Genetics

stripes of various colors
Output from the genetic analysis program STRUCTURE, depicting ancestry of native trout based on single nucleotide polymorphism data.

Biodiversity refers to the variety of life in a particular place, conjuring up the image of a diverse array of plants and animals residing in a certain area. However, this term also encompasses diversity found at the DNA-level of all living organisms. Genetics is the study of heredity and of individual genes and traits, while genomics is the study of all genes in an organism and how those genes interact with one another. Genetic and genomic techniques have emerged as valuable tools in addressing a variety of complex issues in fish and wildlife management and law enforcement. How does California Department of Fish and Wildlife (CDFW) apply genetics and genomics in executing its mission to manage California’s diverse fish, wildlife, and plant resources? Similar to how genetics is popularly used to trace human ancestry, it can be used to uncover ancestral lineages of organisms, such as trout and gray wolves, and the geographic distributions associated with those lineages. Additionally, just as genetics can be used to confirm the identity of a perpetrator of a crime, it can be used in wildlife criminal investigations to verify whether a confiscated piece of ivory was derived from a protected species.

There are many specialized fields of study within genetics and genomics, each using molecular genetic techniques to address a suite of questions. The following are examples of some of the fields relevant to fish and wildlife management.

  • Population genetics is essentially a statistical discipline based on models, which focuses on the genetic composition of populations and can be useful for informing management units (or stocks) of species. Population genetic analyses can provide insight into genetic diversity, genetic connectivity, population structure, and effective population size (how many individuals are passing on their genes to the next generation).
  • Taxonomy deals with the classification of organisms and traditionally has relied on morphology and physiology. Molecular genetic data can assist with defining classifications and shed light on evolutionary relationships between species. In particular, taxonomy plays a key role in defining conservation units, such as distinct population segments (DPSs) and evolutionary significant units (ESUs).
  • Molecular ecology is the use of molecular analysis to study ecological questions, such as assessing how populations are responding to changing environments.
  • Adaptive genetic variation (landscape genomics) is the study of how particular regions of the genome respond to natural selection and environmental stressors.
  • Phylogeography is the study of principles and processes underlying the geographic distributions of genetic lineages.
  • Conservation genetics incorporates methods and theories from other fields, such as evolutionary biology, population genetics, and molecular ecology, applying genetics to the conservation and restoration of biodiversity.
  • Molecular forensics applies molecular analysis to criminal investigations, such as identifying the species of origin of confiscated items.
  • Environmental DNA (eDNA) is the genetic material shed by organisms as they pass through an environment and is collected from environmental samples (e.g., soil, sediment, water). Analyzing eDNA can provide information on the biodiversity present at a particular location and the presence/absence of species of interest.

CDFW Genetics Research Laboratory

The Genetics Research Laboratory (GRL) was established in 2018 to focus scientific efforts on the genetic priorities of CDFW. The GRL is a collaboration between the Law Enforcement Division and Wildlife and Fisheries Branches. The GRL coordinates statewide genetics priorities with direct input from the three (3) branches to support CDFW management, conservation, and enforcement mandates.

Funding from passage of Assembly Bill 96 (AB 96), which made the commercialization of ivory and rhinoceros horn illegal in California, supported the creation of the GRL. CDFW invested in equipping the GRL with state-of-the-art equipment and several research scientists. The GRL carries out genetic analyses to support a wide variety of projects in CDFW Branches and Regions. The GRL also has the ability to execute interagency contracts to work on non-CDFW projects, and GRL staff collaborate with external partners (e.g., academia, other government agencies, non-governmental organizations) on a variety of projects to leverage different areas of expertise and capabilities.

As demonstrated by the examples below, the capabilities of the GRL are broadly applicable to both aquatic and terrestrial species, regardless of whether they are native or invasive.

Fisheries Genetics Program

Current Projects

fish with bands and spots being held by a human hand
Lahontan cutthroat trout (Oncorhynchus clarki henshawi)

  • Genetic stock identification of Chinook Salmon (Oncorhynchus tshawytscha)
  • Independence Lake Lahontan Cutthroat Trout (O. clarkii henshawi) hybridization with Rainbow Trout (O. mykiss)
  • Post-drought genetic diversity of California Golden Trout (O. mykiss aguabonita) and population genetics of Little Kern Golden Trout (O. mykiss whitei), including hybridization with other non-native O. mykiss
  • Genetic characterization of interior Redband Trout
  • Assessing detection rates of special-status fishes using eDNA and determining the efficacy of a new monitoring tool for Mountain Whitefish (Prosopium williamsoni)
    • Creation of an eDNA assay for Mountain Whitefish
    • Comparing fish detection rates for eDNA methodology with single-pass electrofishing data
  • Co-principal investigators on studies of Tui Chub, Arroyo Chub, Rainbow Trout and Cutthroat Trout, funded through California Conservation Genomics Project

Completed Projects

Wildlife Genetics Program

Current Projects

group of desert bighorn sheep
Group of desert bighorn sheep (Ovis canadensis nelsoni) ewes. Photo courtesy of Regina Abella (CDFW).

  • Genetic assessment of peninsular bighorn sheep (Ovis canadensis nelsoni)
  • Local adaptation in bighorn sheep (O. canadensis)
  • Phylogeography and local adaptation in mule deer (Odocoileus hemionus)
  • Genomics of white-nose syndrome pathogen susceptibility in Myotis bat species
  • Population genomics, landscape connectivity, and demographic history of invasive nutria (Myocastor coypus) in California
  • Statewide assessment of mountain lions (Puma concolor) using non-invasive, fecal DNA-based mark-recapture methods
  • Greater white-fronted goose (Anser albifrons) and tule goose (A. a. elgasi) annual harvest abundance estimates using genetic stock identification
  • Co-principal investigators on studies of mule deer, bobcat (Lynx rufus), golden eagle (Aquila chrysaetos), Townsend’s big-eared bat (Corynorhinus townsendii), and Yuma bat (Myotis yumanensis), funded through California Conservation Genomics Project

CDFW Wildlife Forensic Laboratory

The Wildlife Forensic Laboratory serves as the wildlife “crime lab” for the CDFW Law Enforcement Division by providing scientific analyses to assist in the determination of whether wildlife laws have been broken. The Wildlife Forensic Laboratory uses accepted forensic science procedures, including DNA analysis, to examine, analyze, report, and testify on physical evidence seized by CDFW Wildlife Officers. Over the years, the Wildlife Forensic Laboratory has assisted CDFW Wildlife Officers with thousands of investigations into wildlife crimes, such as poaching, trafficking, and illegally marketed products.

Current Projects

California Conservation Genomics Project

Led by the University of California Los Angeles, the link opens in new windowCalifornia Conservation Genomics Project (CCGP) is a three-year, state-funded $10 million effort to produce and analyze a genomic database of about 150 species, with a focus on those that are threatened and endangered, commercially exploited, or of great ecological significance. Faculty and researchers from across the University of California system were eligible to apply for funding through the CCGP, and some CDFW staff are engaged with this effort as well. The ultimate goal for the CCGP is to provide state officials with a genomic dataset to inform management of regional biodiversity in California. The genomic data will allow for: identification of populations and regions of greatest genomic diversity that are most resilient to climate change and other human disturbances; assessment of genomic health of keystone species; and analyses of genetic variation and connectivity to identify the most intact and resilient watersheds, landscapes, and marine regions.

Led by the University of California Los Angeles, the California Conservation Genomics Project (CCGP) is a three-year, state-funded $10 million effort to produce and analyze a genomic database of about 150 species, with a focus on those that are threatened and endangered, commercially exploited, or of great ecological significance. Faculty and researchers from across the University of California system were eligible to apply for funding through the CCGP, and some CDFW staff are engaged with this effort as well. The ultimate goal for the CCGP is to provide state officials with a genomic dataset to inform management of regional biodiversity in California. The genomic data will allow for: identification of populations and regions of greatest genomic diversity that are most resilient to climate change and other human disturbances; assessment of genomic health of keystone species; and analyses of genetic variation and connectivity to identify the most intact and resilient watersheds, landscapes, and marine regions.