Kurt M. Neubig

Evolution along the crassulacean acid metabolism continuum

Crassulaceanacid metabolism(CAM) isaspecialised modeof photosynthesisthat improves atmospheric CO2 assimilationinwater-limited terrestrial andepiphytichabitatsandinCO2-limited aquatic environments.Incontrast withC3 and C4 plants, CAM plants take up CO2 from the atmosphere partially or predominantly at night. CAM is taxonomically widespreadamongvascularplantsandispresentinmanysucculentspeciesthatoccupysemiaridregions,aswellasintropical epiphytesandinsomeaquaticmacrophytes.Thiswater-conservingphotosyntheticpathwayhasevolvedmultipletimesand isfoundincloseto6%ofvascularplantspeciesfromatleast35families.AlthoughmanyaspectsofCAMmolecularbiology, biochemistryandecophysiologyarewellunderstood,relativelylittleisknownabouttheevolutionaryoriginsofCAM.This review focuses on five main topics: (1) the permutations and plasticity of CAM, (2) the requirements for CAM evolution, (3) the drivers of CAM evolution, (4) the prevalence and taxonomic distribution of CAM among vascular plants with emphasisontheOrchidaceaeand(5)themolecularunderpinningsofCAMevolutionincludingcircadianclockregulationof gene expression.

Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

Plastid DNA sequences have been widely used by systematists for reconstructing plant phylogenies. The utility of any DNA region for phylogenetic analysis is determined by ease of amplification and sequencing, confidence of assessment in phylogenetic character alignment, and by variability across broad taxon sampling. Often, a compromise must be made between using relatively highly conserved coding regions or highly variable introns and intergenic spacers. Analyses of a combination of these types of DNA regions yield phylogenetic structure at various levels of a tree (i.e., along the spine and at the tips of the branches). Here, we demonstrate the phylogenetic utility of a heretofore unused portion of a plastid protein-coding gene, hypothetical chloroplast open reading frame 1 (ycf1), in orchids. All portions of ycf1 examined are highly variable, yet alignable across Orchidaceae, and are phylogenetically informative at the level of species. In Orchidaceae, ycf1 is more variable than matK both in total number of parsimony informative characters and in percent variability. The nrITS region is more variable than ycf1, but is more difficult to align. Although we only demonstrate the phylogenetic utility of ycf1 in orchids, it is likely to be similarly useful among other plant taxa.

Floral convergence in Oncidiinae (Cymbidieae; Orchidaceae): an expanded concept of Gomesa and a new genus Nohawilliamsia

BACKGROUND Floral morphology, particularly the angle of lip attachment to the column, has historically been the fundamental character used in establishing generic limits in subtribe Oncidiinae (Orchidaceae), but it has also been long recognized that reliance on this character alone has produced a highly artificial set of genera. In essence, lip/column relationships reflect syndromes associated with pollinator preferences; most genera of Oncidiinae as previously defined have consisted of a single floral type. Here, the degree to which this has influenced generic delimitation in Brazilian members of the largest genus of Oncidiinae, Oncidium, which previous molecular (DNA) studies have demonstrated to be polyphyletic, is evaluated. METHODS Phylogenetic analyses of the following multiple DNA regions were used: the plastid psbA-trnH intergenic spacer, matK exon and two regions of ycf1 exon and nuclear ribosomal DNA, comprised of the two internal transcribed spacers, ITS1 and ITS2, and the 5.8S gene. Results from all regions analysed separately indicated highly similar relationships, so a combined matrix was analysed. KEY RESULTS Nearly all species groups of Brazilian Oncidium are only distantly related to the type species of the genus, O. altissimum, from the Caribbean. There are two exceptions to this geographical rule: O. baueri is related to the type group and O. orthostates, an isolated species that lacks the defining tabula infrastigmata of Oncidium, is not exclusively related to any previously described genus in the subtribe. Several well-supported subclades can be observed in these results, but they do not correspond well to sections of Oncidium as previously circumscribed or to segregate genera as defined by several recent authors. In spite of their floral differences, these groups of Oncidium, formerly treated as O. sections Barbata, Concoloria pro parte, Crispa, Ranifera, Rhinocerotes, Rostrata (only O. venustum), Synsepala, Verrucituberculata pro parte and Waluewa, form a well-supported clade with Gomesa (including Rodrigueziella and Rodrigueziopsis) embedded in it. Two often recognized segregate genera, Baptistonia and Ornithophora, and the recently described Carriella are also embedded within the Brazilian clade. The level of variation within major subclades of the Gomesa clade is low and similar to that observed within other genera of Oncidiinae. CONCLUSIONS Convergence on a stereotypical syndrome of floral traits associated with pollination by oil-collecting bees has resulted in these characters not being reliable for producing monophyletic taxa, and the genus Oncidium, defined by these characters, is grossly polyphyletic. Vegetative and a few floral/inflorescence characters link these taxa with a mainly Brazilian distribution, and they were all transferred to Gomesa on this basis rather than separated from Gomesa based on their floral differences, which we hypothesize to be simple shifts in pollination strategies. Other authors have described a large number of new genera for these former members of Oncidium, but most of these are not supported by the results presented here (i.e. they are not monophyletic). A new genus, Nohawilliamsia, is described for O. orthostates because it does not fit in any currently recognized genus and is only distantly related to any other member of Oncidiinae.

Recent gene-capture on the UV sex chromosomes of the moss Ceratodon purpureus.

Sex chromosomes evolve from ordinary autosomes through the expansion and subsequent degeneration of a region of suppressed recombination that is inherited through one sex. Here we investigate the relative timing of these processes in the UV sex chromosomes of the moss Ceratodon purpureus using molecular population genetic analyses of eight newly discovered sex‐linked loci. In this system, recombination is suppressed on both the female‐transmitted (U) sex chromosome and the male‐transmitted (V) chromosome. Genes on both chromosomes therefore should show the deleterious effects of suppressed recombination and sex‐limited transmission, while purifying selection should maintain homologs of genes essential for both sexes on both sex chromosomes. Based on analyses of eight sex‐linked loci, we show that the nonrecombining portions of the U and V chromosomes expanded in at least two events (∼0.6–1.3 MYA and ∼2.8–3.5 MYA), after the divergence of C. purpureus from its dioecious sister species, Trichodon cylindricus and Cheilothela chloropus. Both U‐ and V‐linked copies showed reduced nucleotide diversity and limited population structure, compared to autosomal loci, suggesting that the sex chromosomes experienced more recent selective sweeps that the autosomes. Collectively these results highlight the dynamic nature of gene composition and molecular evolution on nonrecombining portions of the U and V sex chromosomes.

Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries.

Earlier research has revealed that the ndh loci have been pseudogenized, truncated, or deleted from most orchid plastomes sequenced to date, including in all available plastomes of the two most species-rich subfamilies, Orchidoideae and Epidendroideae. This study sought to resolve deeper-level phylogenetic relationships among major orchid groups and to refine the history of gene loss in the ndh loci across orchids. The complete plastomes of seven orchids, Oncidium sphacelatum (Epidendroideae), Masdevallia coccinea (Epidendroideae), Sobralia callosa (Epidendroideae), Sobralia aff. bouchei (Epidendroideae), Elleanthus sodiroi (Epidendroideae), Paphiopedilum armeniacum (Cypripedioideae), and Phragmipedium longifolium (Cypripedioideae) were sequenced and analyzed in conjunction with all other available orchid and monocot plastomes. Most ndh loci were found to be pseudogenized or lost in Oncidium, Paphiopedilum and Phragmipedium, but surprisingly, all ndh loci were found to retain full, intact reading frames in Sobralia, Elleanthus and Masdevallia. Character mapping suggests that the ndh genes were present in the common ancestor of orchids but have experienced independent, significant losses at least eight times across four subfamilies. In addition, ndhF gene loss was correlated with shifts in the position of the junction of the inverted repeat (IR) and small single-copy (SSC) regions. The Orchidaceae have unprecedented levels of homoplasy in ndh gene presence/absence, which may be correlated in part with the unusual life history of orchids. These results also suggest that ndhF plays a role in IR/SSC junction stability.

Miconia cineana (Melastomataceae: Miconieae), a New Species from the Massif de la Hotte, Haiti, Based on Morphological and Molecular Evidence

Abstract We describe a new species, Miconia cineana (Melastomataceae: Miconieae), from the Massif de la Hotte, Haiti. Although this species has been known from sterile collections since the early 1980s, its phylogenetic position was unknown, although it was presumed to be closely related to species of Pachyanthus s. l. The phylogenetic reconstruction presented here, based on a recent collection of the species, clearly places M. cineana in a clade comprised of Cuban species of the polyphyletic genera Tetrazygia s. l. and Pachyanthus s. l. Thus, M. cineana represents the sole Hispaniolan member of an otherwise Cuban clade, and an uncommon biogeographic pattern in melastomes. Miconia cineana, although described here from sterile specimens, is easily distinguished from the other species of this clade using vegetative morphology, as well as phylogenetic placement. This study highlights the utility of molecular data when coupled with morphology, allowing for the discovery of an unrecognized species in a region of high diversity and endemism, i.e. the Massif de la Hotte.

Primer development for the plastid region ycf1 in Annonaceae and other magnoliids.

UNLABELLED PREMISE OF THE STUDY Primers were developed for a portion of the ycf1 plastid gene in magnoliid taxa to investigate the utility of ycf1 in phylogenetic analyses. • METHODS AND RESULTS Twenty-six species across six families within the magnoliid group (Canellales, Piperales, Laurales, and Magnoliales) were sampled to examine the ability to amplify ycf1. Additionally, 29 accessions of Asimina and Deeringothamnus (Annonaceae) were sequenced to assess levels of variation in ycf1 compared to matK and trnL-F. • CONCLUSIONS Results indicate that ycf1 is easily amplified and sequenced. In Annonaceae, ycf1 provides more informative phylogenetic characters than commonly used markers such as matK and trnL-F.

Molecular phylogenetics and the evolution of fruit and leaf morphology of Dichaea (Orchidaceae: Zygopetalinae).

BACKGROUND AND AIMS The orchid genus Dichaea, with over 100 species found throughout the neotropics, is easily recognized by distichous leaves on long stems without pseudobulbs and flowers with infrastigmatic ligules. The genus has previously been divided into four sections based primarily on presence of ovary bristles and a foliar abscission layer. The aim of this work is to use DNA sequence data to estimate phylogenetic relationships within Dichaea and map the distribution of major morphological characters that have been used to delimit subgenera/sections. METHODS Sequence data for the nuclear ribosomal internal transcribed spacers and plastid matK, trnL intron, trnL-F spacer and ycf1 for 67 ingroup and seven outgroup operational taxonomic units were used to estimate phylogenetic relationships within Dichaea. Taxa from each of the four sections were sampled, with the greatest representation from section Dichaea, the most diverse and taxonomically puzzling group. KEY RESULTS Molecular data and morphology support monophyly of Dichaea. Results indicate that section Dichaeopsis is polyphyletic and based on symplesiomorphies, including deciduous leaves and smooth ovaries that are widespread in Zygopetalinae. There are at least three well-supported clades within section Dichaeopsis. Section Pseudodichaea is monophyletic and defined by setose ovaries and leaves with an abscission layer. Sections Dichaea and Dichaeastrum are monophyletic and defined by pendent habit and persistent leaves. Section Dichaeastrum, distinguished from section Dichaea primarily by a glabrous ovary, is potentially polyphyletic. CONCLUSIONS The leaf abscission layer was lost once, occurring only in the derived sections Dichaea and Dichaeastrum. The setose fruit is a more homoplasious character with several losses and gains within the genus. We propose an informal division of the genus based upon five well-supported clades.

Evolution of the Sandpaper Clade (Miconieae, Melastomataceae)

Premise of research. The Sandpaper clade comprises a group of taxa endemic to the Greater Antilles and forms a subgroup of a larger Caribbean assemblage of Miconieae. Numerous species within this monophyletic group share striking morphological characters and thus traditionally have been considered close relatives. Recent phylogenetic work has shown that not all of these species are each other’s closest relatives, and they actually form three distinct clades: the Lima, Paralima, and Pseudolima clades. We reconstructed a phylogeny of these poorly known species to test patterns of morphological evolution and the biogeographic history of the clade. Methodology. We reconstructed a phylogeny of the Sandpaper clade using two plastid intergenic spacers (accD-psaI, psbK-psbL) and two nuclear ribosomal spacers (ITS, ETS) and then sequenced three more plastid spacers for the Lima clade (rpl32-trnL, trnV-ndhC, trnH-psbA) to provide better resolution among those species. The biogeographic history and the evolution of morphological traits were tested using maximum parsimony based on 12 mountain ranges in the Greater Antilles and 48 morphological characters, respectively. Pivotal results. The Sandpaper clade most likely originated in eastern Cuba, with subsequent dispersals to other parts of the island, as well as to Jamaica, Hispaniola, and Puerto Rico. In general, morphological characters shared by the Lima, Paralima, and Pseudolima clades evolved independently. All subclades of the Sandpaper clade can be recognized by suites of characters; however, unique synapomorphies for clades are rare. Conclusions. Eastern Cuba formed the starting point for the diversification of the Sandpaper clade, likely as a result of the diverse topography and associated ecological diversity (e.g., serpentine soils). This clade represents only a moderate-sized radiation of the Caribbean clade; however, the convergent nature of character evolution and the lack of unique synapomorphies for subclades underscore the lability of morphological characters in this group and the difficulty in recognizing these clades from a purely morphological standpoint.

Using Comparative Biogeography to Retrace the Origins of an Ecosystem: The Case of Four Plants Endemic to the Central Florida Scrub

Premise of research. Plant communities assemble through historical, adaptive, and stochastic processes, with their relative contributions varying among communities. This study traces the origin of the highly threatened Florida scrub ecosystem, a series of relic sand dunes with exceptionally high endemism. We used dated phylogenies with four endemic angiosperms to test two hypotheses on the origins of the Florida scrub: the western hypothesis, which emphasizes the role of mid-Pliocene fragmentation of the xeric belt between southwestern North America and Florida, and the eastern hypothesis, which emphasizes the glacial cycles of the Pleistocene. Methodology. Augmenting existing phylogenies, we sequenced the nuclear internal transcribed spacer region and several plastid loci of species of Prunus (Rosaceae), Polygala (Polygalaceae), Persea (Lauraceae), and Ilex (Aquifoliaceae) to phylogenetically place the Florida scrub endemics and identify their putative sister taxa. We used topology tests, ancestral area reconstruction analyses, and time-calibrated trees to evaluate the western and eastern hypotheses both geographically and temporally. Pivotal results. Results for Polygala and Ilex support the eastern hypothesis for the origin of the central Florida endemics, while data for Persea and Prunus are ambiguous. However, all species show an eastern ancestral distribution to some degree. Molecular dating analyses suggest that extant Ilex opaca populations diverged in the Pleistocene, with older Pliocene origins for the North American Persea clade, Polygala lewtonii, and Prunus geniculata. Conclusions. Taken together, our results support eastern North America as the dominant origin of the plant species of the central Florida scrub. However, contrary to the current eastern hypothesis, molecular dating suggests that the origins of the four endemics predate the last glacial cycles. These results have implications for the age of the Florida scrub itself as well as its component species, suggesting that the Florida scrub or its precursor existed before Pleistocene glaciation. Furthermore, the more ancient age of this assemblage of species than envisioned by most accounts suggests that interspecific interactions in this community are not recently formed (i.e., since the end of the Pleistocene) and may have been established over much longer periods of geological history. These fundamental associations argue for enhanced conservation efforts of both the individual species and the persistent remnants of the scrub community.