving under selective constraints. Gene loss is more frequent in groups with an increased substitution rate in the plastid genome.
  
  
  CONCLUSIONS
  The number of inferred losses of cysA in liverworts exceeds any other reported plastid gene. Despite frequent losses, cysA is evolving under purifying selection in liverworts that retain the gene. It appears that cysA is lost more frequently in lineages characterized by a higher rate of nucleotide substitutions in the plastid.
authors.affiliation: Department of Biology, Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, Pennsylvania 16802, USA. njw17@psu.edu
authors.forename: Norman J
authors.initials: NJ
authors.lastname: Wickett
authors.forename: Laura L
authors.initials: LL
authors.lastname: Forrest
authors.forename: Jessica M
authors.initials: JM
authors.lastname: Budke
authors.forename: Blanka
authors.initials: B
authors.lastname: Shaw
authors.forename: Bernard
authors.initials: B
authors.lastname: Goffinet
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D019143:Evolution, Molecular; D017343:Genes, Plant; D054627:Genome, Plastid; D035926:Hepatophyta / Q000145:classification / Q000235:genetics*; D009154:Mutation; D010802:Phylogeny; D018087:Plastids / Q000235:genetics*; D011544:Pseudogenes; D012641:Selection, Genetic; D013045:Species Specificity
chemical_list: D017931:DNA Primers