Underwater sound speed profile estimation from vessel traffic recordings and multi-view neural networks.

Sound speed is a critical parameter in ocean acoustic studies, as it determines the propagation and interpretation of recorded sounds. The potential for exploiting oceanic vessel noise as a sound source of opportunity to estimate ocean sound speed profile is investigated. A deep learning-based inversion scheme, relying upon the underwater radiated noise of moving vessels measured by a single hydrophone, is proposed. The dataset used for this study consists of Automatic Identification System data and acoustic recordings of maritime vessels transiting through the Santa Barbara Channel between January 2015 and December 2017. The acoustic recordings and vessel descriptors are used as predictors for regressing sound speed for each meter in the top 200 m of the water column, where sound speeds are most variable. Multiple (typically ranging between 4 and 10) transits were recorded each day; therefore, this dataset provides an opportunity to investigate whether multiple acoustic observations can be leveraged together to improve inversion estimates. The proposed single-transit and multi-transit models resulted in depth-averaged root-mean-square errors of 1.79 and 1.55 m/s, respectively, compared to the seasonal average predictions of 2.80 m/s.

The N-terminal domains of NLR immune receptors exhibit structural and functional similarities across divergent plant lineages.

Nucleotide-binding domain and leucine-rich repeat (NLR) proteins are a prominent class of intracellular immune receptors in plants. However, our understanding of plant NLR structure and function is limited to the evolutionarily young flowering plant clade. Here, we describe an extended spectrum of NLR diversity across divergent plant lineages and demonstrate the structural and functional similarities of N-terminal domains that trigger immune responses. We show that the broadly distributed coiled-coil (CC) and toll/interleukin-1 receptor (TIR) domain families of non-flowering plants retain immune-related functions through trans-lineage activation of cell death in the angiosperm Nicotiana benthamiana. We further examined a CC subfamily specific to non-flowering lineages and uncovered an essential N-terminal MAEPL motif that is functionally comparable to motifs in resistosome-forming CC-NLRs. Consistent with a conserved role in immunity, the ectopic activation of CCMAEPL in the non-flowering liverwort Marchantia polymorpha led to profound growth inhibition, defense gene activation, and signatures of cell death. Moreover, comparative transcriptomic analyses of CCMAEPL activity delineated a common CC-mediated immune program shared across evolutionarily divergent non-flowering and flowering plants. Collectively, our findings highlight the ancestral nature of NLR-mediated immunity during plant evolution that dates its origin to at least ∼500 million years ago.

Transcriptome data from silica-preserved leaf tissue reveal gene flow patterns in a Caribbean bromeliad.

BACKGROUND AND AIMS: Transcriptome sequencing is a cost-effective approach that allows researchers to study a broad range of questions. However, to preserve RNA for transcriptome sequencing, tissue is often kept in special conditions, such as immediate ultracold freezing. Here, we demonstrate that RNA can be obtained from 6-month-old, field-collected samples stored in silica gel at room temperature. Using these transcriptomes, we explore the evolutionary relationships of the genus Pitcairnia (Bromeliaceae) in the Dominican Republic and infer barriers to gene flow. METHODS: We extracted RNA from silica-dried leaf tissue from 19 Pitcairnia individuals collected across the Dominican Republic. We used a series of macro- and micro-evolutionary approaches to examine the relationships and patterns of gene flow among individuals. KEY RESULTS: We produced high-quality transcriptomes from silica-dried material and demonstrated that evolutionary relationships on the island match geography more closely than species delimitation methods. A population genetic examination indicates that a combination of ecological and geographical features presents barriers to gene flow in Pitcairnia. CONCLUSIONS: Transcriptomes can be obtained from silica-preserved tissue. The genetic diversity among Pitcairnia populations does not warrant classification as separate species, but the Dominican Republic contains several barriers to gene flow, notably the Cordillera Central mountain range.

A mixed-method approach to determining contact matrices in the Cox's Bazar refugee settlement.

Contact matrices are an important ingredient in age-structured epidemic models to inform the simulated spread of the disease between subgroups of the population. These matrices are generally derived using resource-intensive diary-based surveys and few exist in the Global South or tailored to vulnerable populations. In particular, no contact matrices exist for refugee settlements-locations under-served by epidemic models in general. In this paper, we present a novel, mixed-method approach for deriving contact matrices in populations, which combines a lightweight, rapidly deployable survey with an agent-based model of the population informed by census and behavioural data. We use this method to derive the first set of contact matrices for the Cox's Bazar refugee settlement in Bangladesh. To validate our approach, we apply it to the UK population and compare our derived matrices with well-known contact matrices collected using traditional methods. Our findings demonstrate that our mixed-method approach successfully addresses some of the challenges faced by traditional and agent-based approaches to deriving contact matrices. It also shows potential for implementation in resource-constrained environments. This work therefore contributes to a broader aim of developing new methods and mechanisms of data collection for modelling disease spread in refugee and internally displaced person (IDP) settlements and better serving these vulnerable communities.

Assessing the global risk of typhoid outbreaks caused by extensively drug resistant Salmonella Typhi.

Since its emergence in 2016, extensively drug resistant (XDR) Salmonella enterica serovar Typhi (S. Typhi) has become the dominant cause of typhoid fever in Pakistan. The establishment of sustained XDR S. Typhi transmission in other countries represents a major public health threat. We show that the annual volume of air travel from Pakistan strongly discriminates between countries that have and have not imported XDR S. Typhi in the past, and identify a significant association between air travel volume and the rate of between-country movement of the H58 haplotype of S. Typhi from fitted phylogeographic models. Applying these insights, we analyze flight itinerary data cross-referenced with model-based estimates of typhoid fever incidence to identify the countries at highest risk of importation and sustained onward transmission of XDR S. Typhi. Future outbreaks of XDR typhoid are most likely to occur in countries that can support efficient local S. Typhi transmission and have strong travel links to regions with ongoing XDR typhoid outbreaks (currently Pakistan). Public health activities to track and mitigate the spread of XDR S. Typhi should be prioritized in these countries.

Epidemiology of SARS-CoV-2 transmission and superspreading in Salt Lake County, Utah, March-May 2020.

BACKGROUND: Understanding the drivers of SARS-CoV-2 transmission can inform the development of interventions. We evaluated transmission identified by contact tracing investigations between March-May 2020 in Salt Lake County, Utah, to quantify the impact of this intervention and identify risk factors for transmission. METHODS: RT-PCR positive and untested symptomatic contacts were classified as confirmed and probable secondary case-patients, respectively. We compared the number of case-patients and close contacts generated by different groups, and used logistic regression to evaluate factors associated with transmission. RESULTS: Data were collected on 184 index case-patients and up to six generations of contacts. Of 1,499 close contacts, 374 (25%) were classified as secondary case-patients. Decreased transmission odds were observed for contacts aged <18 years (OR = 0.55 [95% CI: 0.38-0.79]), versus 18-44 years, and for workplace (OR = 0.36 [95% CI: 0.23-0.55]) and social (OR = 0.44 [95% CI: 0.28-0.66]) contacts, versus household contacts. Higher transmission odds were observed for case-patient's spouses than other household contacts (OR = 2.25 [95% CI: 1.52-3.35]). Compared to index case-patients identified in the community, secondary case-patients identified through contract-tracing generated significantly fewer close contacts and secondary case-patients of their own. Transmission was heterogeneous, with 41% of index case-patients generating 81% of directly-linked secondary case-patients. CONCLUSIONS: Given sufficient resources and complementary public health measures, contact tracing can contain known chains of SARS-CoV-2 transmission. Transmission is associated with age and exposure setting, and can be highly variable, with a few infections generating a disproportionately high share of onward transmission.

Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants.

Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring the phylogenetic relationships among land plants. The organelles are predominantly inherited from the same parent, and therefore should exhibit phylogenetic concordance. In this study, we examine the mitochondrion and chloroplast genomes of 226 land plants to infer the degree of similarity between the organelles' evolutionary histories. Our results show largely concordant topologies are inferred between the organelles, aside from four well-supported conflicting relationships that warrant further investigation. Despite broad patterns of topological concordance, our findings suggest that the chloroplast and mitochondrial genomes evolved with significant differences in molecular evolution. The differences result in the genes from the chloroplast and the mitochondrion preferentially clustering with other genes from their respective organelles by a program that automates selection of evolutionary model partitions for sequence alignments. Further investigation showed that changes in compositional heterogeneity are not always uniform across divergences in the land plant tree of life. These results indicate that although the chloroplast and mitochondrial genomes have coexisted for over 1 billion years, phylogenetically, they are still evolving sufficiently independently to warrant separate models of evolution. As genome sequencing becomes more accessible, research into these organelles' evolution will continue revealing insight into the ancient cellular events that shaped not only their history, but the history of plants as a whole.

Using real-time data to guide decision-making during an influenza pandemic: A modelling analysis.

Influenza pandemics typically occur in multiple waves of infection, often associated with initial emergence of a novel virus, followed (in temperate regions) by a resurgence accompanying the onset of the annual influenza season. Here, we examined whether data collected from an initial pandemic wave could be informative, for the need to implement non-pharmaceutical measures in any resurgent wave. Drawing from the 2009 H1N1 pandemic in 10 states in the USA, we calibrated simple mathematical models of influenza transmission dynamics to data for laboratory confirmed hospitalisations during the initial 'spring' wave. We then projected pandemic outcomes (cumulative hospitalisations) during the fall wave, and compared these projections with data. Model results showed reasonable agreement for all states that reported a substantial number of cases in the spring wave. Using this model we propose a probabilistic decision framework that can be used to determine the need for preemptive measures such as postponing school openings, in advance of a fall wave. This work illustrates how model-based evidence synthesis, in real-time during an early pandemic wave, could be used to inform timely decisions for pandemic response.

Comparing shared decision making using a paper and digital consent process. A multi-site, single centre study in a trauma and orthopaedic department.

INTRODUCTION: The importance of shared decision making (SDM) for informed consent has been emphasised in the updated regulatory guidelines. Errors of completion, legibility and omission have been associated with paper-based consent forms. We introduced a digital consent process and compared it against a paper-based process for quality and patient reported involvement in shared decision making. METHODS: 223 patients were included in this multi-site, single centre study. Patient consent documentation was by either a paper consent form or the Concentric digital consent platform. Consent forms were assessed for errors of legibility, completion and accuracy of content. Core risks for 20 orthopaedic operations were pre-defined by a Delphi round of experts and forms analysed for omission of these risks. SDM was determined via the 'collaboRATE Top Score', a validated measure for gold-standard SDM. RESULTS: 72% (n = 78/109) of paper consent forms contained ≥1 error compared to 0% (n = 0/114) of digital forms (P < 0.0001). Core risks were unintentionally omitted in 63% (n = 68/109) of paper-forms compared to less than 2% (n = 2/114) of digital consent forms (P < 0.0001). 72% (n = 82/114) of patients giving consent digitally reported gold-standard SDM compared to 28% (n = 31/109) with paper consent (P < 0.001). CONCLUSION: Implementation of a digital consent process has been shown to reduce both error rate and the omission of core risks on consent forms whilst increasing the quality of SDM. This novel finding suggests that using digital consent can improve both the quality of informed consent and the patient experience of SDM.

Cuticle chemistry drives the development of diffraction gratings on the surface of Hibiscus trionum petals.

Plants combine both chemical and structural means to appear colorful. We now have an extensive understanding of the metabolic pathways used by flowering plants to synthesize pigments, but the mechanisms remain obscure whereby cells produce microscopic structures sufficiently regular to interfere with light and create an optical effect. Here, we combine transgenic approaches in a novel model system, Hibiscus trionum, with chemical analyses of the cuticle, both in transgenic lines and in different species of Hibiscus, to investigate the formation of a semi-ordered diffraction grating on the petal surface. We show that regulating both cuticle production and epidermal cell growth is insufficient to determine the type of cuticular pattern produced. Instead, the chemical composition of the cuticle plays a crucial role in restricting the formation of diffraction gratings to the pigmented region of the petal. This suggests that buckling, driven by spatiotemporal regulation of cuticle chemistry, could pattern the petal surface at the nanoscale.

Anionic polymers amplify electrokinetic perfusion through extracellular matrices.

Electrical stimulation (ES) promotes healing of chronic epidermal wounds and delays degeneration of articular cartilage. Despite electrotherapeutic treatment of these non-excitable tissues, the mechanisms by which ES promotes repair are unknown. We hypothesize that a beneficial role of ES is dependent on electrokinetic perfusion in the extracellular space and that it mimics the effects of interstitial flow. In vivo, the extracellular space contains mixtures of extracellular proteins and negatively charged glycosaminoglycans and proteoglycans surrounding cells. While these anionic macromolecules promote water retention and increase mechanical support under compression, in the presence of ES they should also enhance electro-osmotic flow (EOF) to a greater extent than proteins alone. To test this hypothesis, we compare EOF rates between artificial matrices of gelatin (denatured collagen) with matrices of gelatin mixed with anionic polymers to mimic endogenous charged macromolecules. We report that addition of anionic polymers amplifies EOF and that a matrix comprised of 0.5% polyacrylate and 1.5% gelatin generates EOF with similar rates to those reported in cartilage. The enhanced EOF reduces mortality of cells at lower applied voltage compared to gelatin matrices alone. We also use modeling to describe the range of thermal changes that occur during these electrokinetic experiments and during electrokinetic perfusion of soft tissues. We conclude that the negative charge density of native extracellular matrices promotes electrokinetic perfusion during electrical therapies in soft tissues and may promote survival of artificial tissues and organs prior to vascularization and during transplantation.

Eco-Evo-Devo of petal pigmentation patterning.

Colourful spots, stripes and rings decorate the corolla of most flowering plants and fulfil important biotic and abiotic functions. Spatial differences in the pigmentation of epidermal cells can create these patterns. The last few years have yielded new data that have started to illuminate the mechanisms controlling the function, formation and evolution of petal patterns. These advances have broad impacts beyond the immediate field as pigmentation patterns are wonderful systems to explore multiscale biological problems: from understanding how cells make decisions at the microscale to examining the roots of biodiversity at the macroscale. These new results also reveal there is more to petal patterning than meets the eye, opening up a brand new area of investigation. In this mini-review, we summarise our current knowledge on the Eco-Evo-Devo of petal pigmentation patterns and discuss some of the most exciting yet unanswered questions that represent avenues for future research.

A feasibility study on yoga's mechanism of action for chronic low back pain: psychological and neurophysiological changes, including global gene expression and DNA methylation, following a yoga intervention for chronic low back pain.

INTRODUCTION: Yoga has been shown to reduce pain and improve function in populations with chronic low back pain (cLBP), yet the underlying molecular mechanisms remain elusive. This study examined the feasibility and acceptability of a yoga research protocol, including recruitment, retention, and data collection, and investigated the preliminary effects of yoga on psychological and neurophysiological functions, including gene expression and DNA methylation profiles, in participants with cLBP. METHODS: A one-arm trial was conducted with 11 participants with cLBP who enrolled in a 12-week yoga intervention. Data on subjective pain characteristics, quantitative sensory testing, and blood for analysis of differentially expressed genes and CpG methylation was collected prior to the start of the intervention and at study completion. RESULTS: Based on pre-determined feasibility and acceptability criteria, the yoga intervention was found to be feasible and highly acceptable to participants. There was a reduction in pain severity, interference, and mechanical pain sensitivity post-yoga and an increase in emotion regulation and self-efficacy. No adverse reactions were reported. Differential expression analysis demonstrated that the yoga intervention induced increased expression of antisense genes, some of which serve as antisense to known pain genes. In addition, there were 33 differentially hypomethylated positions after yoga (log2 fold change ≥ 1), with enrichment of genes involved in NIK/NF-kB signaling, a major pathway that modulates immune function and inflammation. DISCUSSION/CONCLUSIONS: The study supports the feasibility and acceptability of the proposed protocol to test a specific mechanism of action for yoga in individuals with cLBP. These results also support the notion that yoga may operate through our identified psychological and neurophysiologic pathways to influence reduced pain severity and interference.

Consent for orthopaedic trauma surgery during the COVID-19 pandemic.

INTRODUCTION: The COVID-19 pandemic has brought a series of new challenges to the management of surgical patients. The consent process relies on a foundation of open and non-coerced discussion between clinician and patient, which includes all the potential risks of surgery. This must be updated to incorporate the additional risks of surgery during the pandemic including infection with the SARS-CoV-2 and increased risks of complications with the potential requirement for intensive care support. AIM: The aim of this multi-cycle quality improvement project was to ensure all patients were fully informed of the risks of developing COVID-19 and the possible need for intensive care unit (ICU) support. METHODS: We investigated the quality of the consent process for patients undergoing surgery for trauma at our major trauma centre. Our baseline data collection included a review of all orthopaedic trauma consent forms over a 4-week period in March 2020. We subsequently undertook three further Plan-Do-Study-Act (PDSA) cycles over separate 4-week periods. First, in June 2020, after education measures and presentation of baseline data, second in July 2020 after further education and regular digital reminders were sent to staff, and third in September 2021 after the implementation of an electronic consent form. RESULTS: At baseline, only 2.6% of consent forms mentioned the risk of COVID-19 and none mentioned the risk of requiring ITU support. Through three PDSA cycles this increased to 97% of cases where consent forms displayed the additional risks of COVID-19 and the potential need for ITU admission. CONCLUSION: Our quality improvement project improved the informed consent procedure at our trust. By incorporating these additional risks into the template of an electronic consent form, we hope to achieve sustained improvement in practice.

De-escalation of asymptomatic testing and potential of future COVID-19 outbreaks in US nursing homes amidst rising community vaccination coverage: A modeling study.

As of 2 September 2021, United States nursing homes have reported >675,000 COVID-19 cases and >134,000 deaths according to the Centers for Medicare & Medicaid Services (CMS). More than 205,000,000 persons in the United States had received at least one dose of a COVID-19 vaccine (62% of total population) as of 2 September 2021. We investigate the role of vaccination in controlling future COVID-19 outbreaks. We developed a stochastic, compartmental model of SARS-CoV-2 transmission in a 100-bed nursing home with a staff of 99 healthcare personnel (HCP) in a community of 20,000 people. We parameterized admission and discharge of residents in the model with CMS data, for a within-facility basic reproduction number (R0) of 3.5 and a community R0 of 2.5. The model also included: importation of COVID-19 from the community, isolation of SARS-CoV-2 positive residents, facility-wide adherence to personal protective equipment (PPE) use by HCP, and testing. We systematically varied coverage of mRNA vaccine among residents, HCP, and the community. Simulations were run for 6 months after the second dose in the facility, with results summarized over 1,000 simulations. Expected resident cases decreased as community vaccination increased, with large reductions at high HCP coverage. The probability of a COVID-19 outbreak was lower as well: at HCP vaccination coverage of 60%, probability of an outbreak was below 20% for community coverage of 50% or above. At high coverage, stopping asymptomatic screening and facility-wide testing yielded similar results. Results suggest that high coverage among HCP and in the community can prevent infections in residents. When vaccination is high in nursing homes, but not in their surrounding communities, asymptomatic and facility-wide testing remains necessary to prevent the spread of COVID-19. High adherence to PPE may increase the likelihood of containing future COVID-19 outbreaks if they occur.

Modeling strategies for the allocation of SARS-CoV-2 vaccines in the United States.

The Advisory Committee on Immunization Practices (ACIP) recommended phased allocation of SARS-CoV-2 vaccines in December 2020. To support the development of this guidance, we used a mathematical model of SARS-CoV-2 transmission to evaluate the relative impact of three vaccine allocation strategies on infections, hospitalizations, and deaths. All three strategies initially prioritized healthcare personnel (HCP) for vaccination. Strategies of subsequently prioritizing adults aged ≥65 years, or a combination of essential workers and adults aged ≥75 years, prevented the most deaths. Meanwhile, prioritizing adults with high-risk medical conditions immediately after HCP prevented the most infections. All three strategies prevented a similar fraction of hospitalizations. While no model is capable of fully capturing the complex social dynamics which shape epidemics, exercises such as this one can be a useful way for policy makers to formalize their assumptions and explore the key features of a problem before making decisions.

Transcription Factors Evolve Faster Than Their Structural Gene Targets in the Flavonoid Pigment Pathway.

Dissecting the relationship between gene function and substitution rates is key to understanding genome-wide patterns of molecular evolution. Biochemical pathways provide powerful systems for investigating this relationship because the functional role of each gene is often well characterized. Here, we investigate the evolution of the flavonoid pigment pathway in the colorful Petunieae clade of the tomato family (Solanaceae). This pathway is broadly conserved in plants, both in terms of its structural elements and its MYB, basic helix-loop-helix, and WD40 transcriptional regulators, and its function has been extensively studied, particularly in model species of petunia. We built a phylotranscriptomic data set for 69 species of Petunieae to infer patterns of molecular evolution across pathway genes and across lineages. We found that transcription factors exhibit faster rates of molecular evolution (dN/dS) than their targets, with the highly specialized MYB genes evolving fastest. Using the largest comparative data set to date, we recovered little support for the hypothesis that upstream enzymes evolve slower than those occupying more downstream positions, although expression levels do predict molecular evolutionary rates. Although shifts in floral pigmentation were only weakly related to changes affecting coding regions, we found a strong relationship with the presence/absence patterns of MYB transcripts. Intensely pigmented species express all three main MYB anthocyanin activators in petals, whereas pale or white species express few or none. Our findings reinforce the notion that pathway regulators have a dynamic history, involving higher rates of molecular evolution than structural components, along with frequent changes in expression during color transitions.

The Sea Spray Chemistry and Particle Evolution study (SeaSCAPE): overview and experimental methods.

Marine aerosols strongly influence climate through their interactions with solar radiation and clouds. However, significant questions remain regarding the influences of biological activity and seawater chemistry on the flux, chemical composition, and climate-relevant properties of marine aerosols and gases. Wave channels, a traditional tool of physical oceanography, have been adapted for large-scale ocean-atmosphere mesocosm experiments in the laboratory. These experiments enable the study of aerosols under controlled conditions which isolate the marine system from atmospheric anthropogenic and terrestrial influences. Here, we present an overview of the 2019 Sea Spray Chemistry and Particle Evolution (SeaSCAPE) study, which was conducted in an 11 800 L wave channel which was modified to facilitate atmospheric measurements. The SeaSCAPE campaign sought to determine the influence of biological activity in seawater on the production of primary sea spray aerosols, volatile organic compounds (VOCs), and secondary marine aerosols. Notably, the SeaSCAPE experiment also focused on understanding how photooxidative aging processes transform the composition of marine aerosols. In addition to a broad range of aerosol, gas, and seawater measurements, we present key results which highlight the experimental capabilities during the campaign, including the phytoplankton bloom dynamics, VOC production, and the effects of photochemical aging on aerosol production, morphology, and chemical composition. Additionally, we discuss the modifications made to the wave channel to improve aerosol production and reduce background contamination, as well as subsequent characterization experiments. The SeaSCAPE experiment provides unique insight into the connections between marine biology, atmospheric chemistry, and climate-relevant aerosol properties, and demonstrates how an ocean-atmosphere-interaction facility can be used to isolate and study reactions in the marine atmosphere in the laboratory under more controlled conditions.

Concordance-Based Approaches for the Inference of Relationships and Molecular Rates with Phylogenomic Data Sets.

Gene tree conflict is common and finding methods to analyze and alleviate the negative effects that conflict has on species tree analysis is a crucial part of phylogenomics. This study aims to expand the discussion of inferring species trees and molecular branch lengths when conflict is present. Conflict is typically examined in two ways: inferring its prevalence and inferring the influence of the individual genes (how strongly one gene supports any given topology compared to an alternative topology). Here, we examine a procedure for incorporating both conflict and the influence of genes in order to infer evolutionary relationships. All supported relationships in the gene trees are analyzed and the likelihood of the genes constrained to these relationships is summed to provide a likelihood for the relationship. Consensus tree assembly is conducted based on the sum of likelihoods for a given relationship and choosing relationships based on the most likely relationship assuming it does not conflict with a relationship that has a higher likelihood score. If it is not possible for all most likely relationships to be combined into a single bifurcating tree then multiple trees are produced and a consensus tree with a polytomy is created. This procedure allows for more influential genes to have a greater influence on an inferred relationship, does not assume conflict has arisen from any one source and does not force the data set to produce a single bifurcating tree. Using this approach, on three empirical data sets, we examine and discuss the relationship between influence and prevalence of gene tree conflict. We find that in one of the data sets, assembling a bifurcating consensus tree solely composed of the most likely relationships is impossible. To account for conflict in molecular rate analysis we also introduce a concordance-based approach to the summary and estimation of branch lengths suitable for downstream comparative analyses. We demonstrate through simulation that even under high levels of stochastic conflict, the mean and median of the concordant rates recapitulate the true molecular rate better than using a supermatrix approach. Using a large phylogenomic data set, we examine rate heterogeneity across concordant genes with a focus on the branch subtending crown angiosperms. Notably, we find highly variable rates of evolution along the branch subtending crown angiosperms. The approaches outlined here have several limitations, but they also represent some alternative methods for harnessing the complexity of phylogenomic data sets and enrich our inferences of both species relationships and evolutionary processes.[Branch length estimation; consensus tree; gene tree conflict; gene tree filtering; phylogenetics; phylogenomics.].

Monocotyledonous plants graft at the embryonic root-shoot interface.

Grafting is possible in both animals and plants. Although in animals the process requires surgery and is often associated with rejection of non-self, in plants grafting is widespread, and has been used since antiquity for crop improvement1. However, in the monocotyledons, which represent the second largest group of terrestrial plants and include many staple crops, the absence of vascular cambium is thought to preclude grafting2. Here we show that the embryonic hypocotyl allows intra- and inter-specific grafting in all three monocotyledon groups: the commelinids, lilioids and alismatids. We show functional graft unions through histology, application of exogenous fluorescent dyes, complementation assays for movement of endogenous hormones, and growth of plants to maturity. Expression profiling identifies genes that unify the molecular response associated with grafting in monocotyledons and dicotyledons, but also gene families that have not previously been associated with tissue union. Fusion of susceptible wheat scions to oat rootstocks confers resistance to the soil-borne pathogen Gaeumannomyces graminis. Collectively, these data overturn the consensus that monocotyledons cannot form graft unions, and identify the hypocotyl (mesocotyl in grasses) as a meristematic tissue that allows this process. We conclude that graft compatibility is a shared ability among seed-bearing plants.