Implications from molecular phylogenetic data for systematics, biogeography and growth form evolution of Thottea (Aristolochiaceae)

Volume: 63Start Page: 259End Page: 27

The emergence of earliest angiosperms may be earlier than fossil evidence indicates

Gaps between molecular ages and fossils undermine the validity of time-calibrated molecular phylogenies. An example of the time gap surrounds the age of angiosperms' origin. We calculate molecular ages of the earliest flowering plant lineages using 22 fossil calibrations (101 genera, 40 families). Our results reveal the origin of angiosperms at the late Permian,; 275 million years ago. Different prior probability curves of molecular age calculations on dense calibration point distributions had little effect on overall age estimates compared to the effects of altered calibration points. The same is true for reasonable root age constraints. We conclude that our age estimates based on multiple datasets, priors, and calibration points are robust and the true ages are likely between our extremes. Our results, when integrated with the ecophysiological evolution of early angiosperms, imply that the ecology of the earliest angiosperms is critical to understand the pre-Cretaceous evolution of flowering plants

Data from: The emergence of earliest angiosperms may be earlier than fossil evidence indicates

Gaps between molecular ages and fossils undermine the validity of time-calibrated molecular phylogenies. An example of the time gap surrounds the age of angiosperms' origin. We calculate molecular ages of the earliest flowering plant lineages using 22 fossil calibrations (101 genera, 40 families). Our results reveal the origin of angiosperms at the late Permian, ∼275 million years ago. Different prior probability curves of molecular age calculations on dense calibration point distributions had little effect on overall age estimates compared to the effects of altered calibration points. The same is true for reasonable root age constraints. We conclude that our age estimates based on multiple datasets, priors, and calibration points are robust and the true ages are likely between our extremes. Our results, when integrated with the ecophysiological evolution of early angiosperms, imply that the ecology of the earliest angiosperms is critical to understand the pre-Cretaceous evolution of flowering plants

The emergence of earliest angiosperms may be earlier than fossil evidence indicates

Gaps between molecular ages and fossils undermine the validity of time-calibrated molecular phylogenies. An example of the time gap surrounds the age of angiosperms' origin. We calculate molecular ages of the earliest flowering plant lineages using 22 fossil calibrations (101 genera, 40 families). Our results reveal the origin of angiosperms at the late Permian,; 275 million years ago. Different prior probability curves of molecular age calculations on dense calibration point distributions had little effect on overall age estimates compared to the effects of altered calibration points. The same is true for reasonable root age constraints. We conclude that our age estimates based on multiple datasets, priors, and calibration points are robust and the true ages are likely between our extremes. Our results, when integrated with the ecophysiological evolution of early angiosperms, imply that the ecology of the earliest angiosperms is critical to understand the pre-Cretaceous evolution of flowering plants

Present trans-Pacific disjunct distribution of Aristolochia subgenus Isotrema (Aristolochiaceae) was shaped by dispersal, vicariance and extinction

International audienceAim: Isotrema is a monophyletic subgenus of Aristolochia with species in East Asia and North/Central America. Earlier studies, based on limited sampling, suggested that the Asian and American species do not form two reciprocal sister clades. We reconstructed phylogenetic relationships within Isotrema to infer the biogeographical events that have shaped its present-day distribution. Location: Eastern Asia, North America, Mexico, Central America. Methods: We performed parsimony and Bayesian phylogenetic analyses of 54 accessions using three chloroplast regions. The temporal origins were traced with relaxed phylogenetics and penalized likelihood using fossil calibrations; these methods were combined with ancestral area reconstructions in a comparative approach using statistical dispersal-vicariance analysis (S-DIVA) and dispersal-extinction-cladogenesis (DEC) analyses. Results: The ancestors of the herbaceous eastern North American species and the woody species probably diverged during the Oligocene. The woody species form a Neotropical and a North American/Eastern Asian clade. Diversification in the Neotropical and North American/Eastern Asian clades occurred mostly in the Miocene. In the latter clade, two further intercontinental splits are reconstructed: between the exclusively western North American Aristolochia californica and most of the Asian taxa, and between A. manshuriensis and A. tomentosa. Main conclusions : The present distribution of Isotrema developed via a number of dispersal, vicariance and extinction events. The disjunct distributions observed may be the result mainly of non-synchronous events (e.g. a decrease of mean annual temperature in the Oligocene and the development of unfavourable conditions across the Bering land bridge) that were responsible for the fragmentation of the mesophytic forests. Later diversifications may be correlated with events such as the orogeny of the Western Cordillera and Appalachian Mountains, the development of extensive grasslands in North America, and the mainland extension of Central America southwards to western and central Panam

Urinary MicroRNAs as Potential Markers for Non-Invasive Diagnosis of Bladder Cancer

Currently, voided urine cytology (VUC) serves as the gold standard for the detection of bladder cancer (BCa) in urine. Despite its high specificity, VUC has shortcomings in terms of sensitivity. Therefore, alternative biomarkers are being searched, which might overcome these disadvantages as a useful adjunct to VUC. The aim of this study was to evaluate the diagnostic potential of the urinary levels of selected microRNAs (miRs), which might represent such alternative biomarkers due to their BCa-specific expression. Expression levels of nine BCa-associated microRNAs (miR-21, -96, -125b, -126, -145, -183, -205, -210, -221) were assessed by quantitative PCR in urine sediments from 104 patients with primary BCa and 46 control subjects. Receiver operating characteristic (ROC) curve analyses revealed a diagnostic potential for miR-96, -125b, -126, -145, -183, and -221 with area under the curve (AUC) values between 0.605 and 0.772. The combination of the four best candidates resulted in sensitivity, specificity, positive and negative predictive values (NPV), and accuracy of 73.1%, 95.7%, 97.4%, 61.1%, and 80.0%, respectively. Combined with VUC, sensitivity and NPV could be increased by nearly 8%, each surpassing the performance of VUC alone. The present findings suggested a diagnostic potential of miR-125b, -145, -183, and -221 in combination with VUC for non-invasive detection of BCa in urine

Table S2

Regions removed from the alignment of DNA sequences and rationale for the removal

BA Method Paper combined 2 with hotspots 17.06.2013

combined data, indels include

BA Method Paper combined 2 without hotspots 21.06.2013

combined data indels exclude