Diverse fates of ancient horizontal gene transfers in extremophilic red algae.

Horizontal genetic transfer (HGT) is a common phenomenon in eukaryotic genomes. However, the mechanisms by which HGT-derived genes persist and integrate into other pathways remain unclear. This topic is of significant interest because, over time, the stressors that initially favoured the fixation of HGT may diminish or disappear. Despite this, the foreign genes may continue to exist if they become part of a broader stress response or other pathways. The conventional model suggests that the acquisition of HGT equates to adaptation. However, this model may evolve into more complex interactions between gene products, a concept we refer to as the 'Integrated HGT Model' (IHM). To explore this concept further, we studied specialized HGT-derived genes that encode heavy metal detoxification functions. The recruitment of these genes into other pathways could provide clear examples of IHM. In our study, we exposed two anciently diverged species of polyextremophilic red algae from the Galdieria genus to arsenic and mercury stress in laboratory cultures. We then analysed the transcriptome data using differential and coexpression analysis. Our findings revealed that mercury detoxification follows a 'one gene-one function' model, resulting in an indivisible response. In contrast, the arsH gene in the arsenite response pathway demonstrated a complex pattern of duplication, divergence and potential neofunctionalization, consistent with the IHM. Our research sheds light on the fate and integration of ancient HGTs, providing a novel perspective on the ecology of extremophiles.

Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts.

Geothermal springs house unicellular red algae in the class Cyanidiophyceae that dominate the microbial biomass at these sites. Little is known about host-virus interactions in these environments. We analyzed the virus community associated with red algal mats in three neighboring habitats (creek, endolithic, soil) at Lemonade Creek, Yellowstone National Park (YNP), USA. We find that despite proximity, each habitat houses a unique collection of viruses, with the giant viruses, Megaviricetes, dominant in all three. The early branching phylogenetic position of genes encoded on metagenome assembled virus genomes (vMAGs) suggests that the YNP lineages are of ancient origin and not due to multiple invasions from mesophilic habitats. The existence of genomic footprints of adaptation to thermophily in the vMAGs is consistent with this idea. The Cyanidiophyceae at geothermal sites originated ca. 1.5 Bya and are therefore relevant to understanding biotic interactions on the early Earth.

Clinical context and communication in shared decision-making about major surgery: Findings from a qualitative study with colorectal, orthopaedic and cardiac patients.

Increasing numbers of older people undergo major surgery in the United Kingdom (UK), with many at high risk of complications due to age, co-morbidities or frailty. This article reports on a study of such patients and their clinicians engaged in shared decision-making. Shared decision-making is a collaborative approach that seeks to value and centre patients' preferences, potentially addressing asymmetries of knowledge and power between clinicians and patients by countering medical authority with greater patient empowerment. We studied shared decision-making practices in the context of major surgery by recruiting 16 patients contemplating either colorectal, cardiac or joint replacement surgery in the UK National Health Service (NHS). Over 18 months 2019-2020, we observed and video-recorded decision-making consultations, studied the organisational and clinical context for consultations, and interviewed patients and clinicians about their experiences of making decisions. Linguistic ethnography, the study of communication and interaction in context, guided us to analyse the interplay between interactions (during consultations between clinicians, patients and family members) and clinical and organisational features of the contexts for those interactions. We found that the framing of consultations as being about life-saving or life-enhancing procedures was important in producing three different genres of consultations focused variously on: resolving problems, deliberation of options and evaluation of benefits of surgery. We conclude that medical authority persists, but can be used to create more deliberative opportunities for decision-making through amending the context for consultations in addition to adopting appropriate communication practices during surgical consultations.

Facultative lifestyle drives diversity of coral algal symbionts.

The photosynthetic symbionts of corals sustain biodiverse reefs in nutrient-poor, tropical waters. Recent genomic data illuminate the evolution of coral symbionts under genome size constraints and suggest that retention of the facultative lifestyle, widespread among these algae, confers a selective advantage when compared with a strict symbiotic existence. We posit that the coral symbiosis is analogous to a 'bioreactor' that selects winner genotypes and allows them to rise to high numbers in a sheltered habitat prior to release by the coral host. Our observations lead to a novel hypothesis, the 'stepping-stone model', which predicts that local adaptation under both the symbiotic and free-living stages, in a stepwise fashion, accelerates coral alga diversity and the origin of endemic strains and species.

Supporting effective shared decision-making in surgical context: Why framing of choices matters for high-risk patients and clinicians.

AIM: In the context of high-risk surgery, shared decision-making (SDM) is important. However, the effectiveness of SDM can be hindered by misalignment between patients and clinicians in their expectations of postoperative outcomes. This study investigated the extent and the effects of this misalignment, as well as its amenability to interventions that encourage perspective-taking. METHOD: Lay participants with a Charlson Comorbidity Index of ≥4 (representing patients) and surgeons and anaesthetists (representing doctors) were recruited. During an online experiment, subjects in both groups forecast their expectations regarding short-term (0, 1 and 3 months after treatment) and long-term (6, 9 and 12 months after treatment) outcomes of different treatment options for one of three hypothetical clinical scenarios - ischaemic heart disease, colorectal cancer or osteoarthritis of the hip - and then chose between surgical or non-surgical treatment. Subjects in both groups were asked to consider the scenarios from their own perspective (Estimation task), and then to adopt the perspective of subjects in the other study group (Perspective task). The decisions of all participants (surgery vs. non-surgical alternative) were analysed using binomial generalized linear mixed models. RESULTS: In total, 55 lay participants and 54 doctors completed the online experiment. Systematic misalignment in expectations between high-risk patients and doctors was observed, with patients expecting better surgical outcomes than clinicians. Patients forecast a significantly higher likelihood of engaging in normal activities in the long term (ß = -1.09, standard error [SE] = 0.20, t = -5.38, p < 0.001), a lower likelihood of experiencing complications in the long term (ß = 0.92, SE = 0.21, t = 4.45, p < 0.001) and a lower likelihood of experiencing depression in both the short term and the long term (ß = 1.01, SE = 0.19, t = 5.38, p < 0.001), than did doctors. Compared with doctors, patients forecast higher estimates of experiencing complications in the short term when a non-surgical alternative was selected (ß = -0.91, SE = 0.26, t = -3.50, p = 0.003). Despite this misalignment, in both groups surgical treatment was strongly preferred (estimation task: 88.7% of doctors and 80% of patients; perspective task: 82.2% of doctors and 90.1% of patients). CONCLUSION: When high-risk surgery is discussed, a non-surgical option may be viewed as 'doing nothing', hence reducing the sense of agency and control. This biases the decision-making process, regardless of the expectations that doctors and patients might have about the outcomes of surgery. Therefore, to improve SDM and to increase the agency and control of patients regarding decisions about their care, we advocate framing the non-surgical treatment options in a way that emphasizes action, agency and change.

Peeling back the layers of coral holobiont multi-omics data.

The integration of multiple 'omics' datasets is a promising avenue for answering many important and challenging questions in biology, particularly those relating to complex ecological systems. Although multi-omics was developed using data from model organisms with significant prior knowledge and resources, its application to non-model organisms, such as coral holobionts, is less clear-cut. We explore, in the emerging rice coral model Montipora capitata, the intersection of holobiont transcriptomic, proteomic, metabolomic, and microbiome amplicon data and investigate how well they correlate under high temperature treatment. Using a typical thermal stress regime, we show that transcriptomic and proteomic data broadly capture the stress response of the coral, whereas the metabolome and microbiome datasets show patterns that likely reflect stochastic and homeostatic processes associated with each sample. These results provide a framework for interpreting multi-omics data generated from non-model systems, particularly those with complex biotic interactions among microbial partners.

Ploidy Variation and Its Implications for Reproduction and Population Dynamics in Two Sympatric Hawaiian Coral Species.

Standing genetic variation is a major driver of fitness and resilience and therefore of fundamental importance for threatened species such as stony corals. We analyzed RNA-seq data generated from 132 Montipora capitata and 119 Pocillopora acuta coral colonies collected from Kane'ohe Bay, O'ahu, Hawai'i. Our goals were to determine the extent of colony genetic variation and to study reproductive strategies in these two sympatric species. Surprisingly, we found that 63% of the P. acuta colonies were triploid, with putative independent origins of the different triploid clades. These corals have spread primarily via asexual reproduction and are descended from a small number of genotypes, whose diploid ancestor invaded the bay. In contrast, all M. capitata colonies are diploid and outbreeding, with almost all colonies genetically distinct. Only two cases of asexual reproduction, likely via fragmentation, were identified in this species. We report two distinct strategies in sympatric coral species that inhabit the largest sheltered body of water in the main Hawaiian Islands. These data highlight divergence in reproductive behavior and genome biology, both of which contribute to coral resilience and persistence.

A k-mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data.

In the age of genome sequencing, whole-genome data is readily and frequently generated, leading to a wealth of new information that can be used to advance various fields of research. New approaches, such as alignment-free phylogenetic methods that utilize k-mer-based distance scoring, are becoming increasingly popular given their ability to rapidly generate phylogenetic information from whole-genome data. However, these methods have not yet been tested using environmental data, which often tends to be highly fragmented and incomplete. Here, we compare the results of one alignment-free approach (which utilizes the D2 statistic) to traditional multi-gene maximum likelihood trees in 3 algal groups that have high-quality genome data available. In addition, we simulate lower-quality, fragmented genome data using these algae to test method robustness to genome quality and completeness. Finally, we apply the alignment-free approach to environmental metagenome assembled genome data of unclassified Saccharibacteria and Trebouxiophyte algae, and single-cell amplified data from uncultured marine stramenopiles to demonstrate its utility with real datasets. We find that in all instances, the alignment-free method produces phylogenies that are comparable, and often more informative, than those created using the traditional multi-gene approach. The k-mer-based method performs well even when there are significant missing data that include marker genes traditionally used for tree reconstruction. Our results demonstrate the value of alignment-free approaches for classifying novel, often cryptic or rare, species, that may not be culturable or are difficult to access using single-cell methods, but fill important gaps in the tree of life.

Building consensus around the assessment and interpretation of Symbiodiniaceae diversity.

Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.

The Pediatrician Workforce in the United States and China.

ABSTRACT: From 2019 to 2022, the For Our Children project gathered a team of Chinese and American pediatricians to explore the readiness of the pediatric workforce in each country to address pressing child health concerns. The teams compared existing data on child health outcomes, the pediatric workforce, and education and combined qualitative and quantitative comparisons centered on themes of effective health care delivery outlined in the World Health Organization Workforce 2030 Report. This article describes key findings about pediatric workload, career satisfaction, and systems to assure competency. We discuss pediatrician accessibility, including geographic distribution, practice locations, trends in pediatric hospitalizations, and payment mechanisms. Pediatric roles differed in the context of each country's child health systems and varied teams. We identified strengths we could learn from one another, such as the US Medical Home Model with continuity of care and robust numbers of skilled clinicians working alongside pediatricians, as well as China's Maternal Child Health system with broad community accessibility and health workers who provide preventive care.In both countries, notable inequities in child health outcomes, evolving epidemiology, and increasing complexity of care require new approaches to the pediatric workforce and education. Although child health systems in the United States and China have significant differences, in both countries, a way forward is to develop a more inclusive and broad view of the child health team to provide truly integrated care that reaches every child. Training competencies must evolve with changing epidemiology as well as changing health system structures and pediatrician roles.

Opportunities for shared decision-making about major surgery with high-risk patients: a multi-method qualitative study.

BACKGROUND: Little is known about the opportunities for shared decision-making when older high-risk patients are offered major surgery. This study examines how, when, and why clinicians and patients can share decision-making about major surgery. METHODS: This was a multi-method qualitative study, combining video recordings of preoperative consultations, interviews, and focus groups (33 patients, 19 relatives, 36 clinicians), with observations and documentary analysis in clinics in five hospitals in the UK undertaking major orthopaedic, colorectal, and/or cardiac surgery. RESULTS: Three opportunities for shared decision-making about major surgery were identified. Resolution-focused consultations (cardiac/colorectal) resulted in a single agreed preferred option related to a potentially life-threatening problem, with limited opportunities for shared decision-making. Evaluative and deliberative consultations offered more opportunity. The former focused on assessing the likelihood of benefits of surgery for a presenting problem that was not a threat to life for the patient (e.g., orthopaedic consultations) and the latter (largely colorectal) involved discussion of a range of options while also considering significant comorbidities and patient preferences. The extent to which opportunities for shared decision-making were available, and taken up by surgeons, was influenced by the nature of the presenting problem, clinical pathway, and patient trajectory. CONCLUSIONS: Decisions about major surgery were not always shared between patients and doctors. The nature of the presenting problem, comorbidities, clinical pathways, and patient trajectories all informed the type of consultation and opportunities for sharing decision-making. Our findings have implications for clinicians, with shared decision-making about major surgery most feasible when the focus is on life-enhancing treatment.

Algae obscura: The potential of rare species as model systems.

Model organism research has provided invaluable knowledge about foundational biological principles. However, most of these studies have focused on species that are in high abundance, easy to cultivate in the lab, and represent only a small fraction of extant biodiversity. Here, we present three examples of rare algae with unusual features that we refer to as "algae obscura." The Cyanidiophyceae (Rhodophyta), Glaucophyta, and Paulinella (rhizarian) lineages have all transitioned out of obscurity to become models for fundamental evolutionary research. Insights have been gained into the prevalence and importance of eukaryotic horizontal gene transfer, early Earth microbial community dynamics, primary plastid endosymbiosis, and the origin of Archaeplastida. By reviewing the research that has come from the exploration of these organisms, we demonstrate that underappreciated algae have the potential to help us formulate, refine, and substantiate core hypotheses and that such organisms should be considered when establishing future model systems.

Endosymbiotic ratchet accelerates divergence after organelle origin: The Paulinella model for plastid evolution: The Paulinella model for plastid evolution.

We hypothesize that as one of the most consequential events in evolution, primary endosymbiosis accelerates lineage divergence, a process we refer to as the endosymbiotic ratchet. Our proposal is supported by recent work on the photosynthetic amoeba, Paulinella, that underwent primary plastid endosymbiosis about 124 Mya. This amoeba model allows us to explore the early impacts of photosynthetic organelle (plastid) origin on the host lineage. The current data point to a central role for effective population size (Ne ) in accelerating divergence post-endosymbiosis due to limits to dispersal and reproductive isolation that reduce Ne , leading to local adaptation. We posit that isolated populations exploit different strategies and behaviors and assort themselves in non-overlapping niches to minimize competition during the early, rapid evolutionary phase of organelle integration. The endosymbiotic ratchet provides a general framework for interpreting post-endosymbiosis lineage evolution that is driven by disruptive selection and demographic and population shifts. Also see the video abstract here: https://youtu.be/gYXrFM6Zz6Q.

Multiple waves of viral invasions in Symbiodiniaceae algal genomes.

Dinoflagellates from the family Symbiodiniaceae are phototrophic marine protists that engage in symbiosis with diverse hosts. Their large and distinct genomes are characterized by pervasive gene duplication and large-scale retroposition events. However, little is known about the role and scale of horizontal gene transfer (HGT) in the evolution of this algal family. In other dinoflagellates, high levels of HGTs have been observed, linked to major genomic transitions, such as the appearance of a viral-acquired nucleoprotein that originated via HGT from a large DNA algal virus. Previous work showed that Symbiodiniaceae from different hosts are actively infected by viral groups, such as giant DNA viruses and ssRNA viruses, that may play an important role in coral health. Latent viral infections may also occur, whereby viruses could persist in the cytoplasm or integrate into the host genome as a provirus. This hypothesis received experimental support; however, the cellular localization of putative latent viruses and their taxonomic affiliation are still unknown. In addition, despite the finding of viral sequences in some genomes of Symbiodiniaceae, viral origin, taxonomic breadth, and metabolic potential have not been explored. To address these questions, we searched for putative viral-derived proteins in thirteen Symbiodiniaceae genomes. We found fifty-nine candidate viral-derived HGTs that gave rise to twelve phylogenies across ten genomes. We also describe the taxonomic affiliation of these virus-related sequences, their structure, and their genomic context. These results lead us to propose a model to explain the origin and fate of Symbiodiniaceae viral acquisitions.

High-quality genome assembles from key Hawaiian coral species.

BACKGROUND: Coral reefs house about 25% of marine biodiversity and are critical for the livelihood of many communities by providing food, tourism revenue, and protection from wave surge. These magnificent ecosystems are under existential threat from anthropogenic climate change. Whereas extensive ecological and physiological studies have addressed coral response to environmental stress, high-quality reference genome data are lacking for many of these species. The latter issue hinders efforts to understand the genetic basis of stress resistance and to design informed coral conservation strategies. RESULTS: We report genome assemblies from 4 key Hawaiian coral species, Montipora capitata, Pocillopora acuta, Pocillopora meandrina, and Porites compressa. These species, or members of these genera, are distributed worldwide and therefore of broad scientific and ecological importance. For M. capitata, an initial assembly was generated from short-read Illumina and long-read PacBio data, which was then scaffolded into 14 putative chromosomes using Omni-C sequencing. For P. acuta, P. meandrina, and P. compressa, high-quality assemblies were generated using short-read Illumina and long-read PacBio data. The P. acuta assembly is from a triploid individual, making it the first reference genome of a nondiploid coral animal. CONCLUSIONS: These assemblies are significant improvements over available data and provide invaluable resources for supporting multiomics studies into coral biology, not just in Hawai'i but also in other regions, where related species exist. The P. acuta assembly provides a platform for studying polyploidy in corals and its role in genome evolution and stress adaptation in these organisms.

Surgery in older patients: learning from shared decision-making in intensive care.

An increasing number of older patients are having surgical treatments. Similar to older patients admitted to intensive care, they present with additional problems including multimorbidity, frailty, and cognitive impairment. In both intensive care and surgical settings, comprehensive assessment can inform targeted interventions and shared decision-making. We explore the challenges faced by older patients, and by the clinicians treating them.

Loss of key endosymbiont genes may facilitate early host control of the chromatophore in Paulinella.

The primary plastid endosymbiosis (∼124 Mya) that occurred in the heterotrophic amoeba lineage, Paulinella, is at an earlier stage of evolution than in Archaeplastida, and provides an excellent model for studying organelle integration. Using genomic data from photosynthetic Paulinella, we identified a plausible mechanism for the evolution of host control of endosymbiont (termed the chromatophore) biosynthetic pathways and functions. Specifically, random gene loss from the chromatophore and compensation by nuclear-encoded gene copies enables host control of key pathways through a minimal number of evolutionary innovations. These gene losses impact critical enzymatic steps in nucleotide biosynthesis and the more peripheral components of multi-protein DNA replication complexes. Gene retention in the chromatophore likely reflects the need to maintain a specific stoichiometric balance of the encoded products (e.g., involved in DNA replication) rather than redox state, as in the highly reduced plastid genomes of algae and plants.