The Molecular Ecology Laboratory applies genetic and genomic technologies to address a variety of complex questions and conservation issues facing the management of the Nation's fish and wildlife resources. Together with our partners, we design and implement studies to document genetic diversity and the distribution of genetic variation among individuals, populations, and species. Information from these studies is used to support wildlife-management planning and conservation actions. Current and past studies have provided information to assess taxonomic boundaries, inform listing decisions made under the Endangered Species Act, identify unique or genetically depauperate populations, estimate population size or survival rates, develop management or recovery plans, breed wildlife in captivity, relocate wildlife from one location to another, and assess the effects of environmental change.
Conservation genomics is a new field of science that applies novel whole-genome sequencing technology to problems in conservation biology. Rapidly advancing molecular technologies are revolutionizing wildlife ecology, greatly expanding our understanding of wildlife and their interactions with the environment. In the same way that molecular tools such as microsatellites revolutionized wildlife management in the past, evolving genomic-level data collection techniques are beginning to offer powerful ways to assess biodiversity, taxonomy, hybridization, diets, demography, disease resistance and outbreaks, and even local adaptation.
Landscape genetics is a recently developed discipline that involves the merger of molecular population genetics and landscape ecology. The goal of this new field of study is to provide information about the interaction between landscape features and microevolutionary processes such as gene flow, genetic drift, and selection allowing for the understanding of processes that generate genetic structure across space.
Population genetics is an area of research that examines the distribution of genetic variation and levels of genetic diversity within and between populations. This information provides insights into the level of connectedness of populations throughout a species’ range and can be used to identify unique populations or those with low levels of genetic diversity.
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.
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.
Taxonomic uncertainty can be assessed using genetic data, along with other lines of evidence (such as morphological and behavioral characteristics). Such data can be used to identify and assess taxonomic boundaries (species, subspecies, hybrids) and in many cases redefine them. Such delineations are highly relevant for species status determinations (endangered, threatened, or at-risk).
Family Relationships and Mating Systems
Family relationships and mating systems can be investigated and defined using genetic data. This information is potentially important for conservation and management as it may influence effective population size and levels of genetic diversity.
Population models can incorporate genetic data to assess potential impacts of different management strategies on connectivity, effective population size, and genetic diversity.
Below are other science projects associated with this project.
Real-World Applications of Molecular Genetics
Conservation Genomics
Landscape Genetics
Population Genetics
Molecular Tagging
Environmental DNA (eDNA) Sampling Improves Occurrence and Detection Estimates of Invasive Burmese Pythons and Other Constrictor Snakes in Florida
Taxonomic Uncertainty
Family Relationships and Mating Systems
Population Models
Below are multimedia items associated with this project.
Below are publications associated with this project.
Critical considerations for the application of environmental DNA methods to detect aquatic species
A field ornithologist’s guide to genomics: Practical considerations for ecology and conservation
Rangewide genetic analysis of Lesser Prairie-Chicken reveals population structure, range expansion, and possible introgression
Contrasting evolutionary histories of MHC class I and class II loci in grouse—Effects of selection and gene conversion
Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds
Potential demographic and genetic effects of a sterilant applied to wild horse mares
Landscape characteristics influencing the genetic structure of greater sage-grouse within the stronghold of their range: a holistic modeling approach
Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive Burmese pythons
Development of 13 microsatellites for Gunnison Sage-grouse (Centrocercus minimus) using next-generation shotgun sequencing and their utility in Greater Sage-grouse (Centrocercus urophasianus)
Genomic single-nucleotide polymorphisms confirm that Gunnison and Greater sage-grouse are genetically well differentiated and that the Bi-State population is distinct
Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences
Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies
Below are partners associated with this project.
- Overview
The Molecular Ecology Laboratory applies genetic and genomic technologies to address a variety of complex questions and conservation issues facing the management of the Nation's fish and wildlife resources. Together with our partners, we design and implement studies to document genetic diversity and the distribution of genetic variation among individuals, populations, and species. Information from these studies is used to support wildlife-management planning and conservation actions. Current and past studies have provided information to assess taxonomic boundaries, inform listing decisions made under the Endangered Species Act, identify unique or genetically depauperate populations, estimate population size or survival rates, develop management or recovery plans, breed wildlife in captivity, relocate wildlife from one location to another, and assess the effects of environmental change.
A male Greater Sage-grouse. Photo by: Stephen Ting, Fish and Wildlife Service. Public domain. Conservation genomics is a new field of science that applies novel whole-genome sequencing technology to problems in conservation biology. Rapidly advancing molecular technologies are revolutionizing wildlife ecology, greatly expanding our understanding of wildlife and their interactions with the environment. In the same way that molecular tools such as microsatellites revolutionized wildlife management in the past, evolving genomic-level data collection techniques are beginning to offer powerful ways to assess biodiversity, taxonomy, hybridization, diets, demography, disease resistance and outbreaks, and even local adaptation.
Sagebrush lands in southwestern Wyoming (photograph by Anna Wilson, USGS). Landscape genetics is a recently developed discipline that involves the merger of molecular population genetics and landscape ecology. The goal of this new field of study is to provide information about the interaction between landscape features and microevolutionary processes such as gene flow, genetic drift, and selection allowing for the understanding of processes that generate genetic structure across space.
A male lesser prairie-chicken. Photo by Dan Wundrock, Public domain. Population genetics is an area of research that examines the distribution of genetic variation and levels of genetic diversity within and between populations. This information provides insights into the level of connectedness of populations throughout a species’ range and can be used to identify unique populations or those with low levels of genetic diversity.
A mountain lion in a pen at the Colorado Parks and Wildlife offices in Fort Collins, CO. 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.
A brown treesnake in the grass. USGS photo. 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.
A Cascades frog perched on moss. Public domain. Taxonomic uncertainty can be assessed using genetic data, along with other lines of evidence (such as morphological and behavioral characteristics). Such data can be used to identify and assess taxonomic boundaries (species, subspecies, hybrids) and in many cases redefine them. Such delineations are highly relevant for species status determinations (endangered, threatened, or at-risk).
A female broad-tailed hummingbird visiting a flower near the Rocky Mountain Biological Laboratory in Colorado. Public domain. Family Relationships and Mating Systems
Family relationships and mating systems can be investigated and defined using genetic data. This information is potentially important for conservation and management as it may influence effective population size and levels of genetic diversity.
A female grizzly with a cub. Public domain. Population models can incorporate genetic data to assess potential impacts of different management strategies on connectivity, effective population size, and genetic diversity.
- Science
Below are other science projects associated with this project.
Real-World Applications of Molecular Genetics
Recent advances in molecular biology allow us to develop and apply the tools and concepts of molecular genetics to the conservation of biological resources. Working with our partners, we design and implement studies that provide genetic and genomic information for a broad range of applications, as detailed below.Conservation Genomics
Conservation genomics is a new field of science that applies novel whole-genome sequencing technology to problems in conservation biology. Rapidly advancing molecular technologies are revolutionizing wildlife ecology, greatly expanding our understanding of wildlife and their interactions with the environment. In the same way that molecular tools such as microsatellites revolutionized wildlife...Landscape Genetics
Landscape genetics is a recently developed discipline that involves the merger of molecular population genetics and landscape ecology. The goal of this new field of study is to provide information about the interaction between landscape features and microevolutionary processes such as gene flow, genetic drift, and selection allowing for the understanding of processes that generate genetic...Population Genetics
Population genetics is an area of research that examines the distribution of genetic variation and levels of genetic diversity within and between populations. This information provides insights into the level of connectedness of populations throughout a species’ range and can be used to identify unique populations or those with low levels of genetic diversity.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...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...Taxonomic Uncertainty
Taxonomic uncertainty can be assessed using genetic data, along with other lines of evidence (such as morphological and behavioral characteristics). Such data can be used to identify and assess taxonomic boundaries (species, subspecies, hybrids) and in many cases redefine them. Such delineations are highly relevant for species status determinations (endangered, threatened, or at-risk).Family Relationships and Mating Systems
Family relationships and mating systems can be investigated and defined using genetic data. This information is potentially important for conservation and management as it may influence effective population size and levels of genetic diversity.Population Models
Population models can incorporate genetic data to assess potential impacts of different management strategies on connectivity, effective population size, and genetic diversity. - Multimedia
Below are multimedia items associated with this project.
- Publications
Below are publications associated with this project.
Filter Total Items: 42Critical considerations for the application of environmental DNA methods to detect aquatic species
Species detection using environmental DNA (eDNA) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods, however, rAuthorsCaren S. Goldberg, Cameron R. Turner, Kristy Deiner, Katy E. Klymus, Philip Francis Thomsen, Melanie A. Murphy, Stephen F. Spear, Anna McKee, Sara J. Oyler-McCance, Robert S. Cornman, Matthew B. Laramie, Andrew R. Mahon, Richard F. Lance, David S. Pilliod, Katherine M. Strickler, Lisette P. Waits, Alexander K. Fremier, Teruhiko Takahara, Jelger E. Herder, Pierre TaberletA field ornithologist’s guide to genomics: Practical considerations for ecology and conservation
Vast improvements in sequencing technology have made it practical to simultaneously sequence millions of nucleotides distributed across the genome, opening the door for genomic studies in virtually any species. Ornithological research stands to benefit in three substantial ways. First, genomic methods enhance our ability to parse and simultaneously analyze both neutral and non-neutral genomic regiAuthorsSara J. Oyler-McCance, Kevin Oh, Kathryn Langin, Cameron L. AldridgeRangewide genetic analysis of Lesser Prairie-Chicken reveals population structure, range expansion, and possible introgression
The distribution of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus) has been markedly reduced due to loss and fragmentation of habitat. Portions of the historical range, however, have been recolonized and even expanded due to planting of conservation reserve program (CRP) fields that provide favorable vegetation structure for Lesser Prairie-Chickens. The source population(s) feeding the raAuthorsSara J. Oyler-McCance, Randall W DeYoung, Jennifer A. Fike, Christian A. Hagen, Jeff A. Johnson, Lena C. Larsson, Michael PattenContrasting evolutionary histories of MHC class I and class II loci in grouse—Effects of selection and gene conversion
Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promoteAuthorsPiotr Minias, Zachary W. Bateson, Linda A. Whittingham, Jeff A. Johnson, Sara J. Oyler-McCance, Peter O. DunnZ chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds
Sex chromosomes contribute disproportionately to species boundaries as they diverge faster than autosomes and often have reduced diversity. Their hemizygous nature contributes to faster divergence and reduced diversity, as do some types of selection. In birds, other factors (mating system and bottlenecks) can further decrease the effective population size of Z-linked loci and accelerate divergenceAuthorsSara J. Oyler-McCance, Robert S. Cornman, Kenneth L. Jones, Jennifer A. FikePotential demographic and genetic effects of a sterilant applied to wild horse mares
Wild horse populations on western ranges can increase rapidly, resulting in the need for the Bureau of Land Management (BLM) to remove animals in order to protect the habitat that horses share with numerous other species. As an alternative to removals, BLM has sought to develop a long-term, perhaps even permanent, contraceptive to aid in reducing population growth rates. With long-term (perhaps evAuthorsJames E. Roelle, Sara J. Oyler-McCanceLandscape characteristics influencing the genetic structure of greater sage-grouse within the stronghold of their range: a holistic modeling approach
Given the significance of animal dispersal to population dynamics and geographic variability, understanding how dispersal is impacted by landscape patterns has major ecological and conservation importance. Speaking to the importance of dispersal, the use of linear mixed models to compare genetic differentiation with pairwise resistance derived from landscape resistance surfaces has presented new oAuthorsJeff R Row, Sara J. Oyler-McCance, Jennifer A. Fike, Michael O'Donnell, Kevin E. Doherty, Cameron L. Aldridge, Zachary H. Bowen, Brad C. FedyEnvironmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive Burmese pythons
Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence pAuthorsMargaret E. Hunter, Sara J. Oyler-McCance, Robert M. Dorazio, Jennifer A. Fike, Brian J. Smith, Charles T. Hunter, Robert N. Reed, Kristen M. HartDevelopment of 13 microsatellites for Gunnison Sage-grouse (Centrocercus minimus) using next-generation shotgun sequencing and their utility in Greater Sage-grouse (Centrocercus urophasianus)
Gunnison Sage-grouse are an obligate sagebrush species that has experienced significant population declines and has been proposed for listing under the U.S. Endangered Species Act. In order to examine levels of connectivity among Gunnison Sage-grouse leks, we identified 13 novel microsatellite loci though next-generation shotgun sequencing, and tested them on the closely related Greater Sage-grousAuthorsJennifer A. Fike, Sara J. Oyler-McCance, Shawna J Zimmerman, Todd A. CastoeGenomic single-nucleotide polymorphisms confirm that Gunnison and Greater sage-grouse are genetically well differentiated and that the Bi-State population is distinct
Sage-grouse are iconic, declining inhabitants of sagebrush habitats in western North America, and their management depends on an understanding of genetic variation across the landscape. Two distinct species of sage-grouse have been recognized, Greater (Centrocercus urophasianus) and Gunnison sage-grouse (C. minimus), based on morphology, behavior, and variation at neutral genetic markers. A parapaAuthorsSara J. Oyler-McCance, Robert S. Cornman, Kenneth L. Jones, Jennifer A. FikeBlood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences
Next generation sequencing methods allow rapid, economical accumulation of data that have many applications, even at relatively low levels of genome coverage. However, the utility of shotgun sequencing data sets for specific goals may vary depending on the biological nature of the samples sequenced. We show that the ability to assemble mitogenomes from three avian samples of two different tissue tAuthorsF. Keith Barker, Sara Oyler-McCance, Diana F. TombackTwo low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies
As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novAuthorsDaren C. Card, Drew R. Schield, Jacobo Reyes-Velasco, Matthre K. Fujita, Audra L. Andrew, Sara J. Oyler-McCance, Jennifer A. Fike, Diana F. Tomback, Robert P. Ruggiero, Todd A. Castoe - Partners
Below are partners associated with this project.