Understanding how biodiversity is shaped through time is a fundamental question in biology. Even though tropical rain forests (TRF) represent the most diverse terrestrial biomes on the planet, the ...timing, location and mechanisms of their diversification remain poorly understood. Molecular phylogenies are valuable tools for exploring these issues, but to date most studies have focused only on recent time scales, which minimises their explanatory potential. In order to provide a long-term view of TRF diversification, we constructed the first complete genus-level dated phylogeny of a largely TRF-restricted plant family with a known history dating back to the Cretaceous. Palms (Arecaceae/Palmae) are one of the most characteristic and ecologically important components of TRF worldwide, and represent a model group for the investigation of TRF evolution.
We provide evidence that diversification of extant lineages of palms started during the mid-Cretaceous period about 100 million years ago. Ancestral biome and area reconstructions for the whole family strongly support the hypothesis that palms diversified in a TRF-like environment at northern latitudes. Finally, our results suggest that palms conform to a constant diversification model (the 'museum' model or Yule process), at least until the Neogene, with no evidence for any change in diversification rates even through the Cretaceous/Paleogene mass extinction event.
Because palms are restricted to TRF and assuming biome conservatism over time, our results suggest the presence of a TRF-like biome in the mid-Cretaceous period of Laurasia, consistent with controversial fossil evidence of the earliest TRF. Throughout its history, the TRF biome is thought to have been highly dynamic and to have fluctuated greatly in extent, but it has persisted even during climatically unfavourable periods. This may have allowed old lineages to survive and contribute to the steady accumulation of diversity over time. In contrast to other plant studies, our results suggest that ancient and steady evolutionary processes dating back to the mid-Cretaceous period can contribute, at least in part, to present day species richness in TRF.
Collections‐based research in the genomic era Buerki, Sven; Baker, William J
Biological Journal of the Linnean Society/Biological journal of the Linnean Society,
January 2016, Letnik:
117, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Biological collections are at the front line of biodiversity research, informing taxonomy, evolution, conservation and sustainable livelihoods. In April 2014, we organised a meeting at the Linnean ...Society (UK) discussing the impact of next‐generation sequencing (NGS) methods on collections‐based research. Here, we explore the main themes of this meeting and outline the incredible potential of NGS to reinvent collections‐based research. Among the many opportunities at the interface of genomics and collections, we focus specifically on (1) the genomic characterisation of biological collections, (2) the enhancement and development of DNA‐based identification, (3) the tree of life and (4) interdisciplinary research addressing the most pressing environmental challenges of our times. Across the world, biological collections are at risk, primarily due to declining funding and shifts in scientific fashions. We encourage all users of collections to embrace the genomic era, not only because of the unparalleled scientific potential that it presents, but also because new cross‐disciplinary synergies will reinvigorate and secure the collections for future generations.
18FTHK5351, a recently-developed positron emission tomography (PET) tracer for measuring tau neurofibrillary tangle accumulation, may help researchers examine aging, disease, and tau pathology in ...living human brains. We examined THK5351 tracer pharmacokinetics to define an optimal acquisition time for static late images.
Primary measurements were calculation of regional values of distribution volume ratios (DVR) and standardized uptake value ratios (SUVR) in 6 healthy older control and 10 Alzheimer's disease (AD) participants. We examined associations between DVR and SUVR, searching for a 20 min SUVR time window that was stable and comparable to DVR. We additionally examined diagnostic group differences in this 20 min SUVR.
In healthy controls, 18FTHK5351 uptake was low, with increased temporal relative to frontal binding. In AD, regional uptake was substantially higher than in healthy controls, with temporal exceeding frontal binding. Retention in cerebellar gray matter, which was used as the reference region, was low compared to other regions. Both DVR and SUVR values showed minimal change over time after 40 min. SUVR 20-40, 30-50, and 40-60 min were most consistently correlated with DVR; SUVR 40-60 min, the most stable time window, was used in further analyses. Significant (AD > healthy control) group differences existed in temporoparietal regions, with marginal medial temporal differences. We found high basal ganglia SUVR 40-60 min signal, with no group differences.
We examined THK5351, a new PET tracer for measuring tau accumulation, and compared multiple analysis methods for quantifying regional tracer uptake. SUVR 40-60 min performed optimally when examining 20 min SUVR windows, and appears to be a practical method for quantifying relative regional tracer retention. The results of this study offer clinical potential, given the usefulness of THK5351-PET as a biomarker of tau pathology in aging and disease.
18F-AV-1451 is a leading tracer used with positron emission tomography (PET) to quantify tau pathology. However, 18F-AV-1451 shows “off target” or non-specific binding, which we define as binding of ...the tracer in unexpected areas unlikely to harbor aggregated tau based on autopsy literature 1. Along with caudate, putamen, pallidum and thalamus non-specific binding 2,3, we have found binding in the superior portion of the cerebellar gray matter, leading us to use inferior cerebellar gray as the reference region. We also addressed binding in the posterior portion of the choroid plexus. PET signal unlikely to be associated with tau also occurs in skull, meninges and soft tissue (see e.g. 4). We refer to 18F-AV-1451 binding in the skull and meninges as extra-cortical hotspots (ECH) and find them near lateral and medial orbitofrontal, lateral occipital, inferior and middle temporal, superior and inferior parietal, and inferior cerebellar gray matter. Lastly, the choroid plexus also shows non-specific binding that bleeds into hippocampus. We are providing the code (http://www.runmycode.org/companion/view/2798) used to create different regions of interest (ROIs) that we then used to perform Partial Volume Correction (PVC) using the Rousset geometric transfer matrix method (GTM, 5). This method was used in the companion article, “Comparison of multiple tau-PET measures as biomarkers in aging and Alzheimer's Disease” (6, DOI 10.1016/j.neuroimage.2017.05.058).
A major unanswered question in the dementia field is whether cognitively unimpaired individuals who harbor both Alzheimer's disease neuropathological hallmarks (that is, amyloid-β plaques and tau ...neurofibrillary tangles) can preserve their cognition over time or are destined to decline. In this large multicenter amyloid and tau positron emission tomography (PET) study (n = 1,325), we examined the risk for future progression to mild cognitive impairment and the rate of cognitive decline over time among cognitively unimpaired individuals who were amyloid PET-positive (A
) and tau PET-positive (T
) in the medial temporal lobe (A
T
) and/or in the temporal neocortex (A
T
) and compared them with A
T
and A
T
groups. Cox proportional-hazards models showed a substantially increased risk for progression to mild cognitive impairment in the A
T
(hazard ratio (HR) = 19.2, 95% confidence interval (CI) = 10.9-33.7), A
T
(HR = 14.6, 95% CI = 8.1-26.4) and A
T
(HR = 2.4, 95% CI = 1.4-4.3) groups versus the A
T
(reference) group. Both A
T
(HR = 6.0, 95% CI = 3.4-10.6) and A
T
(HR = 7.9, 95% CI = 4.7-13.5) groups also showed faster clinical progression to mild cognitive impairment than the A
T
group. Linear mixed-effect models indicated that the A
T
(β = -0.056 ± 0.005, T = -11.55, P < 0.001), A
T
(β = -0.024 ± 0.005, T = -4.72, P < 0.001) and A
T
(β = -0.008 ± 0.002, T = -3.46, P < 0.001) groups showed significantly faster longitudinal global cognitive decline compared to the A
T
(reference) group (all P < 0.001). Both A
T
(P < 0.001) and A
T
(P = 0.002) groups also progressed faster than the A
T
group. In summary, evidence of advanced Alzheimer's disease pathological changes provided by a combination of abnormal amyloid and tau PET examinations is strongly associated with short-term (that is, 3-5 years) cognitive decline in cognitively unimpaired individuals and is therefore of high clinical relevance.
Few studies have evaluated the relationship between in vivo18F-flortaucipir PET and post-mortem pathology. We sought to compare antemortem 18F-flortaucipir PET to neuropathology in a consecutive ...series of patients with a broad spectrum of neurodegenerative conditions. Twenty patients were included mean age at PET 61 years (range 34-76); eight female; median PET-to-autopsy interval of 30 months (range 4-59 months). Eight patients had primary Alzheimer's disease pathology, nine had non-Alzheimer tauopathies (progressive supranuclear palsy, corticobasal degeneration, argyrophilic grain disease, and frontotemporal lobar degeneration with MAPT mutations), and three had non-tau frontotemporal lobar degeneration. Using an inferior cerebellar grey matter reference, 80-100-min 18F-flortaucipir PET standardized uptake value ratio (SUVR) images were created. Mean SUVRs were calculated for progressive supranuclear palsy, corticobasal degeneration, and neurofibrillary tangle Braak stage regions of interest, and these values were compared to SUVRs derived from young, non-autopsy, cognitively normal controls used as a standard for tau negativity. W-score maps were generated to highlight areas of increased tracer retention compared to cognitively normal controls, adjusting for age as a covariate. Autopsies were performed blinded to PET results. There was excellent correspondence between areas of 18F-flortaucipir retention, on both SUVR images and W-score maps, and neurofibrillary tangle distribution in patients with primary Alzheimer's disease neuropathology. Patients with non-Alzheimer tauopathies and non-tau frontotemporal lobar degeneration showed a range of tracer retention that was less than Alzheimer's disease, though higher than age-matched, cognitively normal controls. Overall, binding across both tau-positive and tau-negative non-Alzheimer disorders did not reliably correspond with post-mortem tau pathology. 18F-flortaucipir SUVRs in subcortical regions were higher in autopsy-confirmed progressive supranuclear palsy and corticobasal degeneration than in controls, but were similar to values measured in Alzheimer's disease and tau-negative neurodegenerative pathologies. Quantification of 18F-flortaucipir SUVR images at Braak stage regions of interest reliably detected advanced Alzheimer's (Braak VI) pathology. However, patients with earlier Braak stages (Braak I-IV) did not show elevated tracer uptake in these regions compared to young, tau-negative controls. In summary, PET-to-autopsy comparisons confirm that 18F-flortaucipir PET is a reliable biomarker of advanced Braak tau pathology in Alzheimer's disease. The tracer cannot reliably differentiate non-Alzheimer tauopathies and may not detect early Braak stages of neurofibrillary tangle pathology.
Improving the reproducibility of biomedical research is a major challenge. Transparent and accurate reporting is vital to this process; it allows readers to assess the reliability of the findings and ...repeat or build upon the work of other researchers. The ARRIVE guidelines (Animal Research: Reporting In Vivo Experiments) were developed in 2010 to help authors and journals identify the minimum information necessary to report in publications describing in vivo experiments. Despite widespread endorsement by the scientific community, the impact of ARRIVE on the transparency of reporting in animal research publications has been limited. We have revised the ARRIVE guidelines to update them and facilitate their use in practice. The revised guidelines are published alongside this paper. This explanation and elaboration document was developed as part of the revision. It provides further information about each of the 21 items in ARRIVE 2.0, including the rationale and supporting evidence for their inclusion in the guidelines, elaboration of details to report, and examples of good reporting from the published literature. This document also covers advice and best practice in the design and conduct of animal studies to support researchers in improving standards from the start of the experimental design process through to publication.
Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal ...research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work adequately, evaluate its methodological rigour, and reproduce the methods and results. Despite considerable levels of endorsement by funders and journals over the years, adherence to the guidelines has been inconsistent, and the anticipated improvements in the quality of reporting in animal research publications have not been achieved. Here, we introduce ARRIVE 2.0. The guidelines have been updated and information reorganised to facilitate their use in practice. We used a Delphi exercise to prioritise and divide the items of the guidelines into 2 sets, the “ARRIVE Essential 10,” which constitutes the minimum requirement, and the “Recommended Set,” which describes the research context. This division facilitates improved reporting of animal research by supporting a stepwise approach to implementation. This helps journal editors and reviewers verify that the most important items are being reported in manuscripts. We have also developed the accompanying Explanation and Elaboration document, which serves (1) to explain the rationale behind each item in the guidelines, (2) to clarify key concepts, and (3) to provide illustrative examples. We aim, through these changes, to help ensure that researchers, reviewers, and journal editors are better equipped to improve the rigour and transparency of the scientific process and thus reproducibility.
Shifts in species' distribution and abundance in response to climate change have been well documented, but the underpinning processes are still poorly understood. We present the results of a ...systematic literature review and meta‐analysis investigating the frequency and importance of different mechanisms by which climate has impacted natural populations. Most studies were from temperate latitudes of North America and Europe; almost half investigated bird populations. We found significantly greater support for indirect, biotic mechanisms than direct, abiotic mechanisms as mediators of the impact of climate on populations. In addition, biotic effects tended to have greater support than abiotic factors in studies of species from higher trophic levels. For primary consumers, the impact of climate was equally mediated by biotic and abiotic mechanisms, whereas for higher level consumers the mechanisms were most frequently biotic, such as predation or food availability. Biotic mechanisms were more frequently supported in studies that reported a directional trend in climate than in studies with no such climatic change, although sample sizes for this comparison were small. We call for more mechanistic studies of climate change impacts on populations, particularly in tropical systems.
Tau pathology first appears in the transentorhinal and anterolateral entorhinal cortex (alEC) in the aging brain. The transition to Alzheimer's disease (AD) is hypothesized to involve amyloid-β (Aβ) ...facilitated tau spread through neural connections. We contrasted functional connectivity (FC) of alEC and posteromedial EC (pmEC), subregions of EC that differ in functional specialization and cortical connectivity, with the hypothesis that alEC-connected cortex would show greater tau deposition than pmEC-connected cortex. We used resting state fMRI to measure FC, and PET to measure tau and Aβ in cognitively normal older adults. Tau preferentially deposited in alEC-connected cortex compared to pmEC-connected or non-connected cortex, and stronger connectivity was associated with increased tau deposition. FC-tau relationships were present regardless of Aβ, although strengthened with Aβ. These results provide an explanation for the anatomic specificity of neocortical tau deposition in the aging brain and reveal relationships between normal aging and the evolution of AD.
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