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Annual Report of the U.S. Atlantic Salmon Assessment Committee

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Annual Report of the U.S. Atlantic Salmon Assessment Committee U.S. ATLANTIC SALMON ANNUAL REPORT 2007/20 ASSESSMENT COMMITTEE 9 July 2008 ANNUAL REPORT OF THE U.S. ATLANTIC SALMON ASSESSMENT COMMITTEE REPORT NO. 20 - 2007 ACTIVITIES PORTLAND, MAINE March 11 – March 13, 2008 PREPARED FOR U.S. SECTION TO NASCO Table of Contents Table of Contents…………………………………………….…………………………………....i Index of Tables and Figures………….…………………………………………………………..iv List of Historical Tables…………………………………………………………………………vi 1.0 Executive Summary…………………………………………………………………………...1 1.1 Abstract ……………….………...……………………………………………….……1 1.2 Description of Fisheries ………………………………………………………………1 1.3 Adult Returns …………………………………………………………………………1 1.4 Stock Enhancement Programs………………….…………………..............................2 1.5 Tagging and Marking Programs………………………………………………………2 1.6 Farm Production……………………………………………………………………….3 1.7 Highlights……………………………………………………………………………...3 1.7.1 IPNV………………………………………………………………...............3 1.7.2 Didymo……………………………………………………………...............4 2.0 Status of Stocks…………………………………………………………………..................11 3.0 Program Summaries………………………………………………………………...............16 3.1 Connecticut River………….………………………………………………...........................16 3.1.1 Adult Returns……………………………………………….……...........................16 3.1.2 Hatchery Operations……………………………………….………………………16 3.1.3 Stocking…………………………………………………….……...........................18 3.1.4 Juvenile Population Status……………………………….………...........................18 3.1.5 Fish Passage…………………………………….……………….…………………19 3.1.6 Genetics……………………………………...……….…………………………….20 3.1.7 General Program Information……………………………………...........................22 3.1.8 Salmon Habitat Enhancement and Conservation…………………………………..22 3.2 Maine Program……………………………………………………………………………….23 3.2.1 Adult Returns………………………………………………………………………23 3.2.2 Hatchery Operations……………………………………………………………….28 3.2.3 Stocking……………………………………………………………………………29 3.2.4 Juvenile Population Status…………………………………………………………33 3.2.5 Fish Passage………………………………………………………………………..41 3.2.6 Genetic sampling…………………………………………………………………..42 3.2.7 General Program Information……………………………………...........................43 3.2.8 Salmon Habitat Enhancement and Conservation…………………………………..44 3.3 Merrimack River……………………………………………………………………………..48 3.3.1 Adult Returns………………………………………………………………………48 3.3.2 Hatchery Operations……………………………………………………………….50 3.3.3. Stocking…………………………………………………………...........................51 3.3.4 Juvenile Population Status…………………………………………………………51 3.3.5 Upstream and Downstream Fish Passage – Mainstem…………………………….54 3.3.6 Genetics…………………………………………………………………………….55 3.3.8 Salmon Habitat Enhancement and Conservation…………………………………..58 3.4 Pawcatuck River……………………………………………………………………………..60 3.4.1 Adult Returns………………………………………………………………………60 3.4.2 Hatchery Operations……………………………………………………………….60 ii 3.4.3 Stocking ……………………………………………………………………………60 3.4.4 Juvenile Population Status…………………………………………………………62 3.4.5 Fish Passage………………………………………………………………………..63 3.4.6 Genetics…………………………………………………………………………….63 3.4.7 General Program Information……………………………………...........................63 3.4.8 Salmon Habitat Enhancement and Conservation…………………………………..63 4.0 Terms of Reference and Emerging Issues in New England Salmon………………...............64 4.1 Regional Assessment Products………………………………………………………64 4.2 Biological Characteristics of Smolts and Fecundity of Adults: Presentations and Discussion Topic……………… ………………………………………………...68 4.2.1 2008 WGNAS biological characteristics ……………………..…………..68 4.2.2 Merrimack River Fry Evaluation and Update .…………………………….68 4.2.3 Changes in Penobscot River Atlantic Salmon Fecundity ..………………..68 4.3 ICES Marine Survival………………………………………………………………..70 4.3.1 Penobscot River Atlantic Salmon Studies, 2000-2006 – Using VIE Tag Data to Influence Stocking Decisions……………………………………70 4.3.2 Estuarine and Coastal Migration and Survival of Wild Atlantic Salmon Smolts in Maine Using Ultrasonic Telemetry…………………………...70 4.3.3 Feeding Ecology of Atlantic Salmon Postsmolts in Penobscot Bay, Maine – Does Origin Matter? ………………..……..…………………...71 4.4 NASCO Rivers Database ……………………………………………………………72 4.5 Emerging Issues – Coastal Fish Communities…………………………………….....73 4.6 Juvenile Production Estimates or Indices ……………………………………………74 4.7 Emerging Issues: Disease and Management of Diseases ……………………………76 4.7.1 IPN at Cronin in Connecticut – the Pathology ..…………………………...76 4.7.2 Didymo Effects of Fry Production – briefing in CT River ..………………77 5.0 Appendices………..……………………………………………………………………...…78 5.1 List of Attendees……………………………………………………………………..78 5.2 List of Program Summary and Technical Working Papers including PowerPoint Presentation Reports………………………………..…………….……………...79 5.3 Glossary of Abbreviations…………………………………………………………...82 5.4 Glossary of Definitions………………………………………………………………84 5.5 Abstracts from Regional Atlantic Salmon Assessment Committee Meeting………..89 5.5.1 Maine Atlantic Salmon and their Ecosystems (2008 Meeting) ……………89 5.6 Historical Tables…….…….……………………………………start on page ….. 107 iii List of Tables and Figures Table 1.3.1 Documented Atlantic salmon returns to USA rivers, 2007. "Natural" includes fish originating from natural spawning and hatchery fry………………………….4 Table 1.3.2 Documented Atlantic salmon returns to the USA, 1967-2007. "Natural" includes fish originating from natural spawning and hatchery fry. Starting in 2003 estimated returns based on redds are included…………………………………….5 Table 1.3.4 Two sea winter (2SW) returns for 2007 in relation to spawner requirements for USA rivers.………………………...…………………………………………..6 Table 1.4.1 Number of juvenile Atlantic salmon stocked in USA, 2007………………....6 Table 1.4.2 Stocking summary for sea-run, captive, and domestic adult Atlantic salmon for the USA in 2007 by river……………………………………………………...7 Table 1.5.1 Summary of tagged and marked Atlantic salmon released in USA, 2007…...8 Table 1.6.1 Aquaculture production (metric tones) in New England from 1997 to 2007...9 Figure 1.3.1 Origin and sea age of Atlantic salmon returning to USA rivers, 1967 to 2007…….………………………………………………………………………….9 Figure 1.3.2 Return rate of 2SW adults by cohort of hatchery-reared Atlantic salmon smolts released into the Penobscot River (solid line) and wild smolt emigration estimated on the Narraguagus River (dashed line), Maine, USA………………..10 Figure 2.1 Estimated total returns to New England since 1967 from USASAC databases. ……………………………………………………………………………………14 Figure 2.2 Return rates of 2SW Atlantic salmon from the Connecticut, Narraguagus, and Penobscot populations estimated from numbers of stocked smolts for the Penobscot and Connecticut populations and from estimated smolt emigration from the Narraguagus River population…………………………………………15 Figure 3.2.1 Narraguagus River fish arrivals relative to flows during the 2007 adult salmon trapping season…………………………………………………………..24 Table 3.2.1.2 Regression estimates and confidence intervals (90% CI) of adult Atlantic salmon in the core GOM DPS rivers from 1991 to 2007………………...……...26 Table 3.2.2.1 Fry development index (DI) and environmental conditions for stocking events from CBNFS in 2007……………………………………………………..31 Table 3.2.3.2 River pH conditions for stocking events from CBNFH in 2007………….32 Table 3.2.4.1 Minimum (min), median, and maximum (max) large parr Atlantic salmon population densities (fish/100m2) based on multiple pass electrofishing estimates in selected Maine Rivers, 2007…………………………………………………..34 Table 3.2.4.2 Minimum (min), median, and maximum (max) relative abundance of large parr Atlantic salmon population (fish/minute) based on timed single pass catch per unit effort (CPUE) sampling in selected Maine Rivers, 2007……………….34 iv Table 3.2.4.3 Mean fork length (mm) by origin of smolts captured in Rotary Screw Traps in Maine………………………………………………………………………….37 Table 3.2.4.4 Mean smolt weight (g) by origin of smolts captured in Rotary Screw Traps in Maine………………………………………………………………………….37 Table 3.2.4.5 Freshwater age of naturally reared smolts collected in Rotary Screw Traps on selected Maine rivers…………………………………………………………37 Figure 3.2.4.1 Mean fork length (mm) of age 2+ smolts collected in selected Maine Rivers, 2000-2007………………………………………………………………..38 Figure 3.2.4.2 Mean wet weight (g) of age 2+ smolts, collected in selected Maine Rivers, 2000-2007………………………………………………………………………..38 Figure 3.2.4.3 Population estimates (± Std. Error) of emigrating smolts in the Narraguagus River, Maine from 1997 to2007…………………………………...39 Figure 3.2.4.4 Cumulative percentage smolt catch in Rotary Screw Traps by date (run timing) on the Narraguagus and Sheepscot Rivers, Maine, for years 2004 to 2007. The Piscataquis traps did not fish in 2004……………………………………….40 Table 3.2.4.6. Ordinal day (days from January) of median smolt catch in rotary screw traps on the Narraguagus and Sheepscot Rivers, 1997-2007. ……………………41 Table 3.2.8.1 Stream connectivity projects in Atlantic salmon watersheds in Downeast Maine…………………………………………………………………………….46 Table 3.3.1.1 Fry origin adult Atlantic salmon returns, Merrimack River, Years 1994- 2004………………………………………………………………………………49 Table 3.3.1.2 Hatchery smolt origin adult Atlantic salmon returns, Merrimack River, Years 1996 - 2006……………………………………………………………..…49 Table 3.3.4.1 Estimated statistics for yearling parr per habitat unit at Index Sites (IS) and sample sites in the Merrimack River watershed, 1994 – 2007…………………..52 Table 3.4.3.1 Summary of fry stocking by the Rhode Island Salmon in the Classroom program…..………………………………………………………………………61 Table 3.4.3.2 Locations of smolt stocking in the Pawcatuck River, Rhode Island……..62 Figure 4.1.1 Map
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