Matching seed to site by climate similarity: Techniques to prioritize plant materials development and use in restoration

Land management agencies are increasing the use of native plant materials for vegetation treatments to restore ecosystem function and maintain natural ecological integrity. This shift toward the use of natives has highlighted a need to increase the diversity of materials available. A key problem is agreeing on how many, and which, new accessions should be developed. Here we describe new methods that address this problem. Our methods use climate data to calculate a climate similarity index between two points in a defined extent. This index can be used to predict relative performance of available accessions at a target site. In addition, the index can be used in combination with standard cluster analysis algorithms to quantify and maximize climate coverage (mean climate similarity), given a modeled range extent and a specified number of accessions. We demonstrate the utility of this latter feature by applying it to the extents of 11 western North American species with proven or potential use in restoration. First, a species-specific seed transfer map can be readily generated for a species by predicting performance for accessions currently available; this map can be readily updated to accommodate new accessions. Next, the increase in climate coverage achieved by adding successive accessions can be explored, yielding information that managers can use to balance ecological and economic considerations in determining how many accessions to develop. This approach identifies sampling sites, referred to as climate centers, which contribute unique, complementary, climate coverage to accessions on hand, thus providing explicit sampling guidance for both germplasm preservation and research. We examine how these and other features of our approach add to existing methods used to guide plant materials development and use. Finally, we discuss how these new methods provide a framework that could be used to coordinate native plant materials development, evaluation, and use across agencies, regions, and research groups.

Landscape genetic approaches to guide native plant restoration in the Mojave Desert

Restoring dryland ecosystems is a global challenge due to synergistic drivers of disturbance coupled with unpredictable environmental conditions. Dryland plant species have evolved complex life-history strategies to cope with fluctuating resources and climatic extremes. Although rarely quantified, local adaptation is likely widespread among these species and potentially influences restoration outcomes. The common practice of reintroducing propagules to restore dryland ecosystems, often across large spatial scales, compels evaluation of adaptive divergence within these species. Such evaluations are critical to understanding the consequences of large-scale manipulation of gene flow and to predicting success of restoration efforts. However, genetic information for species of interest can be difficult and expensive to obtain through traditional common garden experiments. Recent advances in landscape genetics offer marker-based approaches for identifying environmental drivers of adaptive genetic variability in non-model species, but tools are still needed to link these approaches with practical aspects of ecological restoration. Here, we combine spatially explicit landscape genetics models with flexible visualization tools to demonstrate how cost-effective evaluations of adaptive genetic divergence can facilitate implementation of different seed sourcing strategies in ecological restoration. We apply these methods to Amplified Fragment Length Polymorphism (AFLP) markers genotyped in two Mojave Desert shrub species of high restoration importance: the long-lived, wind-pollinated gymnosperm Ephedra nevadensis, and the short-lived, insect-pollinated angiosperm Sphaeralcea ambigua. Mean annual temperature was identified as an important driver of adaptive genetic divergence for both species. Ephedra showed stronger adaptive divergence with respect to precipitation variability, while temperature variability and precipitation averages explained a larger fraction of adaptive divergence in Sphaeralcea. We describe multivariate statistical approaches for interpolating spatial patterns of adaptive divergence while accounting for potential bias due to neutral genetic structure. Through a spatial bootstrapping procedure, we also visualize patterns in the magnitude of model uncertainty. Finally, we introduce an interactive, distance-based mapping approach that explicitly links marker-based models of adaptive divergence with local or admixture seed sourcing strategies, promoting effective native plant restoration.

Climate change perils for dioecious plant species

Climate change, particularly increased aridity, poses a significant threat to plants and the biotic communities they support. Dioecious species may be especially vulnerable to climate change given that they often exhibit spatial segregation of the sexes, reinforced by physiological and morphological specialization of each sex to different microhabitats. In dimorphic species, the overexpression of a trait by one gender versus the other may become suppressed in future climates. Data suggest that males will generally be less sensitive to increased aridity than co-occurring females and, consequently, extreme male-biased sex ratios are possible in a significant number of populations. The effects of male-biased sex ratios are likely to cascade to dependent community members, especially those that are specialized on one sex.

CA19-9 decrease at 8 weeks as a predictor of overall survival in a randomized phase III trial (MPACT) of weekly nab-paclitaxel plus gemcitabine versus gemcitabine alone in patients with metastatic pancreatic cancer

Any CA19-9 decline at week 8 and radiologic response by week 8 each predicted longer OS in both treatment arms. In the nab-P + Gem arm, the higher proportion of patients with week 8 CA19-9 decrease [82% (206/252); median OS 13.2 months] than a RECIST-defined response [16% (40/252); median OS 13.7 months] suggests that CA19-9 decline is a predictor of OS applicable to a larger population.

Background

A phase I/II study and subsequent phase III study (MPACT) reported significant correlations between CA19-9 decreases and prolonged overall survival (OS) with nab-paclitaxel plus gemcitabine (nab-P + Gem) treatment for metastatic pancreatic cancer (MPC). CA19-9 changes at week 8 and potential associations with efficacy were investigated as part of an exploratory analysis in the MPACT trial.

Patients and methods

Untreated patients with MPC (N = 861) received nab-P + Gem or Gem alone. CA19-9 was evaluated at baseline and every 8 weeks.

Results

Patients with baseline and week-8 CA19-9 measurements were analyzed (nab-P + Gem: 252; Gem: 202). In an analysis pooling the treatments, patients with any CA19-9 decline (80%) versus those without (20%) had improved OS (median 11.1 versus 8.0 months; P = 0.005). In the nab-P + Gem arm, patients with (n = 206) versus without (n = 46) any CA19-9 decrease at week 8 had a confirmed overall response rate (ORR) of 40% versus 13%, and a median OS of 13.2 versus 8.3 months (P = 0.001), respectively. In the Gem-alone arm, patients with (n = 159) versus without (n = 43) CA19-9 decrease at week 8 had a confirmed ORR of 15% versus 5%, and a median OS of 9.4 versus 7.1 months (P = 0.404), respectively. In the nab-P + Gem and Gem-alone arms, by week 8, 16% (40/252) and 6% (13/202) of patients, respectively, had an unconfirmed radiologic response (median OS 13.7 and 14.7 months, respectively), and 79% and 84% of patients, respectively, had stable disease (SD) (median OS 11.1 and 9 months, respectively). Patients with SD and any CA19-9 decrease (158/199 and 133/170) had a median OS of 13.2 and 9.4 months, respectively.

Conclusion

This analysis demonstrated that, in patients with MPC, any CA19-9 decrease at week 8 can be an early marker for chemotherapy efficacy, including in those patients with SD. CA19-9 decrease identified more patients with survival benefit than radiologic response by week 8.

The genetic basis of speciation in the Giliopsis lineage of Ipomopsis (Polemoniaceae)

One of the most powerful drivers of speciation in plants is pollinator-mediated disruptive selection, which leads to the divergence of floral traits adapted to the morphology and behavior of different pollinators. Despite the widespread importance of this speciation mechanism, its genetic basis has been explored in only a few groups. Here, we characterize the genetic basis of pollinator-mediated divergence of two species in genus Ipomopsis, I. guttata and I. tenuifolia, using quantitative trait locus (QTL) analyses of floral traits and other variable phenotypes. We detected one to six QTLs per trait, with each QTL generally explaining small to modest amounts of the phenotypic variance of a backcross hybrid population. In contrast, flowering time and anthocyanin abundance (a metric of color variation) were controlled by a few QTLs of relatively large effect. QTLs were strongly clustered within linkage groups, with 26 of 37 QTLs localized to six marker-interval 'hotspots,' all of which harbored pleiotropic QTLs. In contrast to other studies that have examined the genetic basis of pollinator shifts, our results indicate that, in general, mutations of small to modest effect on phenotype were involved. Thus, the evolutionary transition between the distinct pollination modes of I. guttata and I. tenuifolia likely proceeded incrementally, rather than saltationally.

The investigation of copper-based impregnated activated carbons prepared from water-soluble materials for broad spectrum respirator applications

The preparation of impregnated activated carbons (IACs) from aqueous, copper-containing solutions for broad spectrum gas filtration applications is studied here. Several samples were studied to determine the effect that impregnant loading, impregnant distribution and impregnant recipe had on the overall performance. Dynamic flow testing was used to determine the gas filtration capacity of the IAC samples versus a variety of challenge gases. X-ray diffraction (XRD), scanning electron microscopy (SEM) and energy dispersive X-ray analysis (EDX) were used to characterize the impregnant distribution on the carbon as a function of impregnant loading. Oven tests were performed to determine the thermal stability of the IAC samples exposed to elevated temperatures. The role impregnant distribution plays in gas filtration capacity and the overall performance of the IAC samples is discussed. The IAC samples prepared in this work were found to have gas filtration capacities as good as or better than broad spectrum respirator carbon samples prepared from the patent literature. IACs impregnated with an aqueous 2.4 M Cu(NO(3))(2)/0.04 M H(3)PO(4).12MoO(3)/4M HNO(3) solution that were heated to 200 degrees C under argon were found to have the best overall performance of the samples studied in this work.

The frequency of polyploid speciation in vascular plants

Since its discovery in 1907, polyploidy has been recognized as an important phenomenon in vascular plants, and several lines of evidence indicate that most, if not all, plant species ultimately have a polyploid ancestry. However, previous estimates of the frequency of polyploid speciation suggest that the formation and establishment of neopolyploid species is rare. By combining information from the botanical community's vast cytogenetic and phylogenetic databases, we establish that 15% of angiosperm and 31% of fern speciation events are accompanied by ploidy increase. These frequency estimates are higher by a factor of four than earlier estimates and lead to a standing incidence of polyploid species within genera of 35% (n = 1,506). Despite this high incidence, we find no direct evidence that polyploid lines, once established, enjoy greater net species diversification. Thus, the widespread occurrence of polyploid taxa appears to result from the substantial contribution of polyploidy to cladogenesis, but not from subsequent increases in diversification rates of polyploid lines.

Investigating species boundaries in the Giliopsis group of Ipomopsis (Polemoniaceae): Strong discordance among molecular and morphological markers

As a first step in elucidating mechanisms of speciation in the Giliopsis group of Ipomopsis (Polemoniaceae), we examined patterns of morphological and genetic differentiation and crossability. This group comprises three species that diverged very recently: two perennials, I. guttata and I. tenuifolia, and one annual, I. effusa. Analysis of phenotypic variation established that the three species are distinct for floral characters, and this differentiation is maintained in a locality containing both perennial species. Next, we assessed the genealogical relationships with AFLPs. All sampled individuals of I. effusa clustered together, a result in accord with its genetic isolation. The perennials, which retain interfertility, were not resolved as sister taxa. Rather, individuals sampled from the single I. guttata population that is sympatric with I. tenuifolia were genetically more similar to I. tenuifolia samples than they were to conspecifics. This pattern may be due to substantial introgression of I. tenuifolia genomic regions that do not contribute to floral phenotype in I. guttata. Our result adds to mounting evidence that plant species, as defined by morphological characters, are often not genomically cohesive. Taken together, our data warrant caution in delimiting species with genetic markers alone, and, importantly, suggest that selection on species-diagnostic morphological characters can be sufficiently strong to counteract extensive gene flow.

Molecular ecology of global change

Global environmental change is altering the selection regime for all biota. The key selective factors are altered mean, variance and seasonality of climatic variables and increase in CO(2) concentration itself. We review recent studies that document rapid evolution to global climate change at the phenotypic and genetic level, as a response to shifts in these factors. Among the traits that have changed are photoperiod responses, stress tolerance and traits associated with enhanced dispersal. The genetic basis of two traits with a critical role under climate change, stress tolerance and photoperiod behaviour, is beginning to be understood for model organisms, providing a starting point for candidate gene approaches in targeted nonmodel species. Most studies that have documented evolutionary change are correlative, while selection experiments that manipulate relevant variables are rare. The latter are particularly valuable for prediction because they provide insight into heritable change to simulated future conditions. An important gap is that experimental selection regimes have mostly been testing one variable at a time, while synergistic interactions are likely under global change. The expanding toolbox available to molecular ecologists holds great promise for identifying the genetic basis of many more traits relevant to fitness under global change. Such knowledge, in turn, will significantly advance predictions on global change effects because presence and polymorphism of critical genes can be directly assessed. Moreover, knowledge of the genetic architecture of trait correlations will provide the necessary framework for understanding limits to phenotypic evolution; in particular as lack of critical gene polymorphism or entire pathways, metabolic costs of tolerance and linkage or pleiotropy causing negative trait correlations. Synergism among stressor impacts on organismal function may be causally related to conflict among transcriptomic syndromes specific to stressor types. Because adaptation to changing environment is always contingent upon the spatial distribution of genetic variation, high-resolution estimates of gene flow and hybridization should be used to inform predictions of evolutionary rates.

The nature of plant species

Many botanists doubt the existence of plant species, viewing them as arbitrary constructs of the human mind, as opposed to discrete, objective entities that represent reproductively independent lineages or 'units of evolution'. However, the discreteness of plant species and their correspondence with reproductive communities have not been tested quantitatively, allowing zoologists to argue that botanists have been overly influenced by a few 'botanical horror stories', such as dandelions, blackberries and oaks. Here we analyse phenetic and/or crossing relationships in over 400 genera of plants and animals. We show that although discrete phenotypic clusters exist in most genera (> 80%), the correspondence of taxonomic species to these clusters is poor (< 60%) and no different between plants and animals. Lack of congruence is caused by polyploidy, asexual reproduction and over-differentiation by taxonomists, but not by contemporary hybridization. Nonetheless, crossability data indicate that 70% of taxonomic species and 75% of phenotypic clusters in plants correspond to reproductively independent lineages (as measured by postmating isolation), and thus represent biologically real entities. Contrary to conventional wisdom, plant species are more likely than animal species to represent reproductively independent lineages.

Parallel genotypic adaptation: when evolution repeats itself

Until recently, parallel genotypic adaptation was considered unlikely because phenotypic differences were thought to be controlled by many genes. There is increasing evidence, however, that phenotypic variation sometimes has a simple genetic basis and that parallel adaptation at the genotypic level may be more frequent than previously believed. Here, we review evidence for parallel genotypic adaptation derived from a survey of the experimental evolution, phylogenetic, and quantitative genetic literature. The most convincing evidence of parallel genotypic adaptation comes from artificial selection experiments involving microbial populations. In some experiments, up to half of the nucleotide substitutions found in independent lineages under uniform selection are the same. Phylogenetic studies provide a means for studying parallel genotypic adaptation in non-experimental systems, but conclusive evidence may be difficult to obtain because homoplasy can arise for other reasons. Nonetheless, phylogenetic approaches have provided evidence of parallel genotypic adaptation across all taxonomic levels, not just microbes. Quantitative genetic approaches also suggest parallel genotypic evolution across both closely and distantly related taxa, but it is important to note that this approach cannot distinguish between parallel changes at homologous loci versus convergent changes at closely linked non-homologous loci. The finding that parallel genotypic adaptation appears to be frequent and occurs at all taxonomic levels has important implications for phylogenetic and evolutionary studies. With respect to phylogenetic analyses, parallel genotypic changes, if common, may result in faulty estimates of phylogenetic relationships. From an evolutionary perspective, the occurrence of parallel genotypic adaptation provides increasing support for determinism in evolution and may provide a partial explanation for how species with low levels of gene flow are held together.

Articulated Palaeozoic fossil with 17 plates greatly expands disparity of early chitons

Modern chitons (Mollusca: Polyplacophora) possess a highly conserved skeleton of eight shell plates (valves) surrounded by spicules or scales, and fossil evidence suggests that the chiton skeleton has changed little since the first appearance of the class in the Late Cambrian period (about 500 million years before present, Myr bp). However, the Palaeozoic problematic taxon Multiplacophora, in spite of having a more complex skeleton, shares several derived characters with chitons. The enigmatic status of the Multiplacophora is due in part to the fact that its members had an exoskeleton of numerous calcium carbonate valves that usually separated after death. A new articulated specimen from the Carboniferous period (about 335 Myr bp) of Indiana reveals that multiplacophorans had a dorsal protective surface composed of head and tail valves, left and right columns of overlapping valves (five on each side), and a central zone of five smaller valves, all surrounded by an annulus of large spines. Here we describe and name the articulated specimen and present evidence that multiplacophorans were chitons. Thus the highly conserved body plan of living chitons belies the broad disparity of this clade during the Palaeozoic era.

Theophylline for irreversible chronic airflow limitation: a randomized study comparing n of 1 trials to standard practice

STUDY OBJECTIVE

To compare quality of life and exercise capacity (primary aim), and drug usage (secondary aim), between groups of patients with irreversible chronic airflow limitation (CAL) who were undergoing theophylline Theo-Dur; Key Pharmaceuticals; Kenilworth, NJ) therapy guided by n of 1 trials or standard practice.

DESIGN

Randomized study of n of 1 trials vs standard practice.

SETTING

Outpatient departments in two tertiary care centers.

PATIENTS

Sixty-eight patients with irreversible CAL who were symptomatic despite the use of inhaled bronchodilators, and who were unsure whether theophylline was helping them following open treatment, were randomized into n of 1 trials (N=34) or standard practice.

INTERVENTIONS

The n of 1 trials (single-patient, randomized, double-blind, multiple crossover comparisons of the effect on dyspnea of theophylline vs a placebo) followed published guidelines. Standard practice patients stopped taking theophylline but resumed it if their dyspnea worsened. If their dyspnea then improved, theophylline was continued. In both groups, a decision about continuing or stopping the use of theophylline was made within 3 months of randomization.

MEASUREMENTS AND RESULTS

The primary outcomes (the chronic respiratory disease questionnaire [CRQ] and 6-min walk) were measured at baseline, 6 months, and 12 months by personnel blinded to treatment group allocation. No between-group differences (n of 1 minus standard practice) were seen in within-group changes over time (1 year minus baseline) in the CRQ Physical Function score (point estimate on the difference, -2.8; 95% confidence limits [CLs], -8.2, 2.5), CRQ Emotional Function score (point estimate on the difference, 0.5; 95% CLs, -4.7, 5.7), or 6-min walk (point estimate on the difference, 8 m; 95% CLs, -26, 44 m). No differences between groups were seen in the secondary outcome of the proportion of patients taking theophylline at 6 and 12 months. In 7 of 34 n of 1 trial patients (21%), dyspnea improved during theophylline treatment compared with placebo treatment.

CONCLUSIONS

Using n of 1 trials to guide theophylline therapy in patients with irreversible CAL did not improve their quality of life or exercise capacity, or reduce drug usa e, over 1 year compared to standard practice. Under the objective conditions of an n of 1 trial, 21% of patients with CAL responded to theophylline. There remains a rationale for considering theophylline in patients with irreversible CAL who remain symptomatic despite the use of inhaled bronchodilators, but the use of n of 1 trials to guide this decision did not yield clinically important advantages over standard practice.

Proton magnetic resonance imaging to stage activity of interstitial lung disease

Patients with active interstitial lung disease (ILD) are often treated with high-dose corticosteroids, although such therapy is not universally effective and has significant risks. Clinicians have utilized various ancillary diagnostic techniques to help with difficult treatment decisions. Since magnetic resonance imaging (MRI) has the theoretic and experimental potential of differentiating various stages of ILD, we prospectively studied 34 adult patients in a 0.15 Tesla resistive magnet body imager. The most severely affected patients, who were thought to warrant a steroid trial, had the greatest MRI image intensity, and dramatic improvement was seen following successful treatment. Qualitative MRI data were as useful as any other ancillary diagnostic technique (radiographic, physiologic, scintigraphic) in predicting clinical course. Computer-generated relaxation times were not sufficiently precise to differentiate active from inactive disease. Although limited by availability and cost, MRI appears to be a useful ancillary diagnostic technique in ILD patients facing immunomodulating therapy.

Mediastinal lymph-node biopsy is a definitive staging procedure for bronchogenic carcinoma

Mediastinal lymph-node biopsy has been performed as a staging procedure in most cases of bronchogenic carcinoma since 1965. This study was carried out to assess the results of staging by this method in 75 patients. Biopsy sites were marked with hemoclips. Three zones were defined: zone 3 (inoperable), beyond the midline and above the lower border of the aortic arch; zone 1 (operable), more than 3 cm from the carcinoma, ipsilateral to the tumour; and zone 2, between zones 1 and 3. Forty of 75 patients had biopsy specimens showing carcinoma. The proportion was highest in small cell anaplastic carcinoma and lowest in squamous cell tumours. Of the 40 positive biopsies 35 were from zone 3. All the positive biopsy specimens showing small cell anaplastic carcinoma were from zone 3. Positive specimens correlated strongly with other evidence of inoperability. Mediastinal lymph-node biopsy is a definitive staging procedure.

Locomotor activity in morphine-treated rats: effects of and comparisons between cocaine, procaine, and lidocaine

The effects of cocaine, procaine, and lidocaine on open field and spontaneous (actophotometer) locomotor activities were assessed and compared in rats (1) treated acutely with morphine (single injection), (2) made dependent on morphine (SC pellets), (3) implanted with morphine and withdrawn at the time of peak dependence, and (4) implanted SC with lactose-containing pellets (sham). Cocaine-induced (10 or 30 mg/kg) open field and spontaneous locomotor activities were significantly greater in each of the four groups than those of the corresponding groups administered saline. Procaine (50 or 100 mg/kg) significantly reduced open field locomotor activity in all morphine-treated rats and spontaneous locomotor activity in acute rats. Lidocaine (30 mg/kg) significantly depressed spontaneous locomotor activity in acute rats. Upon comparison of the activities induced by the three local anesthetics, open field locomotor activity of sham-implanted rats was greater following cocaine (10 or 30 mg/kg) than following procaine (50 or 100 mg/kg). Only morphine withdrawn rats manifested greater activity following cocaine (10 mg/kg) than following either procaine (50 mg/kg) or lidocaine (10 mg/kg); activities were equivalent in dependent and acute rats. In contrast, cocaine-induced (30 mg/kg) open field locomotor activity of all morphine-treated rats was greater than either procaine- (100 mg/kg) or lidocaine- (30 mg/kg) induced activities. Spontaneous locomotor activity of all groups except acute morphine was greater following both doses of cocaine than following both doses of either procaine or lidocaine. In acute rats, only cocaine (10 mg/kg, induced greater activity than the other local anesthetics. Thus, stimulation of locomotor activity following cocaine treatment is a pharmacological property unique to cocaine and not shared by either procaine or lidocaine. Further, the data indicate that the methods selected for assessing locomotor activity may not give comparable results.

The application of 67Ga scanning in determining the operability of bronchogenic carcinoma

In a prospective study of 34 patients with histologically proven bronchogenic carcinoma, 67Ga scanning of the chest was used to screen for mediastinal involvement. Mediastinal scans and pathologic findings were in agreement in 27 patients. Two patients had false-negative scans and 5 had positive scans but no evidence of mediastinal tumor. These results indicate a sensitivity of 89%, a specificity of 66.6%, an accuracy of 77% for positive scans, and an accuracy of 83% for negative scans. Overall correlation between 67Ga scanning of the chest and mediastinal-tumor involvement is statistically significant (P = 0.003).

Recovery from inhalation of diquat aerosol

A patient developed high fever, cough, changing consolidations on chest roentgenograms, jaundice, and skin rash following inhalation of diquat aerosol. To our knowledge this is the first report of diquat inhalation and only the second report of aerosol damage from any part of the dipyridyl herbicides.

The electronic spectrum of KCoF3: Exchange effects

An analysis of the absorption spectrum of KcoF3 based on the weak field spin-orbit matrices has led to an assignment of all the doublet states of the d7 configuration using the parameters Dq = 780 cm-l, F2 = 1440cm-l, F4 = 104.5 cm-l and the spin-orbit coupling constant 5 = 490 cm-l. F2 F4, and < correspond to 91%, 94%, and 91% of their respective free ion values. The spectral absorption intensities of the spin forbidden transitions between 26000 and 40000 cm-l are much too large to be accounted for by the conventional spin-orbit coupling mechanism and one involving exchange interactions between pairs of ions is indicated. Consistent with this mechanism 1s the appearance of nine absorption regions which correspond to the simultaneous electronic excitation of pairs of ions.