Speciation dynamics during the global radiation of extant bats

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/1/evo12681-sup-0008-FIGURE7.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/2/evo12681-sup-0003-FIGURE2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/3/evo12681.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/4/evo12681-sup-0002-FIGURE1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/5/evo12681-sup-0009-FIGURE8.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/6/evo12681-sup-0007-FIGURE6.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/7/evo12681-sup-0006-FIGURE5.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/8/evo12681-sup-0004-FIGURE3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/9/evo12681-sup-0005-FIGURE4.pd

Ecomorphological and phylogenetic controls on sympatry across extant bats

AimMacroecological patterns of sympatry can inform our understanding of how ecological and evolutionary processes govern species distributions. Following speciation, both intrinsic and extrinsic factors may determine how readily sympatry occurs. One possibility is that sympatry most readily occurs with ecological divergence, especially if broad‐scale co‐occurrence is mediated by niche differentiation. Time since divergence may also predict sympatry if hybridization and gene flow lead to the collapse of species boundaries between closely related taxa. Here, we test for ecological and phylogenetic predictors of sympatry across the global radiation of extant bats.LocationGlobal.TaxonBats (Order Chiroptera).MethodsWe used a combination of linear mixed‐modelling, simulations and maximum‐likelihood modelling to test whether phylogenetic and ecomorphological divergence between species predict sympatry. We further assess how these relationships vary based on biogeographic realm.ResultsWe find that time since divergence does not predict sympatry in any biogeographic realm. Morphological divergence is negatively related to sympatry in the Neotropics, but shows no relationship with sympatry elsewhere.Main conclusionsWe find that bats in most biogeographic realms co‐occur at broad spatial scales regardless of phylogenetic similarity. Neotropical bats, however, appear to co‐occur most readily when morphologically similar. To the extent that pairwise phylogenetic and morphological divergence reflect ecological differentiation, our results suggest that abiotic and environmental factors may be more important than species interactions in determining patterns of sympatry across bats.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/144581/1/jbi13353-sup-0005-FigureS5.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144581/2/jbi13353.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144581/3/jbi13353-sup-0006-FigureS6.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144581/4/jbi13353-sup-0003-FigureS3.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144581/5/jbi13353-sup-0004-FigureS4.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144581/6/jbi13353_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144581/7/jbi13353-sup-0002-FigureS2.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144581/8/jbi13353-sup-0001-FigureS1.pd

Synthesis of freestanding HfO2 nanostructures

Two new methods for synthesizing nanostructured HfO2 have been developed. The first method entails exposing HfTe2 powders to air. This simple process resulted in the formation of nanometer scale crystallites of HfO2. The second method involved a two-step heating process by which macroscopic, freestanding nanosheets of HfO2 were formed as a byproduct during the synthesis of HfTe2. These highly two-dimensional sheets had side lengths measuring up to several millimeters and were stable enough to be manipulated with tweezers and other instruments. The thickness of the sheets ranged from a few to a few hundred nanometers. The thinnest sheets appeared transparent when viewed in a scanning electron microscope. It was found that the presence of Mn enhanced the formation of HfO2 by exposure to ambient conditions and was necessary for the formation of the large scale nanosheets. These results present new routes to create freestanding nanostructured hafnium dioxide

An Integrative Model for Soil Biogeochemistry and Methane Processes: I. Model Structure and Sensitivity Analysis

Environmental changes are anticipated to generate substantial impacts on carbon cycling in peatlands, affecting terrestrial-climate feedbacks. Understanding how peatland methane (CH4) fluxes respond to these changing environments is critical for predicting the magnitude of feedbacks from peatlands to global climate change. To improve predictions of CH4 fluxes in response to changes such as elevated atmospheric CO2 concentrations and warming, it is essential for Earth system models to include increased realism to simulate CH4 processes in a more mechanistic way. To address this need, we incorporated a new microbial-functional group-based CH4 module into the Energy Exascale Earth System land model (ELM) and tested it with multiple observational data sets at an ombrotrophic peatland bog in northern Minnesota. The model is able to simulate observed land surface CH4 fluxes and fundamental mechanisms contributing to these throughout the soil profile. The model reproduced the observed vertical distributions of dissolved organic carbon and acetate concentrations. The seasonality of acetoclastic and hydrogenotrophic methanogenesis—two key processes for CH4 production—and CH4 concentration along the soil profile were accurately simulated. Meanwhile, the model estimated that plant-mediated transport, diffusion, and ebullition contributed to ∼23.5%, 15.0%, and 61.5% of CH4 transport, respectively. A parameter sensitivity analysis showed that CH4 substrate and CH4 production were the most critical mechanisms regulating temporal patterns of surface CH4 fluxes both under ambient conditions and warming treatments. This knowledge will be used to improve Earth system model predictions of these high-carbon ecosystems from plot to regional scales

Unmanned Aerial Vehicles for High-Throughput Phenotyping and Agronomic Research

Advances in automation and data science have led agriculturists to seek real-time, high-quality, high-volume crop data to accelerate crop improvement through breeding and to optimize agronomic practices. Breeders have recently gained massive data-collection capability in genome sequencing of plants. Faster phenotypic trait data collection and analysis relative to genetic data leads to faster and better selections in crop improvement. Furthermore, faster and higher-resolution crop data collection leads to greater capability for scientists and growers to improve precision-agriculture practices on increasingly larger farms; e.g., site-specific application of water and nutrients. Unmanned aerial vehicles (UAVs) have recently gained traction as agricultural data collection systems. Using UAVs for agricultural remote sensing is an innovative technology that differs from traditional remote sensing in more ways than strictly higher-resolution images; it provides many new and unique possibilities, as well as new and unique challenges. Herein we report on processes and lessons learned from year 1-the summer 2015 and winter 2016 growing seasons-of a large multidisciplinary project evaluating UAV images across a range of breeding and agronomic research trials on a large research farm. Included are team and project planning, UAV and sensor selection and integration, and data collection and analysis workflow. The study involved many crops and both breeding plots and agronomic fields. The project's goal was to develop methods for UAVs to collect high-quality, high-volume crop data with fast turnaround time to field scientists. The project included five teams: Administration, Flight Operations, Sensors, Data Management, and Field Research. Four case studies involving multiple crops in breeding and agronomic applications add practical descriptive detail. Lessons learned include critical information on sensors, air vehicles, and configuration parameters for both. As the first and most comprehensive project of its kind to date, these lessons are particularly salient to researchers embarking on agricultural research with UAVs

Scientific imperatives, clinical implications, and theoretical underpinnings for the investigation of the relationship between genetic variables and patient-reported quality-of-life outcomes

Objectives There is emerging evidence for a genetic basis of patient-reported quality-of-life (QOL) outcomes that can ultimately be incorporated into clinical research and practice. Objectives are (1) to provide arguments for the timeliness of investigating the genetic basis of QOL given the scientific advances in genetics and patient-reported QOL research; (2) to describe the clinical implications of such investigations; (3) to present a theoretical foundation for investigating the genetic underpinnings of QOL; and (4) to describe a series of papers resulting from the GENEQOL Consortium that was established to move this work forward. Methods Discussion of scientific advances based on relevant literature. Results In genetics, technological advances allow for increases in speed and efficiency and decreases in costs in exploring the genetic underpinnings of disease processes, drug metabolism, treatment response, and survival. In patient-based research, advances yield empirically based and stringent approaches to measurement that are scientifically robust. Insights into the genetic basis of QOL will ultimately allow early identification of patients susceptible to QOL deficits and to target care. The Wilson and Cleary model for patient-reported outcomes was refined by incorporating the genetic underpinnings of QOL. Conclusions This series of papers provides a path for QOL and genetics researchers to work together to move this field forward and to unravel the intricate interplay of the genetic underpinnings of patient-reported QOL outcomes. The ultimate result will be a greater understanding of the process relating disease, patient, and doctor that will have the potential to lead to improved survival, QOL, and health services deliver

The establishment of the GENEQOL consortium to investigate the genetic disposition of patient-reported quality-of-life outcomes

To our knowledge, no comprehensive, interdisciplinary initiatives have been taken to examine the role of genetic variants on patient-reported quality-of-life outcomes. The overall objective of this paper is to describe the establishment of an international and interdisciplinary consortium, the GENEQOL Consortium, which intends to investigate the genetic disposition of patient-reported quality-of-life outcomes. We have identified five primary patient-reported quality-of-life outcomes as initial targets: negative psychological affect, positive psychological affect, self-rated physical health, pain, and fatigue. The first tangible objective of the GENEQOL Consortium is to develop a list of potential biological pathways, genes and genetic variants involved in these quality-of-life outcomes, by reviewing current genetic knowledge. The second objective is to design a research agenda to investigate and validate those genes and genetic variants of patient-reported quality-of-life outcomes, by creating large datasets. During its first meeting, the Consortium has discussed draft summary documents addressing these questions for each patient-reported quality-of-life outcome. A summary of the primary pathways and robust findings of the genetic variants involved is presented here. The research agenda outlines possible research objectives and approaches to examine these and new quality-of-life domains. Intriguing questions arising from this endeavor are discussed. Insight into the genetic versus environmental components of patient-reported quality-of-life outcomes will ultimately allow us to explore new pathways for improving patient care. If we can identify patients who are susceptible to poor quality of life, we will be able to better target specific clinical interventions to enhance their quality of life and treatment outcome

In-Silico Patterning of Vascular Mesenchymal Cells in Three Dimensions

Cells organize in complex three-dimensional patterns by interacting with proteins along with the surrounding extracellular matrix. This organization provides the mechanical and chemical cues that ultimately influence a cell's differentiation and function. Here, we computationally investigate the pattern formation process of vascular mesenchymal cells arising from their interaction with Bone Morphogenic Protein-2 (BMP-2) and its inhibitor, Matrix Gla Protein (MGP). Using a first-principles approach, we derive a reaction-diffusion model based on the biochemical interactions of BMP-2, MGP and cells. Simulations of the model exhibit a wide variety of three-dimensional patterns not observed in a two-dimensional analysis. We demonstrate the emergence of three types of patterns: spheres, tubes, and sheets, and show that the patterns can be tuned by modifying parameters in the model such as the degradation rates of proteins and chemotactic coefficient of cells. Our model may be useful for improved engineering of three-dimensional tissue structures as well as for understanding three dimensional microenvironments in developmental processes.National Institutes of Health (U.S.) (GM69811)United States. Dept. of Energy (DOE CSGF fellowship

Development, standardization and refinement of procedures for evaluating effects of endocrine active compounds on development and sexual differentiation of Xenopus laevis

Xenopus laevis has been introduced as a model to study effects of endocrine-active compounds (EAC) on development and sexual differentiation. However, variable and inconsistent data have raised questions about the reliability of the test methods applied. The current study was conducted in two laboratories to develop, refine, and standardize procedures and protocols. Larvae were exposed in flow-through systems to 17β-estradiol (E2), at concentrations from 0.2 to 6.0 μg E2 L−1 in Experiment 1A, and 0.015 to 2.0 μg E2 L−1 in Experiment 1B. In both studies survival (92%, 99%) and percentage of animals that completed metamorphosis (97%, 99%) indicated reproducible biological performance. Furthermore, minor variations in husbandry led to significant differences in snout-to-vent length, weight, and gonad size. In Experiment 1A, almost complete feminization occurred in all E2 treatment groups whereas a concentration response was observed in Experiment 1B resulting in an EC50 of 0.12 μg E2 L−1. The final verified protocol is suitable for determining effects of EAC on development and sexual differentiation in X. laevis