Wildlife Genetics Research

Bobcats (Lynx rufus) are an important species for conservation planning with wide distribution throughout California. This species is a valuable model for studying anthropogenic effects associated with urbanization. They are adversely impacted by habitat fragmentation, disease, and rodenticide exposure. Little is known about the bobcat population structure, demographic history, and adaptive variation across the State.

In 2019, Assembly Bill No. 1254 (opens in new tab) banned bobcat hunting until 2025, at which time the Fish and Game Commission must re-evaluate the appropriateness of a hunting season based on the best available science. Statewide genetic study of bobcats is needed. Genetics researchers are collaborating with University of California-Los Angeles on a CCGP funded study to:

• Delineate population structure and generate summary metrics of genetic diversity, effective population size, and demographic history. 
• Evaluate genetic connectivity and identify genetic diversity hotspots and landscape barriers to gene flow.
• Identify functional genomic variation and adaptive potential in future climate scenarios.
• Perform eco-evolutionary demographic simulations explicitly informed by genomic characteristics to predict the population outcome of hunting. Further, assess the impacts of various hunting scenarios, habitat loss, and climate change.
• Inform establishment of sustainable Management Units for bobcats across California and identify the genetic diversity hotspots of high conservation concern.

Yuma Myotis (Myotis yumanensis) is an abundant and widely distributed bat species in California. Detection of the fungus responsible for White-nose syndrome (WNS) in California is a significant threat to this species. WNS has decimated hibernation colonies of other Myotis species in North America. Genomic data is key to conserving bat populations and to understand WNS impacts on populations before declines occur.

Little data exists on Yuma bat population structure, genetic structure, or their movements as they transition between maternity colonies and hibernacula. Genetics researchers are collaborating with the University of California-Los Angeles (opens in new tab) on a CCGP funded study to:

• Provide baseline data on population structure statewide.
• Characterize patterns of gene flow in relation to landscape features.
• Use genetic-environment association methods to characterize genomic variation consistent with local adaptation.
• Estimate demographic population parameters to provide information on historical fluctuations in effective population size.

This research will provide critical baseline data facilitating an integrated statewide approach and establishment of conservation management units. Findings from this study can inform how to prioritize and screen for WNS in California. It can also inform predictions on how WNS may spread and the landscape features (e.g., mountain ranges, watersheds) that may insulate colonies from the pathogen.

The Townsend’s big-eared bat (Corynorhinus townsendii) is as a Species of Special Concern in California. The geographic distribution of this species is thought to include most of the state, though reliable demographic data is lacking. This species was evaluated for listing as threatened or endangered under the California Endangered Species Act with listing ultimately determined to be unwarranted. There is little data regarding genetic population structure, effective population size, heterozygosity, or genomic variation as it relates to local adaptation.

Effective conservation requires identification of Management Units using population genetics techniques, evaluation of genomic health (e.g., presence of deleterious alleles, genetic load) in each unit, and identification of locally adapted ecotypes in the context of climate change resiliency. Genetics research staff are collaborating with the University of California-Los Angeles (opens in new tab) on a CCGP funded study to:

• Delineate population structure, generate standard measures of genetic diversity, and estimate effective population size across the state.
• Identify functional genomic differences among different ecotypes, particularly with respect to climatic and other habitat variables.
• Perform demographic modeling explicitly informed by measures of genetic load, runs of homozygosity, and the prevalence of deleterious recessive alleles.

This research will allow for the establishment of Management Units and evaluation of the threat low genomic variation may pose to this species. Demographic simulations will permit assessment of species persistence in various scenarios of climate change, habitat loss and reduced gene flow.

The golden eagle (Aquila chrysaetos) is widespread across most of California. These birds use different movement strategies that make effective conservation of the species challenging. Movement is complex and variable among golden eagles in California, with telemetry data suggesting there are:

• Seasonal migrants that track optimal thermal conditions.
• Migrants that leave the state during the non-breeding season and return to breed.
• Residents that stay on territory throughout the year.

Genetics research staff are collaborating with the U.S. Geological Survey (opens in new tab) (USGS) and the University of California-Los Angeles (opens in new tab) on a CCGP funded study to examine the landscape genomics of golden eagles in California.

Loss of foraging habitat and large nesting trees is associated with urban and agricultural development, wildfire, and increased outdoor recreation. As a result, golden eagles may suffer range reduction, increased breeding pressures, demographic decline and loss of genomic variation. Existing data identifies California and Alaska populations as genetically distinct from other populations in North America and highlighted the need for higher resolution genetic analysis. A genomic approach to understanding population structure, current levels of heterozygosity, and genomic health are important for effective management of this iconic species.

There are several local and regional projects examining the conservation genetics of bighorn sheep. Bighorn sheep populations have declined due to habitat loss and modification, habitat fragmentation, human disturbance, livestock grazing, disease, fire suppression, poaching, and predation. California is home to three subspecies: Sierra Nevada bighorn sheep, desert bighorn sheep, Peninsular desert bighorn sheep.

• Desert bighorn sheep reference genome – CDFW genetics researchers use a combination of 10X Genomics and Bionano Saphyr technologies to create a chromosome-level assembly that will be fully annotated.
• Peninsular bighorn sheep recovery genetics – The Distinct Population Segment of Peninsular bighorn sheep in the United States has recovered demographically since listing under the Endangered Species Act (opens in new tab). CDFW genetics researchers use genetic methods to examine how the population recovered (i.e., immigration vs. recruitment) and the implications of the demographic decline on genetic diversity.
• Reintroduction genetics – The Sespe Wilderness herd is one of few reintroduced populations of bighorn sheep in California. Source stock were taken from the geographically isolated and low genetic diversity San Gabriel population. This resulted in a reintroduced herd with the lowest heterozygosity ever measured in desert bighorn sheep. CDFW genetics researchers are examining the genomic implications of this extreme founder event.

Mule deer (Odocoileus hemionus) are an intensively managed native species in California There are few population-genetic data and no genomic resources that can be used to inform an effective management strategy, despite this species ecological importance throughout the western United States. Clearer understanding of population structure based on genome-wide assessment for locally adapted ecotypes in terms of climate change; and by evaluation of genomic status of each distinct population in terms of genetic diversity, presence of deleterious alleles, and genetic load related to disease resiliency or susceptibility is critical.

Of particular interest is chronic wasting disease (CWD), for which resistance and progression appear heritable. CWD is steadily increasing its geographic range in wild cervid populations of North America and could soon threaten mule deer in California. Genetics research staff are collaborating with the University of California-Davis (opens in new tab) on a CCGP funded study to:

• Delineate population structure and assess standard measures of genetic diversity across the state.
• Identify functional genomic differences among different ecotypes, particularly with respect to climatic and other habitat variables.
• Assess the frequency and geographic distribution of deleterious alleles at clinically relevant loci (e.g., major histocompatibility complex, prion protein gene) as it pertains to CWD.
• Inform evaluation of the severity of the threat CWD exposure poses to mule deer in California.

Genomics of White-Nose Syndrome Susceptibility

Since the first appearance of white-nose syndrome (WNS) in North America in 2006, some bat populations appear to be stabilizing with less over-winter mortality and colony sizes approaching pre-WNS sizes in some areas of eastern North America. However, the causative fungal pathogen (Psuedogymnoascus destructans) continues its spread across the continent and WNS continues to be detected in new states. The impact of the disease bat populations in western North America remains unknown.

Previous genomic comparisons of pre- and post-WNS populations have provided important insights into this disease. Each study relied on the current genome assembly for the little brown bat (Myotis lucifugus), which was generated by earlier and less robust sequencing technologies. CDFW genetics research staff intend to:

• Create a high quality, annotated reference genome for M. lucifugus using a combination of long range and linked-reads sequencing technologies.
• Produce medium to high coverage resequencing data of M. lucifugus samples from pre- and post-WNS populations in New York and Pennsylvania to identify ‘resistance’ genes.
• Assay standing genetic variation of several western myotis species in order to assess the potential for these populations to respond to and survive the strong selective pressure due to WNS.

Invasive species can significantly impact native species, reduce biodiversity, and cost billions in mitigation efforts and damage. Genetic techniques are an increasingly important tool for invasive species control. These methods can identify discrete breeding populations, estimate population size, detect long-distance migrants, and identify barriers to dispersal.

One invasive species where genetic tools can aid eradication efforts is nutria (Myocastor coypus). Nutria cause substantial damage to native wetland communities, soils, agricultural crops, and water management infrastructure. In California, the removal and eradication of nutria before they spread is vital to conserve native species and habitat. Genetics research staff use a landscape genetic approach to investigate the current population of nutria in California, and assist eradication efforts by:

• Characterizing the genetic diversity, population structure, and effective population size of nutria throughout the invaded area.
• Identifying landscape barriers to gene flow and possible paths of recolonization.
• Reconstructing the demographic history of nutria to examine the origin of the current nutria population.

Mountain lions (Puma concolor) are one of few remaining large predators in California. Research indicates a lack of genetic diversity in specific areas of the state. In April 2020, the mountain lion was designated as a candidate species under the California Endangered Species Act (CESA) within a proposed evolutionarily significant unit located in Southern California and the central coast.

Population monitoring is an important component of conservation and management. Scat survey followed by fecal DNA-based mark-recapture modeling represents a noninvasive and invaluable means of monitoring population density. In fragmented, small subpopulations, genotyping from a limited set of genetic markers is challenging. Proper marker screening and selection is critical.

• CDFW genetics researchers developed a set of 96 SNP markers capable of genotyping individual mountain lions from fecal DNA, using existing sequencing from hundreds of individuals statewide.
• This SNP marker set can differentiate individual mountain lions with high confidence, and mountain lions from bobcats, the most frequent non-target sample type encountered during field surveys.
• This SNP marker set will facilitate population monitoring of mountain lions throughout California, even in subpopulations with low genetic diversity (e.g., southern California).

California provides wintering habitat for most greater white-fronted geese (Answer albifrons) in the Pacific Flyway. Multiple subspecies of greater white-fronted geese utilize this migratory route, each with their own population distribution and trends. Tule geese (A. a. elgasi) are a potentially vulnerable subspecies that winter predominantly in the Sacramento Valley and Suisun and Napa marshes of north-central California.

• Tule geese can be difficult to differentiate from individuals belonging to other greater white-fronted geese subspecies that winter in California.
• A genetic stock identification panel of single nucleotide polymorphisms (SNP), designed and tested for Fluidigm SNP Type technology, is used to assist in an accurate assessment of Tule goose harvest.
• This important genetic research helps to inform the conservation and management of this species.