Leigh A. Johnson

matK DNA sequences and phylogenetic reconstruction in Saxifragaceae s. str.

Comparative DNA sequencing of matK, a maturase coding gene located within the intron of the chloroplast gene trnK, was evaluated for phylogenetic utility using genera of Saxi- fragaceae s. str. The entire matK gene was sequenced for two members of the family, Sullivantia sullivantii and Saxifraga integrifolia. Comparison of base substitution rates between these two species indicated that matK evolves approximately three-fold faster than rbcL. Comparative sequencing of 754 base pairs within matK was subsequently conducted using 25 genera in Saxifragaceae s. str. and two outgroup taxa. Summed over the 31 taxa sequenced for this 754 base pair region, 40% of the base positions were variable and 15.6% were potentially informative. Five insertion/deletion events of three or six base pairs were also detected. Skewness and randomization tests both suggest that significant non-random structure is present in the matK data set. Parsimony analyses provided 72 most parsimonious trees of 223 steps (excluding autapomorphies) with a consistency index of 0.565. Several well-supported groups of genera are highly concordant with relationships suggested by two other chloroplast DNA data sets: chloroplast DNA restriction sites and rbcL sequences.

Assessing Congruence: Empirical Examples from Molecular Data

Numerous DNA regions representing the nuclear and both organellar genomes are now available for comparative sequencing in plants (see Chapter 1); in addition, morphological and chemical data can also be obtained for phylogenetic analyses. With such a diversity of potential data sets available and the relative ease with which DNA sequences can be obtained, the acquisition of multiple data sets for the same suite of taxa is straightforward. As a result, the number of groups for which multiple data sets is available is increasing rapidly. Although it is readily apparent that multiple data sets are needed for estimating phylogenetic relationships reliably, it is also recognized that different genes may, in fact, possess different branching histories (see Chapter 10). Consequently, incorporating multiple data sets into phylogenetic studies is not a casual undertaking. Essential tasks in the analysis of multiple data sets include assessing congruence between different phylogenetic trees and data sets, and ascertaining whether multiple data sets should be combined into a single data matrix prior to phylogenetic reconstruction.

Interfamilial Relationships in Myrtales: Molecular Phylogeny and Patterns of Morphological Evolution

Numerous phenotypic (morphological, palynological, cytological, and anatomical) studies have been conducted on Myrtales, yet the detailed relationships among the families of the order remain elusive. In this paper, the rbcL sequences of 50 taxa (39 representatives of Myrtales and 11 rosid outgroups) were analyzed using parsimony and maximum likelihood to provide a phylogenetic hypothesis of intraordi- nal relationships in Myrtales. The congruence between the phenotypic data from an earlier study and the rbcL topology was assessed to identify the potential synapomorphies that would corroborate the clades supported by the molecular tree. The rbcL consensus tree defined two major clades in the order. The first clade comprised a Myrtaceae lineage sister to a Melastomataceae lineage and the second clade included Onagraceae, a Lythraceae lineage, and Combretaceae. Phenotypic characters suggest that the ancestor of the first clade was characterized by the acquisition of fibrous seed exotegmen, while the ancestor of the second clade had flowers with stamens inserted directly on the rim of the hypanthium. However, branch support for the basal split of Myrtales is weak, possibly as a result of rapid early radiation in the order.

Evolutionary origin of the Asteraceae capitulum: Insights from Calyceraceae

PREMISE OF THE STUDY Phylogenies based on molecular data are revealing that generalizations about complex morphological structures often obscure variation and developmental patterns important for understanding the evolution of forms, as is the case for inflorescence morphology within the well-supported MGCA clade (Menyanthaceae + Goodeniaceae + Calyceraceae + Asteraceae). While the basal families share a basic thyrsic/thyrsoid structure of their inflorescences, Asteraceae possesses a capitulum that is widely interpreted as a racemose, condensed inflorescence. Elucidating the poorly known inflorescence structure of Calyceraceae, sister to Asteraceae, should help clarify how the Asteraceae capitulum evolved from thyrsic/thyrsoid inflorescences. METHODS The early development and structure of the inflorescence of eight species (five genera) of Calyceraceae were studied by SEM, and patterns of evolutionary change were interpreted via phylogenetic character mapping. KEY RESULTS The basic inflorescence structure of Calyceraceae is a cephalioid (a very condensed botryoid/thyrsoid). Optimization of inflorescence characters on a DNA sequence-derived tree suggests that the Asteraceae capitulum derives from a simple cephalioid through two morphological changes: loss of the terminal flower and suppression of the cymose branching pattern in the peripheral branches. CONCLUSIONS Widely understood as a condensed raceme, the Asteraceae capitulum is the evolutionary result of a very reduced, condensed thyrsoid. Starting from that point, evolution worked separately only on the racemose developmental control/pattern within Asteraceae and mainly on the cymose developmental control/pattern within Calyceraceae, producing head-like inflorescences in both groups but with very different diversification potential. We also discuss possible remnants of the ancestral cephalioid structure in some Asteraceae.

Species delimitation and evolution in morphologically and chemically diverse communities of the lichen-forming genus Xanthoparmelia (Parmeliaceae, Ascomycota) in western North America

PREMISE OF THE STUDY Accurate species delimitation is important for understanding the diversification of biota and has critical implications for ecological and conservation studies. However, a growing body of evidence indicates that morphology-based species circumspection in lichenized fungi misrepresents fungal diversity. The foliose lichen genus Xanthoparmelia includes over 800 species displaying a complex array of morphological and secondary metabolite diversity. METHODS We used a multifaceted approach, applying phylogenetic, population genetic, and genealogical analyses to delimit species in a single well-supported monophyletic clade containing 10 morphologically and chemically diverse Xanthoparmelia species in western North America. Sequence data from four ribosomal and two low-copy, protein-coding markers, along with chemical and morphological data were used to assess species diversity. KEY RESULTS We found that traditionally circumscribed species are not supported by molecular data. Rather, all sampled taxa were better represented by three polymorphic population clusters. Our results suggest that secondary metabolite variation may have limited utility in diagnosing lineages within this group, while identified populations clusters did not reflect major phylogeographic or ecological patterns. CONCLUSIONS In contrast to studies revealing previously undiscovered fungal lineages masked within lichen species circumscribed by traditional morphological and chemical concepts, the present study suggests that species diversity has been overestimated in the species-rich genus Xanthoparmelia.

Species delimitation in taxonomically difficult lichen-forming fungi: an example from morphologically and chemically diverse Xanthoparmelia (Parmeliaceae) in North America.

Mounting evidence suggests many morphology-based species circumscriptions in lichenized ascomycetes misrepresent fungal diversity. The lichenized ascomycete genus Xanthoparmelia includes over 800 described species displaying a considerable range of morphological and chemical variation. Species circumscriptions in this genus have traditionally been based on thallus morphology, medullary chemistry, and the presence or absence of sexual or asexual reproductive structures. Notwithstanding concerted effort on the part of taxonomists to arrive at a natural classification, modern taxonomic concepts for the most part remain unclear. Here we assess the evolution of characters traditionally regarded as taxonomically important by reconstructing a phylogenetic hypothesis based on sequence data from four nuclear ribosomal markers as well as fragments from two protein-coding nuclear loci. A total of 414 individuals were tested, representing 19 currently accepted species. Most sampled species, as currently circumscribed, were recovered as polyphyletic, suggesting that major diagnostic characters have evolved in a homoplasious manner. The vagrant growth form, distinct medullary chemistries, and production of vegetative diaspores appear to have evolved independently multiple times. Application of a population assignment test resulted in the recognition of 21 species-level genetic clusters, each of which was supported by a comparison of genetic distances as well as a Bayesian species delimitation method calculating probabilities associated with speciation events. Inferred clusters are largely incongruent with traditionally circumscribed species due to the prevalence of cryptic diversity and, in some cases, high levels of intraspecific morphological and chemical variation. These results call for a major taxonomic revision of Xanthoparmelia species in western North America.

Nuclear and cpDNA sequences combined provide strong inference of higher phylogenetic relationships in the phlox family (Polemoniaceae).

Members of the phlox family (Polemoniaceae) serve as useful models for studying various evolutionary and biological processes. Despite its biological importance, no family-wide phylogenetic estimate based on multiple DNA regions with complete generic sampling is available. Here, we analyze one nuclear and five chloroplast DNA sequence regions (nuclear ITS, chloroplast matK, trnL intron plus trnL-trnF intergeneric spacer, and the trnS-trnG, trnD-trnT, and psbM-trnD intergenic spacers) using parsimony and Bayesian methods, as well as assessments of congruence and long branch attraction, to explore phylogenetic relationships among 84 ingroup species representing all currently recognized Polemoniaceae genera. Relationships inferred from the ITS and concatenated chloroplast regions are similar overall. A combined analysis provides strong support for the monophyly of Polemoniaceae and subfamilies Acanthogilioideae, Cobaeoideae, and Polemonioideae. Relationships among subfamilies, and thus for the precise root of Polemoniaceae, remain poorly supported. Within the largest subfamily, Polemonioideae, four clades corresponding to tribes Polemonieae, Phlocideae, Gilieae, and Loeselieae receive strong support. The monogeneric Polemonieae appears sister to Phlocideae. Relationships within Polemonieae, Phlocideae, and Gilieae are mostly consistent between analyses and data permutations. Many relationships within Loeselieae remain uncertain. Overall, inferred phylogenetic relationships support a higher-level classification for Polemoniaceae proposed in 2000.

Seed Surface Sculpturing and Its Systematic Significance in Gilia (Polemoniaceae) and Segregate Genera

Seed surface sculpturing was examined comparatively from 46 species of Gilia sensu lato and 32 species representing other genera of Polemonioideae. Character states were defined for three primary sculptural characters (cell shape, anticlinal wall fusion, and anticlinal wall relief) and three secondary sculptural characters (periclinal wall embossing, microsculptural relief, and macroprotrusive elements). These surface features define morphotypes that correspond to several monophyletic groups recently defined for Polemoniaceae, including Saltugilia, Lathrocasis, Aliciella, Giliastrum, and a clade comprising Gilia sensu stricto, Allophyllum, Collomia, and Navarretia. Other groups, including Linanthus and Dayia, had diverse seed morphotypes. Considered individually across a phylogenetic hypothesis for Polemonioideae, five of the six surface characters were homoplastic, with consistency indices ranging from 0.71 to 0.88. When applied to specific hypotheses of relationship embedded in two alternative classifications for Gilia sensu lato, seed surface morphotypes agreed with or were equivocal regarding groups also indicated by comparative DNA sequence analyses but were only equivocal at best for alternative groups proposed on the basis of “evolutionary systematics.”

Phylogenetic Systematics of Ipomopsis (Polemoniaceae): Relationships and Divergence Times Estimated from Chloroplast and Nuclear DNA Sequences

Abstract The genus Ipomopsis (Polemoniaceae) encompasses about 29 species and 24 subspecies generally divided into three sections: sect. Ipomopsis, sect. Microgilia, and sect. Phloganthea. We employed maximum likelihood and Bayesian inference of DNA sequences from the nuclear ribosomal ITS region (ITS1, 5.8S ribosomal subunit, ITS2) and the chloroplast trnL—F region (trnL intron + trnL—trnF intergenic spacer) to estimate phylogenetic relationships within this genus and its placement among other genera of Polemoniaceae. The chloroplast and combined sequences provide support for the monophyly of Ipomopsis, but only if four species previously included in the genus are removed: Ipomopsis havardii, I. sonorae, Microgilia minutiflora (= I. minutiflora), and Loeseliastrum depressum (= I. depressa). Of the three sections, two are conditionally supported as being monophyletic. Section Microgilia (with 11 species and 11 infra-specific taxa) is supported as monophyletic if I. polycladon, I. sonorae, I. depressa, and I. minutiflora (the type of the section) are removed. This clade is treated here as section Elaphocera. Section Ipomopsis is inferred to be monophyletic with the inclusion of several members of sect. Phloganthea (I. multiflora, I. pinnata, and I. polyantha). There is no support for monophyly or paraphyly of sect. Phloganthea. The Giliopsis group (I. effusa, I. guttata, and I. tenuifolia) is supported as monophyletic by both data sets, and the cpDNA sequences place it as sister to the remainder of Ipomopsis. This clade is treated as a new section, Giliopsis. Nuclear data place Giliopsis in a clade with Ipomopsis havardii, I. sonorae, Microgilia minutiflora, Loeseliastrum depressum, Eriastrum spp., Langloisia, and Dayia grantii. Using the Eocene fossil Gilisenium hueberii to calibrate the most recent common ancestor of tribe Gilieae, we estimate that Ipomopsis has its origin 28.2 ± 0.40–39.0 ± 1.14 MYA (trnL—F and ITS, respectively). Using this same relaxed clock, the node (or coalescent event) that defines the I. aggregata complex is dated at 16.2 ± 0.38 and 27.1 ± 0.83 MYA (trnL—F and ITS, respectively). The deep divergence of the I. aggregata complex suggests that reticulation, rather than lineage sorting, is the source of conflict among phylogenetic markers used to infer the placement of I. macrosiphon.

Morphological Delimitation and Molecular Evidence for Allopolyploidy in Collomia wilkenii (Polemoniaceae), a New Species from Northern Nevada

Abstract Under the criterion of limited homogenizing gene flow as evidenced through specimen aggregation analysis, and genetic evidence of a barrier to gene exchange with its closest relatives, we describe a new species in Polemoniaceae, Collomia wilkenii. Collomia wilkenii superficially resembles Collomia tinctoria and Collomia linearis in some features, but, upon examination, has consistent, unique character combinations that distinguish it from both species, as well as from sympatric Collomia renacta and Collomia tenella. These features include particulars of calyx morphology, corolla morphology, stamen insertion and exertion, numbers of flowers in inflorescence clusters, and the kinds and distribution of glandular and eglandular trichomes. Comparative DNA sequencing of chloroplast genes indicates Collomia wilkenii has the chloroplast genome of Collomia tenella. Nuclear ITS sequences show additivity in Collomia wilkenii between Collomia linearis and Collomia tenella, a pattern confirmed by cloning this region. Two low copy nuclear loci, idh-A and idh-B, indicate an allopolyploid origin of this previously undescribed species. Collomia wilkenii is endemic to northern Nevada, occurring in several locations across the breadth of the state.