The magnitude of niche shifts associated with ecological speciation and the factors that regulate the process are poorly understood. I propose that ecological transitions most often involve the invasion of habitats most accessible through seed dispersion and by relatively small genetic changes. A significant seed rain is required for the recruitment of chance variants that are somewhat adapted to the novel conditions, as well as for the expansion of the genetic repertoire necessary for the evolution of a well-adapted entity. The probability of exploiting a new niche is an inverse function of the amount of genetic change that is required. Genes with large effect facilitate the change. There is considerable evidence that substantial habitat and pollinator niche shifts may occur with relatively few gene changes. There is speculation that populations may establish in new habitats through adaptive developmental and physiological changes induced by the environment, and then undergo genetic changes that stabilize the new phenotypes. Hybridization provides an unusual opportunity for major ecological change over a relatively short time span.

The monophyly of Campylopus and its relationships to other genera of the Dicranaceae-Campylopodioideae, especially Bryohumbertia and Pilopogon, have been ambiguous. To evaluate inter- and intrageneric relationships of Campylopus, maximum parsimony and maximum likelihood calculations of sequences from the chloroplast DNA (trnT_UGU–trnL_UAA spacer / trnL_UAA 5′ exon / trnL_UAA intron, atpB–rbcL spacer) and the nuclear ribosomal DNA (ITS1 / 5.8S / ITS2 / partial 26S) were performed. Analyses of the cpDNA sequences and the more conserved nrDNA parts (5.8S, partial ITS1, ITS2 and 26S) confirm the monophyly of a clade comprising the Campylopodioideae plus Leucobryum (Leucobryaceae), as proposed by previous molecular studies. Monophyly of Campylopus, including Bryohumbertia, and a sistergroup relationship to Pilopogon are also strongly supported by the cpDNA data. Relationships within Campylopus are only partially resolved due to low sequence variability in the cpDNA and homoplastic substitutions and indels. The present division of Campylopus into three subgenera is not supported by the molecular trees.

It has been suggested in the literature that limited hybridization occurs between Cupressus macnabiana and C. sargentii where the species occur in sympatry. This study confirmed the hybrid origin of specimens from a sympatric population using an objective analysis of morphological and DNA evidence. Fifty–eight individuals from three populations (two pure stands and one mixed population) were sampled. Variation in diagnostic restriction sites within ITS (nrDNA), matK (cpDNA), and NEEDLY intron two (nDNA) were used in combination with 20 quantitative morphological characters to detect and characterize putative hybrids. ITS and NEEDLY were uninformative with respect to hybrid detection, but matK demonstrated species–specific polymorphism. Anomalous combinations of plastid type, Discriminant Function identification, and position in a pictorialized scatter diagram were used to identify putative hybrids. Intermediacy of the putative hybrids was demonstrated statistically (p = 0.005) with 13 out of the 14 diagnostic morphological characters having intermediate values. Hybrids most likely arose from multiple hybridization events with both species acting as the paternal parent. The hybrids are apparently fertile, and may form a complex swarm. The most recognizable morphological characteristics of the hybrids are the partial development of resin glands on leaves of the ultimate branch segments, the penultimate branching pattern, ovulate cone width, and seed mass.

Sequences from the nuclear ribosomal internal transcribed spacer region 1 (nrDNA ITS1) and the plastid rps4 gene from the genus Ephedra (Ephedraceae, Gnetales) were obtained in order to infer phylogenetic relationships, character evolution, and historical biogeography in the genus. Within Ephedra the length of the nrDNA ITS1 varied from 1,081 to 1,143 basepairs (bp), in contrast to dramatically shorter lengths in the outgroups (Gnetum, Welwitschia, and Pinus). The rps4 locus varied in length from 645 to 661 bp in the same set of taxa. Both parsimony and maximum likelihood analyses of these sequences resulted in a well-resolved phylogeny that supports the monophyly of Ephedra, but not its subdivision into the traditional sections Ephedra, Asarca, and Alatae. The resulting phylogeny also indicates a derivation of the New World clade from among the Old World taxa. Among the Old World species three highly-supported monophyletic groups are recognized that are highly concordant with morphological evidence. The New World clade includes two main subclades of North and South American species that are strongly supported, while the position of two, mostly Mexican species E. pedunculata and E. compacta remains unresolved. Character reconstruction of ovulate strobilus types in Ephedra indicates that fleshy bracts are ancestral, with shifts to dry, winged bracts having occurred multiple times. Low levels of sequence divergence within the North American clade suggest either recent and rapid ecological radiation or highly conservative ribosomal DNA evolution within the clade.

Cytogenetic studies of North American Elymus suggest that the genus is an allopolyploid derivative of Pseudoroegneria (St) and Hordeum (H). To test this, we conducted a phylogenetic analysis of North American Elymus species within a broad sample of diploid Triticeae taxa using cloned sequences from one member of the nuclear gene family encoding phosphoenolpyruvate carboxylase. The phylogeny supports the hypothesis that Pseudoroegneria and Hordeum are the diploid progenitors of the North American Elymus tetraploids. Each tetraploid Elymus individual has two distinct forms of the gene, and each form is in a strongly supported clade with sequences from either Pseudoroegneria or Hordeum, suggesting that these Elymus species have an St H genomic content. This pattern is consistent with a single (or multiple very similar) polyploid ancestor(s) of the North American tetraploids, confirming earlier results based on granule-bound starch synthase I gene sequence data. We also examined the utility of the phosphoenolpyruvate carboxylase gene to reconstruct the evolutionary history of the Triticeae by comparing it to starch synthase gene sequence data. Both nuclear data sets are phylogenetically informative, but suggest somewhat different evolutionary histories among genera within the tribe.

The origin of two tetraploid species of Hordeum, H. capense from South Africa and H. secalinum from Eurasia and North Africa, is explored using phylogenetic analyses of two single-copy nuclear genes (DMC1 and EF-G) and one plastid gene (rbcL). By applying copy-specific primers it was possible to obtain sequence data from two copies of each of the nuclear genes from the two tetraploid species. The most parsimonious explanation of the presence of both genes is that each copy was inherited from a different diploid parental species. Hence, H. capense and H. secalinum are allotetraploids. The phylogenetic analyses also demonstrated that the two species have a common hybrid origin involving diploid H. marinum subsp. gussoneanum and H. brevisubulatum. A gene tree derived from the plastid rbcL sequences showed that H. brevisubulatum was the maternal parent. Based on the number of evolutionary changes since polyploidization and subsequent diversification of the two species, H. capense, with an isolated occurrence in South Africa, is best explained as an ancient relict, as opposed to a recent introduction.

Tripogon nicorae Rúgolo & A. S. Vega, a new species from South America, is described and illustrated. A key for the identification of Tripogon species in America is included and a comparative table based on morphology, leaf anatomy, micromorphological features of the spikelets, and ecology. The taxonomic synopsis includes synonymy, geographical distribution and ecology, iconography, vernacular names, and a list of representative specimens examined. Tripogon ekmanii Nicora & Rúgolo is reported for the first time in Uruguay.

Recent phylogenetic analyses of Saxifragales, based on DNA sequences of five plastid and nuclear ribosomal genes under parsimony and likelihood criteria, failed to resolve the branching order of the major lineages of the clade. This lack of resolution was attributed to the rapid radiation of Saxifragales. However, simultaneous origin of the major lineages was rejected by both parametric and non-parametric statistical tests, indicating that there is potential for resolving these relationships using additional analytical procedures and/or additional data. We reanalyzed the original data using a Bayesian approach, by implementing a Markov chain Monte Carlo process. Common-model and mixed-model analyses were conducted. Although Bayesian analyses did not fully resolve the phylogeny of Saxifragales, greater support was indicated for the relationships of Saxifragaceae, Crassulaceae, Haloragaceae, and Paeoniaceae. Relationships of “lower hamamelid” lineages were inconsistently supported, including sister group relationships of Cercidiphyllum-Daphniphyllum and Altingiaiceae-Hamamelidaceae. Simultaneous origin of the major lineages was not supported. We compare parameter estimation in common- and mixed-model Bayesian analyses and find striking differences that may affect the posterior probabilities of clades. Our application of Bayesian methods to discriminate simultaneous speciation from weak phylogenetic signal is a useful addition to the limited set of tools available for this purpose. We discuss important caveats for the interpretation of Bayesian posterior probabilities in this study, especially when a common model is assumed across data partitions.

Leaflet anatomy of 14 taxa in Mimosa sect. Batocaulon, series Quadrivalves is described for the first time, using cleared leaflets and light microscopy. Members of the series have obliquely asymmetric, linear-oblong, narrowly elliptic, or narrowly oblanceolate leaflets with an eccentric primary vein. The venation pattern is brochidodromous with basal lateral veins. In nine of the 14 taxa the lateral loops become notably narrower in the distal portion (anisonerved loops). On the basis of primary vein size and width, and the nature of the loops, the taxa of the series are divided into two groups, one with isonerved loops and a notably thickened primary vein (massive) and the other with anisonerved loops and a stout or moderately thickened primary vein; the primary vein and secondary veins can be sinuate or straight. Idioblasts were observed in association with the ends of the veinlets. These are of three types: polymorphic sclereids, osteosclereids, and tracheoidal elements. Calcium oxalate prisms and druses are present in most taxa of the series. The first are associated with the vascular bundles, while druses are found in mesophyll cells. The systematic value of leaflet anatomical characters is discussed, and leaflet anatomy is found to provide significant characters for distinguishing groups and individual taxa in series Quadrivalves.

Evidence from chloroplast trnK and nuclear ribosomal ITS sequences and morphological data reveals that the monotypic legume genus Wajira is nested within a clade comprising the species of Vigna subgen. Macrorhynchus. This Wajira-containing clade is basally branching in a larger clade that contains many of the genera traditionally referred to as tribe Phaseoleae subtribe Phaseolinae. Wajira is thus recircumscribed to include Vigna subgen. Macrorhynchus. Given the heterogeneity of floral morphology of its constituent species, Wajira is apomorphically diagnosed by woody stems and a pollen brush that comprises an introrse linear array of unicellular hairs. This recircumscribed genus now comprises five species, one of which is described as new, Wajira danissana. Three species require new nomenclatural combinations, Wajira grahamiana, Wajira praecox, and Wajira virescens. Wajira albescens, W. danissana, W. praecox, and W. virescens are woody climbers that are each narrowly distributed in the arid Somalia-Masai region characterized by sparse ground cover not subjected to seasonal burning. Wajira grahamiana has a thick woody subterranean rootstock that resprouts stems, and is widespread in the Sudano-Zambezian Region, southern India, and Sri Lanka, where grasslands subjected to seasonal burning predominate. This species is resolved in all phylogenetic analyses as derived from within the Somalia-Masai clade. An evolutionary rates analysis of trnK sequences suggests that the Wajira stem clade diverged from its closest relatives just over 10 million years ago, the extant diversification of the genus began around 6–7 million years ago, and Wajira grahamiana attained its widespread distribution during the last 2 million years.

Molecular data from Cladopus and Hydrobryum, members of the aquatic angiosperm family Podostemaceae, were analyzed phylogenetically using the chloroplast matK gene and internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA (nrRNA) gene to infer the species relationships and the biogeographic history of the East Asian species. The phylogenies based on matK and ITS were incongruent for relationships in a northern clade of Cladopus, but the pattern of root morphologies (ribbon vs. linear) agreed with the matK phylogeny. The matK phylogeny revealed that all East Asian temperate species of each genus form a monophyletic group that is derived from tropical/subtropical species. A clock-constrained maximum-likelihood tree suggests that the divergence events of the temperate lineages from their tropical sisters occurred coevally in the two genera. Dispersal-vicariance analysis (DIVA) suggests that distribution at the middle latitudes was formed by a wide primary distribution covering tropical and temperate areas and a secondary dispersal event in Cladopus, and by a dispersal event in Hydrobryum. Two Kyushu-Fujian groups are found in Cladopus, one consisting of Japanese C. austro-osumiensis and Chinese C. fukiensis and another consisting of Japanese C. japonicus, C. austrosatsumensis, and C. doianus and Chinese C. chinensis, each of which shows little genetic differentiation between species from Kyushu, southern Japan, and Fujian, China, suggesting parallel biogeographic histories. Disjunct populations of Hydrobryum japonicum from Kyushu in southern Japan and from northern Thailand show little genetic differentiation, whereas a plant from Yunnan, China, diverged earlier than did the Japanese or Thai plants. The DIVA results suggest that the disjunctive distribution of Hydrobryum japonicum was formed by two dispersal events from Kyushu to Yunnan and to northern Thailand.

For the last 150 years, the taxonomy of Hoffmannseggia has been variously entangled with Caesalpinia and Pomaria. Traditionally, Hoffmannseggia consisted of herbaceous or sub-shrubby perennials (rather than trees or vines) that lack spines and usually bear glandular trichomes on portions of the vegetative surfaces. However, the lack of correspondence of other characters such as flower shape, fruit type, and sepal persistence with habit and armament led to the repeated realignment of various species. Recent molecular work has shown that Hoffmannseggia forms a monophyletic group supported with several morphological synapomorphies and that it is not closely related to either Caesalpinia or Pomaria. Here we use molecular data from the nuclear ITS spacer regions, the trnL spacer and trnF intron chloroplast regions, and the rbcL gene to examine the relationships of Hoffmannseggia species. We show that there are two major clades in the genus that do not correspond to any previous infrageneric taxonomy. These clades are supported by morphological differences, the most striking of which is habit with one clade consisting of sub-shrubby species and the other of herbaceous species. We point out other characters that support subgroups within these clades, document one case of hybridization, and identify other suspected cases of hybridization. We also make the new combination Hoffmannseggia pumilio.

The evolution of floral symmetry in Asteridae has been of recent interest. Three genera with full or partial radial floral symmetry are found within tribes Gesnerieae and Gloxinieae of Gesneriaceae where the remaining taxa have bilaterally symmetrical flowers. These tribes have been shown to each be monophyletic and to be sister to each other, but a full analysis within each tribe has not demonstrated strongly supported sister group relationships among genera, especially those with radially symmetrical flowers. To assess sister group relationships more accurately, a phylogenetic analysis using GCYC (a Gesneriaceae homolog of CYCLOIDEA) sequences as well as four regions from the chloroplast genome (ndhF, trnL intron, trnF-trnL spacer, rpl20-rps12 spacer), ITS, and two paralogues of the nuclear encoded chloroplast expressed glutamine synthetase was conducted. The analyses for the most part resolved sister group relationships between radial and bilateral taxa with strong support as well as provided support for several clades within Gloxinieae and indicated that Phinaea is not a monophyletic genus.

Phylogenetic relationships in Mentha were inferred from DNA sequences of the chloroplast (cp) rpl16 intron and trnL-trnF region. The objectives were to test monophyly of Mentha and each of its sections and assess relationships among Mentha species. Based on cpDNA data, Mentha is strongly supported as monophyletic. The suggestions that M. cervina and M. cunninghamii should be placed in other genera gain no support from this analysis. Mentha cervina is sister to M. gattefossei, and the New Zealand endemic, M. cunninghamii, is allied with species from Australia (M. australis, M. diemenica, M. satureioides). No recognized section with more than one species sampled forms a monophyletic group. Section Pulegium may be monophyletic, but the third member of this section, M. grandiflora, was not sampled. Chloroplast DNA sequences of the putative allopolyploids M. canadensis and M. spicata suggest that M. arvensis and M. longifolia, respectively, may be their maternal parents.

We show the power of detailed AFLP study to address questions of species delimitation and genetic diversity in morphologically-cryptic plants. We have combined this technique with karyological studies to explore species boundaries in the Western Mediterranean representatives of Veronica subgen. Pentasepalae. Several members of this subgenus are represented in the Iberian Peninsula and North Africa by morphologically similar populations, which lead to different taxonomic hypotheses. We have analyzed genetic variation with two different objectives: first, to provide a basis on which one taxonomic hypothesis is favored against its alternatives, and second, to obtain a satisfactory interpretation of phylogeographic patterns. The usefulness of several parameters and analyses is considered in order to help rank taxa and to reveal details of their speciation modes. Some of these parameters are presented with a geographical background to facilitate phylogeographic interpretations. The data support one of the previously proposed taxonomic hypotheses, which results in the recognition of eight taxa. An east-to-west migration route within the Iberian Peninsula is hypothesized, coinciding with the general pattern proposed for Veronica subgen. Pentasepalae. Further data on genetic variability and chromosome counts for 41 populations are provided.

A new genus, Salcedoa, is described from the Cordillera Septentrional, northern Dominican Republic. The bilabiate florets, smooth style branches, caudate anthers, and pollen grains size and shape, exine structure and sculpture, and endoaperture shape place it close to the South American genera of the tribe Mutisieae (Asteraceae) centered in the Guayana Shield. Two morphology-based phylogenetic analyses, one using Gochnatia and the other using Chaetanthera as outgroups, and including Salcedoa and the 12 Guayanan genera were performed to determine the sister group relationships of Salcedoa. The results suggest that Salcedoa is sister to Gongylolepis. The unusual distributional pattern of Salcedoa and the Guayanan genera was explored through the dispersal-vicariance method. A trans-oceanic dispersal of fruits is postulated as a probable mechanism by which Salcedoa reached Hispaniola from a South American ancestor.

Phylogenetic analyses of ITS and 5′ trnK/matK spacer sequences were undertaken for 39 species representing the range of morphological variation in the genus Brachyglottis and putative outgroups. Independent analyses of the sequence data were largely congruent, and when combined provided stronger support for relationships. The results suggest that Brachyglottis as currently circumscribed is paraphyletic. However, a more inclusive monophyletic group was supported that consists of the genera Bedfordia, Brachyglottis, Dolichoglottis, Haastia, and Traversia. Short branch lengths suggest that there has been a spectacular adaptive radiation of the Brachyglottis alliance in recent times. The species are morphologically diverse and occupy a wide range of ecological niches in New Zealand, yet exhibit very little sequence variation.

The chloroplast genome has provided sequence data for inferring plant phylogenies for more than a decade. General operational assumptions regarding chloroplast gene sequences are that they are single-copy, under strong functional constraint, and uniparentally inherited. However, studies have demonstrated the transfer of large segments of the chloroplast genome into the nuclear or mitochondrial genomes. Additionally, heteroplasmy and haplotype polymorphism of plastid genomes within and among individuals have been documented. Random sampling of nucleotide sequences from different plastid haplotypes or from paralogous sequences through the course of a systematic investigation may affect the resulting gene tree topology and the inferences drawn from it.