Genetic Analytical Methods

cetacean strip

A few years ago, large numbers of harbor porpoise were being accidentally drowned in gillnets off the coast of central California. We wanted to know whether the population could withstand this kill. But which was the population that was being affected? Was it just the porpoises that lived in Morro Bay, or part of a population that extended to densely populated northern California?

Genetics offer a tool to address how connected populations in different areas are. However, most geneticists are more interested in evolutionary questions and have developed tools to address evolutionary questions. We are entrusted to implement the Marine Mammal Protection Act, which requires that species be managed as “functioning elements of their ecosystems.” NOAA Fisheries has interpreted this to mean that the entire range of a species must be maintained. After all, if harbor porpoise were completely lost from the central California coast, they could not be a functioning element of that ecosystem. This means that we must try to identify and protect those populations which are independent enough from other populations that human-caused mortality cannot be compensated for by immigration from neighboring populations. This may require us to be able to identify populations with dispersal rates that are much higher than the rates usually considered by evolutionary biologists.

Genetics offer a tool to address how connected populations in different areas are. However, most geneticists are more interested in evolutionary questions and have developed tools to address evolutionary questions. We are entrusted to implement the Marine Mammal Protection Act, which requires that species be managed as “functioning elements of their ecosystems.” NOAA Fisheries has interpreted this to mean that the entire range of a species must be maintained. After all, if harbor porpoise were completely lost from the central California coast, they could not be a functioning element of that ecosystem. This means that we must try to identify and protect those populations which are independent enough from other populations that human-caused mortality cannot be compensated for by immigration from neighboring populations. This may require us to be able to identify populations with dispersal rates that are much higher than the rates usually considered by evolutionary biologists.

Because the rates of movement that are of interest under the MMPA are so much higher than the movement rates most analytical methods were designed to detect, many of the evolutionary methods may not perform well as management tools. For example, what if we used a method designed to answer the question, “are these separate sub-species?”, and found no evidence of structure: but the question we really wanted to answer was, “are these independent populations?” With most methods, scientists cannot answer the question, “If these populations did experience only a tenth of a percent per year dispersal, what is the chance that my analysis would detect it?” Furthermore, the difficulty of collecting genetic samples from marine mammals means that our sample sizes are often small, making the detection of population structure even more difficult. Consequently, a major focus of our research is to develop new analytical methods that address these management questions. We are also using computer simulations to test how both these new methods, and already existing methods, perform for actual use in conservation decisions (see Simulation Performance Testing)

Genetic Software Developed by SWFSC Researchers

Chi-Square-Java application for calculating permutation c2 between two populations

 
pinniped strip
Last modified: 12/24/2014