Lower transfer factor of the lung for carbon monoxide in women with a patent foramen ovale.

NEW FINDINGS: What is the central question of this study? Do individuals with a patent foramen ovale (PFO+ ) have a lower lung transfer factor for carbon monoxide than those without (PFO- )? What is the main finding and its importance? We found a lower rate constant for carbon monoxide uptake in PFO+ compared with PFO- women, which was physiologically relevant (≥0.5 z-score difference), but not for PFO+ versus PFO- men. This suggests that factors independent of the PFO are responsible for our findings, possibly inherent structural differences in the lung. ABSTRACT: The transfer factor of the lung for carbon monoxide (TLCO ) measure assumes that all cardiac output flows through the pulmonary circuit. However, right-to-left blood flow through a shunt can result in a lower transfer factor than predicted. A patent foramen ovale (PFO) is a potential source of right-to-left shunt that is present in ∼35% of the population, but the effect of PFO on TLCO is unknown. We sought to determine the effect of PFO on the TLCO . We conducted a retrospective analysis of TLCO data from 239 (101 women) participants. Anthropometrics and lung function, including spirometry, plethysmography and TLCO , were compiled from our previously published work. Women, but not men, with a PFO had a significantly lower TLCO and rate constant for carbon monoxide uptake (KCO ) (percentage of predicted and z-score) than women without a PFO. Women and men with a PFO had normal alveolar volumes that did not differ from those without a PFO. Correcting the data for haemoglobin in a subset of subjects did not change the results (n = 58; 25 women). The lower KCO in women with versus without a PFO was physiologically relevant (≥0.5 z-score difference). There was no effect of PFO in men. This suggests that factors independent of the PFO are responsible for our findings, possibly inherent structural differences in the lung.

Intrapulmonary arteriovenous anastomoses in humans with chronic obstructive pulmonary disease: implications for cryptogenic stroke?

What is the central question of this study? Do individuals with chronic obstructive pulmonary disease have blood flow through intrapulmonary arteriovenous anastomoses at rest or during exercise? What is the main finding and its importance? Individuals with chronic obstructive pulmonary disease have a greater prevalence of blood flow through intrapulmonary arteriovenous anastomoses at rest than age-matched control subjects. Given that the intrapulmonary arteriovenous anastomoses are large enough to permit venous emboli to pass into the arterial circulation, patients with chronic obstructive pulmonary disease and an elevated risk of thrombus formation may be at risk of intrapulmonary arteriovenous anastomosis-facilitated embolic injury (e.g. stroke or transient ischaemic attack). The pulmonary capillaries prevent stroke by filtering venous emboli from the circulation. Intrapulmonary arteriovenous anastomoses are large-diameter (≥50 µm) vascular connections in the lung that may compromise the integrity of the pulmonary capillary filter and have recently been linked to cryptogenic stroke and transient ischaemic attack. Prothrombotic populations, such as individuals with chronic obstructive pulmonary disease (COPD), may be at increased risk of stroke and transient ischaemic attack facilitated by intrapulmonary arteriovenous anastomoses, but the prevalence and degree of blood flow through intrapulmonary arteriovenous anastomoses in this population has not been fully examined and compared with age-matched healthy control subjects. We used saline contrast echocardiography to assess blood flow through intrapulmonary arteriovenous anastomoses at rest (n = 29 COPD and 19 control subjects) and during exercise (n = 10 COPD and 10 control subjects) in subjects with COPD and age-matched healthy control subjects. Blood flow through intrapulmonary arteriovenous anastomoses was detected in 23% of subjects with COPD at rest and was significantly higher compared with age-matched healthy control subjects. Blood flow through intrapulmonary arteriovenous anastomoses at rest was reduced or eliminated in subjects with COPD after breathing hyperoxic gas. Sixty per cent of subjects with COPD who did not have blood flow through the intrapulmonary arteriovenous anastomoses at rest had blood flow through them during exercise. The combination of blood flow through intrapulmonary arteriovenous anastomoses and potential for thrombus formation in individuals with COPD may permit venous emboli to pass into the arterial circulation and cause stroke and transient ischaemic attack. Breathing supplemental oxygen may reduce this risk in COPD. The link between blood flow through intrapulmonary arteriovenous anastomoses, stroke and transient ischaemic attack is worthy of future investigation in COPD and other populations.

Treatment Planning and Delivery of Whole Brain Irradiation with Hippocampal Avoidance in Rats.

BACKGROUND: Despite the clinical benefit of whole brain radiotherapy (WBRT), patients and physicians are concerned by the long-term impact on cognitive functioning. Many studies investigating the molecular and cellular impact of WBRT have used rodent models. However, there has not been a rodent protocol comparable to the recently reported Radiation Therapy Oncology Group (RTOG) protocol for WBRT with hippocampal avoidance (HA) which is intended to spare cognitive function. The aim of this study was to develop a hippocampal-sparing WBRT protocol in Wistar rats. METHODS: The technical and clinical challenges encountered in hippocampal sparing during rat WBRT are substantial. Three key challenges were identified: hippocampal localization, treatment planning, and treatment localization. Hippocampal localization was achieved with sophisticated imaging techniques requiring deformable registration of a rat MRI atlas with a high resolution MRI followed by fusion via rigid registration to a CBCT. Treatment planning employed a Monte Carlo dose calculation in SmART-Plan and creation of 0.5 cm thick lead blocks custom-shaped to match DRR projections. Treatment localization necessitated the on-board image-guidance capability of the XRAD C225Cx micro-CT/micro-irradiator (Precision X-Ray). Treatment was accomplished with opposed lateral fields with 225 KVp X-rays at a current of 13 mA filtered through 0.3 mm of copper using a 40x40 mm square collimator and the lead blocks. A single fraction of 4 Gy was delivered (2 Gy per lateral field) with a 41 second beam on time per field at a dose rate of 304.5 cGy/min. Dosimetric verification of hippocampal sparing was performed using radiochromic film. In vivo verification of HA was performed after delivery of a single 4 Gy fraction either with or without HA using γ-H2Ax staining of tissue sections from the brain to quantify the amount of DNA damage in rats treated with HA, WBRT, or sham-irradiated (negative controls). RESULTS: The mean dose delivered to radiochromic film beneath the hippocampal block was 0.52 Gy compared to 3.93 Gy without the block, indicating an 87% reduction in the dose delivered to the hippocampus. This difference was consistent with doses predicted by Monte Carlo dose calculation. The Dose Volume Histogram (DVH) generated via Monte Carlo simulation showed an underdose of the target volume (brain minus hippocampus) with 50% of the target volume receiving 100% of the prescription isodose as a result of the lateral blocking techniques sparing some midline thalamic and subcortical tissue. Staining of brain sections with anti-phospho-Histone H2A.X (reflecting double-strand DNA breaks) demonstrated that this treatment protocol limited radiation dose to the hippocampus in vivo. The mean signal intensity from γ-H2Ax staining in the cortex was not significantly different from the signal intensity in the cortex of rats treated with WBRT (5.40 v. 5.75, P = 0.32). In contrast, the signal intensity in the hippocampus of rats treated with HA was significantly lower than rats treated with WBRT (4.55 v. 6.93, P = 0.012). CONCLUSION: Despite the challenges of planning conformal treatments for small volumes in rodents, our dosimetric and in vivo data show that WBRT with HA is feasible in rats. This study provides a useful platform for further application and refinement of the technique.

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.

Orchid phylogenomics and multiple drivers of their extraordinary diversification.

Orchids are the most diverse family of angiosperms, with over 25 000 species,more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here,we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. Asupermatrix analysis places an additional 144 species based on three plastid genes. Orchids appear to have arisen roughly 112 million years ago (Mya); the subfamilies Orchidoideae and Epidendroideae diverged from each other at the end of the Cretaceous; and the eight tribes and three previously unplaced subtribes of the upper epidendroids diverged rapidly from each other between 37.9 and 30.8 Mya. Orchids appear to have undergone one significant acceleration of net species diversification in the orchidoids, and two accelerations and one deceleration in the upper epidendroids. Consistent with theory, such accelerations were correlated with the evolution of pollinia, the epiphytic habit, CAM photosynthesis, tropical distribution (especially in extensive cordilleras),and pollination via Lepidoptera or euglossine bees. Deceit pollination appears to have elevated the number of orchid species by one-half but not via acceleration of the rate of net diversification. The highest rate of net species diversification within the orchids (0.382 sp sp(-1) My(-1)) is 6.8 times that at the Asparagales crown.

Exercise- and hypoxia-induced blood flow through intrapulmonary arteriovenous anastomoses is reduced in older adults.

Mean pulmonary arterial pressure (Ppa) during exercise is significantly higher in individuals aged ≥50 yr compared with their younger counterparts, but the reasons for this are unknown. Blood flow through intrapulmonary arteriovenous anastomoses (IPAVA) can be detected during exercise or while breathing hypoxic gas mixtures using saline contrast echocardiography in almost all healthy young individuals. It has been previously hypothesized that a lower degree of exercise-induced blood flow through IPAVA is associated with high Ppa during exercise. This association may suggest that individuals who are known to have high Ppa during exercise, such as those ≥50 yr of age, may have lower blood flow through IPAVA, but the presence and degree of exercise-induced blood flow through IPAVA has not been specifically studied in older populations. Using transthoracic saline contrast echocardiography, we investigated the potential effects of age on exercise-induced blood flow through IPAVA in a cross-section of subjects aged 19-72 yr. To verify our findings, we assessed the effects of age on hypoxia-induced blood flow through IPAVA. Age groups were ≤41 yr (younger, n = 16) and ≥50 yr (older, n = 14). Qualitatively measured exercise- and hypoxia-induced blood flow through IPAVA was significantly lower in older individuals compared with younger controls. Older individuals also had significantly higher pulmonary arterial systolic pressure and total pulmonary resistance (TPR) during exercise. Low blood flow through IPAVA was independently associated with high TPR. The reasons for the age-related decrease in blood flow through IPAVA are unknown.

Convergent evolution of floral signals underlies the success of Neotropical orchids.

The great majority of plant species in the tropics require animals to achieve pollination, but the exact role of floral signals in attraction of animal pollinators is often debated. Many plants provide a floral reward to attract a guild of pollinators, and it has been proposed that floral signals of non-rewarding species may converge on those of rewarding species to exploit the relationship of the latter with their pollinators. In the orchid family (Orchidaceae), pollination is almost universally animal-mediated, but a third of species provide no floral reward, which suggests that deceptive pollination mechanisms are prevalent. Here, we examine floral colour and shape convergence in Neotropical plant communities, focusing on certain food-deceptive Oncidiinae orchids (e.g. Trichocentrum ascendens and Oncidium nebulosum) and rewarding species of Malpighiaceae. We show that the species from these two distantly related families are often more similar in floral colour and shape than expected by chance and propose that a system of multifarious floral mimicry--a form of Batesian mimicry that involves multiple models and is more complex than a simple one model-one mimic system--operates in these orchids. The same mimetic pollination system has evolved at least 14 times within the species-rich Oncidiinae throughout the Neotropics. These results help explain the extraordinary diversification of Neotropical orchids and highlight the complexity of plant-animal interactions.

Longitudinal analysis of pain in patients with metastatic prostate cancer using natural language processing of medical record text.

OBJECTIVES: To test the feasibility of using text mining to depict meaningfully the experience of pain in patients with metastatic prostate cancer, to identify novel pain phenotypes, and to propose methods for longitudinal visualization of pain status. MATERIALS AND METHODS: Text from 4409 clinical encounters for 33 men enrolled in a 15-year longitudinal clinical/molecular autopsy study of metastatic prostate cancer (Project to ELIminate lethal CANcer) was subjected to natural language processing (NLP) using Unified Medical Language System-based terms. A four-tiered pain scale was developed, and logistic regression analysis identified factors that correlated with experience of severe pain during each month. RESULTS: NLP identified 6387 pain and 13 827 drug mentions in the text. Graphical displays revealed the pain 'landscape' described in the textual records and confirmed dramatically increasing levels of pain in the last years of life in all but two patients, all of whom died from metastatic cancer. Severe pain was associated with receipt of opioids (OR=6.6, p<0.0001) and palliative radiation (OR=3.4, p=0.0002). Surprisingly, no severe or controlled pain was detected in two of 33 subjects' clinical records. Additionally, the NLP algorithm proved generalizable in an evaluation using a separate data source (889 Informatics for Integrating Biology and the Bedside (i2b2) discharge summaries). DISCUSSION: Patterns in the pain experience, undetectable without the use of NLP to mine the longitudinal clinical record, were consistent with clinical expectations, suggesting that meaningful NLP-based pain status monitoring is feasible. Findings in this initial cohort suggest that 'outlier' pain phenotypes useful for probing the molecular basis of cancer pain may exist. LIMITATIONS: The results are limited by a small cohort size and use of proprietary NLP software. CONCLUSIONS: We have established the feasibility of tracking longitudinal patterns of pain by text mining of free text clinical records. These methods may be useful for monitoring pain management and identifying novel cancer phenotypes.

Evaluation of a clinically intuitive quality assurance method.

There is a pressing need for clinically intuitive quality assurance methods that report metrics of relevance to the likely impact on tumor control of normal tissue injury. This paper presents a preliminary investigation into the accuracy of a novel "transform method" which enables a clinically relevant analysis through dose-volume-histograms (DVHs) and dose overlays on the patient's CT data. The transform method was tested by inducing a series of known mechanical and delivery errors onto simulated 3D dosimetry measurements of six different head-and-neck IMRT treatment plans. Accuracy was then examined through the comparison of the transformed patient dose distributions and the known actual patient dose distributions through dose-volume histograms and normalized dose difference analysis. Through these metrics, the transform method was found to be highly accurate in predicting measured patient dose distributions for these types of errors.

Description of a rule-based system for the i2b2 challenge in natural language processing for clinical data.

The Obesity Challenge, sponsored by Informatics for Integrating Biology and the Bedside (i2b2), a National Center for Biomedical Computing, asked participants to build software systems that could "read" a patient's clinical discharge summary and replicate the judgments of physicians in evaluating presence or absence of obesity and 15 comorbidities. The authors describe their methodology and discuss the results of applying Lockheed Martin's rule-based natural language processing (NLP) capability, ClinREAD. We tailored ClinREAD with medical domain expertise to create assigned default judgments based on the most probable results as defined in the ground truth. It then used rules to collect evidence similar to the evidence that the human judges likely relied upon, and applied a logic module to weigh the strength of all evidence collected to arrive at final judgments. The Challenge results suggest that rule-based systems guided by human medical expertise are capable of solving complex problems in machine processing of medical text.

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.

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.

Molecular phylogeny of the neotropical genus Christensonella (Orchidaceae, Maxillariinae): species delimitation and insights into chromosome evolution.

BACKGROUND AND AIMS: Species' boundaries applied within Christensonella have varied due to the continuous pattern of variation and mosaic distribution of diagnostic characters. The main goals of this study were to revise the species' delimitation and propose a more stable classification for this genus. In order to achieve these aims phylogenetic relationships were inferred using DNA sequence data and cytological diversity within Christensonella was examined based on chromosome counts and heterochromatin patterns. The results presented describe sets of diagnostic morphological characters that can be used for species' identification. METHODS: Phylogenetic studies were based on sequence data of nuclear and plastid regions, analysed using maximum parsimony and maximum likelihood criteria. Cytogenetic observations of mitotic cells were conducted using CMA and DAPI fluorochromes. KEY RESULTS: Six of 21 currently accepted species were recovered. The results also support recognition of the 'C. pumila' clade as a single species. Molecular phylogenetic relationships within the 'C. acicularis-C. madida' and 'C. ferdinandiana-C. neowiedii' species' complexes were not resolved and require further study. Deeper relationships were incongruent between plastid and nuclear trees, but with no strong bootstrap support for either, except for the position of C. vernicosa. Cytogenetic data indicated chromosome numbers of 2n = 36, 38 and 76, and with substantial variation in the presence and location of CMA/DAPI heterochromatin bands. CONCLUSIONS: The recognition of ten species of Christensonella is proposed according to the molecular and cytogenetic patterns observed. In addition, diagnostic morphological characters are presented for each recognized species. Banding patterns and chromosome counts suggest the occurrence of centric fusion/fission events, especially for C. ferdinandiana. The results suggest that 2n = 36 karyotypes evolved from 2n = 38 through descendent dysploidy. Patterns of heterochromatin distribution and other karyotypic data proved to be a valuable source of information to understand evolutionary patterns within Maxillariinae orchids.

Survival and clinical outcome of SB Charite III disc replacement for back pain.

Between January 1990 and December 2000 we carried out 226 SB Charité III disc replacements for lumbar disc degeneration in 160 patients. They were reviewed at a mean follow-up of 79 months (31 to 161) to determine the clinical and radiological outcome. The clinical results were collected by an independent observer, who was not involved in patient selection, treatment or follow-up, using a combination of outcome measures, including the Oswestry Disability Index. Pain was recorded using a visual analogue score, and the most recent radiographs were reviewed. Survival of the device was analysed by the Kaplan-Meier method and showed a cumulative survival of 35% at 156 months when radiological failure was taken as the endpoint. The mean improvement in the Oswestry disability index scores after disc replacement was 14% (6% to 21%) and the mean improvement in the pain score was 1.6 (0.46 to 2.73), both falling below the clinically significant threshold. Removal of the implant was required in 12 patients, four because of implant failure. These poor results indicate that further use of this implant is not justified.

Molecular phylogenetics of Maxillaria and related genera (Orchidaceae: Cymbidieae) based on combined molecular data sets.

The orchid genus Maxillaria is one of the largest and most common of neotropical orchid genera, but its current generic boundaries and relationships have long been regarded as artificial. Phylogenetic relationships within subtribe Maxillariinae sensu Dressler (1993) with emphasis on Maxillaria s.l. were inferred using parsimony analyses of individual and combined DNA sequence data. We analyzed a combined matrix of nrITS DNA, the plastid matK gene and flanking trnK intron, and the plastid atpB-rbcL intergenic spacer for 619 individuals representing ca. 354 species. The plastid rpoC1 gene (ca. 2600 bp) was sequenced for 84 selected species and combined in a more limited analysis with the other data sets to provide greater resolution. In a well-resolved, supported consensus, most clades were present in more than one individual analysis. All the currently recognized minor genera of "core" Maxillariinae (Anthosiphon, Chrysocycnis, Cryptocentrum, Cyrtidiorchis, Mormolyca, Pityphyllum, and Trigonidium) are embedded within a polyphyletic Maxillaria s.l. Our results support the recognition of a more restricted Maxillaria, of some previously published segregate genera (Brasiliorchis, Camaridium, Christensonella, Heterotaxis, Ornithidium, Sauvetrea), and of several novel clades at the generic level. These revised monophyletic generic concepts should minimize further nomenclatural changes, encourage monographic studies, and facilitate more focused analyses of character evolution within Maxillariinae.

Molecular phylogenetics of Vandeae (Orchidaceae) and the evolution of leaflessness.

Members of tribe Vandeae (Orchidaceae) form a large, pantropical clade of horticulturally important epiphytes. Monopodial leafless members of Vandeae have undergone extreme reduction in habit and represent a novel adaptation to the canopy environment in tropical Africa, Asia, and America. To study the evolution of monopodial leaflessness, molecular and structural evidence was used to generate phylogenetic hypotheses for Vandeae. Molecular analyses used sequence data from ITS nrDNA, trnL-F plastid DNA, and matK plastid DNA. Maximum parsimony analyses of these three DNA regions each supported two subtribes within monopodial Vandeae: Aeridinae and a combined Angraecinae + Aerangidinae. Adding structural characters to sequence data resulted in trees with more homoplasy, but gave fewer trees each with more well-supported clades than either data set alone. Two techniques for examining character evolution were compared: (1) mapping vegetative characters onto a molecular topology and (2) tracing vegetative characters onto a combined structural and molecular topology. In both cases, structural synapomorphies supporting monopodial Vandeae were nearly identical. A change in leaf morphology (usually reduced to a nonphotosynthetic scale), monopodial growth habit, and aeration complexes for gas exchange in photosynthetic roots seem to be the most important characters in making the evolutionary transition to leaflessness.

Infrageneric phylogeny of Schoenocaulon (Liliales: Melanthiaceae) with clarification of cryptic species based on ITS sequence data and geographical distribution.

As currently defined, the 24 species of Schoenocaulon occur in three disjunct areas: north central Florida (one species, S. dubium), southern Peru (portion of the range of S. officinale), and the region from southeastern New Mexico-Texas south to Venezuela; the 20 species endemic to Mexico are geographically restricted. Species delimitations, often based on tepal morphology, have been problematic. Our analyses of ITS sequence data for all 27 species and infraspecific taxa support recognition of two new species and recircumscription and placement of elements of the polyphyletic S. ghiesbreghtii and S. mortonii complexes. For taxa with adequate sampling, our data also indicate 11-12 cladospecies and 3-6 metaspecies according to the apomorphic species concept. The resolved phylogeny, correlated with geography and morphology, allows insight into biogeographical diversification and the evolution of some unusual morphological characters within the genus, such as nectary differentiation and tepal margin type.

Life history evolution and genome size in subtribe Oncidiinae (Orchidaceae).

BACKGROUND AND AIMS: Within Oncidiinae, there are several groups of species that are effectively annuals, and we wished to see if these species had smaller genome sizes than average for the subtribe. METHODS: Fifty-four genome size estimates (50 of which are new) for species in subtribe Oncidiinae (Orchidaceae) were examined for the first time in a phylogenetic context to evaluate hypotheses concerning genome sizes and life history traits. RESULTS AND CONCLUSIONS: Within the limits of still relatively sparse sampling, the species that are effectively annuals do appear to have smaller genome sizes than average. However, the genome sizes of their immediate sister group are also small, indicating that changes in genome size preceded the change in life history traits. Genome sizes and chromosome numbers also do not correlate; some slowly growing species have lower chromosome numbers but large genomes and vice versa. Based on a survey of the literature on orchids, it is also clear that epiphytic species have smaller genome sizes than do terrestrial species, which could be an effect of different water relations or the fact that most terrestrial orchids are geophytic or have distinct growth and dormancy phases.