Conservation Genomics

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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. 

Conservation Genomics - Current Research

A male sage-grouse struts his stuff on his native sage steppe.
A male sage-grouse struts his stuff on his native sage steppe. Doug Ouren, USGS Public domain.

Assembling a High Quality Reference Genome for Sage-grouse to Serve as a Resource for Future Studies - Principal Investigator - Kevin Oh

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. 

This goal of this project is to sequence and assemble a high-quality reference genome for Gunnison Sage-grouse. Assembling such a reference genome can benefit several types of analyses common to conservation genetics. As Gunnison and Greater Sage-grouse are closely related, this reference genome will serve as a resource for future studies in both species, and will inform management and conservation decisions.

 

Greater Sage Grouse Hen with Brood on Seedskadee National Wildlife Refuge
A hen greater sage grouse and her brood head to Seedskadee NWR wetlands to spend the day.

 

Whole Genome Resequencing and Population Genomics of Sage-grouse - Principal Investigator - Kevin Oh

This project aims to identify the precise genomic basis of species differences between Greater and Gunnison Sage-grouse and between different populations of Greater Sage-grouse using whole genome resequencing. These analyses will also examine the adaptive significance of genetic variation identified.  

 

 

Greater Sage Grouse Seedkadee NWR
Greater Sage Grouse on Seedskadee National Wildlife Refuge. USGS photo.

 

 

 

Landscape Genomics and Ecological Adaptation in Wyoming Greater Sage-grouse - Principal Investigator - Kevin Oh

In this project, we are using landscape genomic techniques to identify putative adaptive genetic variation within the Greater Sage-grouse core population in Wyoming.  We are genotyping several hundred tissue samples from across Wyoming at tens of thousands of genomic markers. Regions of the genome determined to show signatures of selection will be investigated and correlated with environmental variables to uncover important gene-environment relation that will be used to assess population vulnerability to climate change and anthropogenic disturbance.

 

 

sandsage landscape Rondeau.JPG
Renée Rondeau, Colorado Natural Heritage Program

 

Genetic Adaptations to Local Sagebrush Diets in Sage-grouse - Principal Investigator - Kevin Oh

In this project we are evaluating the degree to which different Sage-grouse populations might be uniquely adapted to the local sagebrush plants, which make up the bulk of Sage-grouse diets during the fall and winter. Using target resequencing of several candidate genes, we are examining the evidence for functional genetic variation in genes that might allow Sage-grouse to specialize on locally available sagebrush varieties. This research is in collaboration with Boise State University.

 

 

Greater Sage-grouse
Matt Lee, USGS

 

Examining adaptation in Gunnison Sage-grouse - Principal Investigator - Sara Oyler-McCance

The satellite populations of the Gunnison Sage-grouse occupy different areas with a diversity of habitat and local environmental characteristics. With limited gene flow between populations and the potential for different selective pressures acting on each population, there is the potential for locally adapted variation. Local adaptation is important to long-term persistence of populations and pertinent to current management efforts. Pressures of climate change and land-use change differ among the populations, and any existing variation adapted to the unique pressures should be maintained within a population. We are using genomic methods to look within each population for evidence of selection correlated with environmental variation. Identifying adaptive variation can contribute to more targeted management efforts and the intentional maintenance of said variation within populations.

 

 

A white-tailed ptarmigan on Mt. Evans, Colorado
A white-tailed ptarmigan on Mt. Evans, a mountain in Northern Colorado. Cameron Aldridge, USGS, Public domain.

Examining Current Subspecies Delineations in White-tailed Ptarmigan Using Genomic Data - Principal Investigator - Katie Langin

The delineation of populations that are evolutionarily and demographically distinct is an important step in the development of species-specific management plans. Such knowledge is necessary for learning how conservation threats vary across a species’ range, for devising strategies to increase population growth rates, and for providing legal protection at the intraspecific level. It is also essential for conserving long-term evolutionary resilience, given that the genetic diversity that has evolved in response to spatial variation in environmental conditions could provide the raw ingredients necessary to fuel future adaptive evolution. We are using genomic data to delineate distinct evolutionary units across the range of the white-tailed ptarmigan. This information will inform management strategies for this alpine species, which may be vulnerable to climate change.

 

 

Investigating How Landscape and Climate Variables Influence Patterns of Adaptive Genetic Variation in White-tailed Ptarmigan - Principal Investigator - Katie Langin

A white-tailed ptarmigan on Mt. Evans, Colorado
A white-tailed ptarmigan sits on the side of Mt. Evans in Colorado. Cameron Aldridge, USGS Public domain.

We are conducting a landscape genomic analysis to test factors hypothesized to influence spatial patterns of adaptive genetic variation. Genomic data are especially useful for this task because they can capture adaptive divergence along many gradients of variation (e.g., physiological, morphological) – all of which may contribute to a species’ ability to evolve in response to changing environmental conditions. We are conducting this analysis at two spatial scales: broadly across the entire species’ range and at a finer spatial scale within Colorado (the state that has the most ptarmigan habitat in the lower 48 states). We are generating genomic data and will test for outlier genomic sites that are areas of potential adaptation. Those regions will be examined to determine if they are part of or are physically linked with genes of known function (using the annotated chicken genome). We will also examine how variation in those regions of the genome are shaped by landscape variables (which may influence gene flow) and climate variables (which may influence natural selection). This work will inform future work to understand local adaptation in this high-elevation species, and to identify populations that may be adaptively divergent (e.g., adapted to warmer microclimates).

 

A female brown-headed cowbird.
A female brown-headed cowbird. USGS photo.

Evaluating the Gut and Cloacal Bacterial Community of Cowbirds: A Potential Mechanism for Enhanced Immunity - Principal Investigator - Sara Oyler-McCance

The goal of this study is to examine the gut and cloacal communities of brown-headed cowbird, a species that is a generalist parasite that lays its eggs in the nests of more than 200 other avian species. We are comparing cowbird diversity with that of a similar non-parasitic species, red-winged black bird. We hypothesize that one of the reasons that brown-headed cowbirds have such strong immune systems is due to the fact that they have a much more diverse gut and cloacal microbial diversity because their young are raised in such varying environments. We are finding that there is higher microbial diversity in brown-headed cowbird suggesting a possible mechanism for increased immunity in cowbirds. This research is in collaboration with Colorado State University and Cornell University.

 

Greater Sage grouse flying. T. Gettleman USGS photo.
Sage grouse fly along the front range in Wyoming. USGS photo.

Contrasting Evolutionary Histories of MHC Class I and Class II Loci in Grouse - Effects of Selection and Gene Conversion - Principal Investigator - Sara Oyler-McCance

This project examines the evolutionary history of two different classes of MHC genes in five closely related species of grouse.  We are investigating the roles of selection and gene conversion on class I and class II MHC genes and are comparing diversity among the five different prairie grouse. We are finding differences in the strength of balancing selection acting on MHC class I and class II genes. We are also identifying much stronger gene conversion shaping the evolution of MHC class II genes than class I genes. Overall, the combination of strong positive (balancing) selection and frequent gene conversion may be maintaining higher diversity of MHC class II than class I in prairie grouse. This research is in collaboration with University of Łódź, University of Wisconsin-Milwaukee, University of North Texas.

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Conservation Genomics - Completed Research

A male sage grouse. USGS photo gallery.

Conservation genomics is a new field of science that applies novel whole-genome sequencing technology to problems in conservation biology. 

Re-examining Patterns of Genetic Variation in Sage-grouse Using Genomic Techniques - Principal Investigator - Sara Oyler-McCance

The goal of this study was to use new comprehensive genomic markers to re-examine patterns of genetic variation in sage-grouse focusing on differences between Gunnison Sage-grouse, the Bi-State population of Greater Sage-grouse, and the rest of the range of Greater Sage-grouse. We found that by using genomic methods we were able to reveal that Gunnison Sage-grouse are much more diverged from Greater Sage-grouse than the Bi-State population of Greater Sage-grouse is from Greater Sage-grouse. This study confirms definitively that Gunnison Sage-grouse represent a distinct species and that the Bi-State is a distinct population of Greater Sage-grouse.  This study also confirms that Gunnison Sage-grouse have much lower genomic diversity than Greater Sage-grouse. This research was in collaboration with the University of Colorado, Denver.

Z Chromosome Divergence, Polymorphism, and Relative Effective Population Size in a Genus of Lekking Birds - Principal Investigator - Sara Oyler-McCance

The goal of this project was to map genetic markers (Single Nucleotide Polymorphisms or SNPs) that were identified in comparisons of Greater and Gunnison Sage-grouse to the chicken genome and determine the chromosomal location of each SNP. We wanted to determine where in the genome (which chromosome or chromosomes) housed SNPs with the greatest divergence between Greater and Gunnison Sage-grouse. When we found that the divergence SNPs were on the Z chromosome we evaluated the role of the lek mating system on this phenomenon. Species with more skewed mating systems (such as lekking sage-grouse) had smaller effective population sizes on the Z chromosome which may contribute to the increased divergence on the Z. This research was in collaboration with the University of Colorado, Denver.

A genetic analysis illustration

Two Low Coverage Bird Genomes and a Comparison of Reference-Guided Versus de Novo Genome Assemblies - Principal Investigator - Sara Oyler-McCance

The goal of this study was to demonstrate the utility of using low coverage sequence data for genome assembly, comparing reference guided versus de novo assemblies.Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies. This research was in collaboration with the University of Texas, Arlington, and the University of Colorado, Denver.

Tissue Origin of Low-coverage Shotgun Sequencing Libraries Affects Recovery of Mitogenome Sequences - Principal Investigator - Sara Oyler-McCance

This study examined how well complete mitochondrial genomes could be constructed from low coverage shotgun sequencing runs and related the results to tissue type. This study revealed that bird tissue is a much better DNA source for mitochondrial genome assembly than bird blood as it has far more nuclear DNA than mitochondrial DNA. This research was in collaboration with the University of Minnesota and the University of Colorado, Denver.

An agricultural landscape on the Front Range of Colorado. Photo by Katie Walters, USGS.
An agricultural landscape on the Front Range of Colorado. Photo by Katie Walters, USGS.Katie Walters, USGS

Rapid Microsatellite Identification from Illumina Paired-end Genomic Sequencing in Two Birds and a Snake - Principal Investigator - Sara Oyler-McCance

The goal of this study was to develop a new way to isolate microsatellite markers, which in the past has been a time-consuming and costly investment. This method uses Illumina paired-end high throughput sequencing to identify microsatellite loci and a python script (PALfinder) to design PCR primers for those microsatellite loci. This project compared more expensive 454 sequencing with Illumina paired-end sequence data and shows that the new method is even applicable and cost effective for birds which are known to have much fewer microsatellite loci. This research is in collaboration with the University of Colorado School of Medicine, University of Colorado, Denver, University of Georgia, and the University of Texas, Arlington.