University of California, Davis

About: University of California, Davis is a education organization based out in Davis, California, United States. It is known for research contribution in the topics: Population & Gene. The organization has 78770 authors who have published 180033 publications receiving 8064158 citations. The organization is also known as: UC Davis & UCD.

Bayes or Bootstrap? A Simulation Study Comparing the Performance of Bayesian Markov Chain Monte Carlo Sampling and Bootstrapping in Assessing Phylogenetic Confidence

Abstract: Bayesian Markov chain Monte Carlo sampling has become increasingly popular in phylogenetics as a method for both estimating the maximum likelihood topology and for assessing nodal confidence. Despite the growing use of posterior probabilities, the relationship between the Bayesian measure of confidence and the most commonly used confidence measure in phylogenetics, the nonparametric bootstrap proportion, is poorly understood. We used computer simulation to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony bootstrap proportion (MP-BP). We simulated the evolution of DNA sequence on 17-taxon topologies under 18 evolutionary scenarios and examined the performance of these methods in assigning confidence to correct monophyletic and incorrect monophyletic groups, and we examined the effects of increasing character number on support value. BMCMC-PP and ML-BP were often strongly correlated with one another but could provide substantially different estimates of support on short internodes. In contrast, BMCMC-PP correlated poorly with MP-BP across most of the simulation conditions that we examined. For a given threshold value, more correct monophyletic groups were supported by BMCMC-PP than by either ML-BP or MP-BP. When threshold values were chosen that fixed the rate of accepting incorrect monophyletic relationship as true at 5%, all three methods recovered most of the correct relationships on the simulated topologies, although BMCMC-PP and ML-BP performed better than MP-BP. BMCMC-PP was usually a less biased predictor of phylogenetic accuracy than either bootstrapping method. BMCMC-PP provided high support values for correct topological bipartitions with fewer characters than was needed for nonparametric bootstrap.

Loss of functional diversity under land use intensification across multiple taxa.

Abstract: Land use intensification can greatly reduce species richness and ecosystem functioning. However, species richness determines ecosystem functioning through the diversity and values of traits of species present. Here, we analyze changes in species richness and functional diversity (FD) at varying agricultural land use intensity levels. We test hypotheses of FD responses to land use intensification in plant, bird, and mammal communities using trait data compiled for 1600+ species. To isolate changes in FD from changes in species richness we compare the FD of communities to the null expectations of FD values. In over one-quarter of the bird and mammal communities impacted by agriculture, declines in FD were steeper than predicted by species number. In plant communities, changes in FD were indistinguishable from changes in species richness. Land use intensification can reduce the functional diversity of animal communities beyond changes in species richness alone, potentially imperiling provisioning of ecosystem services.

High-risk children in young adulthood: A longitudinal study from birth to 32 years.

Abstract: The developmental courses of high-risk and resilient children were analyzed in a follow-up study of members of a 1955 birth cohort on the island of Kauai, Hawaii. Relative impact of risk and protective factors changed at various life phases, with males displaying greater vulnerability than females in their first decade and less during their second; another shift appears under way at the beginning of their fourth decade. Certain protective factors seem to have a more general effect on adaptation than do specific risk factors.

Increasing CO2 threatens human nutrition.

Abstract: experiments contribute more than tenfold more data regarding both the zinc and iron content of the edible portions of crops grown under FACE conditions than is currently available in the literature. Consistent with earlier meta-analyses of other aspects of plant function under FACE conditions 14,15 , we considered the response comparisons observed from different species, cultivars and stress treatments and from different years to be independent. The natural logarithm of the mean response ratio (r5 response in elevated [CO2]/response in ambient [CO2]) was used as the metric for all analyses. Meta-analysis was used to estimate the overall effect of elevated [CO2] on the concentration of each nutrient in a particular crop and to determine the significance of this effect (see Methods). We found that elevated [CO2] was associated with significant decreases in the concentrations of zinc and iron in all C3 grasses and legumes (Fig. 1 and Extended Data Table 1). For example, wheat grains grown at elevated [CO2] had 9.3% lower zinc (95% confidence interval (CI)212.7% to25.9%) and 5.1% lower iron (95% CI26.5% to23.7%) than those grown at ambient [CO2]. We also found that elevated [CO2] was associated with lower protein content in C3 grasses, with a 6.3% decrease (95% CI27.5% to25.2%) in wheat grains and a 7.8% decrease (95% CI 28.9% to26.8%) in rice grains. Elevated [CO2] was associated with a small decrease in protein in field peas, and there was no significant

Comparison of the total phenolic and ascorbic acid content of freeze-dried and air-dried marionberry, strawberry, and corn grown using conventional, organic, and sustainable agricultural practices.

Abstract: Secondary phenolic metabolites play an important role in plant defense mechanisms, and increasing evidence indicates that many are important in human health. To date, few studies have investigated the impact of various agricultural practices on levels of secondary plant metabolites. To address this issue, the total phenolic (TP) content of marionberries, strawberries, and corn grown by sustainable, organic, or conventional cultural practices were measured. Additionally, the effects of three common postharvest processing treatments (freezing, freeze-drying, and air-drying) on the TP content of these agricultural products were also investigated. Statistically higher levels of TPs were consistently found in organically and sustainably grown foods as compared to those produced by conventional agricultural practices. In all samples, freeze-drying preserved higher levels of TPs in comparison with air-drying.