Data Management Plan

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.

Microsatellite, SNP, and mtDNA sequence data from southern resident killer whales.

NWFSC Montlake: NWFSC Montlake lab

Lineage Statement:
DNA genotyping: These data were collected and processed in accordance with established protocols and best practices under the direction of the project’s Principal Investigator. Contact the dataset Data Manager for full QA/QC methodology.

These data were collected and processed in accordance with established protocols and best practices under the direction of the project’s Principal Investigator. Contact the dataset Data Manager in section 3 for full QA/QC methodology.

At this time, contact the Data Manager for information on obtaining access to this data set. In the near future, the NWFSC will strive to provide all non-sensitive data resources as a web service in order to meet the NOAA Data Access Policy Directive (https://nosc.noaa.gov/EDMC/PD.DA.php).

The Northwest Fisheries Science Center facilitates backup and recovery of all data and IT components which are managed by IT Operations through the capture of static (point-in-time) backup data to physical media. Once data is captured to physical media (every 1-3 days), a duplicate is made and routinely (weekly) transported to an offsite archive facility where it is maintained throughout the data's applicable life-cycle.