Austin Koontz

Research Assistant

Biography

I’m currently a Research Assistant in the Hoban Conservation Lab, with the Center for Tree Science at the Morton Arboretum. Using population genetic data, I work with other members of the lab, and other groups within and outside of the Arboretum, to inform the conservation of rare plant species.

Currently, I’m comparing two types of genetic markers (SNPs generated using RADseq, and more traditional microsatellites) and exploring how the choice of these markers effects measures of ex situ conservation. I’m using genetic sequences from two rare oak species (Quercus boyntonii and Q. acerifola) for the empirical data of this project, which is part of a broader effort by the Global Conservation Consortium for Oaks (GCCO) to protect threatened oak species. Links to the code for this analysis are below.

I received my Master’s of Science degree at Utah State University, where I worked in the Pearse Lab and the Wolf Lab. More information about the research I did in each of these labs can also be found below.

Download my CV.

Interests

Conservation Genetics
Plant Population Genetics
Phylogenetics

Education

MSc in Biology/Ecology, 2020

Utah State University
BSc in Neuroscience, 2014

University of Nevada, Reno

Experience

Research Assistant II

Morton Arboretum

Jul 2021 – Present Lisle, IL

My current role consists of performing genetic analyses for projects focused on the conservation and management of rare trees, both in wild (in situ) and garden (ex situ) scenarios. I also serve as the system administrator for the Hoban Lab Linux server, and the majority of my work consists of bioinformatic analyses.

Applications Specialist

Hamilton Robotics

Jan 2015 – May 2018 Reno, NV

As an Applications Specialist, I wrote and supported method scripts for customers in the OEM setting and internally, for standardized laboratory protocols. I served as the primary application resource for customers from product development to launch, and worked with hardware and software engineers to design automation solutions.

Projects

Primula cusickiana species complex analysis

The four members of the Primula cusickiana species complex were each historically classified as their own species, before a 2001 review subsumed them to varieties of the same species (due to largely similar morphologies). I used RADseeq to examine the genetic separation between these varieties, and to verify past findings of large genetic distance between proximate populations of variety maguirei, the complex member found in Logan Canyon. This research was guided by Dr. Paul Wolf and Dr. Will Pearse, and has been published in Systematic Botany.

Ex situ conservation of oaks using RADseq vs. microsatellite markers

With the Hoban Lab at the Morton Arboretum, I’m performing a comparison of RADseq and microsatellite data, to see how different genetic markers may impact ex situ conservation recommendations for threatened trees. The empirical data for this project comes from two endemic US oaks, Quercus boyntonii and Q. acerifolia. This work is part of the larger Global Conservation Consortium of Oaks, and is funded by the Institute of Museum and Library Services.

Informing OTU thresholds through phylogenetics

Operational taxonomic units (OTUs) are used to group similar microbial taxa together based on DNA sequence similarity, but ambiguity over the value used to determine OTU boundaries persists. This research looks to inform OTU thresholds by using a family of phylogenetic branch length transformations, Pagel’s transformations, and to guide species delimitation by examining the impact different thresholds have on community diversity. This research was guided by Dr. William D. Pearse and the Pearse Lab.

SymbiotaR2 R package

The NSF-ABI project Symbiota2 updates the structure of the widely used Symbiota software platform, a biodiversity data management tool. I’ve developed an R package that allows users to access Symbiota2 function calls within the R environment. This package is now part of ROpenSci!