| 1. |
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| 2. |
- Murari, A., et al.
(author)
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A control oriented strategy of disruption prediction to avoid the configuration collapse of tokamak reactors
- 2024
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In: Nature Communications. - 2041-1723 .- 2041-1723. ; 15:1
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Journal article (peer-reviewed)abstract
- The objective of thermonuclear fusion consists of producing electricity from the coalescence of light nuclei in high temperature plasmas. The most promising route to fusion envisages the confinement of such plasmas with magnetic fields, whose most studied configuration is the tokamak. Disruptions are catastrophic collapses affecting all tokamak devices and one of the main potential showstoppers on the route to a commercial reactor. In this work we report how, deploying innovative analysis methods on thousands of JET experiments covering the isotopic compositions from hydrogen to full tritium and including the major D-T campaign, the nature of the various forms of collapse is investigated in all phases of the discharges. An original approach to proximity detection has been developed, which allows determining both the probability of and the time interval remaining before an incoming disruption, with adaptive, from scratch, real time compatible techniques. The results indicate that physics based prediction and control tools can be developed, to deploy realistic strategies of disruption avoidance and prevention, meeting the requirements of the next generation of devices.
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| 3. |
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| 4. |
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| 5. |
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| 6. |
- Leebens-Mack, James H., et al.
(author)
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One thousand plant transcriptomes and the phylogenomics of green plants
- 2019
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In: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
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Journal article (peer-reviewed)abstract
- Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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| 7. |
- Tobias, Deirdre K, et al.
(author)
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Second international consensus report on gaps and opportunities for the clinical translation of precision diabetes medicine
- 2023
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In: Nature Medicine. - 1546-170X. ; 29:10, s. 2438-2457
-
Research review (peer-reviewed)abstract
- Precision medicine is part of the logical evolution of contemporary evidence-based medicine that seeks to reduce errors and optimize outcomes when making medical decisions and health recommendations. Diabetes affects hundreds of millions of people worldwide, many of whom will develop life-threatening complications and die prematurely. Precision medicine can potentially address this enormous problem by accounting for heterogeneity in the etiology, clinical presentation and pathogenesis of common forms of diabetes and risks of complications. This second international consensus report on precision diabetes medicine summarizes the findings from a systematic evidence review across the key pillars of precision medicine (prevention, diagnosis, treatment, prognosis) in four recognized forms of diabetes (monogenic, gestational, type 1, type 2). These reviews address key questions about the translation of precision medicine research into practice. Although not complete, owing to the vast literature on this topic, they revealed opportunities for the immediate or near-term clinical implementation of precision diabetes medicine; furthermore, we expose important gaps in knowledge, focusing on the need to obtain new clinically relevant evidence. Gaps include the need for common standards for clinical readiness, including consideration of cost-effectiveness, health equity, predictive accuracy, liability and accessibility. Key milestones are outlined for the broad clinical implementation of precision diabetes medicine.
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| 8. |
- Birney, Ewan, et al.
(author)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Journal article (peer-reviewed)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 9. |
- Kilpeläinen, Tuomas O, et al.
(author)
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Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels
- 2016
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
-
Journal article (peer-reviewed)abstract
- Leptin is an adipocyte-secreted hormone, the circulating levels of which correlate closely with overall adiposity. Although rare mutations in the leptin (LEP) gene are well known to cause leptin deficiency and severe obesity, no common loci regulating circulating leptin levels have been uncovered. Therefore, we performed a genome-wide association study (GWAS) of circulating leptin levels from 32,161 individuals and followed up loci reaching P<10(-6) in 19,979 additional individuals. We identify five loci robustly associated (P<5 × 10(-8)) with leptin levels in/near LEP, SLC32A1, GCKR, CCNL1 and FTO. Although the association of the FTO obesity locus with leptin levels is abolished by adjustment for BMI, associations of the four other loci are independent of adiposity. The GCKR locus was found associated with multiple metabolic traits in previous GWAS and the CCNL1 locus with birth weight. Knockdown experiments in mouse adipose tissue explants show convincing evidence for adipogenin, a regulator of adipocyte differentiation, as the novel causal gene in the SLC32A1 locus influencing leptin levels. Our findings provide novel insights into the regulation of leptin production by adipose tissue and open new avenues for examining the influence of variation in leptin levels on adiposity and metabolic health.
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| 10. |
- Middeldorp, Christel M., et al.
(author)
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The Early Growth Genetics (EGG) and EArly Genetics and Lifecourse Epidemiology (EAGLE) consortia : design, results and future prospects
- 2019
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In: European Journal of Epidemiology. - : Springer Science and Business Media LLC. - 0393-2990 .- 1573-7284. ; 34:3, s. 279-300
-
Journal article (peer-reviewed)abstract
- The impact of many unfavorable childhood traits or diseases, such as low birth weight and mental disorders, is not limited to childhood and adolescence, as they are also associated with poor outcomes in adulthood, such as cardiovascular disease. Insight into the genetic etiology of childhood and adolescent traits and disorders may therefore provide new perspectives, not only on how to improve wellbeing during childhood, but also how to prevent later adverse outcomes. To achieve the sample sizes required for genetic research, the Early Growth Genetics (EGG) and EArly Genetics and Lifecourse Epidemiology (EAGLE) consortia were established. The majority of the participating cohorts are longitudinal population-based samples, but other cohorts with data on early childhood phenotypes are also involved. Cohorts often have a broad focus and collect(ed) data on various somatic and psychiatric traits as well as environmental factors. Genetic variants have been successfully identified for multiple traits, for example, birth weight, atopic dermatitis, childhood BMI, allergic sensitization, and pubertal growth. Furthermore, the results have shown that genetic factors also partly underlie the association with adult traits. As sample sizes are still increasing, it is expected that future analyses will identify additional variants. This, in combination with the development of innovative statistical methods, will provide detailed insight on the mechanisms underlying the transition from childhood to adult disorders. Both consortia welcome new collaborations. Policies and contact details are available from the corresponding authors of this manuscript and/or the consortium websites.
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| 11. |
- van Akkooi, Alexander C. J., et al.
(author)
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Neoadjuvant Systemic Therapy (NAST) in Patients with Melanoma: Surgical Considerations by the International Neoadjuvant Melanoma Consortium (INMC)
- 2022
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In: ANNALS OF SURGICAL ONCOLOGY. - : Springer Science and Business Media LLC. - 1068-9265 .- 1534-4681. ; 29:6, s. 3694-3708
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Journal article (peer-reviewed)abstract
- Exciting advances in melanoma systemic therapies have presented the opportunity for surgical oncologists and their multidisciplinary colleagues to test the neoadjuvant systemic treatment approach in high-risk, resectable metastatic melanomas. Here we describe the state of the science of neoadjuvant systemic therapy (NAST) for melanoma, focusing on the surgical aspects and the key role of the surgical oncologist in this treatment paradigm. This paper summarizes the past decade of developments in melanoma treatment and the current evidence for NAST in stage III melanoma specifically. Issues of surgical relevance are discussed, including the risk of progression on NAST prior to surgery. Technical aspects, such as the definition of resectability for melanoma and the extent and scope of routine surgery are presented. Other important issues, such as the utility of radiographic response evaluation and method of pathologic response evaluation, are addressed. Surgical complications and perioperative management of NAST related adverse events are considered. The International Neoadjuvant Melanoma Consortium has the goal of harmonizing NAST trials in melanoma to facilitate rapid advances with new approaches, and facilitating the comparison of results across trials evaluating different treatment regimens. Our ultimate goals are to provide definitive proof of the safety and efficacy of NAST in melanoma, sufficient for NAST to become an acceptable standard of care, and to leverage this platform to allow more personalized, biomarker-driven, tailored approaches to subsequent treatment and surveillance.
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| 12. |
- Block, Keith I., et al.
(author)
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Designing a broad-spectrum integrative approach for cancer prevention and treatment
- 2015
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In: Seminars in Cancer Biology. - : Academic Press. - 1044-579X .- 1096-3650. ; 35, s. S276-S304
-
Research review (peer-reviewed)abstract
- Targeted therapies and the consequent adoption of "personalized" oncology have achieved notable successes in some cancers; however, significant problems remain with this approach. Many targeted therapies are highly toxic, costs are extremely high, and most patients experience relapse after a few disease-free months. Relapses arise from genetic heterogeneity in tumors, which harbor therapy-resistant immortalized cells that have adopted alternate and compensatory pathways (i.e., pathways that are not reliant upon the same mechanisms as those which have been targeted). To address these limitations, an international task force of 180 scientists was assembled to explore the concept of a low-toxicity "broadspectrum" therapeutic approach that could simultaneously target many key pathways and mechanisms. Using cancer hallmark phenotypes and the tumor microenvironment to account for the various aspects of relevant cancer biology, interdisciplinary teams reviewed each hallmark area and nominated a wide range of high-priority targets (74 in total) that could be modified to improve patient outcomes. For these targets, corresponding low-toxicity therapeutic approaches were then suggested, many of which were phytochemicals. Proposed actions on each target and all of the approaches were further reviewed for known effects on other hallmark areas and the tumor microenvironment Potential contrary or procarcinogenic effects were found for 3.9% of the relationships between targets and hallmarks, and mixed evidence of complementary and contrary relationships was found for 7.1%. Approximately 67% of the relationships revealed potentially complementary effects, and the remainder had no known relationship. Among the approaches, 1.1% had contrary, 2.8% had mixed and 62.1% had complementary relationships. These results suggest that a broad-spectrum approach should be feasible from a safety standpoint. This novel approach has potential to be relatively inexpensive, it should help us address stages and types of cancer that lack conventional treatment, and it may reduce relapse risks. A proposed agenda for future research is offered. (C) 2015 The Authors. Published by Elsevier Ltd.
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| 13. |
- Beaumont, Robin N, et al.
(author)
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Genome-wide association study of offspring birth weight in 86,577 women identifies five novel loci and highlights maternal genetic effects that are independent of fetal genetics.
- 2018
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In: Human molecular genetics. - : Oxford University Press (OUP). - 1460-2083 .- 1460-2083 .- 0964-6906. ; 27:4, s. 742-756
-
Journal article (peer-reviewed)abstract
- Genome-wide association studies (GWAS) of birth weight have focused on fetal genetics, while relatively little is known about the role of maternal genetic variation. We aimed to identify maternal genetic variants associated with birth weight that could highlight potentially relevant maternal determinants of fetal growth. We meta-analysed data on up to 8.7 million SNPs in up to 86,577 women of European descent from the Early Growth Genetics (EGG) Consortium and the UK Biobank. We used structural equation modelling (SEM) and analyses of mother-child pairs to quantify the separate maternal and fetal genetic effects. Maternal SNPs at 10 loci (MTNR1B, HMGA2, SH2B3, KCNAB1, L3MBTL3, GCK, EBF1, TCF7L2, ACTL9, CYP3A7) were associated with offspring birth weight at P<5x10-8. In SEM analyses, at least 7 of the 10 associations were consistent with effects of the maternal genotype acting via the intrauterine environment, rather than via effects of shared alleles with the fetus. Variants, or correlated proxies, at many of the loci had been previously associated with adult traits, including fasting glucose (MTNR1B, GCK and TCF7L2) and sex hormone levels (CYP3A7), and one (EBF1) with gestational duration. The identified associations indicate genetic effects on maternal glucose, cytochrome P450 activity and gestational duration, and potentially on maternal blood pressure and immune function, are relevant for fetal growth. Further characterization of these associations in mechanistic and causal analyses will enhance understanding of the potentially modifiable maternal determinants of fetal growth, with the goal of reducing the morbidity and mortality associated with low and high birth weights.
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| 14. |
- Davies, Neil, et al.
(author)
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The founding charter of the Genomic Observatories Network
- 2014
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In: GigaScience. - 2047-217X. ; 3:2
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Journal article (peer-reviewed)abstract
- Abstract The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.
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| 15. |
- Pinto, Dalila, et al.
(author)
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Convergence of Genes and Cellular Pathways Dysregulated in Autism Spectrum Disorders.
- 2014
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In: American journal of human genetics. - : Elsevier BV. - 1537-6605 .- 0002-9297. ; 94:5, s. 677-694
-
Journal article (peer-reviewed)abstract
- Rare copy-number variation (CNV) is an important source of risk for autism spectrum disorders (ASDs). We analyzed 2,446 ASD-affected families and confirmed an excess of genic deletions and duplications in affected versus control groups (1.41-fold, p = 1.0× 10(-5)) and an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated with dominant or X-linked ASD and intellectual disability (odds ratio = 12.62, p = 2.7× 10(-15), ∼3% of ASD subjects). Pathogenic CNVs, often showing variable expressivity, included rare de novo and inherited events at 36 loci, implicating ASD-associated genes (CHD2, HDAC4, and GDI1) previously linked to other neurodevelopmental disorders, as well as other genes such as SETD5, MIR137, and HDAC9. Consistent with hypothesized gender-specific modulators, females with ASD were more likely to have highly penetrant CNVs (p = 0.017) and were also overrepresented among subjects with fragile X syndrome protein targets (p = 0.02). Genes affected by de novo CNVs and/or loss-of-function single-nucleotide variants converged on networks related to neuronal signaling and development, synapse function, and chromatin regulation.
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| 16. |
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| 17. |
- Tyrrell, Jessica, et al.
(author)
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Genetic Evidence for Causal Relationships Between Maternal Obesity-Related Traits and Birth Weight.
- 2016
-
In: JAMA. - : American Medical Association (AMA). - 1538-3598 .- 0098-7484. ; 315:11, s. 1129-40
-
Journal article (peer-reviewed)abstract
- Neonates born to overweight or obese women are larger and at higher risk of birth complications. Many maternal obesity-related traits are observationally associated with birth weight, but the causal nature of these associations is uncertain.To test for genetic evidence of causal associations of maternal body mass index (BMI) and related traits with birth weight.Mendelian randomization to test whether maternal BMI and obesity-related traits are potentially causally related to offspring birth weight. Data from 30,487 women in 18 studies were analyzed. Participants were of European ancestry from population- or community-based studies in Europe, North America, or Australia and were part of the Early Growth Genetics Consortium. Live, term, singleton offspring born between 1929 and 2013 were included.Genetic scores for BMI, fasting glucose level, type 2 diabetes, systolic blood pressure (SBP), triglyceride level, high-density lipoprotein cholesterol (HDL-C) level, vitamin D status, and adiponectin level.Offspring birth weight from 18 studies.Among the 30,487 newborns the mean birth weight in the various cohorts ranged from 3325 g to 3679 g. The maternal genetic score for BMI was associated with a 2-g (95% CI, 0 to 3 g) higher offspring birth weight per maternal BMI-raising allele (P=.008). The maternal genetic scores for fasting glucose and SBP were also associated with birth weight with effect sizes of 8 g (95% CI, 6 to 10 g) per glucose-raising allele (P=7×10(-14)) and -4 g (95% CI, -6 to -2 g) per SBP-raising allele (P=1×10(-5)), respectively. A 1-SD (≈4 points) genetically higher maternal BMI was associated with a 55-g higher offspring birth weight (95% CI, 17 to 93 g). A 1-SD (≈7.2 mg/dL) genetically higher maternal fasting glucose concentration was associated with 114-g higher offspring birth weight (95% CI, 80 to 147 g). However, a 1-SD (≈10 mm Hg) genetically higher maternal SBP was associated with a 208-g lower offspring birth weight (95% CI, -394 to -21 g). For BMI and fasting glucose, genetic associations were consistent with the observational associations, but for systolic blood pressure, the genetic and observational associations were in opposite directions.In this mendelian randomization study, genetically elevated maternal BMI and blood glucose levels were potentially causally associated with higher offspring birth weight, whereas genetically elevated maternal SBP was potentially causally related to lower birth weight. If replicated, these findings may have implications for counseling and managing pregnancies to avoid adverse weight-related birth outcomes.
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| 18. |
- Baruch, Zdravko, et al.
(author)
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Functional acclimation across microgeographic scales in Dodonaea viscosa
- 2018
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In: AoB Plants. - : Oxford University Press (OUP). - 2041-2851. ; 10:3
-
Journal article (peer-reviewed)abstract
- Intraspecific plant functional trait variation provides mechanistic insight into persistence and can infer population adaptive capacity. However, most studies explore intraspecific trait variation in systems where geographic and environmental distances co-vary. Such a design reduces the certainty of trait-environment associations, and it is imperative for studies that make trait-environment associations be conducted in systems where environmental distance varies independently of geographic distance. Here we explored trait variation in such a system, and aimed to: (i) quantify trait variation of parent and offspring generations, and associate this variation to parental environments; (ii) determine the traits which best explain population differences; (iii) compare parent and offspring trait-trait relationships. We characterized 15 plant functional traits in eight populations of a shrub with a maximum separation ca. 100 km. Populations differed markedly in aridity and elevation, and environmental distance varied independently of geographic distance. We measured traits in parent populations collected in the field, as well as their offspring reared in greenhouse conditions. Parent traits regularly associated with their environment. These associations were largely lost in the offspring generation, indicating considerable phenotypic plasticity. An ordination of parent traits showed clear structure with strong influence of leaf area, specific leaf area, stomatal traits, isotope delta C-13 and delta N-15 ratios, and N-area, whereas the offspring ordination was less structured. Parent trait-trait correlations were in line with expectations from the leaf economic spectrum. We show considerable trait plasticity in the woody shrub over microgeographic scales (<100 km), indicating it has the adaptive potential within a generation to functionally acclimate to a range of abiotic conditions. Since our study shrub is commonly used for restoration in southern Australia and local populations do not show strong genetic differentiation in functional traits, the potential risks of transferring seed across the broad environmental conditions are not likely to be a significant issue.
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| 19. |
- Cumming, Graeme S., et al.
(author)
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Research priorities for the sustainability of coral-rich western Pacific seascapes
- 2023
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In: Regional Environmental Change. - 1436-3798 .- 1436-378X. ; 23:2
-
Journal article (peer-reviewed)abstract
- Nearly a billion people depend on tropical seascapes. The need to ensure sustainable use of these vital areas is recognised, as one of 17 policy commitments made by world leaders, in Sustainable Development Goal (SDG) 14 (‘Life below Water’) of the United Nations. SDG 14 seeks to secure marine sustainability by 2030. In a time of increasing social-ecological unpredictability and risk, scientists and policymakers working towards SDG 14 in the Asia–Pacific region need to know: (1) How are seascapes changing? (2) What can global society do about these changes? and (3) How can science and society together achieve sustainable seascape futures? Through a horizon scan, we identified nine emerging research priorities that clarify potential research contributions to marine sustainability in locations with high coral reef abundance. They include research on seascape geological and biological evolution and adaptation; elucidating drivers and mechanisms of change; understanding how seascape functions and services are produced, and how people depend on them; costs, benefits, and trade-offs to people in changing seascapes; improving seascape technologies and practices; learning to govern and manage seascapes for all; sustainable use, justice, and human well-being; bridging communities and epistemologies for innovative, equitable, and scale-crossing solutions; and informing resilient seascape futures through modelling and synthesis. Researchers can contribute to the sustainability of tropical seascapes by co-developing transdisciplinary understandings of people and ecosystems, emphasising the importance of equity and justice, and improving knowledge of key cross-scale and cross-level processes, feedbacks, and thresholds.
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| 20. |
- Liu, Xueping, et al.
(author)
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Variants in the fetal genome near pro-inflammatory cytokine genes on 2q13 associate with gestational duration.
- 2019
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
-
Journal article (peer-reviewed)abstract
- The duration of pregnancy is influenced by fetal and maternal genetic and non-genetic factors. Here we report a fetal genome-wide association meta-analysis of gestational duration, and early preterm, preterm, and postterm birth in 84,689 infants. One locus on chromosome 2q13 is associated with gestational duration; the association is replicated in 9,291 additional infants (combined P=3.96×10-14). Analysis of 15,588 mother-child pairs shows that the association is driven by fetal rather than maternal genotype. Functional experiments show that the lead SNP, rs7594852, alters the binding of the HIC1 transcriptional repressor. Genes at the locus include several interleukin 1 family members with roles in pro-inflammatory pathways that are central to the process of parturition. Further understanding of the underlying mechanisms will be of great public health importance, since giving birth either before or after the window of term gestation is associated with increased morbidity and mortality.
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| 21. |
- Alfoeldi, Jessica, et al.
(author)
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The genome of the green anole lizard and a comparative analysis with birds and mammals
- 2011
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 477:7366, s. 587-591
-
Journal article (peer-reviewed)abstract
- The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments(1). Among amniotes, genome sequences are available for mammals and birds(2-4), but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes(2). Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds(5). We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.
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| 22. |
- Breed, Martin, 1981-, et al.
(author)
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Pollen diversity matters : revealing the neglected effect of pollen diversity on fitness in fragmented landscapes
- 2012
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In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 21:24, s. 5955-5968
-
Journal article (peer-reviewed)abstract
- Few studies have documented the impacts of habitat fragmentation on plant mating patterns together with fitness. Yet, these processes require urgent attention to better understand the impact of contemporary landscape change on biodiversity and for guiding native plant genetic resource management. We examined these relationships using the predominantly insect-pollinated Eucalyptus socialis. Progeny were collected from trees located in three increasingly disturbed landscapes in southern Australia and were planted out in common garden experiments. We show that individual mating patterns were increasingly impacted by lower conspecific density caused by habitat fragmentation. We determined that reduced pollen diversity probably has effects over and above those of inbreeding on progeny fitness. This provides an alternative mechanistic explanation for the indirect density dependence often inferred between conspecific density and offspring fitness.
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| 23. |
- Blyth, Colette, et al.
(author)
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Genomic, Habitat, and Leaf Shape Analyses Reveal a Possible Cryptic Species and Vulnerability to Climate Change in a Threatened Daisy
- 2021
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In: Life. - : MDPI. - 2075-1729. ; 11:6
-
Journal article (peer-reviewed)abstract
- Olearia pannosa is a plant species listed as vulnerable in Australia. Two subspecies are currently recognised (O. pannosa subsp. pannosa (silver daisy) and O. pannosa subsp. cardiophylla (velvet daisy)), which have overlapping ranges but distinct leaf shape. Remnant populations face threats from habitat fragmentation and climate change. We analysed range-wide genomic data and leaf shape variation to assess population diversity and divergence and to inform conservation management strategies. We detected three distinct genetic groupings and a likely cryptic species. Samples identified as O. pannosa subsp. cardiophylla from the Flinders Ranges in South Australia were genetically distinct from all other samples and likely form a separate, range-restricted species. Remaining samples formed two genetic clusters, which aligned with leaf shape differences but not fully with current subspecies classifications. Levels of genetic diversity and inbreeding differed between the three genetic groups, suggesting each requires a separate management strategy. Additionally, we tested for associations between genetic and environmental variation and carried out habitat suitability modelling for O. pannosa subsp. pannosa populations. We found mean annual maximum temperature explained a significant proportion of genomic variance. Habitat suitability modelling identified mean summer maximum temperature, precipitation seasonality and mean annual rainfall as constraints on the distribution of O. pannosa subsp. pannosa, highlighting increasing aridity as a threat for populations located near suitability thresholds. Our results suggest maximum temperature is an important agent of selection on O. pannosa subsp. pannosa and should be considered in conservation strategies. We recommend taxonomic revision of O. pannosa and provide conservation management recommendations.
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| 24. |
- Blyth, Colette, et al.
(author)
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Increased Genetic Diversity via Gene Flow Provides Hope for Acacia whibleyana, an Endangered Wattle Facing Extinction
- 2020
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In: Diversity. - : MDPI AG. - 1424-2818. ; 12:8
-
Journal article (peer-reviewed)abstract
- In this paper we apply a conservation genomics approach to make evidence-based management recommendations forAcacia whibleyana,an endangered shrub endemic to Eyre Peninsula, South Australia. We used population genomic analysis to assess genetic connectivity, diversity, and historical inbreeding across all known stands of the species sampling remnant stands, revegetated stands of unknown origin, and a post-fire seedling cohort. Our results indicate a degree of historical connectivity across the landscape, but habitat loss and/or pollinator community disruption are potential causes of strong genetic structure across the remnant stands. Remnant stands had low genetic diversity and showed evidence of historical inbreeding, but only low levels of intra-stand relatedness indicating that risks of contemporary inbreeding are low. Analysis of a post-fire first generation cohort of seedlings showed they likely resulted from intra-stand matings, resulting in reduced genetic diversity compared to the parents. However, admixed seedlings in this cohort showed an increase in heterozygosity relative to likely sources and the non-admixed seedlings of the same stand. Assisted inter-stand gene flow may prove an effective management strategy to boost heterozygosity and corresponding increases in adapting capacity in this endangered species.
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| 25. |
- Breed, Martin F., 1981-, et al.
(author)
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Clarifying climate change adaptation responses for scattered trees in modified landscapes
- 2011
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In: Journal of Applied Ecology. - : Wiley. - 0021-8901 .- 1365-2664. ; 48:3, s. 637-641
-
Journal article (peer-reviewed)abstract
- 1. Many studies have investigated adaptation to climate change. However, the term ‘adaptation’ has been used ambiguously and sometimes included parts of both classic evolutionary processes and conservation planning measures (i.e. human-mediated adaptation).2. To reduce ambiguity, we define three classes of evolutionary processes involved in adaptation – migrational, novel-variant and plasticity. Migrational adaptation describes the process of redistribution of standing genetic variation among populations. Novel-variant adaptation describes the increase in frequency of beneficial, new genetic variants. Plasticity adaptation refers to adaptive plastic responses of organisms to environmental stressors. Quite separately, human-mediated adaptation aims to maintain these evolutionary processes.3. Whilst the role of scattered trees in migrational adaptation of fauna may have been neglected in the past, their capacity to assist migrational adaptation of trees has been previously documented. However, their role in novel-variant and plasticity adaptation is generally unrecognised, and warrants further attention.4. Synthesis and applications. By defining different aspects of adaptation carefully, we show that scattered trees should not be cleared since they may facilitate gene flow across fragmented landscapes. However, they should be avoided as dominant seed sources since their stock may be of poor quality.
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| 26. |
- Breed, Martin F., 1981-, et al.
(author)
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Which provenance and where? : Seed sourcing strategies for revegetation in a changing environment
- 2013
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In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 14:1, s. 1-10
-
Research review (peer-reviewed)abstract
- Revegetation is one practical application of science that should ideally aim to combine ecology with evolution to maximise biodiversity and ecosystem outcomes. The strict use of locally sourced seed in revegetation programs is widespread and is based on the expectation that populations are locally adapted. This practice does not fully integrate two global drivers of ecosystem change and biodiversity loss: habitat fragmentation and climate change. Here, we suggest amendments to existing strategies combined with a review of alternative seed-sourcing strategies that propose to mitigate against these drivers. We present a provenancing selection guide based on confidence surrounding climate change distribution modelling and data on population genetic and/or environmental differences between populations. Revegetation practices will benefit from greater integration of current scientific developments and establishment of more long-term experiments is key to improving the long-term success. The rapid growth in carbon and biodiversity markets creates a favourable economic climate to achieve these outcomes.
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| 27. |
- Breed, Martin, 1981-, et al.
(author)
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Shifts in reproductive assurance strategies and inbreeding costs associated with habitat fragmentation in Central American mahogany
- 2012
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In: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 15:5, s. 444-452
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Journal article (peer-reviewed)abstract
- The influence of habitat fragmentation on mating patterns and progeny fitness in trees is critical for understanding the long-term impact of contemporary landscape change on the sustainability of biodiversity. We examined the relationship between mating patterns, using microsatellites, and fitness of progeny, in a common garden trial, for the insect-pollinated big-leaf mahogany, Swietenia macrophylla King, sourced from forests and isolated trees in 16 populations across Central America. As expected, isolated trees had disrupted mating patterns and reduced fitness. However, for dry provenances, fitness was negatively related to correlated paternity, while for mesic provenances, fitness was correlated positively with outcrossing rate and negatively with correlated paternity. Poorer performance of mesic provenances is likely because of reduced effective pollen donor density due to poorer environmental suitability and greater disturbance history. Our results demonstrate a differential shift in reproductive assurance and inbreeding costs in mahogany, driven by exploitation history and contemporary landscape context.
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| 28. |
- Christmas, Matthew, et al.
(author)
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Measuring genome-wide genetic variation to reassess subspecies classifications in Dodonaea viscosa (Sapindaceae)
- 2018
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In: Australian Journal of Botany. - : CSIRO PUBLISHING. - 0067-1924 .- 1444-9862. ; 66:4, s. 287-297
-
Journal article (peer-reviewed)abstract
- Subspecies are traditionally defined on the basis of geographic discontinuities in phenotypic traits, and their circumscription is useful to distinguish morphologically differentiated populations. However, the robustness of morphology-based subspecies classifications in the genomics era is coming under increasing scrutiny, and phylogenies inferred from molecular data may not match with morphological approaches. The division of the shrub Dodonaea viscosa into seven subspecies within Australia has been based mainly on variation in leaf shape, which is a notably variable phenotypic character in this species. So as to assess the alignment between genetic variation and subspecies assignment, we genotyped 67 D. viscosa plants, including representatives from each of the seven subspecies, for 941 single nucleotide polymorphisms. Weused network-and Bayesian-based methods to assess genetic relatedness between sampled individuals. Structure analysis identified two genetic clusters, with a further substructure being identified within one of the clusters. Genetic clusters partially aligned with subspecies classifications, particularly for the three most morphologically distinct subspecies (ssp. mucronata, ssp. viscosa and ssp. burmanniana). Subspecies inhabiting the arid zone (ssp. mucronata and ssp. angustissima) exhibited the most distinct genetic clustering. For subspecies inhabiting more temperate regions of its range (ssp. angustifolia, ssp. cuneata and ssp. spatulata), genetic groups did not correspond well with subspecies classifications, but rather were better explained by the geographic origin of individuals. We suggest that the current subspecific classification of the hopbush does not accurately reflect the evolutionary history of this species, and recommend that phenotypic variation be reassessed in light of the genetic structure we describe here. The roles of environmental change, selection and geographic isolation are discussed in an attempt to explain the contemporary distribution of genetic variation in D. viscosa in Australia.
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| 29. |
- Jones, Richard W., et al.
(author)
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A framework for intelligent medical diagnosis using the theory of evidence
- 2002
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In: Knowledge-Based Systems. - 0950-7051 .- 1872-7409. ; 15:1-2, s. 77-84
-
Journal article (peer-reviewed)abstract
- In designing fuzzy logic systems for fault diagnosis, problems can be encountered in the choice of symptoms to use fuzzy operators and an inability to convey the reliability of the diagnosis using just one degree of membership for the conclusion. By turning to an evidential framework, these problems can be resolved whilst still preserving a fuzzy relational model structure. The theory of evidence allows for utilisation of all available information. Relationships between sources of evidence determine appropriate combination rules. By generating belief and plausibility measures it also communicates the reliability of the diagnosis, and completeness of information. In this contribution medical diagnosis is considered using the theory of evidence, in particular the diagnosis of inadequate analgesia is considered
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| 30. |
- Jones, Richard W., et al.
(author)
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Computerised anaesthesia monitoring using fuzzy trend templates
- 2001
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In: Artificial Intelligence in Medicine. - 0933-3657 .- 1873-2860. ; 21:1-3, s. 247-251
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Journal article (peer-reviewed)abstract
- The task of administering anaesthesia requires the clinician to be vigilant for long periods of time to detect the onset of adverse conditions. Large amounts of data must be analysed in real-time and, if a problem is detected, it must be diagnosed as a matter of urgency, this being done while other management protocols are being carried out. For these reasons it would be of benefit if automated decision support could be provided for anaesthesia monitoring, to lighten the cognitive load on the anaesthetist. The Sentinel anaesthesia monitor has been developed with this objective in mind. It uses a fuzzy time-domain pattern matching technique, termed fuzzy trend templates, to detect vaguely specified patterns in multiple physiological data streams. These patterns are representative of symptoms associated with undesirable patient states. The system is capable of detecting trends and states such as 'significant rise' and 'high', and associating vague duration and temporal intervals with individual trends. Fuzzy trend templates have proven to be quite intuitive to specify, given linguistic (anaesthetists') knowledge about the problem domain. Sentinel's implementation of fuzzy trend templates also uses an extension to fuzzy logic based on the theory of evidence, to handle situations where desired information is not available, for example, when sensors are not being used. In off-line testing, Sentinel has achieved sensitivity and specificity of above 90% in the diagnosis of seven common or serious conditions that can arise during anaesthesia
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| 31. |
- Kireta, Dona, et al.
(author)
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Disentangling the evolutionary history of three related shrub species using genome-wide molecular markers
- 2019
-
In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 20:5, s. 1101-1112
-
Journal article (peer-reviewed)abstract
- Understanding population genetic structure provides insight into historic population connectivity, and is largely driven by migration, population size, and species life history. During the last glacial maximum, sea levels around the biogeographically interesting, but poorly studied, South Australian coastal plains and geosyncline were thought to be sufficiently low that three prominent peninsulas (Fleurieu, Yorke, Eyre) and a large offshore island (Kangaroo Island) formed a continuous landmass. However, the degree to which population genetic structure in this region has been shaped by biogeography remains largely untested. Here, we use genome-wide SNP data from three Goodenia shrub species with contrasting growth forms to assess how historical and contemporary processes have shaped population genetic structure. These species occur commonly throughout South Australia and are used extensively in revegetation. The two woody species (Goodenia varia, G. ovata) displayed low genetic differentiation across the southern parts of the peninsulas and island, reflecting historical landscape connectivity. The third more-herbaceous species (G. amplexans) displayed higher genetic structure across the land features, reflecting contemporary disconnectivity. Kangaroo Island and the southern Flinders Ranges had relatively high genetic diversity, providing further evidence that they were important putative Pleistocene refugia. We demonstrate that historic changes in landscape and possible migration to and from refugia, have shaped the population genetic structure in these closely related shrubs, which may have been influenced by contemporary factors and small population sizes. We highlight the importance of using multi-species designs when studying historical population connectivity in understudied regions of the world.
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| 32. |
- Lowe, Andrew, et al.
(author)
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The graphical presentation of decision support information in an intelligent anaesthesia monitor
- 2001
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In: Artificial Intelligence in Medicine. - 0933-3657 .- 1873-2860. ; 22:2, s. 173-191
-
Journal article (peer-reviewed)abstract
- This contribution examines the graphical presentation of decision support information generated by an intelligent monitor, named SENTINEL, developed for use during anaesthesia. Clinicians make diagnoses in real-time during operations by examining clinically significant trends in multiple signals. SENTINEL attempts to mimic this decision process by using a system of fuzzy trend templates. SENTINEL's implementation of fuzzy trend templates is capable of providing the dual fuzzy measures of belief and plausibility, which are derived from the theory of evidence. It is thus capable of generating fairly rich diagnostic decision support information. However, for SENTINEL to be effective, the visual presentation of this information must be intuitive to the anaesthetist, who may not be familiar with the theory of evidence.This paper discusses techniques that are being evaluated to meet the requirements of the SENTINEL anaesthesia monitor. Specifically, the paper presents methods for highlighting clinically significant trends in physiological (or derived) signals by superimposing a coloured band on the signal that reflects fuzzy output from the intelligent monitor. This paper also discusses the intuitive graphical presentation of binary diagnostic fuzzy measures, including their further interpretation and presentation as crisp 'alarm' and 'warning' conditions
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| 33. |
- Nafalski, Andrew, et al.
(author)
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Collaborative Learning in Engineering Remote Laboratories
- 2009
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Conference paper (peer-reviewed)abstract
- This paper reports on practices in national and international on-line cooperation in engineering remote laboratories (RLs) to support student collaborative activities. A structured aid enables them, in addition to acquiring technical skills and knowledge, to develop intercultural communication skills and the global perspectives sought by their profession. The concept of a Community of Practice (CoP) is a central pedagogical consideration for collaborative learning and is discussed in the paper. After reviewing practices of others, an emphasis will be placed on a team-based laboratory environment of NetLab – a remote laboratory framework created at the University of South Australia (UniSA).
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| 34. |
- Solé Navais, Pol, et al.
(author)
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Genetic effects on the timing of parturition and links to fetal birth weight.
- 2023
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In: Nature genetics. - 1546-1718. ; 55:4, s. 559-567
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Journal article (peer-reviewed)abstract
- The timing of parturition is crucial for neonatal survival and infant health. Yet, its genetic basis remains largely unresolved. We present a maternal genome-wide meta-analysis of gestational duration (n=195,555), identifying 22 associated loci (24 independent variants) and an enrichment in genes differentially expressed during labor. A meta-analysis of preterm delivery (18,797 cases, 260,246 controls) revealed six associated loci and large genetic similarities with gestational duration. Analysis of the parental transmitted and nontransmitted alleles (n=136,833) shows that 15 of the gestational duration genetic variants act through the maternal genome, whereas 7 act both through the maternal and fetal genomes and 2 act only via the fetal genome. Finally, the maternal effects on gestational duration show signs of antagonistic pleiotropy with the fetal effects on birth weight: maternal alleles that increase gestational duration have negative fetal effects on birth weight. The present study provides insights into the genetic effects on the timing of parturition and the complex maternal-fetal relationship between gestational duration and birth weight.
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