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.
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.
2020 Awards: Brad McRae Fellowship for Innovation in Conservation Biology; Jeff Whitney Forestry Ecosystems Scholarship
2019 Award: National Park Service Arrowhead and Shoulders Above Award
Prior to beginning the MSF program at NAU, I spent three years as a wildlife technician at Grand Canyon National Park where I studied the canyon’s 22 bat species, collared and monitored bison herds on the North Rim, tracked California condors using radio telemetry, and launched the herpetofauna survey and monitoring program. My research at NAU surrounds using microsatellite DNA to study gene-flow in post-Glen Canyon dam populations of reptiles and amphibians in Grand Canyon National Park. I hope to determine if the dam has created a cold water barrier to movement and gene-glow through the Grand Canyon. This study is the first that we know of to address the impact of dam-altered flow regimes on gene flow in ectotherms. I expect this research will contribute to our understanding of the impact of human ecosystem manipulation on herpetofauna and will give us more information on how to best preserve this globally threatened group.
Undergraduate Genetics Researcher – Team eDNA, Species from Feces Team
2021 Award: NAU Intern2Scholars
I am a sophomore 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.
Genetics Research Specialist
I have worked with non-invasive genetic samples for 10 years, first at PMI as an undergraduate, and then with the Species from Feces program and the Bat Ecology & Genetics Lab. I manage the Ancient DNA Lab 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 which bat species use two Mayan temples. I enjoy communicating our exciting research to STEM students. I will soon be pursuing more wombat DNA for my Ph. D. at the University of Adelaide.
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 – 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.