Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.

/pdf/phyloseq-an-r-package-for-reproducible-interactive-analysis-1ez1xx3dlr.pdf

phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.

Summary

The use of both linear and generalized linear mixed-effects models (LMMs and GLMMs) has become popular not only in social and medical sciences, but also in biological sciences, especially in the field of ecology and evolution. Information criteria, such as Akaike Information Criterion (AIC), are usually presented as model comparison tools for mixed-effects models.


The presentation of ‘variance explained’ (R2) as a relevant summarizing statistic of mixed-effects models, however, is rare, even though R2 is routinely reported for linear models (LMs) and also generalized linear models (GLMs). R2 has the extremely useful property of providing an absolute value for the goodness-of-fit of a model, which cannot be given by the information criteria. As a summary statistic that describes the amount of variance explained, R2 can also be a quantity of biological interest.


One reason for the under-appreciation of R2 for mixed-effects models lies in the fact that R2 can be defined in a number of ways. Furthermore, most definitions of R2 for mixed-effects have theoretical problems (e.g. decreased or negative R2 values in larger models) and/or their use is hindered by practical difficulties (e.g. implementation).


Here, we make a case for the importance of reporting R2 for mixed-effects models. We first provide the common definitions of R2 for LMs and GLMs and discuss the key problems associated with calculating R2 for mixed-effects models. We then recommend a general and simple method for calculating two types of R2 (marginal and conditional R2) for both LMMs and GLMMs, which are less susceptible to common problems.


This method is illustrated by examples and can be widely employed by researchers in any fields of research, regardless of software packages used for fitting mixed-effects models. The proposed method has the potential to facilitate the presentation of R2 for a wide range of circumstances.

https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/j.2041-210x.2012.00261.x

A general and simple method for obtaining R2 from generalized linear mixed-effects models

Humans are altering the composition of biological communities through a variety of activities that increase rates of species invasions and species extinctions, at all scales, from local to global. These changes in components of the Earth's biodiversity cause concern for ethical and aesthetic reasons, but they also have a strong potential to alter ecosystem properties and the goods and services they provide to humanity. Ecological experiments, observations, and theoretical developments show that ecosystem properties depend greatly on biodiversity in terms of the functional characteristics of organisms present in the ecosystem and the distribution and abundance of those organisms over space and time. Species effects act in concert with the effects of climate, resource availability, and disturbance regimes in influencing ecosystem properties. Human activities can modify all of the above factors; here we focus on modification of these biotic controls. The scientific community has come to a broad consensus on many aspects of the re- lationship between biodiversity and ecosystem functioning, including many points relevant to management of ecosystems. Further progress will require integration of knowledge about biotic and abiotic controls on ecosystem properties, how ecological communities are struc- tured, and the forces driving species extinctions and invasions. To strengthen links to policy and management, we also need to integrate our ecological knowledge with understanding of the social and economic constraints of potential management practices. Understanding this complexity, while taking strong steps to minimize current losses of species, is necessary for responsible management of Earth's ecosystems and the diverse biota they contain.

/pdf/effects-of-biodiversity-on-ecosystem-functioning-a-consensus-13j8vabcus.pdf

Effects of biodiversity on ecosystem functioning: a consensus of current knowledge

http://talklab.psy.gla.ac.uk/KeepItMaximalR2.pdf

Random effects structure for confirmatory hypothesis testing: Keep it maximal

Landfills are ideal locations for short-rotation forestry, tree-based bioremediation, and wildlife habitat reconstruction. However, tree survival is reduced by harsh growing conditions and poor soil quality. This study was designed to determine survival of tree seedlings and test effects of different mulch types and depths on edaphic properties and herb emergence on a closed Ohio landfill. In spring 2002, five species of hardwood tree seedlings (Fraxinus pennsylvanica, Robinia pseudoacacia, Prunus serotina, Quercus macrocarpa, and Populus sp.) were planted in a clustered fashion on 35 plots. Each plot received a mulch treatment consisting of one type of mulch (hardwood, leaf, or mixed) at a specific depth (5 or 15 cm) or was designated as a nonmulched control. The status of each seedling and edaphic qualities (soil moisture, temperature, and nutrients) were recorded for two growing seasons. Aboveground herbaceous biomass was sampled at the end of each growing season. We found that survival and growth were species dependent. At the conclusion of the experiment, Fraxinus had the highest survival rate (70%) and Prunus the lowest (7%). The use of leaf mulch (15 cm deep) increased organic matter and various edaphic properties (cation exchange capacity, P, Mg) after the second growing season. Mulch treatments did not significantly affect aboveground herbaceous biomass when compared to nonmulched controls. These results suggest Fraxinus as a good candidate for landfill plantings. Additionally, leaves and yard waste are plentiful and could quickly enrich poor soils on a landfill if left to decompose aboveground.

Effects of Mulch on Seedlings and Soil on a Closed Landfill

Background
Spore discharge in the majority of the 30,000 described species of Basidiomycota is powered by the rapid motion of a fluid droplet, called Buller's drop, over the spore surface. In basidiomycete yeasts, and phytopathogenic rusts and smuts, spores are discharged directly into the airflow around the fungal colony. Maximum discharge distances of 1–2 mm have been reported for these fungi. In mushroom-forming species, however, spores are propelled over much shorter ranges. In gilled mushrooms, for example, discharge distances of <0.1 mm ensure that spores do not collide with opposing gill surfaces. The way in which the range of the mechanism is controlled has not been studied previously.

/pdf/adaptation-of-the-spore-discharge-mechanism-in-the-19cod9g7f8.pdf

Adaptation of the spore discharge mechanism in the basidiomycota.

Herbaceous plant species richness typically declines with increasing productivity, but differences in the resources underlying these gradients are often ignored. This study adds to the small number of studies examining the effects of water and mineral nutrients on biomass and richness in oldfield communities. We established 60 4 m2 plots in a goldenrod-dominated oldfield to test the differential effects of water and mineral nutrients on community properties. Species richness declined with added nutrients, but increased with added water. Aboveground biomass increased only when both nutrients and water were added. Leaf area index increased with added nutrients alone, although the increase was greater when water was also added. Understory light levels decreased with added nutrients, but not with added water; however, the per-gram effect of biomass on understory light levels did not vary significantly among nutrient and water treatments. Our results suggest that water tends to enhance productivity, but does not cause the common decline in species richness that typically accompanies nitrogen additions. Rather, water increased richness through positivie effects on either germination and establishment, or increased survival. These results are consistent with either increased light limitation or increased water limitation causing loss of species from nitrogen-rich habitats.

Water and fertilizer have opposite effects on plant species richness in a mesic early successional habitat

We assessed the influence of riparian disturbance on 26 stream variables in Linesville Creek and six tributaries, in northwestern Pennsylvania, USA. Redundancy analysis, a canonical ordination technique, was used in three separate analyses to test for significant relationships between riparian characteristics and the multivariate stream data (aspects of geomorphology, substrate composition, leaf litter processing and macroinvertebrate shredder species composition). Ordination (PCA) showed riparian vegetation to be strongly related to land use. Pasture sites, characterized by grasses and Eupatorium spp., had the most distinctive plant assemblages, while species composition was most variable among woodland sites. In-stream variables were significantly related to both land use and riparian vegetation. Generally, disturbed sites tended to have more silt and higher populations of Gammarus sp. Land use, in particular, had a great effect on detritus processing and storage. Stream reaches in pastures ten...

Effects of Long-Term Disturbance on Riparian Vegetation and In-Stream Characteristics

Different disturbances in similar habitats can produce unique successional assemblages of plants. We collected plant species composition and cover data to investigate the effects of three common types of disturbances—fire, anthropogenic clearing (‘cleared’), and clearing followed by goat grazing (‘cleared‐and‐grazed’)—on early‐successional coppice (dry forest) community structure and development on Eleuthera, Bahamas. For each disturbance type, both the ground layer ( 0.5 m height) were sampled in eight patches ( > 1 ha) of varying age (1–28 yr) since large‐scale mature coppice disturbance. Overall, plant communities differed among disturbance types; several common species had significantly higher cover in the shrub layer of fire patches, and cleared‐ and‐grazed patches exhibited higher woody ground cover. Total percent cover in the shrub layer increased in a similar linear fashion along the investigated chronosequence of each disturbance type; however, cover of the common tree species, Bursera simaruba, increased at a notably slower rate in cleared‐and‐grazed patches. The pattern of increase and subsequent decrease in cover of Lantana spp. and Zanthoxylum fagara in the shrub layer was characterized by longer persistence and higher covers, respectively, in cleared‐and‐grazed patches, which also exhibited low peak cover and fast decline of nonwoody ground cover. Our results suggest that goats may accelerate some aspects of succession (e.g., quickly removing nonwoody ground cover) and retard other aspects (e.g., inhibiting growth of tree species and maintaining early‐successional shrubs in the shrub layer). These effects may lead to different successional trajectories, and have important conservation implications.

https://www.fs.fed.us/global/iitf/pubs/ja_iitf_2012_Larkin001.pdf

M. Henry H. Stevens

Papers

Effects of Mulch on Seedlings and Soil on a Closed Landfill

Adaptation of the spore discharge mechanism in the basidiomycota.

Water and fertilizer have opposite effects on plant species richness in a mesic early successional habitat

Effects of Long-Term Disturbance on Riparian Vegetation and In-Stream Characteristics

Disturbance Type and Plant Successional Communities in Bahamian Dry Forests