title: Multiplexed-shotgun-genotyping data resolve phylogeny within a very recently derived insular lineage.
abstract: OBJECTIVE
  Endemic plants on oceanic islands have long served as model systems for studying patterns and processes of evolution. However, phylogenetic studies of island plants frequently illustrate a decoupling of molecular divergence and ecological/morphological diversity, resulting in phylogenies lacking the resolution required to interpret patterns of evolution in a phylogenetic context. The current study uses the primarily Macaronesian flowering plant genus Tolpis to illustrate the utility of multiplexed shotgun genotyping (MSG) for resolving relationships at relatively deep (among archipelagos) and very shallow (within archipelagos) nodes in this small, yet diverse insular plant lineage that had not been resolved with other molecular markers.
  
  
  METHODS
  Genomic libraries for 27 accessions of Macaronesian Tolpis were generated for genotyping individuals using MSG, a form of reduced-representation sequencing, similar to restriction-site-associated DNA markers (RADseq). The resulting data files were processed using the program pyRAD, which clusters MSG loci within and between samples. Phylogenetic analyses of the aligned data matrix were conducted using RAxML.
  
  
  RESULTS
  Analysis of MSG data recovered a highly resolved phylogeny with generally strong support, including the first robust inference of relationships within the highly diverse Canary Island clade of Tolpis.
  
  
  CONCLUSIONS
  The current study illustrates the utility of MSG data for resolving relationships in lineages that have undergone recent, rapid diversification resulting in extensive ecological and morphological diversity. We suggest that a similar approach may prove generally useful for other rapid plant radiations where resolving phylogeny has been difficult.
authors: Department of Ecology and Evolutionary Biology, and Biodiversity Institute; University of Kansas, 1200 Sunnyside Ave, Lawrence, Kansas 66045 USA.
authors: Mark E
authors: ME
authors: Mort
authors: Department of Ecology and Evolutionary Biology, and Biodiversity Institute; University of Kansas, 1200 Sunnyside Ave, Lawrence, Kansas 66045 USA.
authors: Daniel J
authors: DJ
authors: Crawford
authors: Department of Ecology and Evolutionary Biology, 1200 Sunnyside Ave, Lawrence, Kansas 66045 USA.
authors: John K
authors: JK
authors: Kelly
authors: Calle Guaidil 16, Urbanización Tamarco, Tegueste, Tenerife, Canary Islands, Spain 38280.
authors: Arnoldo
authors: A
authors: Santos-Guerra
authors: Universidade da Madeira, Centro de Ciências da Vida, Campus da Penteada, Funchal, Portugal.
authors: Miguel
authors: M
authors: Menezes de Sequeira
authors: Universidade dos Açores, Departamento de Biologia, Rua da Mãe de Deus, Ponta Delgada, Azores, Portugal.
authors: Mónica
authors: M
authors: Moura
authors: Jardin Botanico Canario "Viera y Clavijo"-Unidad Asociada CSIC, Cabildo de Gran Canaria; Camino al Palmeral 15, Tafira Alta 35017 Las Palmas de Gran Canaria, Spain.
authors: Juli
authors: J
authors: Caujapé-Castells
mesh_terms: D019659:Asteraceae / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D018745:Genome, Plant; D015698:Genomic Library; D060005:Genotyping Techniques / Q000379:methods*; D062312:Islands; D017422:Sequence Analysis, DNA; D013030:Spain
keywords: Asteraceae; Canary Islands; Macaronesia; Tolpis; genome sequencing; multiplexed shotgun genotyping; phylogenomics; phylogeny; radiation