http://www.ices.dk/reports/FTC/2005/WKSAD05.pdf
They ran these two survey types on two different simulated oceans of fish. One ocean had high variability and low spatial autocorrelation (don't know what that is), and the other had low variability and high correlation. (each ocean had 1x10^7 fish).
The random sample did a better job estimating the population in the high variability ocean, but the systematic sample did a better job with low variability. Implies that sample method selection should correlate to spatial distribution of fish. ("Further investigation of a wider range of surfaces with different properties should help to refine the parameters that influence the point at which different survey strategies are more efficient estimators...")
The international bottom trawl survey used stratification based on depth. There is evidence that in some areas, bottom sediment type makes a significant difference in fish populations, so characteristics of the seabed will be incorporated into future stratification designs. Stratification can become a confounding factor in samples of several different species where the species have different spatial distribution characteristics. Preliminary analysis is need to know how to stratify when surveying several species.
(this is where I got bored of reading most of the document, and it is 174 pages, so the rest is just a summary of a skim reading).
There is a detailed graphic on printed page 24 that describes how to chose what type of survey to use to get good population estimates.
Starting on printed page 39 the report talks about integrating trawl survey data and SONAR data.
Printed page 49 starts talking about estimating population parameters from survey data.
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