FORT researchers Sara Oyler-McCance and Jenny Fike discuss genetic data in the Molecular Ecology Lab.
The Molecular Ecology Laboratory applies innovative genetic and genomic technologies to address a variety of complex questions and issues facing the Nation's natural resources. While we continually update the scale and efficiency of laboratory procedures to meet stakeholder needs, we must also be innovative and flexible in addressing those needs that have no off-the-shelf solution.
We help characterize known and emerging pathogens that impact natural resources such as game fish, avian species, and pollinators. These innovations arise out of close partnership between the benchtop and data analysis realms. Our lab also develops and evaluates novel methods for detecting unobserved species (such as invasive species) via the trace DNA they leave in their environment. We identify signatures of local adaptation and the means to monitor these critical genomic regions in populations. We apply cutting-edge sequencing and bioinformatic methods to generate reference-quality genome assemblies that support diverse partnerships and research goals.
Pathogen Genomics
Pathogen Genomics
Many commercially important animal species as well as natural populations are impacted by pathogens that are poorly understood and difficult to detect. Metagenomics is the field of identifying microbial genomes present in a host species or an environmental sample. Application of metagenomics to fishery and wildlife disease include identifying novel viruses associated with symptoms, monitoring the dynamics of known viruses and how they spread in a population, and characterizing the immune response of hosts in different environments or at different life-history stages.
Environmental DNA (eDNA)
Environmental DNA (eDNA)
Media
Sources/Usage: Some content may have restrictions. View Media Details
Environmental DNA (eDNA) is organismal DNA that can be found in the environment. Environmental DNA originates from cellular material shed by organisms (via skin, excrement, etc.) into aquatic or terrestrial environments that can be sampled and monitored using new molecular methods. Such methodology is important for the early detection of invasive species as well as the detection of rare and cryptic species.
Genome sequencing and genomics
Genome sequencing and genomics
The latest generation of sequencing technologies now allows high-quality reference genome sequences to be developed by a single lab with modest investment. For research programs such as ours that that use genetic methods, the benefits of a reference genome are many and profound. In our lab we use genomics to assess disease resistance and outbreaks, diets, demography, and even adaptation
Landscape Genetics
Landscape Genetics
Media
Sources/Usage: Public Domain. View Media Details
The field of landscape genetics provides information about the interaction between landscape features and microevolutionary processes such as gene flow, genetic drift, and selection which can help guide efficient planning.
Molecular Tagging
Molecular Tagging
Molecular tagging is a new application of molecular genetic techniques to traditional mark-recapture methodology designed to address situations where traditional methods fail. In such studies, non-invasively collected samples (such as feces, feathers, or fur) are used as a source of DNA that is then genotyped at multiple loci such that each individual animal can be uniquely identified. Thus, each individual’s DNA represents a unique tag analogous to a band or other mark used in traditional mark-recapture studies.
Population Models
Population Models
Media
Sources/Usage: Public Domain. View Media Details
Population models can incorporate genetic data to assess potential impacts of different management strategies on connectivity, effective population size, and genetic diversity. Models that can guide the selection, implementation, and anticipated outcome of management actions are powerful tools for managers to maintain healthy wildlife populations amidst the complexities of balancing multiple land uses.
Diet Analysis
Diet Analysis
Genetic “barcodes” are short DNA sequences, obtained from many organisms using a single “universal” method. These barcodes are then compared to genetic databases to identify the source of the DNA. When applied to samples containing may different sources mixed together, a semi-quantitative table of the DNA sources can be obtained. This metabarcoding approach is frequently used to characterize the diet of focal species, in order to better understand habitat requirements and trophic interactions. Metabarcoding data can often be obtained more quickly, with higher throughput, and sometimes with greater resolution, than traditional methods of direct observation.
Below are other science projects associated with this project.
Developing and evaluating a point-of-use environmental DNA test for rapid field detection of highly invasive brown treesnakes
New terrestrial environmental DNA (eDNA) sampling techniques are sensitive tools for early detection of the highly invasive brown treesnakes (BTS). In a new collaborative research effort involving four USGS science centers, scientists have initiated the development of an innovative point-of-use (POU) assay for BTS. POU assays are tests that can be run in the field with minimal equipment and no...
Characterizing the environmental drivers of range-wide gene flow for greater sage-grouse
Widespread anthropogenic development in the sagebrush steppe and shifting climatic patterns have contributed to the observed dramatic declines of the greater sage-grouse since the 1960s. Alteration of the sagebrush habitat can affect many aspects of the species life history, including survival and local resource use. Over many years, the combined effects of landscape composition on these traits...
Development and application of genomic resources for the greater sage-grouse
The greater sage-grouse is a sagebrush-obligate species that has experienced dramatic range-wide declines since the 1960s, causing significant conservation concern. Genetic information has refined our understanding of population structure, the levels of inbreeding or relatedness, allowed the ability to monitor for change over time, and has been used to understand the outcome of management actions...
Synthesis of sage-grouse genetic information to support conservation and land management actions
Sage-grouse, iconic birds of the American West, have experienced dramatic reductions and fragmentation of habitat, resulting in significant conservation concern. Genetic information can help inform priorities for protection and habitat restoration as well as strategies for translocations, but may be difficult for resource managers to find, interpret, and use in their decision making. In this work...
Genomic Scans for Local Adaptation in Greater Sage-Grouse
USGS scientists are identifying local adaptation in sage-grouse by modeling allelic variation at large numbers of single-nucleotide polymorphisms (SNPs) in relation to environmental and climate variables.
Integration of Genetic and Demographic Data to Assess the Relative Importance of Connectivity and Habitat in Sage-Grouse Populations
Using the existing rangewide genetic and demographic data, scientists from the USGS, USDA Forest Service, and University of Waterloo will assess the relative contributions of habitat and genetic connectivity to lek size and stability.
Using Genetic Analyses To Inform On-The-Ground Conservation for Multiple Sagebrush-Associated Wildlife Species
Recent analyses of greater sage-grouse genetics have delineated areas of key genetic connectivity for this species and provided a prioritization tool for conservation and restoration of habitats essential for genetic exchange.
Non-invasive Genetic Sampling of Free-roaming Horses to Estimate Population Size, Genetic Diversity, and Consumption of Invasive Species
Molecular tagging is a new application of molecular genetic techniques to traditional mark-recapture methodology designed to address situations where traditional methods fail. In such studies, non-invasively collected samples (such as feces, feathers, or fur) are used as a source of DNA that is then genotyped at multiple loci such that each individual animal can be uniquely identified. Thus, each...
Incorporating Genetic Data into Spatially-explicit Population Viability Models for Gunnison Sage-grouse
This goal of this study is to develop a spatially explicit habitat-population modeling framework to assess the viability of Gunnison sage-grouse and each of the seven populations (Gunnison Basin and six satellite populations).
Genomics and Bioinformatics
Genetic analysis is increasingly used to understand ecosystem processes and inform conservation, management, and policy. I assist USGS researchers and their collaborators in the design, analysis, and interpretation of high-throughput genetic studies. Common applications include: detecting genes responsive to particular environmental stressors in a sentinel species or species of conservation...
Environmental DNA (eDNA) Sampling Improves Occurrence and Detection Estimates of Invasive Burmese Pythons and Other Constrictor Snakes in Florida
Environmental DNA (eDNA) is organismal DNA that can be found in the environment. Environmental DNA originates from cellular material shed by organisms (via skin, excrement, etc.) into aquatic or terrestrial environments that can be sampled and monitored using new molecular methods. Such methodology is important for the early detection of invasive species as well as the detection of rare and...
Landscape Influence on Gene Flow in Greater Sage-grouse
US Geological Survey scientists and collaborators are using genetic information contained in sage-grouse feathers collected at leks to define the rangewide network of breeding populations.
Below are multimedia items associated with this project.
Researchers look at genetic data in the Molecular Ecology Lab
FORT researchers Sara Oyler-McCance and Jenny Fike discuss genetic data in the Molecular Ecology Lab.
Sara Oyler-McCance working in the Molecular Ecology Lab
Sara Oyler-McCance uses a pipette to complete research in the FORT Molecular Ecology Lab.
Sara Oyler-McCance uses a pipette to complete research in the FORT Molecular Ecology Lab.
Sara Oyler-McCance and Jenny Fike in the Molecular Ecology Lab
Sara Oyler-McCance and Jenny Fike in the FORT Molecular Ecology Lab, where they complete research on the genetics and genomics of natural resources.
Sara Oyler-McCance and Jenny Fike in the FORT Molecular Ecology Lab, where they complete research on the genetics and genomics of natural resources.
The Molecular Ecology Laboratory applies innovative genetic and genomic technologies to address a variety of complex questions and issues facing the Nation's natural resources. While we continually update the scale and efficiency of laboratory procedures to meet stakeholder needs, we must also be innovative and flexible in addressing those needs that have no off-the-shelf solution.
We help characterize known and emerging pathogens that impact natural resources such as game fish, avian species, and pollinators. These innovations arise out of close partnership between the benchtop and data analysis realms. Our lab also develops and evaluates novel methods for detecting unobserved species (such as invasive species) via the trace DNA they leave in their environment. We identify signatures of local adaptation and the means to monitor these critical genomic regions in populations. We apply cutting-edge sequencing and bioinformatic methods to generate reference-quality genome assemblies that support diverse partnerships and research goals.
Pathogen Genomics
Pathogen Genomics
Many commercially important animal species as well as natural populations are impacted by pathogens that are poorly understood and difficult to detect. Metagenomics is the field of identifying microbial genomes present in a host species or an environmental sample. Application of metagenomics to fishery and wildlife disease include identifying novel viruses associated with symptoms, monitoring the dynamics of known viruses and how they spread in a population, and characterizing the immune response of hosts in different environments or at different life-history stages.
Environmental DNA (eDNA)
Environmental DNA (eDNA)
Media
Sources/Usage: Some content may have restrictions. View Media Details
Environmental DNA (eDNA) is organismal DNA that can be found in the environment. Environmental DNA originates from cellular material shed by organisms (via skin, excrement, etc.) into aquatic or terrestrial environments that can be sampled and monitored using new molecular methods. Such methodology is important for the early detection of invasive species as well as the detection of rare and cryptic species.
Genome sequencing and genomics
Genome sequencing and genomics
The latest generation of sequencing technologies now allows high-quality reference genome sequences to be developed by a single lab with modest investment. For research programs such as ours that that use genetic methods, the benefits of a reference genome are many and profound. In our lab we use genomics to assess disease resistance and outbreaks, diets, demography, and even adaptation
Landscape Genetics
Landscape Genetics
Media
Sources/Usage: Public Domain. View Media Details
The field of landscape genetics provides information about the interaction between landscape features and microevolutionary processes such as gene flow, genetic drift, and selection which can help guide efficient planning.
Molecular Tagging
Molecular Tagging
Molecular tagging is a new application of molecular genetic techniques to traditional mark-recapture methodology designed to address situations where traditional methods fail. In such studies, non-invasively collected samples (such as feces, feathers, or fur) are used as a source of DNA that is then genotyped at multiple loci such that each individual animal can be uniquely identified. Thus, each individual’s DNA represents a unique tag analogous to a band or other mark used in traditional mark-recapture studies.
Population Models
Population Models
Media
Sources/Usage: Public Domain. View Media Details
Population models can incorporate genetic data to assess potential impacts of different management strategies on connectivity, effective population size, and genetic diversity. Models that can guide the selection, implementation, and anticipated outcome of management actions are powerful tools for managers to maintain healthy wildlife populations amidst the complexities of balancing multiple land uses.
Diet Analysis
Diet Analysis
Genetic “barcodes” are short DNA sequences, obtained from many organisms using a single “universal” method. These barcodes are then compared to genetic databases to identify the source of the DNA. When applied to samples containing may different sources mixed together, a semi-quantitative table of the DNA sources can be obtained. This metabarcoding approach is frequently used to characterize the diet of focal species, in order to better understand habitat requirements and trophic interactions. Metabarcoding data can often be obtained more quickly, with higher throughput, and sometimes with greater resolution, than traditional methods of direct observation.
Below are other science projects associated with this project.
Developing and evaluating a point-of-use environmental DNA test for rapid field detection of highly invasive brown treesnakes
New terrestrial environmental DNA (eDNA) sampling techniques are sensitive tools for early detection of the highly invasive brown treesnakes (BTS). In a new collaborative research effort involving four USGS science centers, scientists have initiated the development of an innovative point-of-use (POU) assay for BTS. POU assays are tests that can be run in the field with minimal equipment and no...
Characterizing the environmental drivers of range-wide gene flow for greater sage-grouse
Widespread anthropogenic development in the sagebrush steppe and shifting climatic patterns have contributed to the observed dramatic declines of the greater sage-grouse since the 1960s. Alteration of the sagebrush habitat can affect many aspects of the species life history, including survival and local resource use. Over many years, the combined effects of landscape composition on these traits...
Development and application of genomic resources for the greater sage-grouse
The greater sage-grouse is a sagebrush-obligate species that has experienced dramatic range-wide declines since the 1960s, causing significant conservation concern. Genetic information has refined our understanding of population structure, the levels of inbreeding or relatedness, allowed the ability to monitor for change over time, and has been used to understand the outcome of management actions...
Synthesis of sage-grouse genetic information to support conservation and land management actions
Sage-grouse, iconic birds of the American West, have experienced dramatic reductions and fragmentation of habitat, resulting in significant conservation concern. Genetic information can help inform priorities for protection and habitat restoration as well as strategies for translocations, but may be difficult for resource managers to find, interpret, and use in their decision making. In this work...
Genomic Scans for Local Adaptation in Greater Sage-Grouse
USGS scientists are identifying local adaptation in sage-grouse by modeling allelic variation at large numbers of single-nucleotide polymorphisms (SNPs) in relation to environmental and climate variables.
Integration of Genetic and Demographic Data to Assess the Relative Importance of Connectivity and Habitat in Sage-Grouse Populations
Using the existing rangewide genetic and demographic data, scientists from the USGS, USDA Forest Service, and University of Waterloo will assess the relative contributions of habitat and genetic connectivity to lek size and stability.
Using Genetic Analyses To Inform On-The-Ground Conservation for Multiple Sagebrush-Associated Wildlife Species
Recent analyses of greater sage-grouse genetics have delineated areas of key genetic connectivity for this species and provided a prioritization tool for conservation and restoration of habitats essential for genetic exchange.
Non-invasive Genetic Sampling of Free-roaming Horses to Estimate Population Size, Genetic Diversity, and Consumption of Invasive Species
Molecular tagging is a new application of molecular genetic techniques to traditional mark-recapture methodology designed to address situations where traditional methods fail. In such studies, non-invasively collected samples (such as feces, feathers, or fur) are used as a source of DNA that is then genotyped at multiple loci such that each individual animal can be uniquely identified. Thus, each...
Incorporating Genetic Data into Spatially-explicit Population Viability Models for Gunnison Sage-grouse
This goal of this study is to develop a spatially explicit habitat-population modeling framework to assess the viability of Gunnison sage-grouse and each of the seven populations (Gunnison Basin and six satellite populations).
Genomics and Bioinformatics
Genetic analysis is increasingly used to understand ecosystem processes and inform conservation, management, and policy. I assist USGS researchers and their collaborators in the design, analysis, and interpretation of high-throughput genetic studies. Common applications include: detecting genes responsive to particular environmental stressors in a sentinel species or species of conservation...
Environmental DNA (eDNA) Sampling Improves Occurrence and Detection Estimates of Invasive Burmese Pythons and Other Constrictor Snakes in Florida
Environmental DNA (eDNA) is organismal DNA that can be found in the environment. Environmental DNA originates from cellular material shed by organisms (via skin, excrement, etc.) into aquatic or terrestrial environments that can be sampled and monitored using new molecular methods. Such methodology is important for the early detection of invasive species as well as the detection of rare and...
Landscape Influence on Gene Flow in Greater Sage-grouse
US Geological Survey scientists and collaborators are using genetic information contained in sage-grouse feathers collected at leks to define the rangewide network of breeding populations.
Below are multimedia items associated with this project.
Researchers look at genetic data in the Molecular Ecology Lab
FORT researchers Sara Oyler-McCance and Jenny Fike discuss genetic data in the Molecular Ecology Lab.
FORT researchers Sara Oyler-McCance and Jenny Fike discuss genetic data in the Molecular Ecology Lab.
Sara Oyler-McCance working in the Molecular Ecology Lab
Sara Oyler-McCance uses a pipette to complete research in the FORT Molecular Ecology Lab.
Sara Oyler-McCance uses a pipette to complete research in the FORT Molecular Ecology Lab.
Sara Oyler-McCance and Jenny Fike in the Molecular Ecology Lab
Sara Oyler-McCance and Jenny Fike in the FORT Molecular Ecology Lab, where they complete research on the genetics and genomics of natural resources.
Sara Oyler-McCance and Jenny Fike in the FORT Molecular Ecology Lab, where they complete research on the genetics and genomics of natural resources.