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.
2017-2020 Award: National Science Foundation Graduate Research Fellow
2019 Award: ARCS Scholarship
2018 Award: ARCS Scholarship
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 recently awarded an NSF graduate research fellowship to determine dietary preferences and microbiome signatures of the New Mexico meadow jumping mouse across the species’ distribution.
José Gabriel Martinez-Fonseca
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.
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 am an undergraduate majoring in Biology at NAU. As a member of the Ancient DNA Core, my projects start in the School of Forestry’s Ancient DNA Lab, where I handle and extract DNA from sensitive samples, and finish at PMI, where I amplify gene targets of interest. I am currently working on a project that extracts DNA from sediment cores and uses metagenomics and metabarcoding to identify plant and animal species in order to understand past ecosystems. Additionally, I assist with the Bat Ecology & Genetics Lab’s Species from Feces projects, which involves analyzing DNA from bat guano to reveal the species that produced it. This technique is noninvasive, and the information gathered from the process can be used to help track, understand, and protect bats species. My ultimate career goal is to continue contributing to research, and I’m excited to see where my experiences here take me.
2019 Award: NAU Biology’s Pacius Award
2018 Award: Recipient of an Office of Undergraduate Research Mini Grant
I am a senior in the NAU honors program pursuing 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 focuses on 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 aim to barcode 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 assist 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 has expanded my understanding of ecological and genetic research; I intend to continue studying Biology to increase knowledge of lesser known species and their relationships to the environment.
Undergraduate Genetics Researcher – Team Wombat
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’m a senior Biology major at NAU and began working with the Bat Ecology & Genetics Lab (BEGL) last fall through the Intern 2 Scholars program, successfully organizing thousands of bat team genetic samples in -80C freezers and refining our Access database (‘BEGLbase’). In January 2018 I will begin the genetic portion of a follow-up study to Dr. Walker’s Ph.D. research in the early 2000’s, which was the largest non-invasive genetic study of the time and uncovered social structure and population dynamics of South Australia’s southern hairy-nosed wombat (Lasiorhinus latifrons). Because the species is long-lived (over 30 years in the wild) and Dr. Walker’s genetic methods identify all wombats in an area, we can determine if the same individuals are still alive, how their use of space differs from 16 years ago, and whether population size has changed after episodes of drought and mange. To this end, the Walker Lab collected hair samples from Brookfield Conservation Park in April 2017, and we now have DNA extractions from 810 hairs. This will be one of the few studies of Australian wildlife that follows individuals through time
Genetics research specialists
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.
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
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.
Master’s Degree in Forestry, Spring 2016; 2015 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.
B.S. Forestry, Spring 2014; 2013 recipient of NAU’s 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.