Evaluation of parameter estimation and field application of transgenerational genetic mark-recapture
Graduation Date
Fall 2016
Document Type
Dissertation/Thesis
Program
Master of Science degree with a major in Natural Resources, option Fisheries
Committee Chair Name
Dr. Andrew Kinziger
Committee Chair Affiliation
HSU Faculty or Staff
Second Committee Member Name
Dr. David Hankin
Second Committee Member Affiliation
HSU Faculty or Staff
Third Committee Member Name
Dr. Darren Ward
Third Committee Member Affiliation
HSU Faculty or Staff
Keywords
Mark-recapture, Genetics, Coho salmon, Population genetics, Escapement estimates, Lincoln Peterson
Abstract
Use of a genetic-based analogue of the traditional mark-recapture method (transgenerational genetic mark-recapture, tGMR) is rapidly expanding as a means to estimate total escapement of Pacific salmon. The tGMR approach is similar to the simple Lincoln-Peterson mark-recapture method. In tGMR, adults returning to fresh water to spawn are collected in the first sampling occasion and their juvenile offspring that are migrating out to sea are collected during the second sampling occasion. Recaptures are determined by the number of parent-offspring pairs identified through genetic parentage analysis of the adult and juvenile collections. Two versions of tGMR are currently in use, referred to as the “with replacement” and the “without replacement” models. For each version, parentage analysis is used to estimate model parameters. I evaluated accuracy of tGMR parameters estimated by genetic parentage analysis by conducting a series of simulations that mimicked application of the approach for estimating escapement of a small northern California coho salmon population. Accuracy was evaluated by comparing known values of the parameters taken from the simulated pedigrees to estimated values based upon parentage analysis of SNP genotypes using the software COLONY. All parentage-based parameter estimates were biased, (ranging from -0.40 to 0.23) indicating improvements in parentage analysis are needed for applications of tGMR. To further evaluate tGMR, I applied this method to coho salmon in two northern California streams resulting in total escapement estimates using the “with replacement” and “without replacement” models of 576 and 444 (Mill Creek, 2011-2012), 131 and 193 (Mill Creek, 2012-2013), and 430 and 468 (Freshwater Creek, 2012-2013). The tGMR approach shows promise for highly fecund species because the number of individuals captured during the second sampling occasion can greatly exceed the adult population size. This can possibly lead to lower variance in tGMR estimates in comparison to traditional mark-recapture estimators, but improvements in genetic parentage analysis are needed to reduce or eliminate bias from parentage analysis that results in biased estimates of total escapement using tGMR.
Citation Style
American Fisheries Society
Recommended Citation
Whitmore, Ryan W., "Evaluation of parameter estimation and field application of transgenerational genetic mark-recapture" (2016). Cal Poly Humboldt theses and projects. 5.
https://digitalcommons.humboldt.edu/etd/5