title: Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata; Asteraceae).
abstract: OBJECTIVE
  Hybridization has played an important role in the evolution and ecological adaptation of diploid and polyploid plants. Artemisia tridentata (Asteraceae) tetraploids are extremely widespread and of great ecological importance. These tetraploids are often taxonomically identified as A. tridentata subsp. wyomingensis or as autotetraploids of diploid subspecies tridentata and vaseyana. Few details are available as to how these tetraploids are formed or how they are related to diploid subspecies. •
  
  
  METHODS
  We used amplicon sequencing to assess phylogenetic relationships among three recognized subspecies: tridentata, vaseyana, and wyomingensis. DNA sequence data from putative genes were pyrosequenced and assembled from 329 samples. Nucleotide diversity and putative haplotypes were estimated from the high-read coverage. Phylogenies were constructed from Bayesian coalescence and neighbor-net network analyses. •
  
  
  RESULTS
  Analyses support distinct diploid subspecies of tridentata and vaseyana in spite of known hybridization in ecotones. Nucleotide diversity estimates of populations compared to the total diversity indicate the relationships are predominately driven by a small proportion of the amplicons. Tetraploids, including subspecies wyomingensis, are polyphyletic occurring within and between diploid subspecies groups. •
  
  
  CONCLUSIONS
  Artemisia tridentata is a species comprising phylogenetically distinct diploid progenitors and a tetraploid complex with varying degrees of phylogenetic and morphological affinities to the diploid subspecies. These analyses suggest tetraploids are formed locally or regionally from diploid tridentata and vaseyana populations via autotetraploidy, followed by introgression between tetraploid groups. Understanding the phylogenetic vs. ecological relationships of A. tridentata subspecies will have bearing on how to restore these desert ecosystems.
authors.affiliation: Rocky Mountain Research Station, USDA Forest Service, Provo, Utah 84606, USA. brichardson02@fs.fed.us
authors.forename: Bryce A
authors.initials: BA
authors.lastname: Richardson
authors.forename: Justin T
authors.initials: JT
authors.lastname: Page
authors.forename: Prabin
authors.initials: P
authors.lastname: Bajgain
authors.forename: Stewart C
authors.initials: SC
authors.lastname: Sanderson
authors.forename: Joshua A
authors.initials: JA
authors.lastname: Udall
mesh_terms: D019306:Artemisia / Q000033:anatomy & histology* / Q000145:classification / Q000235:genetics / Q000502:physiology*; D020451:Contig Mapping; D018744:DNA, Plant / Q000235:genetics*; D019143:Evolution, Molecular; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D015205:Northwestern United States; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D011123:Polyploidy; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D015206:Southwestern United States
chemical_list: D018744:DNA, Plant