Wildlife Genetics Research

Desert bighorn sheep on trail
Black bear hiding in tree
Golden eagle in flight
Bobcat in snow
Mule deer buck standing still
Little brown bats in flight

The Genetics Research Unit was established in 2018 to improve wildlife population monitoring data, analyze species taxonomic status, identify management and conservation priorities based on genetic variation, and develop an archive of reference genetic samples for future research. These statewide priorities directly support CDFW management, conservation, and enforcement mandates.

Genetics researchers use state-of-the art equipment and provide “in-house” expertise that supports large mammal and carnivore focused genetic research and management, as well as a greater diversity of native species. This function is consistent with California's scientific initiative to increase scientific capacity (Fish and Game Code Section 715(opens in new tab)). Learn more!

California Wildlife DNA Biobank

The California Wildlife DNA Biobank is a valuable archive of extracted DNA and tissues maintained by the Genetics Research Unit. The biobank holds nearly 10,000 genetic samples and counting. The biobank supplies the CDFW and scientific community with high quality genetic materials for research on California's wildlife. The samples are of significant value to the science community for current and future research.

  • The collection is statewide in scope, with especially strong mammalian big game and carnivore holdings. Samples are taken predominantly from mammals and birds.
  • Each sample is uniquely date and geo-referenced allowing for comparison of genetic diversity over space and time.
  • Most samples are extracted for high molecular weight DNA. Many samples have associated tissues frozen or stored on silica desiccant in -80°C freezers to ensure long-term viability for DNA sequencing.

laboratory test tubesThe California Wildlife DNA Biobank is used in California Conservation Genomics Project (opens in new tab) funded studies and by researchers from around the world.

For information on available samples and the biobank loan policy, contact Dr. Michael Buchalski, Research Scientist.

California Conservation Genomics Project

The California Conservation Genomics Project (opens in new tab) (CCGP) is a state-funded initiative, directed by the University of California-Los Angeles, to produce comprehensive, multispecies genomic datasets to help manage regional biodiversity. The CCGP draws upon scientists from all ten University of California campuses and officials from state and federal regulatory agencies. CDFW genetics staff were instrumental in securing CCGP funding for multiple wildlife species and serve as co-investigators on these studies.

Bobcats

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:Bobcat standing in field

  • 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 bats

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:Yuma bat on gloved hand

  • 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.

Townsend’s Big-Eared Bat

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: Townsend's big-eared bat in gloved hand

  • 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.

Golden Eagles

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.Profile of golden eagle
  • 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.

Current Research

Genetic sampling is an invaluable method for estimating population distribution, diversity, and dispersal patterns. The Genetics Research Unit conducts scientific investigations to assist ongoing management efforts for California’s diverse native wildlife. These important research efforts help to improve population monitoring, support biodiversity conservation, and manage healthy wildlife populations. Research projects cover a wide range of species and utilize many techniques in the field of molecular ecology. CDFW genetics researchers use both traditional and new technologies (e.g., high-throughput DNA sequencing) to address ecological and evolutionary questions at a variety of spatial and temporal scales.

Bighorn Sheep Conservation Genetics

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.Three bighorn sheep on mountaintop

  • 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 Disease Genomics

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:Mule deer doe looking over shoulder

  • 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

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.<Little brown bat with white-nose syndrome

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.

Invasion Genetics of Nutria

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. Invasive nutria standing on grass

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.

Statewide Mountain Lion Assessment

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 Mountain lion crouching on rock 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).

Tule Goose Harvest Abundance Estimates

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.Two tule geese standing

  • 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.

Research Staff

Dr. Michael Buchalski, Research Scientist III

Michael Buchalski, Ph.D., Research Scientist III

Michael.buchalski@wildlife.ca.gov

Since 2016, I have led a team of post-doctoral and graduate researchers within the CDFW Genetics Research Laboratory conducting statewide genetics research. I have a broad range of research interests which lie at the intersections of evolutionary biology, ecology, behavior, and biological conservation. My current research primarily focuses on characterizing both neutral and adaptive variation for several of California’s wide-ranging species to better delineate conservation units and protect biodiversity. I am currently collaborating on several California Conservation Genomics Project (opens in new tab) funded studies.

I use a combination of genetic and genomic techniques to investigate numerous questions related to the conservation and management of wildlife species. I use traditional population genetic methodologies to investigate questions fundamental to the field of conservation genetics, including genetic variability, population connectivity and gene flow, as well as small population effects such as genetic drift and inbreeding. I use non-invasive genetic techniques to assist with applied management problems such as species identification and individual genotyping for abundance estimation.

Kristen Ahrens, Research Scientist IKristen Ahrens, MS, Research Scientist I

Kristen.ahrens@wildlife.ca.gov

Kristen is a Research Scientist I and has worked at the CDFW Genetics Research Laboratory since 2019. Prior to joining the Wildlife Genetics Program, her previous research experience included use of environmental DNA and population genetic approaches for species monitoring and management. Her current work is focused on use of RAD-seq methods to conduct a landscape-level study on invasive nutria to aid eradication efforts through better understanding of the invasion dynamics. She is also responsible for the optimization and implementation of multiple genetic assays that support ongoing monitoring projects. Her work includes mountain lion fecal genotyping for population density estimates and Greater White-fronted Goose subspecies typing to refine harvest limits.

Kristen is a part-time lecturer at Sacramento State University in the Department of Biological Sciences where she teaches an undergraduate mammalogy lecture and lab course.

Alciia Kubicki, Fish and Wildlife Scientific Aid Alicia Kubicki, B.S., Fish and Wildlife Scientific Aid

Alicia.kubicki@wildlife.ca.gov

Alicia is a Scientific Aid who joined the CDFW Genetics Research Lab in 2019. She holds a Bachelor of Science degree in Animal Biology from the University of California, Davis. She has a background in disease ecology and researched infectious diseases in rodents for her undergraduate thesis. Alicia assists with various management and monitoring projects for California species including mountain lion and bobcat. She maintains the tissue and DNA archive and helps train volunteers.

Alicia has experience in Sanger sequencing, use of automated DNA extraction robotics, as well as genotyping and species-typing using Fluidigm chemistry.