Reassessment of phylogenetic relationships in Clarkia sect. Sympherica

Abstract

Clarkia (Onagraceae) is a genus of 42 annual species, mostly native to California, that has served as a model for many studies of plant evolutionary biology, particularly morphological, cytological, and genetic divergence; reproductive isolation; and speciation. Section Sympherica is the largest section with eight diploid and one allotetraploid species. Species in the section have provided important evidence about the evolution of reproductive isolation (C. lingulata derived from C. biloba) and large morphological change (C. dudleyana thought to be sister to the morphologically distinct C. heterandra, recently transferred into Clarkia from the monotypic Heterogaura). Clarkia epilobioides, another diploid species in the section, was previously shown to be one parent of the allotetraploid C. delicata, the other parent being C. unguiculata from sect. Phaeostoma. Lewis and Lewis (1955) interpreted the parentage of C. delicata and other evidence of intersectional hybridization to mean that the diploid sections of the genus, though highly diverse, were closely related and should be maintained in the single genus Clarkia. Here we assess phylogenetic relationships among the species of sect. Sympherica and related species by analyzing the nucleotide sequences of PgiC1 and PgiC2, a pair of paralogous genes that encode the cytosolic isozyme of phosphoglucose isomerase (EC 5.3.1.9). The major results were the following: (1) C. unguiculata and both genomes of C. delicata are within a well-defined "Sympherica" clade; thus, C. delicata should not be considered an intersectional hybrid; (2) C. heterandra belongs in the clade and is closely related to C. unguiculata; and (3) on the evidence of PgiC1, C. dudleyana is not in the clade and is not closely related to C. heterandra.

Paraphyly in Tribe Onagreae: Insights into Phylogenetic Relationships of Onagraceae Based on Nuclear and Chloroplast Sequence Data

“…The monophyly of Clarkia is supported by a PgiC gene duplication (Gottlieb and Ford 1996;Ford and Gottlieb 2003) and the shared presence of unicellular papillae on the stigmatic surface (Heslop-Harrison 1990;Hoch et al 1993). Relationships among the sections of Clarkia generally agree with other more detailed analyses (Sytsma et al 1990;Gottlieb and Ford 1996;Ford and Gottlieb 2003;W. J. Hahn et al, in mss.…”

“…Connubium) and C. pulchella (sect. Clarkia), associate with the sectional representative of one of their presumed parents determined from more detailed studies (Lewis and Lewis 1955;Gottlieb and Ford 1996;Ford and Gottlieb 2003). Thus, Clarkia delicata groups with C. heterandra (sect.…”

“…Thus, Clarkia delicata groups with C. heterandra (sect. Heterogaura; ''Sympherica'' clade of Ford and Gottlieb 2003) in the ITS analysis and with C. rostrata (sect. Sympherica) in the cp analyses.…”

“…There have also been various phylogenetic studies of individual genera within the family, including Fuchsia Smith 1988, 1992;Sytsma et al 1991a; P. Berry et al, U. WisconsinMadison, in mss. ), Lopezia (O'Kane and Schaal 1998), Clarkia Smith 1988, 1992;Sytsma et al 1990;Gottlieb and Ford 1996;Ford and Gottlieb 2003;W. J. Hahn et al, in mss.…”

Plant sex and the evolution of plant defenses against herbivores

“…To estimate the phylogeny of Onagreae, we combined existing datasets from GenBank for 2 plastid regions [trnL-trnF spacer (54) and rps16 intron (55)(56)(57)] and 3 nuclear regions [introns 1-6 (plus exons) of the cytosolic isozyme phosphoglucose isomerase (PgiC) (58,59), nuclear ribosomal internal transcribed spacer region (ITS) and the external transcribed spacer (ETS) (55,56)] (Table S1). We expanded the existing dataset to include additional species in clades exhibiting variation in sexual reproduction by sequencing trnL-trnF and ITS from 33 species and PgiC from 43 species by using standard PCR conditions (Table S1 and Table S5) (55,56,60). In total, our taxon sampling encompassed 113 species of Onagreae (44% of described species) plus 8 outgroup taxa (Fig.…”