ANNUAL REPORT OF THE U.S. ATLANTIC SALMON ASSESSMENT COMMITTEE REPORT NO. 32 - 2019 ACTIVITIES Portland, Maine March 2 – 6, 2020 PREPARED FOR U.S. SECTION TO NASCO Contents 1 Executive Summary ............................................................................................................................... 4 1.1 Abstract ......................................................................................................................................... 4 1.2 Description of Fisheries and By-catch in USA Waters ................................................................... 4 1.3 Adult Returns to USA Rivers .......................................................................................................... 4 1.4 Stock Enhancement Programs ...................................................................................................... 5 1.5 Tagging and Marking Programs .................................................................................................... 5 1.6 Farm Production ........................................................................................................................... 5 1.7 Smolt Emigration ........................................................................................................................... 6 1.8 References .................................................................................................................................... 6 2 Viability Assessment - Gulf of Maine Atlantic Salmon ........................................................................ 22 2.1 Overview of DPS and Annual Viability Synthesis ........................................................................ 22 2.1.1 Change in Status Assessment Approach ............................................................................. 22 2.1.2 DPS Boundary Delineation .................................................................................................. 22 2.1.3 Synthesis of 2019 Viability Assessment .............................................................................. 23 2.2 Population Size ............................................................................................................................ 24 2.3 Population Growth Rate ............................................................................................................. 28 2.4 Spatial Structure of DPS .............................................................................................................. 34 2.4.1 Wild Production Areas – Redd Distributions and the 2020 Cohort .................................... 34 2.4.2 2019 Freshwater Cohorts and Hatchery Production Units ................................................. 36 2.5 Genetic Diversity ......................................................................................................................... 40 2.1.1 Allelic Diversity .................................................................................................................... 40 2.1.2 Observed and Expected Heterozygosity ............................................................................. 41 2.1.3 Effective Population Size ..................................................................................................... 42 2.1.4 Inbreeding Coefficient......................................................................................................... 43 2.1.5 Summary ............................................................................................................................. 43 2.6 Literature Cited ........................................................................................................................... 44 3 Long Island Sound ............................................................................................................................... 46 3.1 Long Island Sound: Connecticut River ......................................................................................... 46 3.1.1 Adult Returns ...................................................................................................................... 46 3.1.2 Hatchery Operations ........................................................................................................... 46 3.1.3 Stocking ............................................................................................................................... 46 3.1.4 Juvenile Population Status .................................................................................................. 47 3.1.5 Fish Passage ........................................................................................................................ 47 USASAC ANNUAL REPORT 2019/32 1 3.1.7 General Program Information ............................................................................................. 48 3.2 Long Island Sound: Pawcatuck River ....................................................................................... 48 3.2.3 Stocking ............................................................................................................................... 48 4 Central New England ........................................................................................................................... 50 4.1 Merrimack River .......................................................................................................................... 50 4.1.1 Adult Returns ...................................................................................................................... 50 4.1.2 Hatchery Operations ........................................................................................................... 50 4.1.3 Juvenile population status .................................................................................................. 50 4.1.4 General Program ................................................................................................................. 50 4.2 Saco River .................................................................................................................................... 51 4.2.1 Adult Returns ...................................................................................................................... 51 4.2.2 Hatchery Operations ........................................................................................................... 51 4.2.3 Stocking ............................................................................................................................... 51 4.2.4 Juvenile Population Status .................................................................................................. 51 4.2.5 Fish Passage ........................................................................................................................ 51 4.2.6 Genetics .............................................................................................................................. 51 4.2.7 General Program Information ............................................................................................. 52 4.2.8 Migratory Fish Habitat Enhancement and Conservation .................................................... 52 5 Gulf of Maine ........................................................................................................................................... 53 Summary ................................................................................................................................................. 53 5.1 Adult returns and escapement ......................................................................................................... 55 5.1.1 Merrymeeting Bay ..................................................................................................................... 55 5.1.2 Penobscot Bay ............................................................................................................................ 56 5.1.3 Downeast Coastal ...................................................................................................................... 56 5.2 Juvenile Population Status ................................................................................................................ 63 Juvenile abundance estimate ............................................................................................................. 63 Smolt Abundance ................................................................................................................................ 66 5.3 Fish Passage and Migratory Fish Habitat Enhancement and Conservation...................................... 69 Habitat Assessment ............................................................................................................................ 70 Habitat Connectivity ........................................................................................................................... 70 Habitat Complexity ............................................................................................................................. 76 5.4 Hatchery Operations ......................................................................................................................... 83 Egg Production .................................................................................................................................... 83 Egg Transfers ....................................................................................................................................... 83 Wild Broodstock