title: Resolving incongruence: Species of hybrid origin in Columnea (Gesneriaceae).
abstract: Speciation by hybridization has long been recognized among plants and includes both homoploid and allopolyploid speciation. The numbers of presumed hybrid species averages close to 11% and tends to be concentrated in a subset of angiosperm families. Recent advances in molecular methods have verified species of hybrid origin that had been presumed on the basis of morphology and have identified species that were not initially considered hybrids. Identifying species of hybrid origin is often a challenge and typically based on intermediate morphology, or discrepancies between molecular datasets. Discrepancies between data partitions may result from several factors including poor support, incomplete lineage sorting, or hybridization. A phylogenetic analysis of species in Columnea (Gesneriaceae) indicated significant incongruencies between the cpDNA and nrDNA datasets. Tests that examined whether one or both of the datasets had the phylogenetic signal to reject the topology of the alternate dataset (Shimodaira and Hasegawa [SH] and approximately unbiased [AU] tests) indicated significant differences between the topologies. Splitstree analyses also showed that there was support for the placement of the discrepant taxa in both datasets and that the combined data placed the putative hybrid species in an intermediate position between the two datasets. The genealogical sorting index (GSI) implied that coalescence in nrDNA had occurred in all species where more than a single individual had been sampled, but the GSI value was lower for the cpDNA of most of the putative hybrids, implying that these regions have not yet coalesced in these lineages despite being haploid. The JML test that evaluates simulated species pairwise distances against observed distances also implies that observed nrDNA data generate shorter distances than simulated data, implying hybridization. It is most likely that C. gigantifolia, C. rubriacuta, and C. sp. nov. represent a lineage from a hybrid ancestor, but C. moorei may be a more recent hybrid and may still be undergoing hybridization with sympatric species.
authors.affiliation: Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID 83725-1515, USA. Electronic address: jfsmith@boisestate.edu.
authors.forename: James F
authors.initials: JF
authors.lastname: Smith
authors.affiliation: Department of Biological Sciences, The University of Alabama, Box 870345, Tuscaloosa, AL 35487, USA; The Lawrenceville School: Science Department, The Lawrenceville School, 2500 Main Street, Lawrenceville, NJ 08648, USA.
authors.forename: John L
authors.initials: JL
authors.lastname: Clark
authors.affiliation: Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Apartado 7495, Bogotá, Colombia.
authors.forename: Marisol
authors.initials: M
authors.lastname: Amaya-Márquez
authors.affiliation: Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Apartado 7495, Bogotá, Colombia; Posgrado en Ciencias, Instituto de Ecología, INECOL A.C, Carretera antigua a Coatepec 351, El Haya, Xalapa 91070, Veracruz, Mexico.
authors.forename: Oscar H
authors.initials: OH
authors.lastname: Marín-Gómez
mesh_terms: D001499:Bayes Theorem; D002736:Chloroplasts / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D006824:Hybridization, Genetic; D000068378:Lamiales / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D061350:Sympatry
chemical_list: D018744:DNA, Plant
keywords: Hybrid species; Interspecific hybrids; nrDNA capture