Calibrating fecal NIRS equations for predicting botanical composition of diets

The objectives of this study were to investigate the use of near infrared spectroscopy (NIRS) of fecal samples for predicting the percentage of mountain big sagebrush (Artemisia tridentata Nutt. ssvaseyana (Rydb) Beetle) in sheep diets and to quantify the limitations of using NIRS of fecal samples to predict diet composition. Fecal material from a sheep feeding trial with known levels of sagebrush and several background forages was used to develop fecal NIRS calibration equations validated with fecal material from 2 other sheep feeding trials with known levels of sagebrush in the diets. The 1996 calibration trial varied the level of sagebrush, alfalfa, and grass hay in the diets. The 1998 trial compared frozen to air-dried sagebrush. The Wyoming trial was a metabolism study using frozen sagebrush. Trials used different levels of sagebrush varying from 0 to 30% of the diet in increments of 4 to 10 percentage points. Internal validation of the 1996 trial with a subset of the samples not used for calibration showed that when predicted samples are from the same population as the calibration samples, this procedure can accurately predict percent sagebrush (R2=0.96, SEP=1.6). However, when predicted samples were from a different population than calibration samples, accuracy was much less, but precision was not affected greatly. Low accuracy was caused by a compression of the range of data in the predicted values compared to the reference values, and the predicted sagebrush levels in the diet should be considered to represent an interval scale of measurement. Modified partial least squares regression resulted in better calibration than stepwise regression, and calibration data sets with only high, low, and no sagebrush resulted in calibrations almost as good as data sets with several intermediate levels of sagebrush. High values of the H statistic were related to low precision but did not affect the accuracy of predictions. We believe the interval scale of measurement will contain sufficient information for the purpose of addressing many questions on rangelands

The Ascomycota tree of life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species