title: Evaluating multi-locus phylogenies for species boundaries determination in the genusDiaporthe.
abstract: BACKGROUND
  Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genusDiaporthe. AccurateDiaporthespecies separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem.
  
  
  METHODS
  Here we addressed that problem by identifying five loci that have been sequenced in 142Diaportheisolates representing 96 species:TEF1,TUB,CAL,HISand ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees.
  
  
  RESULTS
  As expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying theTEF1-TUB-CAL-HIS4-loci tree as almost equivalent to the 5-loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus.
  
  
  CONCLUSIONS
  Our results question the current use of the ITS locus for DNA barcoding in the genusDiaportheand suggest thatTEF1might be a better choice if one locus barcoding needs to be done.
authors.affiliation: Departamento de Biologia, CESAM, Universidade de Aveiro , Aveiro , Portugal.
authors.forename: Liliana
authors.initials: L
authors.lastname: Santos
authors.affiliation: Departamento de Biologia, CESAM, Universidade de Aveiro , Aveiro , Portugal.
authors.forename: Artur
authors.initials: A
authors.lastname: Alves
authors.affiliation: Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida and IRBLleida , Lleida , Spain.
authors.forename: Rui
authors.initials: R
authors.lastname: Alves
keywords: Diaporthe; Maximum likelihood; Maximum parsimony; Multi-locus; Phomopsis; Phylogeny