Heritability, covariation and natural selection on 24 traits of common evening primrose (Oenothera biennis) from a field experiment.

This study explored genetic variation and co-variation in multiple functional plant traits. Our goal was to characterize selection, heritabilities and genetic correlations among different types of traits to gain insight into the evolutionary ecology of plant populations and their interactions with insect herbivores. In a field experiment, we detected significant heritable variation for each of 24 traits of Oenothera biennis and extensive genetic covariance among traits. Traits with diverse functions formed several distinct groups that exhibited positive genetic covariation with each other. Genetic variation in life-history traits and secondary chemistry together explained a large proportion of variation in herbivory (r(2) = 0.73). At the same time, selection acted on lifetime biomass, life-history traits and two secondary compounds of O. biennis, explaining over 95% of the variation in relative fitness among genotypes. The combination of genetic covariances and directional selection acting on multiple traits suggests that adaptive evolution of particular traits is constrained, and that correlated evolution of groups of traits will occur, which is expected to drive the evolution of increased herbivore susceptibility. As a whole, our study indicates that an examination of genetic variation and covariation among many different types of traits can provide greater insight into the evolutionary ecology of plant populations and plant-herbivore interactions.

Optimal reference genes for RT-qPCR normalization in the newborn.

It is difficult to identify reliable reference genes for transcriptomic analyses in biofluids such as saliva. This situation is particularly relevant for the newborn population, where rapid development is associated with dynamic changes in gene expression. Real-time gene expression monitoring holds great promise for elucidating disrupted pathways that result in morbidities unique to this population, such as retinopathy of prematurity, but its impact depends on identifying stable and consistently expressed genes across a wide range of gestational ages. We extracted total RNA from 400 neonatal saliva samples (postconceptional ages: 32 5/7 to 48 2/7 weeks), converted it to cDNA, and pre-amplified and analyzed it by qPCR for three commonly used reference genes, ACTB, GAPDH, and YWHAZ. Relative quantification was determined using the Δ Ct method. Data were analyzed as a whole and also stratified by age and sex. Descriptive statistics and homogeneity of variance were performed to identify optimal reference genes. Data analyzed from all ages and both sexes showed significant expression variation for ACTB, while GAPDH and YWHAZ showed greater stability. Male infants exhibited increased expression variation compared to females for ACTB, but neither GAPDH nor YWHAZ showed significant variance for either sex. We suggest that ACTB is an unreliable reference gene for the newborn population. Males showed significantly more variation in ACTB expression compared to females, which suggests a sex-specific developmental role for this biomarker. By contrast, GAPDH and YWHAZ were less variable and therefore preferable for use in neonates. Our findings may improve the use of reference genes for the RT-qPCR platform in the newborn over a wide range of gestational ages, thereby minimizing the likelihood of erroneous interpretation of gene expression during rapid growth, development, and differentiation.

Comparative performance analyses of commercially available products for salivary collection and nucleic acid processing in the newborn.

Analysis of saliva for clinical monitoring and biomarker detection holds great promise for improving health care. Commercially available assays are not intended for use with neonates, however, and collection and processing of saliva for subsequent transcriptomic analysis presents unique challenges in this population. We compared RNA yield, quality, stability and RT-qPCR performance for two commonly used commercial systems: the Qiagen RNeasy Protect Saliva Mini Kit(®) and the DNA Genotek Oragene•RNA(®) assay. Two 10 µl saliva samples were collected from ten newborns and stabilized for each assay. Total RNA was extracted following incubation for 3, 10, 15 or 20 days. Total RNA extracted from each assay was analyzed for integrity, quality and quantity using the Agilent BioAnalyzer 2100. RT-qPCR was performed for the reference gene, GAPDH, to assess subsequent performance of the extracted RNA. Although the DNA Genotek extraction protocol required nearly twice the time of the Qiagen protocol, RNA integrity did not differ between the kits. RNA concentration using the DNA Genotek assay, however, was 3,264 pg/µl (range: 262 - 10,336 pg/µl) compared to 822.4 pg/µl (range: 0 - 1,856 pg/µl) for the Qiagen protocol. Linear regression analysis showed a stronger correlation between the threshold cycle and RNA concentration using DNA Genotek (r(2) = 0.356) compared to Qiagen (r(2) = 0.0331). Our results suggest that although the Qiagen assay may reduce overall extraction time, RNA yield and performance in subsequent transcriptomic analysis is more robust using the DNA Genotek assay.

Fine-scale genetically based differentiation of life-history traits in the perennial shrub Lupinus arboreus.

Across large spatial scales, plants often exhibit genetically based differentiation in traits that allow adaptation to local sites. At smaller spatial scales, sharp boundaries between edaphic conditions also can create strong gradients in selection that counteract gene flow and result in local adaptation. Few studies, however, have examined the degree to which continuous populations of perennial plants exhibit genetically based differentiation in life-history traits over small spatial scales. We quantified the degree of genetically based differentiation in adaptive traits among bush lupine (Lupinus arboreus) from nearby dune and grassland sites (sites separated by < 0.75 km) that formed part of a larger continuous population of L. arboreus. We also investigated the spatial genetic structure of bush lupine by examining how genetic structure differed between seeds and juvenile plants that were less than two years old. We calculated F-statistics from gel electrophoresis of 10 polymorphic loci. We then used these values to infer levels of gene flow. To examine differentiation in adaptive traits, we created full-sibling/half-sibling families of lupine within each area and established reciprocal common gardens at each site. Across two years, we measured canopy volume, flowering time, seed set, and mortality of progeny planted in each garden. Spatial genetic structure among seeds was virtually nonexistent (F(ST) = 0.002), suggesting that gene flow between the three areas could be quite high. However, genetic structure increased 20-fold among juvenile plants (F(ST) = 0.041). We found strong evidence for fine-scale genetically based differentiation and local adaptation in adaptive traits such as plant size, flowering phenology, fecundity, and mortality. Thus, it is likely that strong but differing selection regimes within each area drive spatial differentiation in lupine life-history traits.

Consumer pressure, seed versus safe-site limitation, and plant population dynamics.

Plants often suffer reductions in fecundity due to insect herbivory. Whether this loss of seeds has population-level consequences is much debated and often unknown. For many plants, particularly those with long-lived seedbanks, it is frequently asserted that herbivores have minimal impacts on plant abundance because safe-site availability rather than absolute seed number determines the magnitude of future plant recruitment and hence population abundance. However, empirical tests of this assertion are generally lacking and the interplay between herbivory, spatio-temporal variability in seed- or safe-site-limited recruitment, and seedbank dynamics is likely to be complex. Here we use a stochastic simulation model to explore how changes in the spatial and temporal frequency of seed-limited recruitment, the strength of density-dependent seedling survival, and longevity of seeds in the soil influence the population response to herbivory. Model output reveals several surprising results. First, given a seedbank, herbivores can have substantial effects on mean population abundance even if recruitment is primarily safe-site-limited in either time or space. Second, increasing seedbank longevity increases the population effects of herbivory, because annual reductions in seed input due to herbivory are accumulated in the seedbank. Third, population impacts of herbivory are robust even in the face of moderately strong density-dependent seedling mortality. These results imply that the conditions under which herbivores influence plant population dynamics may be more widespread than heretofore expected. Experiments are now needed to test these predictions.

High mortality, fluctuation in numbers, and heavy subterranean insect herbivory in bush lupine, Lupinus arboreus.

Sporadic patchy die-off of bush lupine, Lupinus arboreus, has long been known. We describe in detail a series of these incidents on the central California coast, based upon observational and comparative evidence. Stands of thousands of plants die, while nearby mature plants live on. In some sites, repeated die-off followed by regeneration from the seed bank has led to the cover and density of this woody, perennial plant fluctuating widely over the 40 year period for which records exist. Root damage by caterpillars of the ghost moth or "swift" Hepialus californicus (Lepidoptera, Hepialidae) is a major cause of individual bush death and a probable cause of die-off of stands of lupine. Hidden from view underground, a few of these insects readily kill a juvenile or young mature plant by girdling and reaming-out roots. The mass mortality of L. arboreus that we observed involved heavy root damage by these caterpillars in evenaged stands of plants in their first (1.5-year-old) or second (2.5-year-old) flowering season. The injured plants set seed before dying. Older, larger bush lupines better withstood root damage. In plants aged 3 or more years, damage and mortality were correlated with the intensity of ghost moth caterpillars in the roots. At the highest intensity (mean = 37.5, maximum = 62 caterpillars/root), a stand of large, old L. arboreus suffered 41% mortality; 45% of root cambium (median value) was destroyed by feeding caterpillars. Mass death of mature L. arboreus was not correlated with folivory, and leaf damage ranged from nil to moderate in instances of die-off. The western tussock moth, Orgyia vetusta, accounted for the highest levels of folivory, but this insect was rare when die-offs occurred. The lowest lupine mortality rates in our study occurred where tussock caterpillar intensities were high and where plants were repeatedly defoliated by this insect. However, experimental defoliation by high, but realistic, intensities of tussock moth caterpillars resulted in some mortality of mature bushes, and the combined effects of leaf and root herbivory have yet to be assessed. In its natural range on the California coast, bush lupine has several additional species of insect herbivores that can be locally abundant and injurious to the plant, although none is associated with die-off. Subterranean natural enemies of ghost moth caterpillars may play a role in the patchy waxing and waning of this shrub. Locally, a new species of entomophagous nematode (Heterorhabditis sp.) cause high mortality in the soil, before ghost moth caterpillars have entered the root. This natural enemy may thus afford lupines protection from heavy underground herbivory.

Entomopathogenic nematodes: natural enemies of root-feeding caterpillars on bush lupine.

A new species of soil-dwelling entomopathogenic nematode Heterorhabditis hepialus killed up to 100% (mean=72%) of root-boring caterpillars of a ghost moth Hepialus californicus in coastal shrub lands. When unchecked, ghost moth caterpillars killed bush lupine, Lupinus arboreus. Here we describe this strange food chain. Although unappreciated by ecologists, entomopathogenic nematodes are widespread and probably one of the most important groups of natural enemies for underground insects. The free-living infective juvenile (IJ) of entomopathogenic nematodes searches for host insects in the soil. A single IJ can kill a host, although several often invade together. After entering the host through a spiracle or other orifice, the IJ regurgitates its symbiotic bacterium, Photorhabdus luminescens, which kills the host within 48 h. The bacteria digest the cadaver and provide food for the exponentially growing nematode population inside. The bacteria produce antibiotics and other noxious substances that protect the host cadaver from other microbes in the soil. When the cadaver is exhausted of resources, IJs break the host integument and can disperse. As many as 420,000 IJs can be produced within a large ghost moth caterpillar. Surface soil of the lupine rhizosphere is the primary habitat of IJs of H. hepialus. Attracted to waste gases emitted by insects, the 0.5-mm-long IJs can move 6 cm/day through moist soil. Prevalences of H. hepialus ranged from as high as 78% of rhizospheres in some lupine stands to almost zero in others, but it was absent from no stand at our study site. Field intensities ranged from 0.003 IJs/cm3 of soil to 7.5 IJs/cm3, and correlated roughly with prevalences among sites. Few ghost moth caterpillars (mean=6.7) succeeded in entering lupine roots where prevalence of H. hepialus was highest, and this stand had lowest mortality (0.02) of mature bush lupine. In the three stands with lowest prevalence (mean = 2%) of this nematode, many caterpillars (mean = 38.5) entered roots, and lupine mortality was high (range = 0.41-1.0). Old aerial photographs indicate that the stands with highest recent nematode prevalence have had little or no mass die-off of lupine over the past 40 years. The photos depict repeated die-offs of lupine during the past four decades in stands with lowest recent prevalence of the nematode. This pattern leads us to entertain the hypothesis that the nematode affects vegetation dynamics indirectly through a trophic cascade. Dispersal of entomopathogenic nematodes is little understood. We found that air drying of soil extirpates H. hepialus and speculate that this nematode is dispersed during the wet season in moist soil bits on the exterior of fossorial insects and mammals. H. hepialus colonized some previously unoccupied lupine rhizospheres during the wet winter-spring season and, obversely, became extinct from some rhizosperes as soil dried in summer. Root-feeding insects have only recently been recognized as a force in communities, and the regulation of these important herbivores is still largely an ecological terra incognita. All evidence indicates that entomopathogenic nematodes are found throughout terrestril ecosystems, and we propose that trophic chains similar to those described in this report should not be uncommon.

Great expectorations: the potential of salivary 'omic' approaches in neonatal intensive care.

Among those that require critical care, preterm neonates have the greatest limitations on available blood or body fluids for clinical or research-based assessments. Recent technological advancements have improved our ability to detect genetic, proteomic and microbial material at the nanoscale level, making analyte and biomarker assessment from even the smallest quantities possible. Saliva is a unique body fluid that not only may be noninvasively and repeatedly obtained, but also contains multiple serum components, making it promising for noninvasive assessment of the newborn. The integration of high-throughput or 'omic' approaches on neonatal saliva holds great potential to improve diagnostic and prognostic accuracy for a wide range of developmental and pathological conditions affecting the vulnerable preterm neonatal population. Herein, we review the clinical applications and technical considerations regarding the integration of salivary 'omic' technology into the neonatal intensive care unit.

Introduced predators transform subarctic islands from grassland to tundra.

Top predators often have powerful direct effects on prey populations, but whether these direct effects propagate to the base of terrestrial food webs is debated. There are few examples of trophic cascades strong enough to alter the abundance and composition of entire plant communities. We show that the introduction of arctic foxes (Alopex lagopus) to the Aleutian archipelago induced strong shifts in plant productivity and community structure via a previously unknown pathway. By preying on seabirds, foxes reduced nutrient transport from ocean to land, affecting soil fertility and transforming grasslands to dwarf shrub/forb-dominated ecosystems.

The embarrassment of riches: atmospheric deposition of nitrogen and community and ecosystem processes.

Anthropogenic sources of nitrogen have exceeded, and will continue to exceed, annual inputs of nitrogen produced by natural processes. Nitrogen enrichment may in plant tissue chemistry and microbial decomposition processes, as well as affecting rates of herbivory, all of which may be expected to result in changes in plant species assemblages Individual concepts, such as nitrogen saturation and critical load, used to describe the effects of enrichment on soil, community, ecosystm processes and species assemblages, cannot accomodate easily the range of interactions and different environmental processes. A number of approaches need to be used in tandem. Major gaps in knowledge are rates of transfer of anthropogenic nitrogen within and between different ecosystem and how these rates affect population dynamic of individual species and trophic relationships. Without this information, predictions of biological effects of enrichment are difficult to make.

Outcrossing rate and inbreeding depression in the perennial yellow bush lupine, Lupinus arboreus (Fabaceae).

Little is known about the breeding systems of perennial Lupinus species. We provide information about the breeding system of the perennial yellow bush lupine, Lupinus arboreus, specifically determining self-compatibility, outcrossing rate, and level of inbreeding depression. Flowers are self-compatible, but autonomous self-fertilization rarely occurs; thus selfed seed are a product of facilitated selfing. Based on four isozyme loci from 34 maternal progeny arrays of seeds we estimated an outcrossing rate of 0.78. However, when we accounted for differential maturation of selfed seeds, the outcrossing rate at fertilization was lower, ∼0.64. Fitness and inbreeding depression of 11 selfed and outcrossed families were measured at four stages: seed maturation, seedling emergence, seedling survivorship, and growth at 12 wk. Cumulative inbreeding depression across all four life stages averaged 0.59, although variation existed between families for the magnitude of inbreeding depression. Inbreeding depression was not manifest uniformly across all four life stages. Outcrossed flowers produced twice as many seeds as selfed flowers, but the mean performance of selfed and outcrossed progeny was not different for emergence, seedling survivorship, and size at 12 wk. Counter to assumptions about this species, L. arboreus is both self-compatible and outcrosses ∼78% of the time.

Saturated state of the nonlinear small-scale dynamo.

We consider the problem of incompressible, forced, nonhelical, homogeneous, and isotropic MHD turbulence with no mean magnetic field and large magnetic Prandtl number. This type of MHD turbulence is the end state of the turbulent dynamo, which generates folded fields with small-scale direction reversals. We propose a model in which saturation is achieved as a result of the velocity statistics becoming anisotropic with respect to the local direction of the magnetic folds. The model combines the effects of weakened stretching and quasi-two-dimensional mixing and produces magnetic-energy spectra in remarkable agreement with numerical results at least in the case of a one-scale flow. We conjecture that the statistics seen in numerical simulations could be explained as a superposition of these folded fields and Alfvén-like waves that propagate along the folds.