Q&A: The Molecular Ecology Lab at the USGS Alaska Science Center Active
The Molecular Ecology Lab at the USGS Alaska Science Center provides genetic information on the health and status of biological resources for diverse local, state, and federal partners. Hypothesis-driven research projects are designed to fill data gaps and inform decisions for Department of Interior and other management agencies. The Molecular Ecology Lab research portfolio currently includes projects pertaining to wildlife health and disease, population genetics, and environmental DNA (eDNA).
Return to USGS Alaska Q&A Series
The USGS provides timely and impartial science information for decision-makers using a wide variety of data types and analytical methods. At the USGS Alaska Science Center, genetic information is one of the primary research directions available to partners and USGS staff to address natural resource questions. The Molecular Ecology Lab has been a critical component of the USGS Alaska Science Center for decades and in late 2021, the Center announced a new Director of the lab who began bringing on new staff to continue important research.
In this Q&A, we introduce new lab members, talk about plans for the research directions of the lab, and highlight the skills and capabilities of the lab that are available to USGS staff and our partners for addressing their science needs.
In October 2021, Dr. Andy Ramey became the new Director of the Molecular Ecology Lab. Though new to this position, Andy has been with the Alaska Science Center for 20 years, much of which has been spent leading research on wildlife health and disease supporting projects pertaining to the population genetics of fish and wildlife. Also in October, Bobbi Pierson stepped into the role as the new Lab Manager, a natural progression given her extensive experience working on projects pertaining to the population genetics wildlife. Meanwhile, Dr. Damian Menning is continuing in his role as a Research Geneticist, focusing on eDNA projects and Dr. Christina Ahlstrom, Geneticist, continues to lead wildlife health and disease-focused projects. Other USGS staff members also continue to support the Molecular Ecology Lab mission in part-time roles.
Three new full-time staff members joined the Molecular Ecology Lab at the end of 2021 and beginning of 2022. Dr. Laura Scott, most recently from New Orleans, and Dr. Cherie McKeeman, from British Columbia, Canada, were hired as Recent Graduates through Pathways Program and Dr. Eleni Petrou, from Seattle, was hired as a Geneticist.
Q: Can you talk about the current research directions of the lab and what capabilities are available in the lab to USGS staff and our partners?
Andy Ramey: The Alaska Science Center Molecular Ecology Lab is currently pursuing research on wildlife health and disease, population genetics, and eDNA. Lab staff are using genomic tools to better understand:
- Ecology of avian influenza viruses in wild birds and the environment
- Distribution and drivers of antimicrobial resistant bacteria in wildlife and on public lands
- Current and potential future distribution of Cryptosporidium and Giardia parasites affecting wildlife in Alaska
- Most efficient molecular tools for sexing wild birds
- Number and genetic relatedness of black bears participating in refuse-foraging and human-bear conflicts in areas of southcentral Alaska
- Distribution of seagrass pathogens in Alaska
- Most efficient molecular tools for detecting fish assemblages in Alaska using eDNA
Staff in the Molecular Ecology Lab are interested and equipped to pursue new hypothesis driven research projects developed with partner input using next-generation sequencing, whole genome sequencing, quantitative PCR, metabarcoding markers, and custom bioinformatics pipelines as well as more traditional genetic tools.
Q: For the new staff, can you briefly describe the research you are doing in the Molecular Ecology Lab?
Laura Scott: I am working on wildlife health and disease projects in the Molecular Ecology Lab. Currently, my work focuses on pathogens in wildlife and the environment. Specifically, I investigate avian influenza in wild birds and antimicrobial resistance in surface water and birds. I have also teamed up with my population genetics colleagues on a project attempting to develop an accurate, high-throughput molecular test to determine the sex of wild birds of Alaska using blood samples.
Cherie McKeeman: I am working on a variety of projects in the Molecular Ecology Lab, with a focus on population genetics. I have a background in using genetics to understand the relationship between species and their environments. For example, I examined the gut contents of larval frogs who inhabit streams in the coastal mountains using the DNA in their digestive tracts. I am also helping to organize archived samples in the Molecular Ecology Lab, which is encouraging me to think of how existing samples might be incorporated in interesting new projects to address research priorities.
Eleni Petrou: My expertise is in population genomics, molecular ecology, and the reconstruction of past environments and social-ecological systems using ancient DNA. Much of my previous work has focused on management and conservation issues in marine fisheries and how those impact human communities. At the USGS Alaska Science Center, I will expand this research to terrestrial ecosystems and continue to explore similar themes.
Q: What does your research look like day-to-day?
Laura: Mostly I work in the lab, but I also do epidemiological analyses on the computer. My work in the lab involves a variety of genomic technologies. For most methods, extracting DNA or RNA from a sample is required to obtain the material needed to analyze genetic questions. For targeted genomic questions (i.e., “How many specific antimicrobial genes are in this water sample?”), I utilize quantitative PCR. I can also use qPCR for detecting pathogens or any other known gene target. I also do a fair share of whole genome sequencing. Currently, I use this to sequence avian influenza viruses or antimicrobial resistant bacteria.
Cherie: Currently, most days are spent making sure project data is reliable and of high quality. I also spend time evaluating appropriate analysis techniques or the best way to visually represent the data. Any days I can spend observing species in their environments are outstanding and helpful.
Eleni: It really depends on the day! Sometimes I am in the laboratory analyzing samples, while other times I am brainstorming with colleagues, writing code for bioinformatic analyses, designing experiments, or interpreting data. A smaller portion of my time is spent collecting samples from the field or engaging in science outreach, but I enjoy those activities very much.
Q: Where did you work prior to this position and what did you do?
Laura: I recently completed my PhD in environmental health at Tulane University School of Public Health and Tropical Medicine, where I also completed my MS in epidemiology. My research highlighted the effects that human activity has on microbes in the environment. I worked with the National Park Service to elucidate how visitors might bring antibiotic resistant bacteria to soil and water in national parks. That research also involved determining the efficacy of backcountry toilets, measuring harmful algal blooms, and disease outbreak investigations. During the pandemic I led a team to screen wastewater across southeastern Louisiana, New Orleanian hospitals, and Tulane University for the COVID-19 virus as an early warning system. Before graduate school I worked at the Oklahoma Medical Research Foundation, a non-profit biomedical research institute, as a transmission electron microscopist and histology technician.
Cherie: I did my PhD in the Natural Resources and Environmental Science Graduate Program at the University of Northern British Columbia in Prince George, BC, Canada. I worked on a variety of research projects focused on the coastal tailed frog (Ascaphus truei), a unique species endemic to the streams and forests of the Coastal and Cascade mountains. Broadly, I used genetics to better understand the northern expansion of the species, as well as the feeding ecology of larvae. I loved the work because I got to know a unique species and spend time in the breathtaking Coastal Mountains.
Eleni: Prior to this position, I was a postdoctoral researcher at the School of Aquatic and Fishery Sciences at the University of Washington. I studied patterns of biodiversity, dispersal, and trophic connectivity in Pacific herring using genomics. I loved that job because I had the opportunity to be a part of a wildly interdisciplinary team that included archaeologists, anthropologists, and fisheries ecologists. I also had the chance to collaborate with several First Nations to assess patterns of herring population structure in their traditional waters.
Q: What do you like best about your work?
Laura: I am always excited when people approach me while working in the field to inquire about my work. They are interested to know about water quality and are usually surprised to learn that contaminants like antibiotic resistant bacteria could be present. I am very flattered when the public finds disease ecology interesting. It is always a win if a visitor walks away with some new knowledge about the ecosystem in which they are recreating, particularly if that knowledge will keep them and the ecosystem a little safer. I am excited to keep working with agency partners on similar questions in the future.
Cherie: The unexpected interactions, experiences, and connections. For example, I once was transporting a coastal tailed frog from Canada to the United States to get its genome sequenced. It was a stressful situation that involved a lot of planning. At the international border, I gave an impromptu lesson on the frogs to border patrol agents. They made excellent students, their interest in frogs was palpable, and all the stress of the situation melted away. Getting to see the excitement that people have for wildlife is one of the best parts of my job.
Eleni: Sometimes, after a lot of effort, all the data snaps into place and you glimpse an unexpected and beautiful pattern in nature. That is one of my favorite parts of the job.
The Molecular Ecology Lab at the USGS Alaska Science Center provides genetic information on the health and status of biological resources for diverse local, state, and federal partners. Hypothesis-driven research projects are designed to fill data gaps and inform decisions for Department of Interior and other management agencies. The Molecular Ecology Lab research portfolio currently includes projects pertaining to wildlife health and disease, population genetics, and environmental DNA (eDNA).
Return to USGS Alaska Q&A Series
The USGS provides timely and impartial science information for decision-makers using a wide variety of data types and analytical methods. At the USGS Alaska Science Center, genetic information is one of the primary research directions available to partners and USGS staff to address natural resource questions. The Molecular Ecology Lab has been a critical component of the USGS Alaska Science Center for decades and in late 2021, the Center announced a new Director of the lab who began bringing on new staff to continue important research.
In this Q&A, we introduce new lab members, talk about plans for the research directions of the lab, and highlight the skills and capabilities of the lab that are available to USGS staff and our partners for addressing their science needs.
In October 2021, Dr. Andy Ramey became the new Director of the Molecular Ecology Lab. Though new to this position, Andy has been with the Alaska Science Center for 20 years, much of which has been spent leading research on wildlife health and disease supporting projects pertaining to the population genetics of fish and wildlife. Also in October, Bobbi Pierson stepped into the role as the new Lab Manager, a natural progression given her extensive experience working on projects pertaining to the population genetics wildlife. Meanwhile, Dr. Damian Menning is continuing in his role as a Research Geneticist, focusing on eDNA projects and Dr. Christina Ahlstrom, Geneticist, continues to lead wildlife health and disease-focused projects. Other USGS staff members also continue to support the Molecular Ecology Lab mission in part-time roles.
Three new full-time staff members joined the Molecular Ecology Lab at the end of 2021 and beginning of 2022. Dr. Laura Scott, most recently from New Orleans, and Dr. Cherie McKeeman, from British Columbia, Canada, were hired as Recent Graduates through Pathways Program and Dr. Eleni Petrou, from Seattle, was hired as a Geneticist.
Q: Can you talk about the current research directions of the lab and what capabilities are available in the lab to USGS staff and our partners?
Andy Ramey: The Alaska Science Center Molecular Ecology Lab is currently pursuing research on wildlife health and disease, population genetics, and eDNA. Lab staff are using genomic tools to better understand:
- Ecology of avian influenza viruses in wild birds and the environment
- Distribution and drivers of antimicrobial resistant bacteria in wildlife and on public lands
- Current and potential future distribution of Cryptosporidium and Giardia parasites affecting wildlife in Alaska
- Most efficient molecular tools for sexing wild birds
- Number and genetic relatedness of black bears participating in refuse-foraging and human-bear conflicts in areas of southcentral Alaska
- Distribution of seagrass pathogens in Alaska
- Most efficient molecular tools for detecting fish assemblages in Alaska using eDNA
Staff in the Molecular Ecology Lab are interested and equipped to pursue new hypothesis driven research projects developed with partner input using next-generation sequencing, whole genome sequencing, quantitative PCR, metabarcoding markers, and custom bioinformatics pipelines as well as more traditional genetic tools.
Q: For the new staff, can you briefly describe the research you are doing in the Molecular Ecology Lab?
Laura Scott: I am working on wildlife health and disease projects in the Molecular Ecology Lab. Currently, my work focuses on pathogens in wildlife and the environment. Specifically, I investigate avian influenza in wild birds and antimicrobial resistance in surface water and birds. I have also teamed up with my population genetics colleagues on a project attempting to develop an accurate, high-throughput molecular test to determine the sex of wild birds of Alaska using blood samples.
Cherie McKeeman: I am working on a variety of projects in the Molecular Ecology Lab, with a focus on population genetics. I have a background in using genetics to understand the relationship between species and their environments. For example, I examined the gut contents of larval frogs who inhabit streams in the coastal mountains using the DNA in their digestive tracts. I am also helping to organize archived samples in the Molecular Ecology Lab, which is encouraging me to think of how existing samples might be incorporated in interesting new projects to address research priorities.
Eleni Petrou: My expertise is in population genomics, molecular ecology, and the reconstruction of past environments and social-ecological systems using ancient DNA. Much of my previous work has focused on management and conservation issues in marine fisheries and how those impact human communities. At the USGS Alaska Science Center, I will expand this research to terrestrial ecosystems and continue to explore similar themes.
Q: What does your research look like day-to-day?
Laura: Mostly I work in the lab, but I also do epidemiological analyses on the computer. My work in the lab involves a variety of genomic technologies. For most methods, extracting DNA or RNA from a sample is required to obtain the material needed to analyze genetic questions. For targeted genomic questions (i.e., “How many specific antimicrobial genes are in this water sample?”), I utilize quantitative PCR. I can also use qPCR for detecting pathogens or any other known gene target. I also do a fair share of whole genome sequencing. Currently, I use this to sequence avian influenza viruses or antimicrobial resistant bacteria.
Cherie: Currently, most days are spent making sure project data is reliable and of high quality. I also spend time evaluating appropriate analysis techniques or the best way to visually represent the data. Any days I can spend observing species in their environments are outstanding and helpful.
Eleni: It really depends on the day! Sometimes I am in the laboratory analyzing samples, while other times I am brainstorming with colleagues, writing code for bioinformatic analyses, designing experiments, or interpreting data. A smaller portion of my time is spent collecting samples from the field or engaging in science outreach, but I enjoy those activities very much.
Q: Where did you work prior to this position and what did you do?
Laura: I recently completed my PhD in environmental health at Tulane University School of Public Health and Tropical Medicine, where I also completed my MS in epidemiology. My research highlighted the effects that human activity has on microbes in the environment. I worked with the National Park Service to elucidate how visitors might bring antibiotic resistant bacteria to soil and water in national parks. That research also involved determining the efficacy of backcountry toilets, measuring harmful algal blooms, and disease outbreak investigations. During the pandemic I led a team to screen wastewater across southeastern Louisiana, New Orleanian hospitals, and Tulane University for the COVID-19 virus as an early warning system. Before graduate school I worked at the Oklahoma Medical Research Foundation, a non-profit biomedical research institute, as a transmission electron microscopist and histology technician.
Cherie: I did my PhD in the Natural Resources and Environmental Science Graduate Program at the University of Northern British Columbia in Prince George, BC, Canada. I worked on a variety of research projects focused on the coastal tailed frog (Ascaphus truei), a unique species endemic to the streams and forests of the Coastal and Cascade mountains. Broadly, I used genetics to better understand the northern expansion of the species, as well as the feeding ecology of larvae. I loved the work because I got to know a unique species and spend time in the breathtaking Coastal Mountains.
Eleni: Prior to this position, I was a postdoctoral researcher at the School of Aquatic and Fishery Sciences at the University of Washington. I studied patterns of biodiversity, dispersal, and trophic connectivity in Pacific herring using genomics. I loved that job because I had the opportunity to be a part of a wildly interdisciplinary team that included archaeologists, anthropologists, and fisheries ecologists. I also had the chance to collaborate with several First Nations to assess patterns of herring population structure in their traditional waters.
Q: What do you like best about your work?
Laura: I am always excited when people approach me while working in the field to inquire about my work. They are interested to know about water quality and are usually surprised to learn that contaminants like antibiotic resistant bacteria could be present. I am very flattered when the public finds disease ecology interesting. It is always a win if a visitor walks away with some new knowledge about the ecosystem in which they are recreating, particularly if that knowledge will keep them and the ecosystem a little safer. I am excited to keep working with agency partners on similar questions in the future.
Cherie: The unexpected interactions, experiences, and connections. For example, I once was transporting a coastal tailed frog from Canada to the United States to get its genome sequenced. It was a stressful situation that involved a lot of planning. At the international border, I gave an impromptu lesson on the frogs to border patrol agents. They made excellent students, their interest in frogs was palpable, and all the stress of the situation melted away. Getting to see the excitement that people have for wildlife is one of the best parts of my job.
Eleni: Sometimes, after a lot of effort, all the data snaps into place and you glimpse an unexpected and beautiful pattern in nature. That is one of my favorite parts of the job.