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 Email

andrew.kinziger@humboldt.edu

Committee Chair Affiliation

HSU Faculty or Staff

Second Committee Member Name

Dr. David Hankin

Second Committee Member Email

david.hankin@humboldt.edu

Second Committee Member Affiliation

HSU Faculty or Staff

Third Committee Member Name

Dr. Darren Ward

Third Committee Member Email

darren.ward@humboldt.edu

Third Committee Member Affiliation

HSU Faculty or Staff

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

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