Community Ecology & Statistics
Much of my research of the last 15 years (as a graduate student and faculty member) has concerned alpine ecology. This includes the use of classic methods in plant synecology and autecology, and the examination of the effect of invasive mountain goats (Oreomnos americanus) on the alpine vegetation of Absaroka-Beartooth mountains.
Figs. Alpine study sites in the Absaroka-Beartooth mountains. (L to R) E. face of Cutoff Pk., looking NW from the summit of the Thunderer, looking NW from the summit of Mineral Pk., and looking S from the summit plateau of Amphitheatre Pk (photos: S. Contor, 2008-2009).
Whitebark pine endophytic ecology
Whitebark pine (Pinus albicaulis), a species of treeline environments in the Western US, is in rapid decline due in part to the exotic fungal pathogen whitebark pine blister rust (Cronartium ribicola). Ehren Moler completed an MS project to ascertain the effect of native endophytic (within-leaf) fungal community structure, and community assembly on C. ribicola infection.
Figs (left) shows whitebark pine study sites in the mountains of South-Central Oregon. (L to R) Parent trees representing a specific type of genetic vulnerability to blister rust infection, view of Crater Lake from Watchman's Peak along the caldera rim (photos: E. Moler, 2013). Fig (right) shows Certhomas Tan and Connor Newman at the top Bonneville Peak near Pocatello, ID, collecting limber pine (P. flexilis) needles. P. flexilis is a close relative of P. albicaulis (photo: K. Aho).
Dwarf mistletoe population ecology
Lodgepole pine dwarf mistletoe (Arceuthobium americanum), is an obligate parasite of lodgepole pine (Pinus contorta). The patterns of genetic variation within A. americanum populations are largely unexplored, and of interest because of the poor gene flow characteristics of the species, due to limited dispersal abilities, and specificity to P. contorta (which itself is limited to montane islands). Roy Hill recently completed an MS project exploring the genetic diversity and phylogeny A. americanum populations using microsatellite markers developed specifically for this species.
Current graduate students
Aurora Bayless-Edwards (MS candidate, FA 2016 - )
My thesis research focuses on classifying plant communities in semi-arid sagebrush steppe on the Snake River Plain. Our classifications involve applications of several hierarchical and non-hierarchical cluster analysis methods evaluated by geometric and non-geometric evaluators to determine optimal community assignments. The goal of the project is a local scale map of plant communities. However, temporal and spatial changes in these communities allow us to investigate interesting ecological processes in semi-arid communities, such as post-fire succession. When I'm not working on research with the Aho Labsters, I am usually mountain biking, running, hiking, snowshoeing, or skiing with my spouse and our dog, Poacea (Po).
Stephanie Zorio (DA candidate, FA 2016 - )
The bulk of my research has focused on plant communities in high-altitude environments and how they change over time, especially due to direct or indirect anthropogenic influence. For my dissertation, I was given the opportunity to expand my investigations of alpine plants to include microbial diversity in soil and the near-terrestrial atmosphere via Next-Gen sequencing. This has been particularly intriguing because the composition and resilience of alpine plant communities may be linked to microbial communities. I primarily use multivariate statistics and a suite of diversity metrics to detect ecologically meaningful patterns. When I’m not working on research, I’m teaching. When I’m not teaching you can find me in the woods or garden.
The R computational environment
R is a computer language and an open source environment for statistics, data management, computation and graphics. Documentation and software can be downloaded for free here.
Asbio (applied statistics for biologists) is an R package that contains functions for statistical pedagogy and biological research. Of particular interest are hundreds of graphical functions for depicting statistical concepts, many with interactive GUIs. Asbio also serves as a software companion to the biostatistical textbook: "Foundational and Applied Statistics for Biologists Using R". Developmental versions of the software for Windows and Unix/Linux can be found in the table below.
MAC OS X users please use the newest R, and download the most recent version of XQuartz to allow implementation of tcltk GUIs. Open XQuartz before using asbio.
ASD associated protein-protein network analysis
- Description of network indices used in Kaushik et al. 2015
- ASD associated PPI network cytoscape file
- Complete dataset for gene sets enriched in fish brains
- Complete dataset for gene sets enriched in human neuronal cells
- Nodal summary statistics of gene set groups
Data from In vivo intestinal and placental transfer of carbamazepine at typical environmental concentrations from drinking water to the developing fetus