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Extensions and Applications of Mean Length Mortality Estimators for Assessment of Data-Limited Fisheries

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Extensions and Applications of Mean Length Mortality Estimators for Assessment of Data-Limited Fisheries W&M ScholarWorks Dissertations, Theses, and Masters Projects Theses, Dissertations, & Master Projects 2017 Extensions and Applications of Mean Length Mortality Estimators for Assessment of Data-Limited Fisheries Quang C. Huynh College of William and Mary - Virginia Institute of Marine Science, [email protected] Follow this and additional works at: https://scholarworks.wm.edu/etd Part of the Aquaculture and Fisheries Commons, and the Natural Resources Management and Policy Commons Recommended Citation Huynh, Quang C., "Extensions and Applications of Mean Length Mortality Estimators for Assessment of Data-Limited Fisheries" (2017). Dissertations, Theses, and Masters Projects. Paper 1516639583. http://dx.doi.org/doi:10.21220/V5CM9D This Dissertation is brought to you for free and open access by the Theses, Dissertations, & Master Projects at W&M ScholarWorks. It has been accepted for inclusion in Dissertations, Theses, and Masters Projects by an authorized administrator of W&M ScholarWorks. For more information, please contact [email protected]. Extensions and applications of mean length mortalit y estimators for assessment of data - limited fisheries A Dissertation Presented to The Faculty of the School of Marine Science The College of William and Mary in Virginia In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Quang C . Huynh January 2018 APPROVAL PAGE This dissertation is submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Quang C . Huynh Approved by the Committee, December, 2017 John M. Hoenig, Ph.D. Committee Chair/ Advisor Mark J. Brush, Ph.D. John E. Graves, Ph.D. Ross J. Iaci, Ph.D. Department of Mathematics John F. Walter III, Ph.D. Southeast Fisheries Science Center Miami, Florida, USA Table of Contents Acknowledgements ................................ ................................ ................................ ........... vii List of Tables ................................ ................................ ................................ ................... viii List of Figures ................................ ................................ ................................ ..................... x Abstract ................................ ................................ ................................ ............................ xvi Author’s Note ................................ ................................ ................................ .................. xvii Chapter 1: Sized - based mortality estimators and diagnostic procedures for assessment of data - limited fisheries ................................ ................................ ................................ ........... 2 1.1. Abstract ................................ ................................ ................................ ................................ 2 1.2. Introduction ................................ ................................ ................................ ........................... 3 1.3. Description of the size - based mortality estimators ................................ ............................... 5 1.3.1. Mean length - based mortality estimators ................................ ................................ ........ 6 1.3.2. Composition - based mortality estimators ................................ ................................ ....... 8 1.4. Violations of model assumptions: implications, diagnostics, a nd solutions ....................... 13 1.4.1. Uncertainty in life history parameters ................................ ................................ .......... 14 1.4.2. Deterministic versus stochastic size - at - age ................................ ................................ .. 17 1.4.3. Knife - edge selectivity versus gradual selectivity ................................ ......................... 18 1.4.4. Flat - top versus dome - shaped selectivity ................................ ................................ ...... 20 1.4.5. Large year class in recruitment ................................ ................................ .................... 22 1.4.6. Trend in mortality ................................ ................................ ................................ ........ 24 1.5. Considerations for applications ................................ ................................ ........................... 25 1.5.1. Biological reference points ................................ ................................ .......................... 26 1.5.2. Software packages ................................ ................................ ................................ ....... 27 1.6. Conclusions ................................ ................................ ................................ ......................... 28 1.7. References ................................ ................................ ................................ ........................... 30 1.8. Tables ................................ ................................ ................................ ................................ .. 36 1.9. Figures ................................ ................................ ................................ ................................ 39 Chapter 2: Comparative performance of three length - based mortality estimators ........... 44 2.1. Abstract ................................ ................................ ................................ ............................... 44 2.2. Introduction ................................ ................................ ................................ ......................... 45 2.3. Metho ds ................................ ................................ ................................ .............................. 50 2.3.1. Simulation design ................................ ................................ ................................ ......... 50 2.3.2. Mortality estimation ................................ ................................ ................................ ..... 54 2.3.3. Performance analysis ................................ ................................ ................................ ... 57 iii 2.3.4. Sensitivity analyses ................................ ................................ ................................ ...... 58 2.4. Results ................................ ................................ ................................ ................................ 59 2.4.1. Performance across factorial variables ................................ ................................ ........ 60 2.4.2. Sensitivity analyses ................................ ................................ ................................ ...... 61 2.5. Discussion ................................ ................................ ................................ ........................... 62 2.5.1. Perfo rmance of mortality estimators ................................ ................................ ............ 62 2.5.2. Sensitivity analyses ................................ ................................ ................................ ...... 65 2.5.3. Life history considerations ................................ ................................ ........................... 67 2.6. Conclusion ................................ ................................ ................................ .......................... 68 2.7. References ................................ ................................ ................................ ........................... 68 2.8. Tables ................................ ................................ ................................ ................................ .. 73 2.9. Figures ................................ ................................ ................................ ................................ 75 Chapter 3: Multispecies Extensions to a Nonequilibrium Length - Based Mortality Estimator ................................ ................................ ................................ ........................... 83 3.1. Abstract ................................ ................................ ................................ ............................... 83 3.2. Introduction ................................ ................................ ................................ ......................... 84 3.3. Methods ................................ ................................ ................................ .............................. 86 3.3.1. Model Development and Model Fitting ................................ ................................ ....... 86 3.3.2. Modifications for Multispecies Estimation ................................ ................................ .. 88 3.3.3. Model Complexity and Model Selection ................................ ................................ ..... 91 3.3.4. Application to Deepwater Snappers in the Puerto Rican Handline Fishery ................ 92 3.4. Results ................................ ................................ ................................ ................................ 95 3.4.1. Application to Snappers in the Puerto Rican Handline Fishery ................................ ... 95 3.4.2. Sensitivity Analysis of Natural Mortality Specification ................................ .............. 97 3.5. Discussion ................................ ................................ ................................ ........................... 97 3.5.1. Selec tion of the Minimum Length of Vulnerability to the Fishery ...........................
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