title: Multilocus phylogenetic inference in subfamily Chlorogaloideae and related genera of Agavaceae - informing questions in taxonomy at multiple ranks.
abstract: A series of taxonomic questions at the subfamilial, generic, and intrageneric levels have remained within subfamily Chlorogaloideae s.s. (comprising Camassia, Chlorogalum, Hastingsia, and Schoenolirion) and relatives in Agavaceae. We present the first phylogenetic hypotheses focused on Chlorogaloideae that are based on multiple independent loci and include a wide sampling of outgroups across Agavaceae. In addition to chloroplast regions ndhF and trnL-trnF, we used nrDNA ITS for phylogenetic inference. Incomplete concerted evolution of the latter is indicated by intra-individual site polymorphisms for nearly half of the individuals. Comparisons of four coding and analysis methods for these characters indicate that the region remains phylogenetically informative. Our results confirm that Chlorogaloideae s.s. is not monophyletic, due to the close relationship of Schoenolirion with Hesperaloe and Hesperoyucca, as well as the likely sister relationship between Hesperocallis and core Chlorogaloideae (Camassia, Chlorogalum, and Hastingsia). Chlorogalum is also not monophyletic, being divided with strong support into vespertine and diurnal clades. This study produced the first phylogenetic hypotheses across Hesperaloe, allowing initial tests of several taxonomic disagreements within this genus. Our results reveal the lack of cohesion of H. funifera, indicating that H. funifera ssp. funifera may be more closely related to H. campanulata than to H. funifera ssp. chiangii (=H. chiangii). With potential gene flow between many members of Hesperaloe and a possible hybrid origin for H. campanulata, the genetic relationships within this genus appear complex. Further population-level investigation of many of the taxa in Chlorogaloideae s.l. would benefit our understanding of the evolution and taxonomy of these groups; Camassia and Hastingsia are the current focus of ongoing study.
authors.affiliation: Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA. Electronic address: jkarchibald@yahoo.com.
authors.forename: Jenny K
authors.initials: JK
authors.lastname: Archibald
authors.affiliation: Department of Biology, Willamette University, Salem, OR 97301, USA. Electronic address: skephart@willamette.edu.
authors.forename: Susan R
authors.initials: SR
authors.lastname: Kephart
authors.affiliation: Department of Biology, Willamette University, Salem, OR 97301, USA. Electronic address: kathryn.theiss@gmail.com.
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Theiss
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, CA 94709, USA. Electronic address: annapetrosky@berkeley.edu.
authors.forename: Anna L
authors.initials: AL
authors.lastname: Petrosky
authors.affiliation: Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA. Electronic address: theresa.culley@uc.edu.
authors.forename: Theresa M
authors.initials: TM
authors.lastname: Culley
mesh_terms: D000070357:Asparagaceae / Q000145:classification*; D001499:Bayes Theorem; D005075:Biological Evolution; D018742:DNA, Chloroplast / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D018742:DNA, Chloroplast; D018744:DNA, Plant; D021903:DNA, Ribosomal Spacer
keywords: Agavaceae; Chlorogaloideae; Chlorogalum; Hesperaloe; Hesperocallis; ITS