Conditional sanctioning in a legume-Rhizobium mutualism.

Legumes are high in protein and form a valuable part of human diets due to their interaction with symbiotic nitrogen-fixing bacteria known as rhizobia. Plants house rhizobia in specialized root nodules and provide the rhizobia with carbon in return for nitrogen. However, plants usually house multiple rhizobial strains that vary in their fixation ability, so the plant faces an investment dilemma. Plants are known to sanction strains that do not fix nitrogen, but nonfixers are rare in field settings, while intermediate fixers are common. Here, we modeled how plants should respond to an intermediate fixer that was otherwise isogenic and tested model predictions using pea plants. Intermediate fixers were only tolerated when a better strain was not available. In agreement with model predictions, nodules containing the intermediate-fixing strain were large and healthy when the only alternative was a nonfixer, but nodules of the intermediate-fixing strain were small and white when the plant was coinoculated with a more effective strain. The reduction in nodule size was preceded by a lower carbon supply to the nodule even before differences in nodule size could be observed. Sanctioned nodules had reduced rates of nitrogen fixation, and in later developmental stages, sanctioned nodules contained fewer viable bacteria than nonsanctioned nodules. This indicates that legumes can make conditional decisions, most likely by comparing a local nodule-dependent cue of nitrogen output with a global cue, giving them remarkable control over their symbiotic partners.

Marked differences in foraging area use and susceptibility to predation between two closely-related tropical seabirds.

Ecological theory predicts that closely-related species must occupy different niches to coexist. How marine top predators achieve this during breeding, when they often gather in large multi-species colonies and are constrained to central-place foraging, has been mostly studied in productive temperate and polar oceans with abundant resources, but less so in poorer, tropical waters. Here, we track the foraging movements of two closely-related sympatric seabirds-the white-tailed and red-tailed tropicbirds Phaethon lepturus and P. rubricauda-breeding on Aldabra Atoll, Seychelles, to investigate potential mechanisms of niche segregation and shed light on their contrasting population trends. Combining data from GPS, immersion, depth and accelerometry loggers, we show that the two species have similar behaviour at sea, but are completely segregated spatially, with red-tailed tropicbirds flying further to feed and using different feeding areas than white-tailed tropicbirds. Using nest-based camera traps, we show that low breeding success of both species-which likely drives observed population declines-is caused by high nest predation. However, the two species are targeted by different predators, with native avian predators mainly targeting red-tailed tropicbird nests, and invasive rats raiding white-tailed tropicbird nests when they leave their eggs unattended. Our findings provide new insight into the foraging ecology of tropicbirds and have important conservation implications. The extensive range and spatial segregation highlight the importance of considering large-scale protection of waters around tropical seabird colonies, while the high level of nest predation provides evidence in support of rat eradication and investigating potential nest protection from native avian predators.

Linking the influence and dependence of people on biodiversity across scales.

Biodiversity enhances many of nature's benefits to people, including the regulation of climate and the production of wood in forests, livestock forage in grasslands and fish in aquatic ecosystems. Yet people are now driving the sixth mass extinction event in Earth's history. Human dependence and influence on biodiversity have mainly been studied separately and at contrasting scales of space and time, but new multiscale knowledge is beginning to link these relationships. Biodiversity loss substantially diminishes several ecosystem services by altering ecosystem functioning and stability, especially at the large temporal and spatial scales that are most relevant for policy and conservation.

The function-dominance correlation drives the direction and strength of biodiversity-ecosystem functioning relationships.

Community composition is a primary determinant of how biodiversity change influences ecosystem functioning and, therefore, the relationship between biodiversity and ecosystem functioning (BEF). We examine the consequences of community composition across six structurally realistic plant community models. We find that a positive correlation between species' functioning in monoculture versus their dominance in mixture with regard to a specific function (the "function-dominance correlation") generates a positive relationship between realised diversity and ecosystem functioning across species richness treatments. However, because realised diversity declines when few species dominate, a positive function-dominance correlation generates a negative relationship between realised diversity and ecosystem functioning within species richness treatments. Removing seed inflow strengthens the link between the function-dominance correlation and BEF relationships across species richness treatments but weakens it within them. These results suggest that changes in species' identities in a local species pool may more strongly affect ecosystem functioning than changes in species richness.

Strong responses from weakly interacting species.

The impact of species loss from competitive communities partly depends on how populations of the surviving species respond. Predicting the response should be straightforward using models that describe population growth as a function of competitor densities; but these models require accurate estimates of interaction strengths. Here, we quantified how well we could predict responses to competitor removal in a community of annual plants, using a combination of observation and experiment. It was straightforward to fit models to multi-species communities, which passed standard diagnostic tests and provided apparently sensible estimates of interaction strengths. However, the models consistently underpredicted the response to competitor removal, by a factor of at least 50%. We argue that this poor predictive ability is likely to be general in plant communities due to 'the ghost of competition present' that confines species to parts of the environment in which they compete best.

Registration of Supine MR Mammography with Breast Ultrasound for Surgical Planning of Breast Conserving Surgery: A Feasibility Study.

Purpose To report the feasibility, accuracy and initial clinical experience of the use of real-time magnetic resonance navigated ultrasound (rtMRnUS) in the surgical planning of breast-conserving surgery (BCS) via guide wire insertion. Materials and Methods 29 participants were recruited into this prospective ethics committee approved study. The first 4 cases were utilized as a training set. Participants underwent a supine contrast-enhanced breast MR examination with external fiducials and corresponding ink marks placed on the skin of the affected breast to act as co-registration pairs. MR examinations included both functional and morphological images. A LOGIQ E9 ultrasound system (GE Healthcare, Milwaukee, WI, USA) equipped with a 6 - 15 MHz transducer was utilized for rtMRnUS. To facilitate point co-registration of the previously acquired MR dataset with the real-time ultrasound, co-registration pairs were identified on both imaging modalities. The following co-registration quality metrics were recorded: root mean square deviation (RMSD), lesion and global accuracies. Post co-registration guide wire insertion was performed. Results Co-registration was successfully undertaken in all participants. Results from 25 participants are presented. The median (min, max) RMSD was 3.3 mm (0.6 mm, 8.8 mm). The global accuracy was assessed as very good (8), good (12), moderate (3) and poor (2) while the median (min, max) lesion accuracy was recorded at 8.9 mm (2.1 mm, 33.2 mm). Conclusion The use of rtMRnUS to facilitate guide wire insertion is a feasible technique. Generally, very good or good global registration can be expected. Lesion accuracy results indicate that a median difference, in 3 D space, of 9 mm can be expected between imaging modalities.

Understanding the value of plant diversity for ecosystem functioning through niche theory.

Biodiversity experiments have generated robust empirical results supporting the hypothesis that ecosystems function better when they contain more species. Given that ecosystems provide services that are valued by humans, this inevitably suggests that the loss of species from natural ecosystems could diminish their value. This raises two important questions. First, will experimental results translate into the real world, where species are being lost at an alarming rate? And second, what are the benefits and pitfalls of such valuation exercises? We argue that the empirical results obtained in experiments are entirely consistent with well-established theories of species coexistence. We then examine the current body of work through the lens of niche theory and highlight where closer links with theory could open up opportunities for future research. We argue that niche theory predicts that diversity-functioning relationships are likely to be stronger (and require more species) in the field than in simplified experimental settings. However, we caution that while many of the biological processes that promote coexistence can also generate diversity-function relationships, there is no simple mapping between the two. This implies that valuation exercises need to proceed with care.

Hierarchical nuclear and cytoplasmic genetic architectures for plant growth and defense within Arabidopsis.

To understand how genetic architecture translates between phenotypic levels, we mapped the genetic architecture of growth and defense within the Arabidopsis thaliana Kas × Tsu recombinant inbred line population. We measured plant growth using traditional size measurements and size-corrected growth rates. This population contains genetic variation in both the nuclear and cytoplasmic genomes, allowing us to separate their contributions. The cytoplasmic genome regulated a significant variance in growth but not defense, which was due to cytonuclear epistasis. Furthermore, growth adhered to an infinitesimal model of genetic architecture, while defense metabolism was more of a moderate-effect model. We found a lack of concordance between quantitative trait loci (QTL) regulating defense and those regulating growth. Given the published evidence proving the link between glucosinolates and growth, this is likely a false negative result caused by the limited population size. This size limitation creates an inability to test the entire potential genetic landscape possible between these two parents. We uncovered a significant effect of glucosinolates on growth once we accounted for allelic differences in growth QTLs. Therefore, other growth QTLs can mask the effects of defense upon growth. Investigating direct links across phenotypic hierarchies is fraught with difficulty; we identify issues complicating this analysis.

Is 'peak N' key to understanding the timing of flowering in annual plants?

Flowering time in annual plants has large fitness consequences and has been the focus of theoretical and empirical study. Previous theory has concluded that flowering time has evolved over evolutionary time to maximize fitness over a particular season length. We introduce a new model where flowering is cued by a growth-rate rule (peak nitrogen (N)). Flowering is therefore sensitive to physiological parameters and to current environmental conditions, including N availability and the presence of competitors. The model predicts that, when overall conditions are suitable for flowering, plants should never flower after 'peak N', the point during development when the whole-plant N uptake rate reaches its maximum. Our model further predicts correlations between flowering time and vegetative growth rates, and that the response to increased N depends heavily on how this extra N is made available. We compare our predictions to observations in the literature. We suggest that annual plants may have evolved to use growth-rate rules as part of the cue for flowering, allowing them to smoothly and optimally adjust their flowering time to a wide range of local conditions. If so, there are widespread implications for the study of the molecular biology behind flowering pathways.

Prognostic value of DCE-MRI in breast cancer patients undergoing neoadjuvant chemotherapy: a comparison with traditional survival indicators.

OBJECTIVES: To determine associations between dynamic contrast-enhanced MR imaging (DCE-MRI) parameters and survival intervals in patients with locally advanced breast cancer treated with neoadjuvant chemotherapy (NAC), surgery, and adjuvant therapies. Further, to compare the prognostic value of DCE-MRI parameters against traditional survival indicators. METHODS: DCE-MRI and MR tumour volume measures were obtained prior to treatment and post 2nd NAC cycle. To demonstrate which parameters were associated with survival, Cox's proportional hazards models (CPHM) were employed. To avoid over-parameterisation, only those MR parameters with at least a borderline significant result were entered into the final CPHM. RESULTS: When considering disease-free survival positive axillary nodal status (hazard ratio [HR] 6.79), younger age (HR 3.37), negative oestrogen receptor status (HR 3.24), pre-treatment Maximum Enhancement Index (MaxEI) (HR 6.51), and percentage change in MaxEI (HR 1.02) represented the retained CPHM covariates. Similarly, positive axillary nodal status (HR 11.47), negative progesterone receptor status (HR 4.37) and percentage change in AUC90 (HR 1.01) represented the retained predictive variables for overall survival. CONCLUSIONS: Multivariate survival analysis has demonstrated that DCE-MRI parameters obtained prior to NAC and/or post 2nd cycle can provide independent prognostic information that can complement traditional prognostic indicators available prior to treatment. KEY POINTS: • MR-derived DCE-MRI parameters obtained prior to treatment have prognostic value. • Early treatment-induced reductions in DCE-MRI parameters represents a positive prognostic indicator. • DCE-MRI parameters provide independent prognostic information that can complement traditional prognostic indicators.

Integration of population genetics with oceanographic models reveals strong connectivity among coral reefs across Seychelles.

Many countries with tropical reef systems face hard choices preserving coral reefs in the face of climate change on limited budgets. One approach to maximising regional reef resilience is targeting management efforts and resources at reefs that export large numbers of larvae to other reefs. However, this requires reef connectivity to be quantified. To map coral connectivity in the Seychelles reef system we carried out a population genomic study of the Porites lutea species complex using 241 sequenced colonies from multiple islands. To identify oceanographic drivers of this connectivity and quantify variability, we further used a 2 km resolution regional ocean simulation coupled with a larval dispersal model to predict the flow of coral larvae between reef sites. Patterns of admixture and gene flow are broadly supported by model predictions, but the realised connectivity is greater than that predicted from model simulations. Both methods detected a biogeographic dispersal barrier between the Inner and Outer Islands of Seychelles. However, this barrier is permeable and substantial larval transport is possible across Seychelles, particularly for one of two putative species found in our genomic study. The broad agreement between predicted connectivity and observed genetic patterns supports the use of such larval dispersal simulations in reef system management in Seychelles and the wider region.

Coexistence, niches and biodiversity effects on ecosystem functioning.

General principles from coexistence theory are often invoked to explain how and why mixtures of species outperform monocultures. However, the complementarity and selection effects commonly measured in biodiversity experiments do not precisely quantify the niche and relative fitness differences that govern species coexistence. Given this lack of direct correspondence, how can we know whether species-rich mixtures are stable and that the benefits of diversity will therefore persist? We develop a resource-based included-niche model in which plant species have asymmetric access to a nested set of belowground resource pools. We use the model to show that positive complementarity effects arise from stabilising niche differences, but do not necessarily lead to stable coexistence and hence can be transient. In addition, these transient complementarity effects occur in the model when there is no complementary resource use among species. Including a trade-off between uptake rates and the size of the resource pool stabilised interactions and led to persistent complementarity coupled with weak or negative selection effects, consistent with results from the longest-running field biodiversity experiments. We suggest that future progress requires a greater mechanistic understanding of the links between ecosystem functions and their underlying biological processes.

Texture analysis in assessment and prediction of chemotherapy response in breast cancer.

PURPOSE: To assess the efficacy of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI)-based textural analysis in predicting response to chemotherapy in a cohort of breast cancer patients. MATERIALS AND METHODS: In all, 100 patients were scanned on a 3.0T HDx scanner immediately prior to neoadjuvant chemotherapy treatment. A software application to use texture features based on co-occurrence matrices was developed. Texture analysis was performed on precontrast and 1-5 minutes postcontrast data. Patients were categorized according to their chemotherapeutic response: partial responders corresponding to a decrease in tumor diameter over 50% (40) and nonresponders corresponding to a decrease of less than 50% (4). Data were also split based on factors that influence response: triple receptor negative phenotype (TNBC) (22) vs. non-TNBC (49); node negative (45) vs. node positive (46); and biopsy grade 1 or 2 (38) vs. biopsy grade 3 (55). RESULTS: Parameters f2 (contrast), f4 (variance), f10 (difference in variance), f6 (sum average), f7 (sum variance), f8 (sum entropy), f15 (cluster shade), and f16 (cluster prominence) showed significant differences between responders and partial responders of chemotherapy. Differences were mainly seen at 1-3 minutes postcontrast administration. No significant differences were found precontrast administration. Node +ve, high grade, and TNBC are associated with poorer prognosis and appear to be more heterogeneous in appearance according to texture analysis. CONCLUSION: This work highlights that textural differences between groups (based on response, nodal status, and triple negative groupings) are apparent and appear to be most evident 1-3 minutes postcontrast administration. The fact that significant differences for certain texture parameters and groupings are consistently observed is encouraging.

Adaptation and extinction in experimentally fragmented landscapes.

Competition and disturbance are potent ecological forces that shape evolutionary trajectories. These forces typically work in opposition: when disturbance is infrequent, densities are high and competition is intense. In contrast, frequent disturbance creates a low-density environment in which competition is weak and good dispersal essential. We exploited recent advances in genomic research to quantify the response to selection by these powerful ecological forces at the phenotypic and molecular genetic level in experimental landscapes. We grew the annual plant Arabidopsis thaliana in discrete patches embedded in a hostile matrix and varied the number and size of patches and the intensity of disturbance, by creating both static and dynamic landscapes. In static landscapes all patches were undisturbed, whereas in dynamic landscapes all patches were destroyed in each generation, forcing seeds to disperse to new locations. We measured the resulting changes in phenotypic, genetic, and genotypic diversity after five generations of selection. Simulations revealed that the observed loss of genetic diversity dwarfed that expected under drift, with dramatic diversity loss, particularly from dynamic landscapes. In line with ecological theory, static landscapes favored good competitors; however, competitive ability was linked to growth rate and not, as expected, to seed mass. In dynamic landscapes, there was strong selection for increased dispersal ability in the form of increased inflorescence height and reduced seed mass. The most competitive genotypes were almost eliminated from highly disturbed landscapes, raising concern over the impact of increased levels of human-induced disturbance in natural landscapes.

The genome sequence of the Hornet Moth, Sesia apiformis (Clerck, 1759).

We present a genome assembly from an individual male Sesia apiformis (the Hornet Moth; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 546.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,358 protein coding genes.

Sources of marine debris for Seychelles and other remote islands in the western Indian Ocean.

Vast quantities of debris are beaching at remote islands in the western Indian Ocean. We carry out marine dispersal simulations incorporating currents, waves, winds, beaching, and sinking, for both terrestrial and marine sources of debris, to predict where this debris comes from. Our results show that most terrestrial debris beaching at these remote western Indian Ocean islands drifts from Indonesia, India, and Sri Lanka. Debris associated with fisheries and shipping also poses a major risk. Debris accumulation at Seychelles is likely seasonal, peaking during February-April. This pattern is driven by monsoonal winds and may be amplified during positive Indian Ocean Dipole and El-Niño events. Our results underline the vulnerability of small island states to marine plastic pollution, and are a crucial step towards improved management of the issue. The trajectories used in this study are available for download, and our analyses can be rerun under different parameter choices.

Fear of the dark or dinner by moonlight? Reduced temporal partitioning among Africa's large carnivores.

Africa is home to the last intact guild of large carnivores and thus provides the only opportunity to investigate mechanisms of coexistence among large predator species. Strong asymmetric dominance hierarchies typically characterize guilds of large carnivores; but despite this asymmetry, subdominant species may persist alongside their stronger counterparts through temporal partitioning of habitat and resources. In the African guild, the subdominant African wild dogs and cheetahs are routinely described as diurnal and crepuscular. These activity patterns have been interpreted to result from the need to avoid encounters with the stronger, nocturnal spotted hyenas and lions. However, the idea that diel activity patterns of carnivore species are strongly shaped by competition and predation has recently been challenged by new observations. In a three-year study in the Okavango Delta, we investigated daily activity patterns and temporal partitioning for wild dogs, cheetahs, spotted hyenas and lions by fitting radio collars that continuously recorded activity bursts, to a total of 25 individuals. Analysis of activity patterns throughout the 24-h cycle revealed an unexpectedly high degree of temporal overlap among the four species. This was mainly due to the extensive and previously undescribed nocturnal activity of wild dogs and cheetahs. Their nocturnal activity fluctuated with the lunar cycle, represented up to 40% of the diel activity budget and was primarily constrained by moonlight availability. In contrast, the nocturnal activity patterns of lions and hyenas were unaffected by moonlight and remained constant over the lunar cycle. Our results suggest that other ecological factors such as optimal hunting conditions have shaped the diel activity patterns of subdominant, large predators. We suggest that they are "starvation driven" and must exploit every opportunity to obtain a meal. The benefits of activity on moonlit nights therefore offset the risks of encountering night-active predators and competitors.

Plant growth rates and seed size: a re-evaluation.

Small-seeded plant species are often reported to have high relative growth rate or RGR. However, because RGR declines as plants grow larger, small-seeded species could achieve higher RGR simply by virtue of their small size. In contrast, size-standardized growth rate or SGR factors out these size effects. Differences in SGR can thus only be due to differences in morphology, allocation, or physiology. We used nonlinear regression to calculate SGR for comparison with RGR for 10 groups of species spanning a wide range of life forms. We found that RGR was negatively correlated with seed mass in nearly all groups, but the relationship between SGR and seed mass was highly variable. We conclude that small-seeded species only sometimes possess additional adaptations for rapid growth over and above their general size advantage.

Low-coverage reduced representation sequencing reveals subtle within-island genetic structure in Aldabra giant tortoises.

Aldabrachelys gigantea (Aldabra giant tortoise) is one of only two giant tortoise species left in the world and survives as a single wild population of over 100,000 individuals on Aldabra Atoll, Seychelles. Despite this large current population size, the species faces an uncertain future because of its extremely restricted distribution range and high vulnerability to the projected consequences of climate change. Captive-bred A. gigantea are increasingly used in rewilding programs across the region, where they are introduced to replace extinct giant tortoises in an attempt to functionally resurrect degraded island ecosystems. However, there has been little consideration of the current levels of genetic variation and differentiation within and among the islands on Aldabra. As previous microsatellite studies were inconclusive, we combined low-coverage and double-digest restriction-associated DNA (ddRAD) sequencing to analyze samples from 33 tortoises (11 from each main island). Using 5426 variant sites within the tortoise genome, we detected patterns of within-island population structure, but no differentiation between the islands. These unexpected results highlight the importance of using genome-wide genetic markers to capture higher-resolution genetic structure to inform future management plans, even in a seemingly panmictic population. We show that low-coverage ddRAD sequencing provides an affordable alternative approach to conservation genomic projects of non-model species with large genomes.

Limited domestic introgression in a final refuge of the wild pigeon.

Domesticated animals have been culturally and economically important throughout history. Many of their ancestral lineages are extinct or genetically endangered following hybridization with domesticated relatives. Consequently, they have been understudied compared to the ancestral lineages of domestic plants. The domestic pigeon Columba livia, which was pivotal in Darwin's studies, has maintained outsized cultural significance. Its role as a model organism spans the fields of behavior, genetics, and evolution. Domestic pigeons have hybridized with their progenitor, the Rock Dove, rendering the latter of dubious genetic status. Here, we use genomic and morphological data from the putative Rock Doves of the British Isles to identify relictual undomesticated populations. We reveal that Outer Hebridean Rock Doves have experienced minimal levels of introgression. Our results outline the contemporary status of these wild pigeons, highlighting the role of hybridization in the homogenization of genetic lineages.