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  • Incidence of inbreeding and inbreeding depression in Southern Resident Killer Whales


Northwest Fisheries Science Center (NWFSC) Conservation Biology CB - Ecosystem Science; CB - Genetics and Evolution


Southern resident killer whale pedigree analysis
Incidence of inbreeding and inbreeding depression in Southern Resident Killer Whales
The southern residents face several well-documented external threats. However, the population might also be subject to internal factors that limit population growth, including a reduction in fitness due to inbreeding. Understanding how inbreeding affects individual fitness and thus the health status of the population is critical for evaluating the relative influence of other factors on southern resident recovery. Assessing the risk of inbreeding depression – specifically called for in the NMFS recovery plan – is important for conducting accurate Population Viability Analyses and correctly understanding the urgency of recovery efforts. Here, we propose using genomic methods to evaluate inbreeding and inbreeding depression in the southern resident population and a comparable but healthier Alaskan resident population. Measures of inbreeding will serve as an important health marker, supporting the integration of individual metrics aimed at understanding population performance.

Measures of inbreeding can be obtained directly by estimating variation at millions of DNA markers in an individual’s genome. Complete genomic sequences for 100 southern and 50 Alaska residents will be collected in collaboration with the genomics company BGI. Inbreeding values for each individual will be obtained using genome wide measures of homozygosity and relatedness. We will then combine measured of inbreeding with data on individual fitness, to evaluate whether inbreeding leads to inbreeding depression. Generalized additive models will be used to determine whether survivorship, fecundity and size-at-age is influenced by different levels of inbreeding. Using this data, we will measure the degree of current and predicted future of inbreeding in the southern residents and compare this risk with the Alaska residents that have experienced consistent population growth. We will then evaluate whether inbreeding depression explains individual variance in fitness, and estimate its influence on the status of southern residents, using Population Viability Analyses.

Research Themes

Recovery and rebuilding of marine and coastal species
The Pacific Northwest is home to several iconic endangered species, including Pacific salmon and killer whales, and several rockfish species. Mandates such as the Endangered Species Act, MagnusonStevens Act, and the Marine Mammal Protection Act, grant NOAA Fisheries the authority to manage the recovery of depleted species and stocks. The NWFSC contributes to species recovery through research, monitoring and analysis, providing NOAA managers and regional stakeholders the tools and information they need to craft effective regulations and develop sustainable plans for recovery.

Research Foci

Characterize the population biology of species, and develop and improve methods for predicting the status of populations
To evaluate species status and recovery, it is necessary to understand key aspects of the population biology of the species in question. This includes basic information on abundance, age structure, recruitment, spatial distribution, life history and how the species interacts with its ecosystem. For some recovering species, including most overfished groundfish stocks, many ESA-listed Pacific salmon stocks, and high profile species such as Southern Resident killer whales, this basic information is often reasonably well understood. For other recovering species, such as Pacific eulachon and some ESA-listed rockfish species, even basic information (e.g. stock abundance) is unknown. Even for well-studied species, key information on survival rates for critical life stages and how the environment affects these vital rates is lacking. Without basic information on species dynamics, achieving other goals such as quantifying relationships between human activities and species recovery or even knowing if species recovery goals are being met will not be successful. The NWFSC, in partnership with regional stakeholders, including states, tribes and industry, is conducting research to collect and monitor critical demographic information for recovering species.
Develop methods to use physiological, biological and behavioral information to predict population-level processes
Understanding the biological processes occurring within organisms is a powerful way of understanding how environmental changes affect those organisms. Genetics, developmental, physiological and behavioral studies all provide important information for effective species recovery and rebuilding. Integrating this information into models is vital to predict how populations will respond to natural or human perturbations, and to assess the constraints to stock rebuilding efforts. For example, data on thermal tolerance and physiological responses to temperature can be used to explore changes caused by shifts in climate on reproductive behavior and productivity, viability, movement, habitat selection, and population dynamics. Similarly, data on contaminants that impact physiological processes (immune system, growth, development, reproduction, and general health) are critical in determining how these compounds affect population dynamics. Data on biological responses of organisms to ocean acidification are useful for understanding how acidification may affect individual development and survival. The NWFSC collects such information for several species that are of concern, targets of fisheries or otherwise important for overall ecosystem function. NWFSC scientists will continue to expand current efforts and develop methods to incorporate physiological, biological and behavioral data into population models in order to predict population-level processes from these individual level data.


Puget Sound
Puget Sound
use of genetic markers to determine differential reproductive success between adults with different life histories
killer whale
focal species


Inbreeding and heterozygosity data are provided the southern resident killer whale health database.
Publication submitted March 2017. Additional publication expected in 2018.


Species Orcinus orca
grampus, killer whale, killer-trasher, orca


Brad Hanson
Internal Collaborator
Kim Parsons
External Collaborator
Linda Park
Principal Investigator
Mike Ford
Principal Investigator