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Duckweeds comprise a distinctive clade of pleustophytic monocots that traditionally has been classified as the family Lemnaceae. However, molecular evidence has called into question their phylogenetic independence, with some authors asserting instead that duckweeds should be reclassified as subfamily Lemnoideae of an expanded family Araceae. Although a close phylogenetic relationship of duckweeds with traditional Araceae has been supported by multiple studies, the taxonomic disposition of duckweeds must be evaluated more critically to promote nomenclatural stability and utility. Subsuming duckweeds as a morphologically incongruent lineage of Araceae effectively eliminates the family category of Lemnaceae that has been widely used for many years. Instead, we suggest that Araceae subfamily Orontioideae should be restored to family status as Orontiaceae, which thereby would enable the recognition of three morphologically and phylogenetically distinct lineages: Araceae, Lemnaceae, and Orontiaceae.

Premise: The submersed aquatic plant Hydrilla verticillata ("hydrilla") is important ecologically and economically due to its aggressive growth in both indigenous and nonindigenous regions. Substantial morphological variation has been documented in hydrilla, including the existence of monoecious and dioecious "biotypes." Whereas plastid sequence data have been used previously to explore intraspecific diversity, nuclear data have yet to be analyzed in a phylogenetic context. Molecular and morphological analyses were used to evaluate the genetic diversity and phylogenetic relationships of native and introduced populations., Methods: Nuclear (internal transcribed spacer-ITS; phytoene desaturase-PDS) and plastid (trnL-F) sequence data were evaluated phylogenetically using likelihood and Bayesian methods. Leaf morphologies were compared among clades that were identified in phylogenetic analyses., Results: Data from both ITS and PDS show multiple instances of polymorphic sequences that could be traced to two or more lineages, including both invasive biotypes in the Americas. Leaf morphological data support the distinctness of lineages and provide a metric for distinguishing monoecious and dioecious biotypes in the United States., Conclusions: Nuclear molecular data indicate far greater genetic diversity than could be estimated using plastid markers. Substantially divergent copies of nuclear genes, found in multiple populations worldwide, likely result from interlineage hybridization. Invasive monoecious and dioecious hydrilla biotypes in the Americas are genetically distinct, with both biotypes resulting from admixture among Eurasian progenitors. Genetic similarity to populations in India and South Korea, respectively, implicates these as likely origins for the dioecious and monoecious biotypes., (© 2019 Botanical Society of America.)

Past phylogenetic studies of the monocot order Alismatales left several higher-order relationships unresolved. We addressed these uncertainties using a nearly complete genus-level sampling of whole plastid genomes (gene sets representing 83 protein-coding and ribosomal genes) from members of the core alismatid families, Tofieldiaceae and additional taxa (Araceae and other angiosperms). Parsimony and likelihood analyses inferred generally highly congruent phylogenetic relationships within the order, and several alternative likelihood partitioning schemes had little impact on patterns of clade support. All families with multiple genera were resolved as monophyletic, and we inferred strong bootstrap support for most inter- and intrafamilial relationships. The precise placement of Tofieldiaceae in the order was not well supported. Although most analyses inferred Tofieldiaceae to be the sister-group of the rest of the order, one likelihood analysis indicated a contrasting Araceae-sister arrangement. Acorus (Acorales) was not supported as a member of the order. We also investigated the molecular evolution of plastid NADH dehydrogenase, a large enzymatic complex that may play a role in photooxidative stress responses. Ancestral-state reconstructions support four convergent losses of a functional NADH dehydrogenase complex in Alismatales, including a single loss in Tofieldiaceae., (© The Willi Hennig Society 2015.)

Nuclear DNA sequence data are essential for obtaining a complete understanding of plant species relationships, yet these data have been conspicuously absent from phylogenetic analyses of Lemnaceae (duckweeds). Using a modified Sanger sequencing protocol, we obtained DNA sequences of duckweed nuclear ribosomal regions, including 18S and 26S rDNA genes, the external transcribed spacer (ETS) and the frequently used internal transcribed spacer (ITS). After obtaining sequence data for all Lemnaceae species, we ascertained that prior difficulty in sequencing the ITS regions likely resulted from extremely rigid secondary structures, precipitated by a high proportion of G/C nucleotides. In phylogenetic analyses, nuclear ribosomal data largely supported relationships that had been inferred using chloroplast DNA sequence data., (© 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.)

Cryptic sympatric species arise when reproductive isolation is established in sympatry, leading to genetically divergent lineages that are highly similar morphologically or virtually indistinguishable. Although cryptic sympatric species have been reported in various animals, fungi, and protists, there are few compelling examples for plants. This investigation presents a case for cryptic sympatric speciation in Najas flexilis, a widespread aquatic plant, which extends throughout northern North America and Eurasia. The taxon is noted for its variable seed morphology, which earlier research associated with cytotypes; i.e., diploids were characterized by thicker seeds and tetraploids by thinner seeds. However, cytotypes are not patterned geographically with diploid and tetraploid plants often found in close proximity within the same lake. Using digital image and DNA sequence analyses, we found that diploids and tetraploids are well-isolated and remain genetically distinct throughout their sympatric range, where sterile hybrids occur frequently. Incorporation of sequence data from the single-copy nuclear phytoene desaturase locus revealed further that the tetraploids are allopolyploid derivatives of N. flexilis and N. guadalupensis, the latter a closely related species with an overlapping distribution. We conclude that the taxon widely known as N. flexilis actually comprises two cryptic, sibling species, which diverged in sympatry by interspecific hybridization and subsequent chromosomal isolation. By comparing seed morphology of type specimens, we associated the names N. flexilis and N. canadensis to the diploids and tetraploids respectively. Additionally, the narrowly restricted taxon known formerly as N. muenscheri is shown via morphological and genetic evidence to be synonymous with N. canadensis., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Haloragaceae are a cosmopolitan plant family with its centre of diversity in Australia. Here, we investigate the historical biogeography of the family and the role of vicariance or dispersal in shaping its current distribution. DNA sequences from ITS, matK and the trnK 5' and trnK 3' introns were obtained for 102 species representing all 8 genera of Haloragaceae for use in Bayesian molecular dating. Molecular dating was conducted using two macrofossils as calibration points for the analyses. Biogeographic history was investigated using a Bayesian dispersal-vicariance analysis and a dispersal-extinction-cladogenesis model. The results suggest that the earliest diversification of the extant Haloragaceae occurred in Australia during the Eocene (37.3-56.3Ma). Early diversification of the family in the Southern Hemisphere is inferred as resulting from vicariance events among Australia, South America and New Zealand. The results also indicate multiple out of Australia dispersal routes, primarily including (1) from Australia to Asia during the Miocene, with subsequent dispersal to Europe and North America; (2) from Australia to New Zealand, then to South America during the Miocene and Pliocene. Most of the inferred dispersal events occurred throughout the Miocene and later, and are biased towards the aquatic Haloragaceae lineages., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Premise of the Study: The discontinuous North American distribution of Najas gracillima has not been explained satisfactorily. Influences of extirpation, nonindigenous introduction, and postglacial migration on its distribution were evaluated using field, fossil, morphological, and molecular data. Najas is a major waterfowl food, and appropriate conservation measures rely on accurate characterization of populations as indigenous or imperiled. •, Methods: Seed lengths of N. gracillima from native Korean populations, a nonindigenous Italian population, and North American populations were compared using digital image analysis. DNA sequence analyses from these regions provided nine nrITS genotypes and eight cpDNA haplotypes. •, Key Results: Najas gracillima seeds from Eurasia and California are shorter than those from eastern North America. Nuclear and chloroplast DNA sequences of N. gracillima from Korea and Italy were identical to California material but differed from native eastern North American plants. Eastern North American specimens of N. gracillima at localities above the last glacial maximum boundary were identical or similar genetically to material from the northeastern United States and Atlantic Coastal Plain and Piedmont but divergent from plants of the Interior Highlands-Mississippi Embayment region. •, Conclusions: In California, N. gracillima is nonindigenous and introduced from Asia. In eastern North America, populations that colonized deglaciated areas were derived primarily from refugia in the Atlantic Coastal Plain and Piedmont. Genetic data indicate initial postglacial migration to northeastern North America, with subsequent westward dispersal into the Upper Great Lakes. These results differentiate potentially invasive California populations from seriously imperiled indigenous eastern North American populations.

The re-colonization of aquatic habitats by angiosperms has presented a difficult challenge to plants whose long evolutionary history primarily reflects adaptations to terrestrial conditions. Many aquatics must complete vital stages of their life cycle on the water surface by means of floating or emergent leaves and flowers. Only a few species, mainly within the order Alismatales, are able to complete all aspects of their life cycle including pollination, entirely underwater. Water-pollinated Alismatales include seagrasses and water nymphs (Najas), the latter being the only freshwater genus in the family Hydrocharitaceae with subsurface water-pollination. We have determined the complete nucleotide sequence of the plastid genome of Najas flexilis. The plastid genome of N. flexilis is a circular AT-rich DNA molecule of 156 kb, which displays a quadripartite structure with two inverted repeats (IR) separating the large single copy (LSC) from the small single copy (SSC) regions. In N. flexilis, as in other Alismatales, the rps19 and trnH genes are localized in the LSC region instead of within the IR regions as in other monocots. However, the N. flexilis plastid genome presents some anomalous modifications. The size of the SSC region is only one third of that reported for closely related species. The number of genes in the plastid is considerably less. Both features are due to loss of the eleven ndh genes in the Najas flexilis plastid. In angiosperms, the absence of ndh genes has been related mainly to the loss of photosynthetic function in parasitic plants. The ndh genes encode the NAD(P)H dehydrogenase complex, believed essential in terrestrial environments, where it increases photosynthetic efficiency in variable light intensities. The modified structure of the N. flexilis plastid genome suggests that adaptation to submersed environments, where light is scarce, has involved the loss of the NDH complex in at least some photosynthetic angiosperms.

Although chloroplast transcriptional and translational mechanisms were derived originally from prokaryote endosymbionts, chloroplasts retain comparatively few genes as a consequence of the overall transfer to the nucleus of functions associated formerly with prokaryotic genomes. Various modifications reflect other evolutionary shifts toward eukaryotic regulation such as posttranscriptional transcript cleavage with individually processed cistrons in operons and gene expression regulated by nuclear-encoded sigma factors. We report a notable exception for the psaA-psaB-rps14 operon of land plant (embryophyte) chloroplasts, where the first two cistrons are separated by a spacer region to which no significant role had been attributed. We infer an important function of this region, as indicated by the conservation of identical, structurally significant sequences across embryophytes and their ancestral protist lineages, which diverged some 0.5 billion years ago. The psaA/psaB spacers of embryophytes and their progenitors exhibit few sequence and length variants, with most modeled transcripts resolving the same secondary structure: a loop with projecting Shine-Dalgarno site and well-defined stem that interacts with adjacent coding regions to sequester the psaB start codon. Although many functions of the original endosymbiont have been usurped by nuclear genes or interactions, conserved functional elements of embryophyte psaA/psaB spacers provide compelling evidence that translation of psaB is regulated here by a cis-acting mechanism comparable to those common in prokaryotes. Modeled transcripts also indicate that spacer variants in some plants (e.g., aquatic genus Najas) potentially reflect ecological adaptations to facilitate temperature-regulated translation of psaB.

Sequences of the nuclear internal transcribed spacer (ITS) regions ITS1 and ITS2 have been used widely in molecular phylogenetic studies because of their relatively high variability and facility of amplification. For phylogenetic applications, most researchers use sequence alignments that are based on nucleotide similarity. However, confidence in the alignment often deteriorates at taxonomic levels above genus, due to increasing variability among sequences. Like ribosomal RNA (rRNA) and other RNA molecules, the ITS transcripts consist in part of conserved secondary structures ('stems' and 'loops') that can be predicted by mathematical algorithm. Researchers have long considered the evolutionary conservation of rRNA secondary structure, but until recently few phylogenetic analyses of the ITS regions specifically incorporated structural data. We outline a novel method by which to derive additional phylogenetic data from ITS secondary structure in order to evaluate support for relationships at higher taxonomic levels. To illustrate the method, we describe an example from the plant family Menyanthaceae. Using predicted ITS secondary structure data, we obtained a well-resolved and moderately supported phylogeny, in which most topological relationships were congruent with the tree constructed using ITS nucleotide sequence data. Furthermore, the explicit encoding of ITS structural data in a phylogenetic framework allowed for the reconstruction of putative ancestral states and structural evolution in the functional but highly variable ITS region.

The poorly known Haloragaceae R. Br. (Saxifragales) are highly diverse in habit (small trees to submerged aquatics) and labile in floral merosity (2-4), both uncommon among the core eudicots. This family has a cosmopolitan distribution, but taxonomic diversity is concentrated in Australia. An explicit phylogenetic approach has not previously been utilized to examine relationships or character evolution in this family. We used molecular evidence from nrDNA ITS and cpDNA trnK and matK regions under both Bayesian and parsimony analyses to address phylogenetic relationships. Combined molecular analyses defined a monophyletic Haloragaceae with the woody genera (Haloragodendron, Glischrocaryon) sister to the rest. Relationships among many genera were well resolved, with genera as currently delimited generally well supported, although there were notable exceptions; a new genus (Trihaloragis) is recognized, and the aquatic genus Meionectes is again distinct from Haloragis. Three new species combinations are also recognized. There are multiple (two or three) origins of the submerged aquatic habit in the family and potentially an intermediate reversal to the terrestrial habit, neither previously demonstrated in a core eudicot family using an explicit phylogenetic hypothesis. Ancestral character analyses suggest two origins of trimerous flowers and multiple reductions to dimerous flowers throughout Haloragaceae.

Field surveys in eastern North America confirm the naturalization of Glossostigma plants at 19 localities in four states: Connecticut, New Jersey, Pennsylvania, and Rhode Island. DNA sequence analysis of individuals from 14 sampled populations identifies these nonindigenous plants as Glossostigma cleistanthum, a species native to Australia and New Zealand. These results correct prior misidentifications of North American plants as G. diandrum. The earliest North American record of G. cleistanthum (1992) is from a Ramsar tidal wetland in Connecticut. Morphological analyses demonstrate that G. cleistanthum differs from G. diandrum by its longer leaves and ability to produce both cleistogamous and chasmogamous flowers in response to ecological conditions. Glossostigma cleistanthum has a high reproductive potential and spreads rapidly within and between both artificial and natural habitats. A survey of more than 100 lakes indicated that G. cleistanthum occurs most often in waters with high clarity and low pH, alkalinity, conductivity, and phosphorous. Because of its affinity for oligotrophic conditions, this species is a particular threat to pristine natural aquatic communities, which often contain imperiled plants.

Invasions of nonindigenous species have caused ecological devastation to natural communities worldwide, yet the biological bases for invasiveness remain poorly understood. Our studies of invasive watermilfoil (Myriophyllum) populations revealed widespread polymorphisms in biparentally inherited nuclear ribosomal DNA sequences, which were not detected in populations of native North American species. Subclones of the polymorphic regions revealed the occurrence of distinct sequences matching those acquired from both nonindigenous and native North American species. Molecular data demonstrate clearly that invasive watermilfoil populations in North America have resulted from hybridization between nonindigenous and native species. These observations suggest that invasiveness in these aggressive aquatic weeds may be linked to heterosis maintained by vegetative propagation.

Simplified DNA sequence acquisition has provided many new data sets that are useful for phylogenetic reconstruction, including single- and multiple-copy nuclear and organellar genes. Although transcribed regions receive much attention, nontranscribed regions have recently been added to the repertoire of sequences suitable for phylogenetic studies, especially for closely related taxa. We evaluated the efficacy of a small portion of the histone repeat for phylogenetic reconstruction among Drosophila species. Histone repeats in invertebrates offer distinct advantages similar to those of widely used ribosomal repeats. First, the units are tandemly repeated and undergo concerted evolution. Second, histone repeats include both highly conserved coding and variable intergenic regions. This composition facilitates application of "universal" primers spanning potentially informative sites. We examined a small region of the histone repeat, including the intergenic spacer segments of coding regions from the divergently transcribed H2A and H2B histone genes. The spacer (about 230 bp) exists as a mosaic with highly conserved functional motifs interspersed with rapidly diverging regions; the former aid in alignment of the spacer. There are no ambiguities in alignment of coding regions. Coding and noncoding regions were analyzed together and separately for phylogenetic information. Parsimony, distance, and maximum-likelihood methods successfully retrieve the corroborated phylogeny for the taxa examined. This study demonstrates the resolving power of a small histone region which may now be added to the growing collection of phylogenetically useful DNA sequences.

The genus Nuphar consists of yellow-flowered waterlilies and is widely distributed in north-temperate bodies of water. Despite regular taxonomic evaluation of these plants, no explicit phylogenetic hypotheses have been proposed for the genus. We investigated phylogenetic relationships in Nuphar using morphology and sequences of the chloroplast gene matK and of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. Two major lineages within Nuphar are consistently resolved with the morphological and molecular data sets. One lineage comprises New World taxa and the other represents a primarily Old World lineage. Relationships within the major lineages were poorly resolved by morphology and ITS, yet certain relationships were elucidated by all analyses. Most notable is the strong support for a monophyletic lineage of dwarf taxa and the alliance of the North American N. microphylla with the Eurasian taxa. Minor discordance between the independent cladograms is accounted for by hybridization. The common taxonomic practice of uniting all North American and Eurasian taxa under one species is not supported phylogenetically.

Within the angiosperm subclass Alismatidae (= superorder Alismatiflorae), contemporary taxonomists have often assigned the families Hydrocharitaceae and Najadaceae to different orders. The Najadaceae are presumably allied to a variety of aquatic families in the order Najadales, whereas the Hydrocharitaceae have been segregated as the order Hydrocharitales or placed within the order Alismatales. Analysis of DNA sequence data from the chloroplast gene rbcL, however, indicate that Najadaceae have a much closer phylogenetic relationship to Hydrocharitaceae than to families of the "Najadales" (Cymodoceaceae, Potamogetonaceae, Ruppiaceae, Scheuchzeriaceae, Zannichelliaceae, Zosteraceae). This association supports previous studies based upon examination of floral structure and seed coat anatomy. The rbcL sequence data also indicate that the Zosteraceae and Potamogetonaceae are closely related families. The rbcL sequence of Zostera is actually more similar to that of Potamogeton richardsonii than is the sequence of the latter to a congener, Potamogeton amplifolius. The marine, dioecious, hydrophilous genus Zostera has acquired a number of distinctive adaptations, but probably diverged relatively rapidly from freshwater Potamogetonaceae. Molecular data place Ruppiaceae as a sister group to the marine Cymodoceaceae and do not support the commonly accepted merger of Ruppiaceae and Potamogetonaceae.

Aquatic plants are notoriously difficult to study systematically due to convergent evolution and reductionary processes that result in confusing arrays of morphological features. Plant systematists have frequently focused their attention on the "water lilies," putative descendants of the most archaic angiosperms. Classification of these 10 plant genera varies from recognition of one to three orders containing three to six families. We have used DNA sequence analysis as a means of overcoming many problems inherent in morphologically based studies of the group. Phylogenetic analyses of sequence data obtained from a 1.2-kilobase portion of the chloroplast gene rbcL provide compelling evidence for the recognition of three distinct lineages of "water lily" plants. Molecular phylogenies including woody Magnoliidae sequences and sequences of these aquatic plants depict Ceratophyllum as an early diverging genus. Our results support hypotheses that most taxonomic concepts of the order Nymphaeales reflect polyphyletic groups and that the unusual genus Ceratophyllum represents descendants of some of the earliest angiosperms.

Aster furcatus is a rare, self-incompatible plant with fewer than 50 known populations throughout its range. We verified self-incompatibility in A. furcatus by conducting experimental self- and cross-pollinations and by examining seed set in a small population comprised of a single clonal genet. We examined variation at 22 electrophoretic loci in 23 populations of A. furcatus from across its range in Wisconsin, Illinois, Indiana, and Missouri. Except for two rare alleles found in single individuals in three populations, all loci but one of those examined were fixed for single alleles. The only variable locus (triosephosphate isomerase, TPI-1) tended to exhibit genotype frequencies in Hardy-Weinberg equilibrium or with a slight excess of heterozygotes. Although overall gene diversity was extremely low, TPI genotype frequencies were indicative of an outcrossing plant. We examined the subpopulation genetic structure among clonal plants within one Wisconsin population in greater detail. F statistics indicated that much of the genetic variation at the polymorphic TPI locus was due to differentiation among populations. We discuss the implications of self-incompatibility and low levels of genetic variation for the evolution and conservation of Aster furcatus and other rare plants with similar breeding systems., (© 1991 The Society for the Study of Evolution.)

Morphologically heterophyllous species of Potamogeton also commonly display biochemical heterophylly with respect to flavonoid compounds. Generally, floating leaves contain an assortment of flavonoids, whereas submersed leaves often exhibit reduced flavonoid profiles. In strictly submersed (homophyllous) species, two patterns occur. Linear-leaved species have few flavonoids and their biochemical profiles resemble those of submersed leaves of heterophyllous species. Broad-leaved homophyllous species possess flavonoid profiles more similar to those of the floating leaves of heterophyllous species. Numerical analysis of these chemical data is consistent with phylogenetic relationships within the genus derived independently on the basis of morphological and chromosomal data. Glycoflavones, which are probably maintained in floating leaves because of their UV filtering ability, exhibit the most pronounced biochemical heterophylly in Potamogeton. The lack of glycoflavones in submersed leaves of heterophyllous species and in linear-leaved homophyllous species is attributable to the ability of naturally colored water to significantly absorb harmful UV radiation. These observations provide strong support for earlier hypotheses suggesting the importance of flavonoid evolution in the conquest of exposed terrestrial habitats by plants., (© 1990 Botanical Society of America.)