Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness.

Target capture sequencing effectively generates molecular marker arrays useful for molecular systematics. These extensive data sets are advantageous where previous studies using a few loci have failed to resolve relationships confidently. Moreover, target capture is well-suited to fragmented source DNA, allowing data collection from species that lack fresh tissues. Herein we use target capture to generate data for a phylogeny of the avian family Pipridae (manakins), a group that has been the subject of many behavioral and ecological studies. Most manakin species feature lek mating systems, where males exhibit complex behavioral displays including mechanical and vocal sounds, coordinated movements of multiple males, and high speed movements. We analyzed thousands of ultraconserved element (UCE) loci along with a smaller number of coding exons and their flanking regions from all but one species of Pipridae. We examined three different methods of phylogenetic estimation (concatenation and two multispecies coalescent methods). Phylogenetic inferences using UCE data yielded strongly supported estimates of phylogeny regardless of analytical method. Exon probes had limited capability to capture sequence data and resulted in phylogeny estimates with reduced support and modest topological differences relative to the UCE trees, although these conflicts had limited support. Two genera were paraphyletic among all analyses and data sets, with Antilophia nested within Chiroxiphia and Tyranneutes nested within Neopelma. The Chiroxiphia-Antilophia clade was an exception to the generally high support we observed; the topology of this clade differed among analyses, even those based on UCE data. To further explore relationships within this group, we employed two filtering strategies to remove low-information loci. Those analyses resulted in distinct topologies, suggesting that the relationships we identified within Chiroxiphia-Antilophia should be interpreted with caution. Despite the existence of a few continuing uncertainties, our analyses resulted in a robust phylogenetic hypothesis of the family Pipridae that provides a comparative framework for future ecomorphological and behavioral studies.

The evolution of a tropical biodiversity hotspot.

The tropics are the source of most biodiversity yet inadequate sampling obscures answers to fundamental questions about how this diversity evolves. We leveraged samples assembled over decades of fieldwork to study diversification of the largest tropical bird radiation, the suboscine passerines. Our phylogeny, estimated using data from 2389 genomic regions in 1940 individuals of 1283 species, reveals that peak suboscine species diversity in the Neotropics is not associated with high recent speciation rates but rather with the gradual accumulation of species over time. Paradoxically, the highest speciation rates are in lineages from regions with low species diversity, which are generally cold, dry, unstable environments. Our results reveal a model in which species are forming faster in environmental extremes but have accumulated in moderate environments to form tropical biodiversity hotspots.

A Comparison of Methods for High-Spatial-Resolution Diffusion-weighted Imaging in Breast MRI.

Background Diffusion-weighted imaging (DWI) shows promise in detecting and monitoring breast cancer, but standard spin-echo (SE) echo-planar DWI methods often have poor image quality and low spatial resolution. Proposed alternatives include readout-segmented (RS) echo-planar imaging and axially reformatted (AR)-simultaneous multislice (SMS) imaging. Purpose To compare the resolution and image quality of standard SE echo-planar imaging DWI with two high-spatial-resolution alternatives, RS echo-planar and AR-SMS imaging, for breast imaging. Materials and Methods In a prospective study (2016-2018), three 5-minute DWI protocols were acquired at 3.0 T, including standard SE echo-planar imaging, RS echo-planar imaging with five segments, and AR-SMS imaging with four times slice acceleration. Participants were women undergoing breast MRI either as part of a treatment response clinical trial or undergoing breast MRI for screening or suspected cancer. A commercial breast phantom was imaged for resolution comparison. Three breast radiologists reviewed images in random order, including clinical images indicating the lesion, images with b value of 800 sec/mm2, and apparent diffusion coefficient (ADC) maps from the three randomly labeled DWI methods. Readers measured the longest dimension and lesion-average ADC on three DWI methods, reported measurement confidence, and rated or ranked the quality of each image. The scores were fit to a linear mixed-effects model with intercepts for reader and subject. Results The smallest feature (1 mm) was only detectible in a phantom on images from AR-SMS DWI. Thirty lesions from 28 women (mean age, 50 years ± 13 [standard deviation]) were evaluated. On the five-point Likert scale for image quality, AR-SMS imaging scored 1.31 points higher than SE echo-planar imaging and 0.74 points higher than RS echo-planar imaging, whereas RS echo-planar imaging scored 0.57 points higher than SE echo-planar imaging (all P < .001). Conclusion The axially reformatted simultaneous multislice protocol was rated highest for image quality, followed by the readout-segmented echo-planar imaging protocol. Both were rated higher than the standard spin-echo echo-planar imaging. © RSNA, 2020 Online supplemental material is available for this article. See also the editorial by Partridge in this issue.

Why is Amazonia a 'source' of biodiversity? Climate-mediated dispersal and synchronous speciation across the Andes in an avian group (Tityrinae).

Amazonia is a 'source' of biodiversity for other Neotropical ecosystems, but which conditions trigger in situ speciation and emigration is contentious. Three hypotheses for how communities have assembled include (1) a stochastic model wherein chance dispersal events lead to gradual emigration and species accumulation, (2) diversity-dependence wherein successful dispersal events decline through time due to ecological limits, and (3) barrier displacement wherein environmental change facilitates dispersal to other biomes via transient habitat corridors. We sequenced thousands of molecular markers for the Neotropical Tityrinae (Aves) and applied a novel filtering protocol to identify loci with high utility for dated phylogenomics. We used these loci to estimate divergence times and model Tityrinae's evolutionary history. We detected a prominent role for speciation driven by barriers including synchronous speciation across the Andes and found that dispersal increased toward the present. Because diversification was continuous but dispersal was non-random over time, we show that barrier displacement better explains Tityrinae's history than stochasticity or diversity-dependence. We propose that Amazonia is a source of biodiversity because (1) it is a relic of a biome that was once more extensive, (2) environmentally mediated corridors facilitated emigration and (3) constant diversification is attributed to a spatially heterogeneous landscape that is perpetually dynamic through time.

Nyquist ghost correction of breast diffusion weighted imaging using referenceless methods.

PURPOSE: Correction of Nyquist ghosts for single-shot spin-echo EPI using the standard 3-line navigator often fails in breast DWI because of incomplete fat suppression, respiration, and greater B0 inhomogeneity. The purpose of this work is to compare the performance of the 3-line navigator with 4 data-driven methods termed "referenceless methods," including 2 previously proposed in literature, 1 introduced in this work, and finally a combination of all 3, in breast DWI. METHODS: Breast DWI was acquired for 41 patients with SS SE-EPI. Raw data was corrected offline with the standard 3-line navigator and 4 referenceless methods, which modeled the ghost as a linear phase error and minimized 3 unique cost functions as well as the median solution of all 3. Ghost levels were evaluated based on the signal intensity in the background region, defined by a mask auto-generated from a T1 -weighted anatomical image. Ghost intensity measurements were fit to a linear mixed model including ghost correction method and b-value as covariates. RESULTS: All 4 referenceless methods outperformed the standard 3-line navigator with statistical significance at all 4 b-values tested (b = 0, 100, 600, and 800 s/mm2 ). CONCLUSIONS: Referenceless methods provide a robust way to reduce Nyquist ghosts in breast DWI without the need for any additional calibration scan.

Quantitative in vivo neurochemical profiling in humans: where are we now?

Proton nuclear magnetic resonance spectroscopy of biofluids has become one of the key techniques for metabolic profiling and phenotyping. This technique has been widely used in a number of epidemiological studies and in a variety of health disorders. However, its utilization in brain disorders is limited due to the blood-brain barrier, which not only protects the brain from unwanted substances in the blood, but also substantially limits the potential of finding biomarkers for neurological disorders in serum. This review article focuses on the potential of localized in vivo proton magnetic resonance spectroscopy (1H-MRS) for non-invasive neurochemical profiling in the human brain. First, methodological aspects of 1H-MRS (data acquisition, processing and metabolite quantification) that are essential for reliable non-invasive neurochemical profiling are described. Second, the power of 1H-MRS-based neurochemical profiling is demonstrated using some examples of its application in neuroscience and neurology. Finally, the authors present their vision and propose necessary steps to establish 1H-MRS as a method suitable for large-scale neurochemical profiling in epidemiological research.

Improved receiver arrays and optimized parallel imaging accelerations applied to time-resolved 3D fluoroscopically tracked peripheral runoff CE-MRA.

OBJECTIVES: Three-station stepping-table time-resolved 3D contrast-enhanced magnetic resonance angiography has conflicting demands in the need to limit acquisition time in proximal stations to match the speed of the advancing contrast bolus and in the distal-most station to avoid venous contamination while still providing clinically useful spatial resolution. This work describes improved receiver coil arrays which address this issue by allowing increased acceleration factors, providing increased spatial resolution per unit time. MATERIALS AND METHODS: Receiver coil arrays were constructed for each station (pelvis, thigh, calf) and then integrated into a 48-element array for three-station peripheral CE-MRA. Coil element sizes and array configurations for these three stations were designed to improve SENSE-type parallel imaging taking advantage of an increase in coil count for all stations versus the previous 32 channel capability. At each station either acceleration apportionment or optimal CAIPIRINHA selection was used to choose the optimum acceleration parameters for each subject. Results were evaluated in both single- and multi-station studies. RESULTS: Single-station studies showed that SENSE acceleration in the thigh station could be readily increased from R=8 to R=10, allowing reduction of the frame time from 2.5 to 2.1 s to better image the typically rapidly advancing bolus at this station. Similarly, the improved coil array for the calf station permitted acceleration increase from R=8 to R=12, providing a 4.0 vs. 5.2 s frame time. Results in three-station studies suggest an improved ability to track the contrast bolus in peripheral CE-MRA. CONCLUSIONS: Modified receiver coil arrays and individualized parameter optimization have been used to provide improved acceleration at all stations in multi-station peripheral CE-MRA and provide high spatial resolution with frame times as short as 2.1 s.