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Environmental Association Analyses in Plants and the Influence of Methodological DecisionsNARA Subscribed
Climate change is predicted to impact existing ecological systems, leading to a requirement to improve our understanding of environmental adaptation in plants, particularly for conservation and the development of environmentally tolerant crop varieties. Environmental association analyses (EAAs) are a group of landscape genomic methods for detecting genetic markers or genes associated with environmental factors and therefore pr...
Interpretable deep learning reveals spatiotemporal MRI features of brain aging that align with neurodegenerationNARA Subscribed
Cortical thinning and atrophy are hallmarks of brain aging that have been characterized using magnetic resonance imaging (MRI). Brain aging involves many neuroanatomic features whose effects on brain structure remain unexplored. To address this challenge, we trained interpretable deep neural networks (DNNs) to estimate brain age (BA) from T 1 -weighted ( T 1 w) MRI. By identifying MRI features unapparent to humans, DNNs can fi...
Alzheimer’s disease (AD) disproportionately affects women and carriers of the apolipoprotein E ε4 allele (APOE4), yet little is known about how sex and APOE interact to influence white matter (WM) integrity during disease progression. We integrated diffusion MRI and matched blood transcriptomic data to investigate these interactions and their underlying biological mechanisms. WM microstructure was quantified using diffusion te...
Genetic variation and synonymous cultivars in the USDA lychee (Litchi chinensis Sonn.) collection assessed using genome-wide SNPsNARA Subscribed
Lychee ( Litchi chinensis ) fruits have high nutritional and pharmacological value, yet the crop is underutilized on global markets partly due to cultivation problems outside the native area and lack of knowledge/misidentification of cultivars. Using reduced representation sequencing, 78 trees representing 57 cultivars plus 13 trees without varietal names from the USDA lychee collection on Hawai’i were analysed. We aimed to (1...
Energetic benefits of prey choice for a shark-eating sharkNARA Subscribed
The migratory behavior of Atlantic salmon ( Salmo salar ) post‐smolts in coastal waters is poorly understood. In this collaborative study, 1914 smolts, from 25 rivers, in four countries were tagged with acoustic transmitters during a single seasonal migration. In total, 1105 post‐smolts entered the marine study areas and 438 (39.6%) were detected on a network of 414 marine acoustic receivers and an autonomous underwater vehicl...
Predicting the progression of MCI and Alzheimer’s disease on structural brain integrity and other features with machine learningNARA Subscribed
Machine learning (ML) on structural MRI data shows high potential for classifying Alzheimer’s disease (AD) progression, but the specific contribution of brain regions, demographics, and proteinopathy remains unclear. Using Alzheimer’s Disease Neuroimaging Initiative (ADNI) data, we applied an extreme gradient-boosting algorithm and SHAP (SHapley Additive exPlanations) values to classify cognitively normal (CN) older adults, th...
Genome resources for underutilised legume crops: genome sizes, genome skimming and marker developmentNARA Subscribed
Underutilised crops suffer from under-investigation relative to more mainstream crops, but often possess improved stress tolerance and/or nutrition, making them potentially important for breeding programmes in the context of climate change and an expanding human population. Developing basic genome resources for underutilised crops may therefore catalyse analyses to facilitate their use, through improved understanding of popula...
Peatlands are globally important stores of soil carbon (C) formed over millennial timescales but are at risk of destabilization by human and climate disturbance. Pools are ubiquitous features of many peatlands and can contain very high concentrations of C mobilized in dissolved and particulate organic form and as the greenhouses gases carbon dioxide (CO 2 ) and methane (CH 4 ). The radiocarbon content ( 14 C) of these aquatic...
Case study: Applying the resist–accept–direct framework to an Ojibwe Tribe's relationship with the natural worldNARA Subscribed
Ojibwe Tribes' approach to the natural world is guided by the original treaties between beings (species and spirits) and the Ojibwe people who reside in lands now known as the United States and Canada. Relationships with these beings, such as ogaa (walleye Sander vitreus ), are best characterised as taking care of a relative/gift for the next seven generations of Ojibwe. Initial denial of treaty rights by the state government...
Mangrove growth response to experimental warming is greatest near the range limit in northeast FloridaNARA Subscribed
Shrubs are invading into grasslands around the world, but we don’t yet know how these shrubs will fare in a warmer future. In ecotonal coastal wetland ecosystems, woody mangroves are encroaching into herbaceous salt marshes owing to changes in temperature, precipitation, and sediment dynamics. Increasing mangrove biomass in wetlands often increases carbon storage, which is high in these productive ecosystems, but little is kno...
Unravelling plant responses to rising atmospheric CO 2 concentration ([CO 2 ]) has largely focussed on plastic functional attributes to single generation [CO 2 ] exposure. Quantifying the consequences of long‐term, decadal multigenerational exposure to elevated [CO 2 ] and the genetic changes that may underpin evolutionary mechanisms with [CO 2 ] as a driver remain largely unexplored. Here, we investigated both plastic and evo...