title: Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.
abstract: OBJECTIVE
  Estimating phylogenetic relationships in relatively recent evolutionary radiations is challenging, especially if short branches associated with recent divergence result in multiple gene tree histories. We combine anchored enrichment next-generation sequencing with species tree analyses to produce a robust estimate of phylogenetic relationships in the genus Protea (Proteaceae), an iconic radiation in South Africa.
  
  
  METHODS
  We sampled multiple individuals within 59 out of 112 species of Protea and 6 outgroup species for a total of 163 individuals, and obtained sequences for 498 low-copy, orthologous nuclear loci using anchored phylogenomics. We compare several approaches for building species trees, and explore gene tree-species tree discrepancies to determine whether poor phylogenetic resolution reflects a lack of informative sites, incomplete lineage sorting, or hybridization.
  
  
  RESULTS
  Phylogenetic estimates from species tree approaches are similar to one another and recover previously well-supported clades within Protea, in addition to providing well-supported phylogenetic hypotheses for previously poorly resolved intrageneric relationships. Individual gene trees are markedly different from one another and from species trees. Nonetheless, analyses indicate that differences among gene trees occur primarily concerning clades supported by short branches.
  
  
  CONCLUSIONS
  Species tree methods using hundreds of nuclear loci provided strong support for many previously unresolved relationships in the radiation of the genus Protea. In cases where support for particular relationships remains low, these appear to arise from few informative sites and lack of information rather than strongly supported disagreement among gene trees.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269 United States nora.mitchell@uconn.edu nora.c.mitchell@gmail.com.
authors.forename: Nora
authors.initials: N
authors.lastname: Mitchell
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269 United States.
authors.forename: Paul O
authors.initials: PO
authors.lastname: Lewis
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32306 United States.
authors.forename: Emily Moriarty
authors.initials: EM
authors.lastname: Lemmon
authors.affiliation: Department of Scientific Computing, Florida State University, Tallahassee, Florida 32306 United States.
authors.forename: Alan R
authors.initials: AR
authors.lastname: Lemmon
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269 United States.
authors.forename: Kent E
authors.initials: KE
authors.lastname: Holsinger
mesh_terms: D019143:Evolution, Molecular; D017343:Genes, Plant / Q000235:genetics; D049810:Genetic Speciation; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D005843:Geography; D059014:High-Throughput Nucleotide Sequencing; D008957:Models, Genetic; D010802:Phylogeny; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development; D039105:Proteaceae / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D013019:South Africa; D013045:Species Specificity
keywords: Proteaceae; anchored phylogenomics; coalescence; phylogenetics; radiation