title: Multilocus phylogeny and phylogenomics of Eriochrysis P. Beauv. (Poaceae-Andropogoneae): Taxonomic implications and evidence of interspecific hybridization.
abstract: Species delimitation is a vital issue concerning evolutionary biology and conservation of biodiversity. However, it is a challenging task for several reasons, including the low interspecies variability of markers currently used in phylogenetic reconstructions and the occurrence of reticulate evolution and polyploidy in many lineages of flowering plants. The first phylogeny of the grass genus Eriochrysis is presented here, focusing on the New World species, in order to examine its relationships to other genera of the subtribe Saccharinae/tribe Andropogoneae and to define the circumscriptions of its taxonomically complicated species. Molecular cloning and sequencing of five regions of four low-copy nuclear genes (apo1, d8, ep2-ex7 and ep2-ex8, kn1) were performed, as well as complete plastome sequencing. Trees were reconstructed using maximum parsimony, maximum likelihood, and Bayesian inference analyses. The present phylogenetic analyses indicate that Eriochrysis is monophyletic and the Old World E. pallida is sister to the New World species. Subtribe Saccharinae is polyphyletic, as is the genus Eulalia. Based on nuclear and plastome sequences plus morphology, we define the circumscriptions of the New World species of Eriochrysis: E. laxa is distinct from E. warmingiana, and E. villosa is distinct from E. cayennensis. Natural hybrids occur between E. laxa and E. villosa. The hybrids are probably tetraploids, based on the number of paralogues in the nuclear gene trees. This is the first record of a polyploid taxon in the genus Eriochrysis. Some incongruities between nuclear genes and plastome analyses were detected and are potentially caused by incomplete lineage sorting and/or ancient hybridization. The set of low-copy nuclear genes used in this study seems to be sufficient to resolve phylogenetic relationships and define the circumscriptions of other species complexes in the grass family and relatives, even in the presence of polyploidy and reticulate evolution. Complete plastome sequencing is also a promising tool for phylogenetic inference.
authors.affiliation: Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Botânica, Av. Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, RS, Brazil. Electronic address: cassiano_welker@yahoo.com.br.
authors.forename: Cassiano A D
authors.initials: CAD
authors.lastname: Welker
authors.affiliation: Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Botânica, Av. Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, RS, Brazil. Electronic address: tatiana.chies@ufrgs.br.
authors.forename: Tatiana T
authors.initials: TT
authors.lastname: Souza-Chies
authors.affiliation: Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Botânica, Av. Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, RS, Brazil. Electronic address: hmlwagner@gmail.com.
authors.forename: Hilda M
authors.initials: HM
authors.lastname: Longhi-Wagner
authors.affiliation: Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias (UNNE), Sargento Cabral 2131, Corrientes 3400, Argentina. Electronic address: mcpeichoto@agr.unne.edu.ar.
authors.forename: Myriam Carolina
authors.initials: MC
authors.lastname: Peichoto
authors.affiliation: Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA. Electronic address: mrmckain@gmail.com.
authors.forename: Michael R
authors.initials: MR
authors.lastname: McKain
authors.affiliation: Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA. Electronic address: ekellogg@danforthcenter.org.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Kellogg
mesh_terms: D001499:Bayes Theorem; D044822:Biodiversity; D004247:DNA / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D018745:Genome, Plant; D006824:Hybridization, Genetic; D010802:Phylogeny; D006109:Poaceae / Q000145:classification / Q000235:genetics*; D011123:Polyploidy; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA
keywords: Incomplete lineage sorting; Low-copy nuclear genes; Plastome; Polyploidy; Saccharinae; Species delimitation