I am a research professor at Northern Arizona University (NAU), Director of Genetics of the Species from Feces Team, Bat Ecology & Genetics Lab, and Ancient DNA lab, and an associate director of NAU’s Pathogen and Microbiome Institute. My team employs a variety of tools in genetics and ecology to understand population biology and natural and evolutionary history of organisms. A uniting theme is how wildlife function in natural systems and are impacted in human-altered ones. I enjoy pairing degraded DNA (feces, ancient, environmental) with emerging technologies to answer difficult questions, and my favorite questions have a management component and involve species that are scientifically intractable because they are cryptic, rare, or endangered. My team is excited about scientific discovery, innovation, and translation, and I work with many excellent collaborators. I foster a global perspective to my research, having spent seven years overseas in various research contexts.
I am a Professor of Wildlife Ecology at NAU and Director of Ecology of the Bat Ecology & Genetics Lab, with a long-term bat ecology and habitat relationships research program. For almost 20 years, my research has focused on bats, resulting in 15 studies encompassing 22 southwestern bat species, some of which are uncommon and rare species. My work covers a variety of roost types such as snags, caves, and mines, as well as a wide range of methods and techniques including live-trapping mark-recapture, track plates, occupancy modeling, radio telemetry, stable isotopes, and others.
2021 Award: AZTWS Roger Hungerford Student Award
2018-2020 Awards: ARCS Scholarships
2017-2020 Award: National Science Foundation Graduate Research Fellow
I use cutting edge genetic and computational tools to study conservation ecology and evolution in wildlife systems. After helping develop Species from Feces in the laboratory, I focused my research on understanding the historical biogeography of the spotted bat as well as designing a metabarcode assay for identifying diet of the endangered New Mexico meadow jumping mouse. Some of the skills that I employ for these projects include next-generation sequencing, microbiome bioinformatics, phylogenetics, ecological niche modeling, and bacterial and fungal microbiology. I was awarded an NSF graduate research fellowship to determine dietary preferences and population signatures of the New Mexico meadow jumping mouse across the species’ distribution.
During my PhD At NAU, I will be investigating the seasonal dynamics and landscape ecology of bat communities in the highly fragmented equatorial dry forests of Peru and Ecuador. Maintaining population connectivity in these ecosystems is essential for ecosystem functioning and community resilience in the face of climate change. Through stable isotope analyses and phylogenetics of bats/their parasites, I will describe habitat use across seasons and population connectivity between forests. Through this work, I hope to understand the impact of landscape connectivity on community composition and functioning in highly seasonal environments.
I am pursuing my PhD at the University of Adelaide with Dr. Jeremy Austin. Dr. Walker is an external supervisor. For my PhD I am using genetic techniques for the conservation and management of the northern hairy-nosed wombat (Lasiorhinus krefftii), one of the most endangered mammals in the world. I am 1) building a phylogeny of northern hairy-nosed wombats and their congener the southern hairy-nosed wombat (Lasiorhinus latifrons) using whole mitochondrial genomes to determine whether genetic diversity is still low; 2) using fecal samples to characterize diet and microbiome, and search for pathogens; 3) developing a science communication program; and, 4) incorporating indigenous communities and histories.
2022-2023 Awards: Jean Shuler Mini Research Grant; Student Mentored Research Grant
I am an Honors student studying biology with a minor in criminal justice. I joined PMI in spring 2022 as a member of the Bat Ecology and Genetics Lab (BEGL), where I work as part of the Species From Feces team. I am also the Undergraduate Lab Manager of the Ancient DNA lab. There, I will study 30,000 year old bat mummies collected in the Grand Canyon. Through my work here I am gaining experience in working with damaged, partial, and trace DNA, which will aid me as I pursue a career in forensic science after college.
2023 Awards: NAU Interns2Scholars; Farrell Family Scholarship; Chemistry and Physics Award for Female or Underrepresented Students; Distinguished Scholars Award Endowment; NAU Honors Merit Scholarship; Nancy and Henry Wettaw Organic Chemistry Scholarship; Jean Shuler Mini Research Grant
I am double majoring in environmental sciences with an emphasis on biology and chemistry with an emphasis on biochemistry. I am joining the team as an undergraduate student researcher. Learning how to use DNA processing equipment and to analyze results during my time at NAU will give me hands-on experience and help me develop the skills needed to pursue medical research after my undergraduate studies.
2023 Awards: Nackard Family Scholarship from the NAU Honors College; Environmental Science Scholarship from the NAU School of Earth and Sustainability
I am an NAU Honors student majoring in Environmental Science with an emphasis in biology. As an undergraduate researcher on the Species from Feces team, I am gaining experience in DNA extraction from environmental DNA sources and am learning how this technology is pivotal to species identification as well as what implications this may have. This research experience will be valuable as I pursue a future career in wildlife conservation.
I am a Research Assistant whose primary focus is the Species From Feces project. Before joining the Bat Ecology and Genetics Lab, I worked at the Translational Genomics Research Institute where I engaged in assay development to better understand the molecular mechanisms of Parkinson’s Disease. Later, I joined W.L. Gore & Associates, where I worked in R&D to improve the biocompatibility of materials in medical devices. Now I am excited to take the experience I gained using molecular biology techniques in those settings to support the capabilities of Dr. Faith Walker’s team in aiding wildlife conservation efforts.
I am an Assistant Professor in the School of Informatics, Computing, and Cyber Systems at NAU. My research focuses on applications of High Throughput Sequencing data to pathogen detection in complex clinical and environmental samples. In humans, this includes detection and transmission tracing (person-to-person, surface-to-person, and animal-to-person) of community-acquired Methicillin Resistant Staphylococcus aureus (MRSA) infections, an important cause of soft tissue and skin infections, with significant ethnic health disparities. In animals, this includes development of tools for pathogen surveillance of wildlife reservoirs, including PCR amplicon and metagenomic sequencing approaches. My particular focus is on bats – an important and ubiquitous animal reservoir of a number of important human-affecting diseases.
I am a professor in NAU’s Pathogen and Microbiome Institute. I work on pathogen evolution and disease ecology in wildlife and livestock. Recent research foci include white-nose syndrome in bats, brucellosis in a range of hosts, and avian cholera and malaria in birds. Much of my training was in avian ecology, focusing on native and introduced birds in Hawaii and elsewhere. I continue to work in the Hawaiian Islands on seed dispersal and native forest birds (vicariously through lucky students).
Undergraduate Genetics Researcher – Team eDNA, Species from Feces Team
2021-2022 Award: NAU Interns2Scholars
I am a junior in the NAU Honors College, pursuing a major in Biomedical Sciences and a minor in Psychology. I started working at the Pathogen and Microbiome Institute (PMI) with the Bat Ecology & Genetics Lab (BEGL) in the summer of 2021 and will continue into the school year as an Interns2scholar undergraduate. My current projects include the testing and applying of qPCR assays on fecal DNA to determine diet and on environmental DNA to detect species presence. I will: 1) determine whether or not predatory sportfish, such as the largemouth bass (Micropterus salmoides) may be contributing to population declines of the threatened northern Mexican garter snake (Thamnophis eques megalops); 2) determine the diet of this snake at Lake Roosevelt, AZ; and, 3) identify the endangered Mexican long-nosed bat (Leptonycteris nivalis) from environmental DNA found on agave flowers. I will also assist with the Species from Feces program, which uses fecal DNA to identify communities for wildlife conservation and management. Additionally, I have helped to develop and run social media accounts for our Species from Feces program. I will work at BEGL throughout my undergraduate career at NAU, where I will gain a hands-on education in molecular conservation, before going to pursue a Master’s focused on genetics.
2022 Award: Jean Shuler Mini-Grant
I am an undergraduate researcher majoring in biology with a minor in chemistry and I am earning a Wildlife Ecology and Management Certificate. I am passionate about wildlife conservation and the importance of communication as a tool to facilitate it. My position within the Walker Lab includes work on Species from Feces at the Pathogen and Microbiome Institute under the Bat Ecology and Genetics Lab. I complete Sanger Sequencing for bat IDs using DNA extracted from bat fecal matter, bat tissue, and the environment. Additionally, I complete work on our public and client outreach, in part by running our Species from Feces Team’s social media. Following my undergraduate career, I will be earning a master’s degree in wildlife biology to pursue a career in wildlife conservation and management.
Before starting as a Research Technician at PMI, I worked for the Forest Service and the National Parks Service in Alaska, the Cascades, Yellowstone and most recently Olympic National Park as a Biological Science Technician where I performed coastal surveys, population studies, and gathered limnological data up at remote mountain lakes. During my undergraduate degree at the University of Arizona, I worked in a Conservation Genetics Lab. I currently am assisting with a rabies project that is showing progress in detecting the rabies virus in fecal samples rather than the more invasive method of gathering brain tissue. Additionally, I am working on the Species From Feces Team to conduct DNA metabarcoding to identify species and determine diet for a wide range of taxa. I also work for Dr. Jeff Foster’s team, applying a genetic assay on wing swabs and feces to test for the fungus that causes white-nose syndrome in bats.
José Gabriel Martinez-Fonseca
2020 Award: BCI Student Research Scholarship
In 2018 I started a PhD program at NAU after 12 years working with amphibians, reptiles, bats and other small mammals in my home country, Nicaragua. Currently, my research focuses on better understanding how different species of bats respond to forest fragmentation and how they move in altered landscapes. To achieve this, I’ll be incorporating different techniques like geographic information systems, machine learning, acoustic monitoring, genetics, and telemetry. I expect the product of my research to positively impact the management of the landscape to promote conservation of bat diversity and ecosystem health.
I have worked with non-invasive genetic samples for 7 years, first at PMI as an undergraduate, and then with the School of Forestry’s Bat Ecology & Genetics Lab. I manage the Ancient DNA Lab, perform our Species from Feces services, and am involved in a suite of different projects. My skills include DNA extraction and amplification from severely degraded sample types, next-generation amplicon sequencing, and bioinformatics. My favorite projects to date include extracting DNA from a 10,000 year old spotted bat mummy, chasing wombat DNA in South Australia, developing an eDNA sampling protocol to detect bat species from water sources, and determining what bat species use two Mayan temples. I enjoy communicating our exciting research to STEM students.
Undergraduate Genetics Researcher – Jumping Mouse Team, Team Lizard
2021 Award: Gold Axe Award; NAU President’s Prize Recipient; Outstanding Researcher Award
2020: NAU Biology’s Kenneth Derifield Award
2019 Award: NAU Biology’s Pacius Award
2018 Award: Recipient of an Office of Undergraduate Research Mini Grant
I graduated from NAU in April 2021, where I pursued a double major in Biology and Spanish with a minor in Chemistry. As an undergraduate research assistant at the Pathogen and Microbiome Institute (PMI) with the Bat Ecology & Genetics Lab, my research focused on the genetic barcoding of plants that are important to the herbaceous diet of the endangered New Mexico meadow jumping mouse (Zapus hudsonius luteus). Currently, our barcoding efforts have genus-level resolution; I barcoded plants that were collected from jumping mouse habitat in order to identify taxa down to the species level. These results will help us understand what plant species are important to jumping mice and will help land managers promote protection of these plant communities. In addition, I assisted with bat Species from Feces projects, which involve the identification of bat species from guano using a DNA mini-barcode assay. Working at the School of Forestry and PMI expanded my understanding of ecological and genetic research; In Fall 2021, I started a dual Ph.D. in molecular biology and an M.S. in genetic counseling at the University of Minnesota.
Undergraduate Genetics Researcher – Team Wombat, Team Rabies, Species from Feces Team
2021 Award: The Keim Award for Excellence in Undergraduate Research; Gold Axe Award; Runner-up for best poster at the American Society for Microbiology Branch Meeting
2020 Awards: Entomological Society of Helsinki Research Grant; 2020-2021 Hooper Undergraduate Research Award
2019 Awards: Selected for Council on Undergraduate Research Posters on the Hill, Washington, DC; National Conference on Undergraduate Research, Kennesaw State University; NAU Biology’s Drickamer-Montgomery Award
2018 Awards: RCN g2p2pop Lab Exchange Fellow to South Australia; NAU Intern2Scholar; Poster Winner at the 20th Anniversary Wombat Conference in Adelaide, South Australia; Recipient of an Office of Undergraduate Research Mini Grant
2017 Award: NAU Intern2Scholar
I graduated from NAU in April 2021, where I was a part of the honors program, and pursued a double major in Biology and Spanish with a minor in Chemistry. I began working with the Bat Ecology & Genetics Lab (BEGL) in 2017 through the Intern2Scholars program, successfully organizing thousands of bat team genetic samples in -80C freezers and refining our Access database (‘BEGLbase’). I conducted the genetic portion of a follow-up study to Dr. Walker’s Ph.D. research in the early 2000s, in order to uncover the population dynamics of South Australia’s southern hairy-nosed wombat (Lasiorhinus latifrons), and see how the population has changed over time. This is described in our 2020 paper. My final project employed a molecular assay to detect rabies through minimally invasive sample types. In addition, I assisted with bat Species from Feces projects, which involve the identification of bat species from guano using a DNA mini-barcode assay. I started a Master’s program at Kennesaw State University in Fall 2021.
Undergraduate Genetics Researcher – Ancient DNA Core
2020: Accepted into the Ph.D. program at UC Santa Cruz
2019 Awards: Hooper Undergraduate Research Award; Jean Shuler Research Mini-Grant; NAU Biology’s Slipher Award and Bayless Award
2018 Awards: Hooper Undergraduate Research Award, NAU/NASA Space Grant Undergraduate Research Intern, and Jerry O Wolf Student Enrichment Scholarship
I graduated from NAU in May 2020 with a degree in Biology. As a 3 year member of the Ancient DNA Core, my projects started in the Ancient DNA Lab, where I handled and extracted DNA from sensitive samples, and finished at PMI, where I amplified gene targets of interest. For my main project, I extracted DNA from sediment cores and used metagenomics and metabarcoding to identify plant and animal species in order to understand past ecosystems. I am preparing a first author paper describing the detection of moose from sediment cores of a lake on the Kenai Peninsula in Alaska. Additionally, I assisted with the Bat Ecology & Genetics Lab’s Species from Feces projects, which involved analyzing DNA from bat guano to reveal the species that produced it. This technique is non-invasive, and the information gathered from the process is used to help track, understand, and protect bat species. I started a Ph.D. program at UC Santa Cruz in fall 2020.
Undergraduate Genetics Researcher
2019 Honors/Awards: Internship at the Curie Institute in Paris; NAU Golden Axe Award
2018 Awards: Goldwater Scholar; Paul A. Sciame Scholarship; NAU Award of Excellence in Undergraduate Inquiry & Creativity; NAU UGRADS 3rd place; Head Undergraduate at PMI.
2017 Awards: Recipient of 2017-2018 Hooper Undergraduate Research Award; 2nd Place in student presentations at The Wildlife Society Joint Annual Meeting.
I graduated from NAU in December 2019 with a Bachelor of Science in Biology, Bachelor of Arts in French, and a minor in Chemistry. As a member of the School of Forestry’s Bat Ecology and Genetics Lab, I performed research that applied noninvasive genetics and genomics to wildlife conservation. I conducted my work at the Pathogen & Microbiome Institute (PMI) using next-generation sequencing to inform management of the endangered New Mexico meadow jumping mouse (Zapus hudsonius luteus). I was awarded a HURA to study E. coli infections that serve as a potential threat to jumping mice. I also helped develop a genetic method to identify herbivore diet. This system has informed management for wildlife such as jumping mice, mule deer, and pronghorn. PMI and the School of Forestry provided stimulating environments to pursue my passion for conservation in an exciting new way through genetics. I plan to pursue a PhD in molecular genetics and continue my career in research.
Clarissa conducted a risk analysis of wind facility development to bats in northern Arizona by identifying areas of high risk via acoustic monitoring and bat capture. She identified migration patterns and routes, characterized the bat community, and located key roost sites, which will allow resource managers to identify options to protect habitat for bats in proximity to wind development sites. This work is important because four factors in northern Arizona create the potential for serious impacts to bat populations if risks are not carefully identified prior to construction of wind facilities: 1) the diversity of bats in the area (≥20 species), 2) the unique types and numbers of roost sites found in canyon areas such as the >300 km long Grand Canyon, 3) the moderate climate that allows year-round occupation and activity for some bat species, and, 4) the use of northern Arizona as flyways for migratory species such as Mexican free-tailed bat (Tadarida brasiliensis). She is now a postdoc at Indiana State University.
2016 Awards: Master’s Degree in Forestry
2015 Awards: Dixie Pierson Scholarship Award
I examined the effects of gating mines on bat use and activity, a project funded by the BLM and Bat Conservation International. Abandoned mines in the Four Corners region of the western U.S. are likely to be gated if they provide habitat for bats. However, these gates have protected sensitive habitat at some sites but caused declines in others. I determined which gate characteristics are detrimental or positive to bat activity. I am now White-nose Syndrome Coordinator at the Washington Department of Fish & Wildlife.
2014 Award: B.S. Forestry
2013 Award: Hooper Undergraduate Research Award
I assisted with a study using radio-telemetry and genetic tools to examine genetic relatedness within maternity colonies of big brown bats (Eptesicus fuscus) in an area with repeated rabies outbreaks. We achieved this entirely by DNA procured from buccal swabs. I received the 2014 Best Student Poster Award at The Wildlife Society’s Joint Annual Meeting in Pinetop, Arizona.