Ecological speciation occurs in saturated floras as well as in unsaturated floras. Whereas much consideration has been given to ecological divergence in open habitats, the process of niche shifting in highly competitive environments hardly has been discussed. I propose that ecological speciation in relatively saturated communities is facilitated by disturbance, which relaxes the competitive pressures on populations entering a new habitat. Disturbance affords marginally adapted immigrants an opportunity to become established and form reproducing populations. These populations then may respond to local selective pressures for greater adaptedness, thereby placing them on a speciation trajectory. This conceptual model is bolstered by the role of disturbance in facilitating the invasion of communities by new entities, as is well documented in the literature on alien species.

Nucleotide sequences from eight nuclear, chloroplast, and mitochondrial genes were obtained from 30 mosses (plus four outgroup liverworts) in order to resolve phylogenetic relationships among the major clades of division Bryophyta. Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood (ML), and Bayesian inference. Inferences were compared from Bayesian analyses using homogeneous and several heterogeneous models. Estimates of clade confidence were based on bootstrap analyses, posterior probabilities (in Bayesian analyses) and novel combined approaches. Most ingroup relationships were congruent among analyses, but support for individual clades depended on the analytical approach. Increasingly parameterized models of nucleotide substitution in the likelihood analyses provided significantly higher goodness-of-fit to the data. The results suggest that 1) the Bryophyta, including Sphagnum and Takakia, are monophyletic, 2) Andreaea and Andreaeobryum form a monophyletic group, 3) Oedipodium griffithianum is sister to all other operculate taxa, 4) mosses with nematodontous peristomes are paraphyletic and basal to arthrodontous mosses, 5) Diphyscium is sister to all other arthrodontous mosses, 6) Encalypta is sister to the Funariaceae, and 6) mosses with diplolepideous-alternate peristomes form a monophyletic group. Implications of the phylogenetic hypothesis for morphological evolution in mosses include 1) a pseudopodium has arisen independently in Sphagnum and Andreaea, 2) the mucilage hairs of Andreaeobryum and Takakia are non-homologous, 3) the stomata found in Sphagnum are not homologous to those of other mosses, and 4) that stomata were absent in the ancestor of all mosses.

Equisetum is a genus of 15 extant species that are the sole surviving representatives of the class Sphenopsida. Chloroplast DNA sequence data were used to examine the monophyly of the two accepted subgenera (Equisetum and Hippochaete) and the putative basal position of Equisetum giganteum. A plastid DNA region that includes rps4 was sequenced for all species of Equisetum. Phylogenetic analyses using parsimony, likelihood or posterior probability criteria, all support the following inferences: (1) Equisetum bogotense is basal within the genus; (2) all other species group in two major sister clades: (i) the rest of subgenus Equisetum (7 species) and (ii) subgenus Hippochaete (7 species). On the basis of the present phylogeny, bisexuality would not be the ancestral state in the Equisetum genus, but characters shared among species of the subgenus Equisetum, such as superficial stomata and protruding antheridia, could be ancestral in the genus.

Molecular phylogenies have been generated to investigate relationships among species and putative segregates in Asplenium, one of the largest genera in ferns. Of the ∼700 described taxa, 71 are included in a phylogenetic analysis using the chloroplast rbcL gene and trnL-F spacer. Our results support Hymenasplenium as the sister lineage to all other asplenioid ferns, and all other putative satellite genera are nested within this asplenioid clade. Instead of the classical and well-recognized separation into Old and New World clades, asplenioid ferns reveal a separation of the deeper branches into tropical and temperate clades. Temperate clades have evolved from tropical, more-basal clades and the phylogeny indicates up to six shifts between temperate and tropical preferences in the evolution of this widespread genus. Implications for speciation processes and biogeographic aspects, including the re-colonization of temperate regions after the last glacial period, are discussed and we present a phylogenetic framework from which the historical biogeography of asplenioid ferns can be inferred for Europe and North America.

Numerous populations from six spruce taxa, including four relict endemics, Picea chihuahuana (Chihuahua spruce), P. martinezii (Martínez spruce), P. mexicana (Mexican spruce), and P. breweriana (Brewer spruce), and two widespread species, P. engelmannii (Engelmann spruce) and P. pungens (blue spruce), were compared at homologous isozyme loci to test various hypotheses about their affinities and origins. Each of the species was clearly separated, and Neighbor-Joining and Unweighted Pair Group analyses of Nei's genetic distance grouped all populations within a taxon into their own clusters. Spruces from Flys Peak, Chiricahua Mountains, Arizona, joined a P. engelmannii cluster and were not a bridge to P. mexicana as previously believed. Spruces from Cerro Mohinora, Chihuahua, were clearly P. mexicana, not phantom hybrids of P. chihuahuana and P. pungens. Nuclear random amplified polymorphic DNA and chloroplast simple sequence repeat and cleaved amplified polymorphic genetic markers were compared in a smaller sample of populations, using distance and parsimony approaches. DNA markers, like isozymes, clearly identified spruces from Cerro Mohinora as P. mexicana. In contradiction to the most recent taxonomic treatment, P. chihuahuana and P. martinezii were separated as distinct species by both isozyme and DNA markers, and formed a sister-species group. Picea engelmannii and P. mexicana formed a separate cluster, and the genetic distance between them was similar to values associated with closely related species but greater than distances typical of subspecies or varieties in conifers. Picea pungens, which is so similar to P. engelmannii that the two are frequently misidentified, was clearly distinguished from it, sometimes joining a P. chihuahuana-martinezii group and sometimes a P. engelmannii-mexicana group, depending on analysis. Picea breweriana was well isolated from all other taxa. Both DNA and isozyme phylogenies agreed with results from crossability studies and contradicted intrageneric relationships constructed largely on cone morphology.

Convergent intron loss in the plastid genome has been reported at a broad phylogenetic level in the flowering plants, but very few cases are known among closely related taxa, aside from those with a propensity for genome rearrangement. We performed a large survey of an intron in the plastid 3′-rps12 locus and found that it is present in all monocots sampled, apart from two closely related families in the order Asparagales, Asphodelaceae and Hemerocallidaceae. However, only a subset of taxa in the latter family lack it. A likelihood-based parametric bootstrapping analysis rejects an hypothesis that intron loss is a marker for the monophyly of all Asparagales lacking it. Reconstructions of evolutionary transformation in intron status (presence versus absence) using an equal weighting scheme (standard parsimony) on optimal and plausible suboptimal trees instead yield two major classes of ancestral-state assignment. These scenarios indicate that introns were either lost in parallel, or there was a single loss and a subsequent secondary origin. Parsimony weighting schemes that are skewed but (arguably) more realistic than equal weighting reject the latter reconstruction, and support the hypothesis that intron loss is not homologous in Asphodelaceae and Hemerocallidaceae. One of the parallel losses supports a recent circumscription of Hemerocallidaceae to incorporate the family Johnsoniaceae.

Morphological and habitat similarities among the five species of the terrestrial orchid genus Calopogon have led to nomenclatural and taxonomic confusion. The taxa are marked by subtle character differences and little apparent reproductive isolation. Here we investigate allozyme diversity at the species level and the partitioning of genetic variation within and among species and their populations. Genetic identities are used to define species boundaries and suggest phylogenetic relationships. All five species of Calopogon maintain high levels of allozyme variation within their populations (P = 50.0%−94.4%, AP = 2.67–3.32, H_e = 0.11–0.43). Calopogon oklahomensis, an autotetraploid that appears to have undergone gene silencing at 13 of its 19 polymorphic loci, consistently had the highest genetic diversity values. Calopogon multiflorus, which has the most restricted range and rarest occurrence, had the lowest mean genetic diversity values. In C. oklahomensis, C. pallidus and C. tuberosus most of the genetic variation exists within rather than among populations (G_ST = 0.037–0.085). The UPGMA phenogram generated using genetic identity data has three phenetic groups and supports designation of the taxa as separate species. The data suggest that C. oklahomensis most closely resembles the basal extant taxon within Calopogon.

A new Neotropical genus of Commelinaceae, Plowmanianthus, is described with five new species. Karyological and morphological data, as well as results of phylogenetic studies, support its inclusion in the subtribe Dichorisandrinae (tribe Tradescantieae) with four other genera (Cochliostema, Dichorisandra, Geogenanthus, and Siderasis). The occurrence of moniliform hairs along the distal margins of the petals is evidence of an even closer relationship with Cochliostema and Geogenanthus, this character being restricted in the family to these three genera. Plowmanianthus may be uniquely characterized as comprising small, perennial rosette herbs with usually one-cymed, axillary inflorescences borne among the lower leaves, an androecium reduced to three fertile stamens, annular, papillate stigmas, and uniseriate to partially biseriate seeds. Plants of the genus are shallowly rooted, the roots not penetrating deeper than the leaf-litter or humus-rich layers of their primary rainforest habitats. Plowmanianthus is also distinctive among the Commelinaceae in the unusually high frequency of cleistogamy in the genus, with some species for which only cleistogamous flowers are known. As currently understood, two species (P. panamensis and P. dressleri) are restricted to the Isthmus of Panama, whereas the remaining four taxa (P. grandifolius subsp. grandifolius, P. grandifolius subsp. robustus, P. perforans, and P. peruvianus) are restricted to lowland Amazonia.

Comparative sequencing of the nuclear ribosomal Internal Transcribed Spacer (ITS) and the chloroplast matK coding and non-coding regions was used to examine the evolutionary relationships among 53 accessions representing 13 genera of the Zingiberaceae, including 31 accessions of Amomum (Alpinioideae). Phylogenetic analyses of the ITS and matK sequences alone and in combination using maximum parsimony methods produced a moderately supported topology within Alpinioideae. Our results indicated that Amomum as currently defined is polyphyletic with three major groups of species that do not correspond with any previously recognized sectional classification of the genus. Our analyses also identified Paramomum as sister to Elettariopsis, which are both embedded within one group of Amomum. The other two groups of Amomum share common ancestors with additional genera of the Alpinioideae. ITS and matK sequences provide new data for inferring relationships within Amomum and allow fresh interpretations of morphological characters (such as anther appendage and fruit type) that may be of value in future classifications.

One-hundred ITS rDNA and 32 trnL-F cpDNA sequences were used to reconstruct the phylogeny of 62 (of 67) species of Delphinium section Diedropetala to test the hypothesized hybrid origins of Delphinium gypsophilum and D. luteum. Delphinium gypsophilum has been proposed to be a hybrid derivative of D. recurvatum and D. hesperium ssp. pallescens; D. luteum is of putative hybrid origin between D. decorum and D. nudicaule. The nuclear and chloroplast sequence data were analyzed separately and, because there was no conflict, in combination. TrnL-F alone did not provide much resolution. The ITS data set and the combined ITS/trnL-F data set resolved several small clades. Delphinium luteum appears in a clade with both of its putative parents, and D. gypsophilum appears in a clade with D. recurvatum. In both cases, the sequence data are consistent with hybrid origin, but are also consistent with the putative hybrids being closely related to one or both of their proposed progenitors. Population-level data (allozymes, RAPDs, and AFLPs) support the latter hypothesis. Although our goal was not to resolve all relationships throughout sect. Diedropetala, the results provide initial information on subsectional relationships.

A brief discussion of the systematics of Swartzia, a large neotropical genus of trees and shrubs, is given in preparation for a comprehensive phylogenetic and revisionary study of the genus. Two new species from Brazilian Amazonia, Swartzia coriaceifolia and Swartzia juruana, are described and illustrated. The former was collected in the basin of the Rio Negro in the state of Amazonas and possesses morphology allying it with S. brachyrachis and its relatives. Swartzia juruana is known from a single collection from the upper Rio Juruá basin of Acre and is closely related to the more widespread species S. jorori. Morphological characters of the new species are discussed, and a key to the unifoliolate species and varieties of Swartzia is provided.

A new papilionoid legume genus, Maraniona, is described based on recent collections from the Marañon Valley in northern Peru. The sister group relationships of Maraniona are analyzed using a combination of non-molecular and chloroplast DNA matK/trnK sequence data that incorporate comprehensive generic level sampling across the dalbergioid legumes. This analysis places Maraniona in a strongly supported subclade of the informal Pterocarpus clade of the dalbergioid legumes. We discuss the endemic status of Maraniona in relation to overall endemism in the upper Marañon Valley as well as the possible affinities of Maraniona to the genus Tipuana from Argentina and Bolivia.

Nuclear ribosomal (ITS) and plastid (trnL-trnF) DNA sequence data from representatives of most New World species of Thlaspi (Brassicaceae), including the widespread North American T. montanum, have been studied to investigate their relationship to the Eurasian members now placed in the genus Noccaea, especially the European T. montanum (= N. montana) complex. ITS sequence data of the New World taxa were added to a previously published data set, which includes sequences of representative taxa of 11 of the 12 genera segregated from Thlaspi, to elucidate overall relationships within Thlaspi s.l. Sequences from Callothlaspi, Kotschyella, Masmenia, Microthlaspi, Neurotropis, Noccaea, Noccidium, Pseudosempervivum, Raparia, Thlaspi s.s., Thlaspiceras, and Vania, as well as of the closely related genera Bivonaea, Alliaria, Peltaria, and Teesdalia, were included in the study. The results show that the New World taxa of Thlaspi form a monophyletic group that should be assigned to Noccaea and that the North American “T. montanum” appear to be unrelated to the European plants referred to this species. Sequence distance values are of an order of magnitude that favors Pleistocene speciation and migration of the perennial Thlaspi species into the New World. It is concluded that the North American infraspecific taxa of T. montanum be recognized as Noccaea fendleri. The new combinations N. fendleri subsp. californica, N. fendleri subsp. glauca, N. fendleri subsp. idahoense, and N. fendleri subsp. siskiyouense are proposed.

Hibiscus section Muenchhusia is a North American taxon with five species as recognized in the most recent taxonomic revision: H. coccineus, H. dasycalyx, H. grandiflorus, H. laevis, and H. moscheutos. To investigate the monophyly of Hibiscus section Muenchhusia, its relationship to other Hibiscus species, and the phylogenetic relationships among its species, DNA sequence data were obtained. To investigate the placement of section Muenchhusia within Hibiscus, chloroplast ndhF gene and rpL16 intron sequences were generated and added to a recently published dataset. To investigate relationships within section Muenchhusia three DNA sequence data sets were generated: a non-coding region of the chloroplast genome (rpL16 intron), nuclear ribosomal ITS, and a nuclear gene encoding granule-bound starch synthase (GBSSI). Analyses of ndhF rpL16 data indicated that section Muenchhusia is indeed monophyletic and is embedded in a clade that includes representatives of Hibiscus section Trionum sensu lato plus other genera segregated from Hibiscus (Abelmoschus, Fioria), and the tribe Malvavisceae. Within section Muenchhusia little to no phylogenetically informative variation was detected in the ITS or rpL16 sequences. The GBSSI data, on the other hand, provided sufficient information to resolve relationships among species. The species of section Muenchhusia fall into two primary clades, one consisting of H. grandiflorus and H. moscheutos sensu lato, the other including H. coccineus, H. dasycalyx, and H. laevis. These phylogenetic data corroborate earlier biosystematic studies that also placed the species into these same two groups. Sequence polymorphism was observed in one accession each of H. dasycalyx and H. grandiflorus and resolution of the underlying alleles indicates that gene flow has occurred from H. moscheutos into both H. dasycalyx and H. grandiflorus.

A systematic treatment is presented for the six species of Pilidiostigma (Myrtaceae), one newly described. Pilidiostigma is distinguished from other fleshy-fruited genera of Myrtaceae by the combination of its elliptic anthers, capitate to peltate stigma, testa usually chartaceous-membranous and covered with numerous large yellow or white oil glands (except for P. tetramerum), 1–3 locular ovary, and globular embryo in which the cotyledons and hypocotyl often are not, or only slightly, differentiated. The genus occurs predominantly in eastern Australia in wet forests east of the Great Dividing Range from near sea level to 1300 meters, although P. papuanum also extends into New Guinea. The new species Pilidiostigma sessile is described from northeastern Queensland and is diagnosed by its sessile or nearly sessile, basally rounded to cordate leaves. Lectotypes are designated for P. rhytispermum and P. glabrum. Detailed descriptions are provided for each species, along with a key, and profiles of essential oils are reviewed for most species.

Titanotrichum oldhamii has been variously placed in Gesneriaceae or Scrophulariaceae, although most recent taxonomic treatments treat it as a monotypic tribe within Gesneriaceae. In this study, we reconstructed a broad-scale phylogeny containing Titanotrichum using gene sequences from four sequence regions (chloroplast trnL-F intron and spacer and atpB-rbcL spacer, nuclear 26S ribosomal DNA, and the low-copy developmental gene CYCLOIDEA, CYC). The phylogenies inferred from each individual data set and the combined data are congruent in placing Titanotrichum inside Gesneriaceae. The phylogenetic tree based on combined chloroplast and nuclear DNA sequences grouped Titanotrichum with subfamilies Gesnerioideae (New World) and Coronantheroideae (South Pacific and Chile). We have isolated CYC, from most of the species of Gesneriaceae and Scrophulariaceae represented in this study, and this gene phylogeny suggests the same placement of Titanotrichum. CYC was found to evolve three times faster than the trnL-F intron and spacer, 3.3 times faster than the atpB-rbcL spacer, and eight times faster than nuclear 26S rDNA. Although there is considerable phylogenetic information in this fast evolving gene, analysis is problematic because of high levels of homoplasy and paralogy. In addition to a duplication predating a split between New World and Old World taxa (Gcyc1 vs. Gcyc2), there are several subsequent lineage-related duplications (mainly within Gcyc1).

Phylogenetic analyses of 159 DNA sequences from the nuclear rDNA internal transcribed spacer region were conducted to evaluate the monophyly of the herbaceous, perennial genera of Apiaceae subfamily Apioideae endemic to North America (north of Mexico) and to determine the relationships of those elements that currently comprise Cymopterus within the group. The results of a previous phylogenetic study were equivocal in suggesting monophyly for these perennial, endemic taxa and revealed Cymopterus to be polyphyletic, with its species closely linked with those of Aletes, Lomatium, Musineon, Oreoxis, Orogenia, Podistera, Pseudocymopterus, Pteryxia, and Tauschia. Herein, we expand sampling to include comprehensive representation of Aletes, Cymopterus, Musineon, Oreoxis, Orogenia, Podistera, Pseudocymopterus, and Pteryxia, and greater representation of Lomatium and Tauschia. We also include all members of two genera not examined previously, Glehnia and Oreonana, as well as additional outgroup genera from the Angelica clade of the apioid superclade. Our results indicate that the perennial, endemic apioid umbellifers of North America constitute a (weakly supported) monophyletic group, with Angelica and the meso-American Arracacia clade comprising two of several possible sister groups. The two subspecies of Glehnia littoralis ally with Angelica and Peucedanum japonicum; Oreonana shows affinity with several species of Cymopterus and Lomatium. The lack of resolution in the ITS trees precludes unambiguous hypotheses of relationship among these perennial, endemic umbellifers but does show that many of these genera, where resolved, are not monophyletic. Indeed, Cymopterus and Lomatium are highly polyphyletic and permeate all major clades resolved in the molecule-derived trees. Evidence from branch lengths and low sequence divergence suggests that this group of North American umbellifers underwent rapid radiation, likely during the geoclimatic events of the Late Tertiary and Quaternary.

Onoseris (Asteraceae, Mutisieae) is a genus of 31 species distributed from Mexico to Argentina through the Andes with its center of diversity in Peru. A phylogenetic analysis based on a detailed morphological study is provided. Urmenetea is used as the outgroup. Three most parsimonious cladograms are obtained based on the complete data set using Paup* 4.0b8. Two monophyletic groups are recognized: 1. Species with petiolate leaves, palmately veined blades with hastate base, and few-headed capitulescences, rarely thyrsoid capitulescences (O. acerifolia, O. alata, O. brasiliensis, O. cabrerae, O. castelnaeana, O. costaricensis, O. donnell-smithii, O. drakeana, O. fraterna, O. hastata, O. macbridei, O. onoseroides, O. peruviana, O. purpurea, O. sagittata, O. silvatica, and O. speciosa). 2. Species with sessile or subsessile leaves, elliptic and pinnately veined blades with attenuate base, and solitary capitula (O. albicans, O. amplexicaulis, O annua, O. chrysactinioides, O cumingii, O. gnaphalioides, O. humboldtiana, O. hyssopifolia, O. linearifolia, O. lopezii, O. minima, O. odorata, O. salicifolia, and O. weberbaueri). These monophyletic groups are recognized as subgenera Onoseris and Hipposeris respectively. Onoseris salicifolia is chosen as the lectotype of Onoseris subg. Hipposeris. Corolla polymorphism within Onoseris shows that corolla morphology alone cannot be used to distinguish between subtribes Mutisiinae and Gochnatiinae. Biogeographically, Onoseris has a continuous distribution from the Southern Andes to Northern Andes and Central America, but no individual species is distributed on both sides of the Huancabamba Zone. A group of species in subgenus Onoseris distributed in Central America and Brazil are regarded as phylogenetically derived (e.g., O. brasiliensis, O. costaricensis, O. onoseroides).

The morphology of branched foliar trichomes in Lobelioideae (Campanulaceae) was studied via scanning electron microscopy. Trichomes of this type are found only in the Neotropical endemics Burmeistera, Centropogon, and Siphocampylus, and in the Hawaiian endemic Cyanea. The 37 species examined included all species with branched trichomes in Burmeistera, Centropogon sect. Burmeisteroides, Centropogon sect. Niveopsis, Centropogon sect. Wimmeriopsis, Cyanea, and Siphocampylus, plus about one- fourth of the 100 species comprising Centropogon sect. Siphocampyloides. Trichomes observed conformed to eight structural types. Dendritic, multangulate, multangulate-dendritic, echinoid, and furcate hairs were found only in Centropogon sect. Siphocampyloides, Cyanea, and Siphocampylus. Echinoid-dendritic hairs were confined to Centropogon sect. Burmeisteroides, stellate hairs to Centropogon sect. Wimmeriopsis, and multiseriate- multangulate hairs to Burmeistera and Centropogon sect. Niveopsis. Within Centropogon, the distribution of trichome types is consistent with the currently accepted classification of the genus. Correlations with other data, both morphological and molecular, suggest that branched trichomes have evolved in the subfamily repeatedly, perhaps as many as 11 times.