Dynamics of the Atlantic salmon (Salmosalar L. ) population of the River Foyle, Ireland. by Patrick Boylan A thesissubndtted for the degreeof Doctor of Philosophy. Division of Environmental and Evolutionary Biology Institute of Biomedical and Life Sciences University of Glasgow March 2004 OPatrick Boylan, 2004 Acknowledgments I wish to acknowledgethe help and support of the Chief Executive, Mr. Derick Anderson,the staff and the Board of the LoughsAgency who providedthe majority funding for this study. I also wish to recognisethe financial supportof the Marine Institute and in particularDr. Niall O'Maoileidigh. Thanksare also due to the rest of Agency's Scientific Advisors Dr. Walter Crozier, Dr. Philip McGinnity and Dr. GershamKennedy for their manyhelpful comments. I wish also to acknowledgethe help and supportI receivedfrom manypeople at GlasgowUniversity and in particular my supervisorDr. Colin Adams. Thanks are also due to Prof. Felicity Huntingford Midam Geurts,Sanne de Boer andthe staff at the University Field Station. Contents Page Page no. Summary i Chapter 1. General Introduction 1 1.1 Atlantic salmonLife-cycle 1 1.2 ConservationStatus of Atlantic salmon 3 1.3 PhysicalDescription of Foyle Catchment 4 1.4 SalmonManagement in the Foyle System 4 1.5 PopulationRegulation 7 1.5.1 Density-DependentFactors 7 1.5.2 Density-IndependentFactors 8 1.6 PopulationRegulation in Salmonids 9 1.6.1 PopulationRegulation Processes in the JuvenileFreshwater 9 Phase 1.6.2 PopulationRegulation Processes in the Marine Phase 11 1.6.3 Population Regulation Processesin the Adult freshwater 13 Phase 1.6.4 MathematicalModels 14 1.7 Modelling of JuvenileSalmonids 17 Chapter 2. Competing modes of exploitation and their effects on 21 spawning successin Atlantic salmon (Salmo salar L. ) in the Foyle catchment, Ireland 2.1 Introduction 21 2.2 Materialsand Methods 23 2.2.1 StudyArea 23 2.2.2 Exploitation Catch Data 24 2.2.3 Salmon Population Size Estimates 26 2.2.4 Analysis 27 2.3 Results 27 2.4 Discussion 37 Chapter 3. Life-stage specific, stochastic environmental effects, 41 overlay density-dependent filial cohort strength effects in an Atlantic salmon (Salmo salar L. ) population from Ireland 3.1 Introduction 41 3.2 Materials and Methods 43 3.2.1 Study Area 43 3.2.2 Salmon Population Estimation 43 3.2.3 Population Structure 46 3.2.4 Data Analysis 47 3.3 Results 54 3.3.1 Density-Dependent Regulation 54 3.3.2 Life-Stage Specific Environmental Effects on Population 57 Size 3.4 Discussion 67 Chapter 4. The influence of broad scale climatic phenomena on long 72 term trends in Atlantic salmon population size: an example from the River Foyle, Ireland 4.1 Introduction 72 4.2 Materials and Methods 75 4.3 Results 77 4.4 Discussion 81 Chapter 5. Local instream and catchment spatial scale habitat 83 characteristics determine 0+ fry density of Atlantic salmon (Salmo salar L. ) in the River Foyle 5.1 Introduction 83 5.2 Materialsand Methods 84 5.2.1 CatchmentScale Characteristics 86 5.2.2 Analysis 89 5.3 Results 90 5.4 Discussion 94 Chapter 6. General Discussion 98 References 104 List of Figures Figure no. Legend Page no. 1.1 Life-cycle of the Atlantic salmon 1 1.2 Location map of the Foyle catchment 4 1.3 Five year running averageof commercial salmon catches 6 in the Foyle 1993-2001 1.4 Hypothetical stock-recruitment model 14 1.5 Three common stock-recruitment curves: 0--Linear; 16 2=Beverton & Holt (1957); 3=Ricker (1954) 2.1 Drift, Draft nets,uncorrected Sport Angling catches& 29 uncorrectedredd counts in the Foyle area1952-2000 2.2 Regressionof total annualcatch of salmonin the Foyle 35 areaand corrected redd counts 2.3 Commercialcatch residuals regressed on correctedangling 37 catch 2.4 Total catchresiduals regressed on correctedredd counts 38 2.5 Total catch residualsregressed on correctedredd counts 38 excludingtwo outlying points 3.1 Salmonlife history stagesfor onelife-cycle 49 3.2a A linear model fitted to parental population size (egg 55 equivalent *100,000) and filial population size (egg equivalent*100,000) 3.2b A Beverton& Holt model fitted to parentalpopulation size 56 (egg equivalent *100,000) and filial population size (egg equivalent*100,000) 3.2c A Ricker model fitted to parental population size (egg 56 equivalent *100,000) and filial population size (egg equivalent*100,000) 3.3 Regressionsof environmentalvariables during life-stage 58 specific eventsand populationsize residualsderived from the Ricker parental-offspringcurves 3.4 Mean residual population size values derived from the 64 Ricker parental-offspring curves for years with high (upper 30 percentile); low (lower 30 percentile) and intermediate (remaining 40 percentile) values for environmental variables during the life-stage specific periods. 4.1 Annual commercial catch of salmon in the Foyle area 77 1875-2000 4.2 The five year averagecommercial catches of migrant 78 Atlantic salmonfrom the Foyle catchment1875 to 2001 & the five yearaverage NAOI: 1875- 2000 4.3 The relationship between the winter NAO and commercial 79 fishery catches of Atlantic salmon returning to the River Foyle over 122 year. Breakpoint analysis shows a uncoupling of a negative relationship about a NAOI of 0.151 4.4 The change in North Atlantic Oscillation predicted by 80 sevenclimate changemodels. Dotted line showsthe mean of the sevenmodels, solid lines showthe 2 extremesof the predictedNAO change 6.1 Foyle area annual commercial salmon catches 1962-2003 102 with regression line List of Tables Table no. Legend Page no. Stock-recruitmentequations for Beverton & Holt (1957) 16 andRicker (1954)models 2.1 Correlations of commercial fishing catches and corrected 32 sport angling catches 2.2 Correlationsof commercialfishing catches,corrected sport 34 angling catches, corrected total catch, corrected redd countsand corrected total population 3.1 Comparisonof predictive linear; Beverton & Holt and 54 Ricker models 3.2 Regressionof environmentalvariables during life-stage 60 specific eventsand populationsize residualsderived from the Ricker parental-offspringcurves 3.3 ANOVA results of environmentalvariables during life- 62 stagespecific eventsand populationsize residualsderived from the Ricker parental-offspringcurves 5.1 Local scale site-specific variables collected for each 85 samplingfor 350 sitesin the Foyle catchment 5.2 Catchmentscale characteristicscalculated from ordnance 86 survey and geological survey maps for each of the 350 samplingsites in the Foyle catchment 5.3 Stepwise regression of local site specific stream 90 characteristics on 0+ salmon numbers for a) all sites (including sites with no 0+ salmon); b) only sites where 0+ salmon were present 5.4 Stepwise regressionof catchmentcharacteristics on 0+ 91 salmonnumbers for a) all sites (including siteswith no 0+ salmon);b) only siteswhere 0+ salmonwere present 5.5 Stepwise regression of local scale and catchment 92 characteristicscombined on 0+ salmonnumbers for a) all sites (including sites with no 0+ salmon); b) only sites where0+ salmonwere present Summary This study examines the dynamics of the Atlantic salmon (Salmo salar L. ) population of the Foyle catchment in Ireland, through the analysis of long-term datasets and extensive field data. In Chapter I the current conservation status of the salmon is discussed with particular reference to the Foyle. A number of methods used in studying the juvenile and adult life-stages are reviewed. Chapter 2 considersthe interaction betweencommercial netting and recreationalsport angling and the effect of total combined exploitation on an independentmeasure of populationsize (redd counts)using a 49 year dataset. While recognisingthat commercial netting had a relatively small negativeimpact on recreationalsport angling, the evidence suggeststhat year class strength is the principal modulator of variation in commercial catches, sport angling catchesand spawning escapement. Chapter 3 examines the role of density-dependencein the Foyle salmon population. A Ricker density-dependent model showed that spawning adult population size significantly predicted variation in the resultant filial generation, however, a significant amount of variation (ca. 68%) remained unexplained. Environmental factors were significant in explaining some of the remaining variance and these influences were linked to specific life stages. This finding strongly suggestspopulation bottlenecks in the complex life cycle of this species, during which specific environmental factors may have an impact, that they do not have during other periods. It was concluded that these life stage specific environmental effects are likely to contribute to the stochastic variation in population size resulting from the application of traditional stock-recruitmentmodels and that the identification and quantification of these effects should allow improved model accuracy. Chapter4 investigatesthe effect of marineclimatic conditionsin the North Atlantic on the abundanceof returningmigrant Atlantic salmon,using a 126 year datasetof commercial catchesand an index of climate in the northernhemisphere, the North Atlantic Oscillation (NAOI). The NAOI when below 0.151 explaineda significant proportionof variation in five year running meancatches of migrant Atlantic salmonreturning to the River Foyle. This indicatesthat a significant proportion of the variancein populationsize in the past was the result of variability in conditionsin the marineenvironment. However, when the NAOI was above0.151, this relationshipuncoupled. Models of climate changeindicate that the NAOI is likely