Genomic variation, environmental adaptation and feralization in ramie, an ancient fiber crop.

Feralization is an important evolutionary process, but the mechanisms behind it remain poorly understood. Here, we use the ancient fiber crop, ramie (Boehmeria nivea (L.) Gaudich.) as a model to investigate genomic changes associated with both domestication and fertilization. We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes. Next, 915 accessions from 20 countries were gathered, comprising cultivars, major landraces, feral populations and wild progenitor. Based on whole genome resequencing of these accessions, the most comprehensive ramie genomic variation map to date was constructed. Phylogenetic, demographic, and admixture signal detection analyses indicate that feral ramie is of exoferal or exo-endo origin, i.e., descended from hybridization between domesticated ramie and wild progenitor or ancient landraces. Feral ramie has greater genetic diversity than wild or domesticated ramie, and genomic regions affected by natural selection during feralization are different from those under selection during domestication. Ecological analyses showed that feral and domesticated ramie have similar ecological niches which are substantially different from the niche of the wild progenitor, and three environmental variables were associated with habitat-specific adaptation in feral ramie. Our findings advance our understanding of feralization, providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.

Conservation genomic investigation of an endangered conifer, Thuja sutchuenensis, reveals low genetic diversity but also low genetic load.

Endangered species generally have small populations with low genetic diversity and a high genetic load. Thuja sutchuenensis is an endangered conifer endemic to southwestern China. It was once considered extinct in the wild, but in 1999 was rediscovered. However, little is known about its genetic load. We collected 67 individuals from five wild, isolated T. sutchuenensis populations, and used 636,151 SNPs to analyze the level of genetic diversity and genetic load in T. sutchuenensis to delineate the conservation units of T. sutchuenensis, based on whole transcriptome sequencing data, as well as target capture sequencing data. We found that populations of T. sutchuenensis could be divided into three groups. These groups had low levels genetic diversity and were moderately genetically differentiated. Our findings also indicate that T. sutchuenensis suffered two severe bottlenecks around the Last Glaciation Period and Last Glacial Maximum. Among Thuja species, T. sutchuenensis presented the lowest genetic load and hence might have purged deleterious mutations efficiently through purifying selection. However, distribution of fitness effects analysis indicated a high extinction risk for T. sutchuenensis. Multiple lines of evidence identified three management units for T. sutchuenensis. Although T. sutchuenensis possesses a low genetic load, low genetic diversity, suboptimal fitness, and anthropogenic pressures all present an extinction risk for this rare conifer. This might also hold true for many endangered plant species in the mountains all over the world.

Detecting value(s): Digital biomarkers for Alzheimer's disease and the valuation of new diagnostic technologies.

This article explores how the meanings and values of diagnosis are being reconfigured at the interface between technological innovation and imaginaries of precision medicine. From genome sequencing to biological and digital 'markers' of disease, technological innovation occupies an increasingly central space in the way we imagine future health and illness. These imaginaries are usually centred on the promise of faster, more precise and personalised diagnosis, and the associated hope that if detected early enough disease can be effectively treated and prevented. Underpinning and reproduced through these narratives of the future is a re-conceptualisation of diagnostic processes and categories around the anticipation of future risk, as noted by recent theoretical developments in the sociology of diagnosis and related disciplines. Adding to this literature, in this article we explore what makes these emerging diagnostic arrangements valuable, to whom and how. Drawing on interviews with experts involved in the development of digital biomarkers for Alzheimer's disease, we trace how multiple and at times conflicting applications of the tools, and the value(s) attached to them, are coproduced. We thus ask what possibilities are pursued, or foreclosed, through the work of imagining the future of diagnosis.

Plastome phylogenomics and morphological traits analyses provide new insights into the phylogenetic position, species delimitation and speciation of Triplostegia (Caprifoliaceae).

BACKGROUND: The genus Triplostegia contains two recognized species, T. glandulifera and T. grandiflora, but its phylogenetic position and species delimitation remain controversial. In this study, we assembled plastid genomes and nuclear ribosomal DNA (nrDNA) cistrons sampled from 22 wild Triplostegia individuals, each from a separate population, and examined these with 11 recently published Triplostegia plastomes. Morphological traits were measured from herbarium specimens and wild material, and ecological niche models were constructed. RESULTS: Triplostegia is a monophyletic genus within the subfamily Dipsacoideae comprising three monophyletic species, T. glandulifera, T. grandiflora, and an unrecognized species Triplostegia sp. A, which occupies much higher altitude than the other two. The new species had previously been misidentified as T. glandulifera, but differs in taproot, leaf, and other characters. Triplotegia is an old genus, with stem age 39.96 Ma, and within it T. glandulifera diverged 7.94 Ma. Triplostegia grandiflora and sp. A diverged 1.05 Ma, perhaps in response to Quaternary climate fluctuations. Niche overlap between Triplostegia species was positively correlated with their phylogenetic relatedness. CONCLUSIONS: Our results provide new insights into the species delimitation of Triplostegia, and indicate that a taxonomic revision of Triplostegia is needed. We also identified that either rpoB-trnC or ycf1 could serve as a DNA barcode for Triplostegia.

Public engagement with genomics.

As detailed in its flagship report, Genome UK, the UK government recognises the vital role that broad public engagement across whole populations plays in the field of genomics. However, there is limited evidence about how to do this at scale. Most public audiences do not feel actively connected to science, are oftenunsure of the relevance to their lives and rarely talk to their family and friends about; we term this dis-connection a 'disengaged public audience'. We use a narrative review to explore: (i) UK attitudes towards genetics and genomics and what may influence reluctance to engage with these topics; (ii) innovative public engagement approaches that have been used to bring diverse public audiences into conversations about the technology. Whilst we have found some novel engagement methods that have used participatory arts, film, social media and deliberative methods, there is no clear agreement on best practice. We did not find a consistently used, evidence-based strategy for delivering public engagement about genomics across diverse and broad populations, nor a specific method that is known to encourage engagement from groups that have historically felt (in terms of perception) and been (in reality) excluded from genomic research. We argue there is a need for well-defined, tailor-made engagement strategies that clearly articulate the audience, the purpose and the proposed impact of the engagement intervention. This needs to be coupled with robust evaluation frameworks to build the evidence-base for population-level engagement strategies.

The legacy of language: What we say, and what people hear, when we talk about genomics.

The way we "talk" about genetics plays a vital role in whether public audiences feel at ease in having conversations about it. Our research explored whether there was any difference between "what we say" and "what people hear" when providing information about genetics to community groups who are known to be missing from genomics datasets. We conducted 16 focus groups with 100 members of the British public who had limited familiarity with genomics and self-identified as belonging to communities with Black African, Black Caribbean, and Pakistani ancestry as well as people of various ancestral heritage who came from disadvantaged socio-economic backgrounds. Participants were presented with spoken messages explaining genomics and their responses to these were analyzed. Results indicated that starting conversations that framed genomics through its potential benefits were met with cynicism and skepticism. Participants cited historical and present injustices as reasons for this as well as mistrust of private companies and the government. Instead, more productive conversations led with an acknowledgment that some people have questions-and valid concerns-about genomics, before introducing any of the details about the science. To diversify genomic datasets, we need to linguistically meet public audiences where they are at. Our research has demonstrated that everyday talk about genomics, used by researchers and clinicians alike, is received differently than it is likely intended. We may inadvertently be further disengaging the very audiences that diversity programs aim to reach.

Genetic imprints of grafting in wild iron walnut populations in southwestern China.

BACKGROUND: Anthropogenic activities are causing unprecedented loss of genetic diversity in many species. However, the effects on genetic diversity from large-scale grafting onto wild plants of crop species are largely undetermined. Iron walnut (Juglans sigillata Dode) is a deciduous nut tree crop endemic to southwestern China with a long history of cultivation. Due to the rapid expansion of the walnut industry, many natural populations are now being replaced by cultivars grafted onto wild rootstocks. However, little is known about the potential genetic consequences of such action on natural populations. RESULTS: We sampled the scion and the rootstock from each of 149 grafted individuals within nine wild populations of J. sigillata from Yunnan Province which is the center of walnut diversity and cultivation in China, and examined their genetic diversity and population structure using 31 microsatellite loci. Scions had lower genetic diversity than rootstocks, and this pattern was repeated in seven of the nine examined populations. Among those seven populations, AMOVA and clustering analyses showed a clear genetic separation between all rootstocks and all scions. However, the two remaining populations, both from northern Yunnan, showed genetic similarity between scions and rootstocks, possibly indicating that wild populations here are derived from feralized local cultivars. Moreover, our data indicated probable crop-to-wild gene flow between scions and rootstocks, across all populations. CONCLUSIONS: Our results indicate that large-scale grafting has been causing genetic diversity erosion and genetic structure breakdown in the wild material of J. sigillata within Yunnan. To mitigate these effects, we caution against the overuse of grafting in wild populations of iron walnut and other crop species and recommend the preservation of natural genotypes through in situ  and ex situ conservation.

Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains.

Mountainous regions provide a multitude of habitats and opportunities for complex speciation scenarios. Hybridization leading to chloroplast capture, which can be revealed by incongruent phylogenetic trees, is one possible outcome. Four allopatric Taxus lineages (three species and an undescribed lineage) from the Hengduan Mountains, southwest China, exhibit conflicting phylogenetic relationships between nuclear and chloroplast phylogenies. Here, we use multi-omic data at the population level to investigate their historical speciation processes. Population genomic analysis based on ddRAD-seq data revealed limited contemporary inter-specific gene flow involving only populations located close to another species. In a historical context, chloroplast and nuclear data (transcriptome) consistently showed conflicting phylogenetic relationships for T. florinii and the Emei type lineage. ILS and chloroplast recombination were excluded as possible causes, and transcriptome and ddRAD-seq data revealed an absence of the mosaic nuclear genomes that characterize hybrid origin scenarios. Therefore, T. florinii appears to have originated when a lineage of T. florinii captured the T. chinensis plastid type, whereas plastid introgression in the opposite direction generated the Emei Type. All four species have distinct ecological niche based on community investigations and ecological niche analyses. We propose that the origins of both species represent very rare examples of chloroplast capture events despite the paternal cpDNA inheritance of gymnosperms. Specifically, allopatrically and/or ecologically diverged parental species experienced a rare secondary contact, subsequent hybridization and reciprocal chloroplast capture, generating two new lineages, each of which acquired a unique ecological niche. These events might have been triggered by orogenic activities of the Hengduan Mountains and an intensification of the Asian monsoon in the late Miocene, and may represent a scenario more common in these mountains than presently known.

Dementia prevention in memory clinics: recommendations from the European task force for brain health services.

Observational population studies indicate that prevention of dementia and cognitive decline is being accomplished, possibly as an unintended result of better vascular prevention and healthier lifestyles. Population aging in the coming decades requires deliberate efforts to further decrease its prevalence and societal burden. Increasing evidence supports the efficacy of preventive interventions on persons with intact cognition and high dementia risk. We report recommendations for the deployment of second-generation memory clinics (Brain Health Services) whose mission is evidence-based and ethical dementia prevention in at-risk individuals. The cornerstone interventions consist of (i) assessment of genetic and potentially modifiable risk factors including brain pathology, and risk stratification, (ii) risk communication with ad-hoc protocols, (iii) risk reduction with multi-domain interventions, and (iv) cognitive enhancement with cognitive and physical training. A roadmap is proposed for concept validation and ensuing clinical deployment.

The establishment of plants following long-distance dispersal.

Long-distance dispersal (LDD) beyond the range of a species is an important driver of ecological and evolutionary patterns, but insufficient attention has been given to postdispersal establishment. In this review, we summarize current knowledge of the post-LDD establishment phase in plant colonization, identify six key determinants of establishment success, develop a general quantitative framework for post-LDD establishment, and address the major challenges and opportunities in future research. These include improving detection and understanding of LDD using novel approaches, investigating mechanisms determining post-LDD establishment success using mechanistic modeling and inference, and comparison of establishment between past and present. By addressing current knowledge gaps, we aim to further our understanding of how LDD affects plant distributions, and the long-term consequences of LDD events.

Ethical Challenges Associated with Pathogen and Host Genetics in Infectious Disease.

The Covid-19 pandemic has demonstrated the potential of genomic technologies for the detection and surveillance of infectious diseases. Pathogen genomics is likely to play a major role in the future of research and clinical implementation of genomic technologies. However, unlike human genetics, the specific ethical and social challenges associated with the implementation of infectious disease genomics has received comparatively little attention. In this paper, we contribute to this literature, focusing on the potential consequences for individuals and communities of the use of these technologies. We concentrate on areas of challenges related to privacy, stigma, discrimination and the return of results in the cases of the surveillance of known pathogens, metagenomics and host genomics.

Ethical issues when using digital biomarkers and artificial intelligence for the early detection of dementia.

Dementia poses a growing challenge for health services but remains stigmatized and under-recognized. Digital technologies to aid the earlier detection of dementia are approaching market. These include traditional cognitive screening tools presented on mobile devices, smartphone native applications, passive data collection from wearable, in-home and in-car sensors, as well as machine learning techniques applied to clinic and imaging data. It has been suggested that earlier detection and diagnosis may help patients plan for their future, achieve a better quality of life, and access clinical trials and possible future disease modifying treatments. In this review, we explore whether digital tools for the early detection of dementia can or should be deployed, by assessing them against the principles of ethical screening programs. We conclude that while the importance of dementia as a health problem is unquestionable, significant challenges remain. There is no available treatment which improves the prognosis of diagnosed disease. Progression from early-stage disease to dementia is neither given nor currently predictable. Available technologies are generally not both minimally invasive and highly accurate. Digital deployment risks exacerbating health inequalities due to biased training data and inequity in digital access. Finally, the acceptability of early dementia detection is not established, and resources would be needed to ensure follow-up and support for those flagged by any new system. We conclude that early dementia detection deployed at scale via digital technologies does not meet standards for a screening program and we offer recommendations for moving toward an ethical mode of implementation. This article is categorized under:Application Areas > Health CareCommercial, Legal, and Ethical Issues > Ethical ConsiderationsTechnologies > Artificial Intelligence.

Genetic analysis of walnut cultivars from southwest China: Implications for germplasm improvement.

Walnuts are highly valued for their rich nutritional profile and wide medicinal applications. This demand has led to the intensification of breeding activities in major walnut production areas such as southwest China, in order to develop more superior cultivars. With the increasing number of cultivars, accurate identification becomes fundamental to selecting the right cultivar for grafting, industrial processing or development of new cultivars. To ensure proper identification of cultivars and understand the genetic structure of wild and cultivated material, we genotyped 362 cultivated and wild individuals of walnut trees from southwest China (with two additional populations from Xinjiang, plus three cultivars from Canada, France and Belgium) using 36 polymorphic microsatellite loci. We found relatively low indices of genetic diversity (H O = 0.570, H E = 0.404, N A = 2.345) as well as a high level of clonality (>85% of cultivars), indicating reliance on genetically narrow sources of parental material for breeding. Our STRUCTURE and PCoA analyses generally delineated the two species, though considerable levels of introgression were also evident. More significantly, we detected a distinct genetic group of cultivated Juglans sigillata, which mainly comprised individuals of the popular 'Yangbidapao' landrace. Finally, a core set of 18 SSR loci was selected, which was capable of identifying 32 cultivars. In a nutshell, our results call for more utilization of genetically disparate material, including wild walnut trees, as parental sources to breed for more cultivars. The data reported herein will significantly contribute towards the genetic improvement and conservation of the walnut germplasm in southwest China.

Ethical Frameworks for Disclosure of Alzheimer Disease Biomarkers to Research Participants: Conflicting Norms and a Nuanced Policy.

More and more frequently, clinical trials for Alzheimer disease (AD) are targeting cognitively unimpaired individuals who are at increased risk of developing the disease. It is not always clear whether AD biomarker information should be disclosed to research participants: on the one hand, research participants may be interested in learning this information because of its perceived utility, but on the other hand, learning this information may be harmful, as there are very few effective preventive or therapeutic options available for AD. In this article, we bring together three separate sets of ethical guidance literature: on the return of individual research results, on an individual's right to access personal data, and on transparent enrollment into clinical trials. Based on these literatures, we suggest policies for the disclosure of AD biomarker test results in longitudinal observational cohort studies, clinical trials, and hybrid research projects, such as the European Prevention of Alzheimer's Dementia (EPAD) project, in which we served as an ethics team. We also present and critically discuss recommendations for disclosure of AD biomarkers in practice. We underscore that, as long as the clinical validity of AD biomarkers remains limited, there are good reasons to avoid actively disclosing them to cognitively unimpaired research participants.

A concentric circles view of health data relations facilitates understanding of sociotechnical challenges for learning health systems and the role of federated data networks.

The ability to use clinical and research data at scale is central to hopes for data-driven medicine. However, in using such data researchers often encounter hurdles-both technical, such as differing data security requirements, and social, such as the terms of informed consent, legal requirements and patient and public trust. Federated or distributed data networks have been proposed and adopted in response to these hurdles. However, to date there has been little consideration of how FDNs respond to both technical and social constraints on data use. In this Perspective we propose an approach to thinking about data in terms that make it easier to navigate the health data space and understand the value of differing approaches to data collection, storage and sharing. We set out a socio-technical model of data systems that we call the "Concentric Circles View" (CCV) of data-relationships. The aim is to enable a consistent understanding of the fit between the local relationships within which data are produced and the extended socio-technical systems that enable their use. The paper suggests this model can help understand and tackle challenges associated with the use of real-world data in the health setting. We use the model to understand not only how but why federated networks may be well placed to address emerging issues and adapt to the evolving needs of health research for patient benefit. We conclude that the CCV provides a useful model with broader application in mapping, understanding, and tackling the major challenges associated with using real world data in the health setting.