EV A LU A TIO N OF GROW TH, SURVIVAL, AND R EC R U ITM EN T OF CH INO O K SALM O N IN SOU TH EA ST A LA SK A RIV ERS
By
Cory J. Graham, B.S., B.A.
A Thesis Subm itted in Partial Fulfillm ent o f the Requirem ents for the D egree o f
M aster o f Science in
Fisheries
U niversity of A laska Fairbanks D ecem ber 2016
A PPR O V ED :
Dr. Trent Sutton, Com m ittee Chair Dr. M ilo Adkison, Com m ittee M em ber Dr. M egan M cPhee, Com m ittee M em ber Dr. G ordon Kruse, Chair
D epartm ent o f Fisheries
Dr. B radley M oran, D ean
College o f F isheries a n d Ocean Sciences
A bstract
R ecent reductions in the run sizes o f Chinook Salm on Oncorhynchus tshawytscha in Southeast A laska have resulted in social and econom ic hardships w ithin the region. Pacific salm on year- class strength may be determ ined by size-selective processes during the early m arine phase of their life cycle; however, the relative im portance of grow th during freshw ater and m arine residence in determ ining recruitm ent success is unknown. A scale-based retrospective analysis w as conducted to exam ine the effects o f freshw ater and annual m arine grow th and early m arine conditions on survival to reproductive m aturity for fem ale Chinook Salm on by brood year (BY) in the Taku (BYs 1979 - 1985, 1990 - 1999, 2002 - 2004) and U nuk (BYs 1981 - 1983, 1986 -
1988, 1994 - 2003, 2005 - 2006) rivers. First-year m arine grow th w as positively related to survival and total return for C hinook Salm on stocks from both systems. G row th during
freshw ater residence (i.e., size-at-ocean entry) w as not related to survival or total return o f either stock. In addition, there w as a positive relationship betw een m arine survival of U nuk R iver Chinook Salm on and sea-surface tem peratures in U pper Chatham Strait, Icy Strait, and A uke Bay M onitor (P = 0.04) during early m arine residence. The results o f my research highlight the im portance of grow th and m arine conditions during the first year at sea in determ ining the survival o f C hinook Salm on in Southeast A laska and suggest that current declines in run sizes and survival o f stocks w ithin this region may be the attributed to poor grow th conditions or grow th during early m arine residence.
Table o f C ontents Title P a g e ... i A bstract ... iii Table o f C on ten ts... v L ist o f F ig u re s... ix L ist o f T a b le s ... xi
A cknow ledgem ents... xiii
General Introduction ... 1
Literature C ite d ...8
Chapter 1: Evaluation o f growth, survival, and recruitm ent o f Chinook Salmon in Southeast A laska r iv e r s ...17
A bstract ... 17
Introduction... 18
M ethods...22
Study s ite s ...22
Scale sam p les...23
Scale reading ...25
R ecruitm ent b en c h m a rk s... 26
Relationship betw een annual grow th zones and recruitm ent b en ch m ark s... 28
Relationship betw een grow th zones...30
Size-selective m ortality at ocean e n try ...31
R esu lts... 32 Page
Relationship betw een brood year recruitm ent success and annual grow th...33
Relationship betw een annual grow th and m arine su rv iv al... 34
Relationship betw een grow th zones...34
Size-selective m ortality at ocean e n try ...35
D iscussion ... 35
Influence o f annual grow th on su rv iv a l... 35
Grow th d ep en d en cy... 40
Size-selective m ortality at ocean e n try ... 41
Literature C ite d ...45
Chapter 2: Influence of abiotic and biotic factors on the freshw ater overw inter survival o f U nuk R iver C hinook Salm on... 67
A bstract ...67
Introduction...68
M ethods...72
Study site...72
Biological d a ta ... 73
P arr and sm olt capture, tagging, and sam plin g...73
Sm olt abundance and freshw ater overw inter su rv iv al... 73
Physical d a ta ... 74
D ata a n a ly se s...75
R esu lts... 77
D iscussion ... 78
Chapter 3: Influence o f sm olt biological attributes and early m arine conditions on the m arine
survival o f U nuk R iver Chinook Salm on...95
A bstract ...95
Introduction...97
M ethods...100
Study site... 100
Biological d a ta ...101
Sm olt length and w e ig h t... 101
Sm olt ab undance... 102
A dult abundance, total return, and m arine su rvival... 102
Physical d a ta ... 103
D ata a n a ly se s...105
R esu lts... 106
D iscu ssio n... 108
Literature C ite d ...115
General C o nclu sio ns...133
L ist o f Figures
Figure 1.1. Location o f the Taku and U nuk riv ers... 57 Figure 1.2. Age-1.4 C hinook Salm on s c a le ...58 Figure 1.3. V isualization o f the m ultiple regression m odels that w ere fitted using w eighted
annual grow th z o n e s ...59 Figure 1.4. Scatter plots showing relationships betw een first- and third-year m arine grow th and m arine survival...60 Figure 1.5. R elationships betw een adjacent grow th z o n e s ... 61 Figure 1.6. Scatter plot w ith skew o f brood-year freshw ater grow th distributions on the y axis and brood year on the x a x is ...62 Figure 2.1. The U nuk R iver in Southeast A laska and B ritish C o lu m b ia... 91 Figure 2.2. Time series o f (a) freshw ater overw inter survival, (b) m ean parr length (mm), (c) m ean parr w eight (g), and (d) log-transform ed parr ab u n d an ce... 92 Figure 3.1. L ocation o f the U nuk R iv e r... 125 Figure 3.2. Time series o f m arine su rv iv a l...126 Figure 3.3. R elationship betw een brood year average sm olt fork length and brood year m arine survival...127 Figure 3.4. V isualization o f the m ultiple regression m o d e ls ... 128 Page
L ist o f Tables
Table 1.1. M ean distance, range, and standard deviation o f w eighted annual grow th z o n e s 63
Table 1.2. R esults o f w eighted m ultiple regression m o dels... 64
Table 1.3. R esults o f w eighted simple linear reg ressio n s...65
Table 1.4. P earson’s product-m om ent correlation coefficient (r) and results o f m ixed-effects m o d e ls...66
Table 2.1. Loadings betw een rotated principal com ponents... 93
Table 2.2. R esults o f m ultiple and simple linear regression analyses... 94
Table 3.1. Locations and coordinates o f sample station s... 129
Table 3.2. Loadings betw een principal com ponents and sm olt biological v ariab les... 130
Table 3.3. L oadings betw een rotated principal com ponents and A uke Bay M onitor (ABM ), U pper Chatham Strait (UCS), Icy Strait (IS) sea-surface te m p eratu res...131
A cknow ledgem ents
F irst and forem ost, I w ould like to thank my advisor, Dr. Trent Sutton, for selecting m e for this research project, providing an abundant am ount of support throughout my graduate studies, and helping m e develop the skills necessary to becom e a fisheries professional. I w ould also like to thank my com m ittee m em bers, Dr. M ilo A dkison and Dr. M egan M cPhee for providing support and helping to develop this project. Thanks to Dr. Ronald Berry for answ ering my num erous questions regarding statistical analyses. I w ould like to thank B ev Alger, Lorna W ilson, Casey M cConnell and the rest o f the A laska D epartm ent o f Fish and G am e (A D F& G ) M ark A ge and Tag Laboratory for preparing the sam ples used in this study. I w ould like to acknow ledge Phil R ichards and Todd Johnson (A D F& G ) for providing data and their expertise relating to Chinook
Salm on in Southeast Alaska. Thanks to the A D F& G field crews that collected the scale samples used in this study. Thanks to Troy Jaecks and Stephen Todd for allow ing m e to be a part o f a great field crew on the Stikine R iver w here I w as able to learn the m ethods used to capture fish in my study. I w ould also like to thank my m om and the rest o f my fam ily for teaching m e how to fish and stressing the im portance o f a college education. Finally, I w ould like to thank my girlfriend, Gina, for supporting m e and staying by my side throughout my undergraduate and graduate studies. This project w ould not have been possible w ithout funding from the Pollock Conservation Cooperative Research Center at the U niversity of A laska Fairbanks, A laska Capital Im provem ent Program , and ADF&G.
G eneral Introduction
G rowth is an im portant process that influences the reproductive success o f fish (Candolin and V oigt 2001; W acker et al. 2012). Fecundity and egg size are positively related to fem ale spaw ner body size for m ost fishes (Beacham et al. 1985; M anzer and M iki 1986; D ickerson et al. 2002). In addition, large body size enables individuals to secure high quality habitats, w hich may lead to fitness advantages over sm aller conspecifics (Candolin and V oigt 2001; W acker et al. 2012). For instance, large Threespine Sticklebacks G asterosteus aculeatus w ere able to defend larger territories and encountered fem ales at higher rates than sm aller individuals in the population (Candolin and V oigt 2001). B oth biotic and abiotic processes regulate grow th in fish, w ith tem perature and food availability being o f prim ary im portance (G root et al. 1995). Fish are poikilotherm s; therefore, the m etabolic rates o f fish are regulated by am bient tem peratures. In general, fish grow th rates increase until an optim um tem perature is reached (G root et al. 1995); once this tem perature is exceeded, grow th rates decline due to high basal m etabolic costs (W ootton 1998). B iotic factors, such as quality and quantity o f food resources, also affect somatic grow th rates (W ootton 1998), as illustrated by a positive relationship betw een the abundance o f drifting invertebrates and juvenile Coho Salm on Oncorhynchus kisutch grow th rates (Rosenfeld et al. 2005). Further, the nutritional quality o f prey resources may also affect grow th rates (W ootton 1998). F or example, in the w estern G ulf o f Alaska, variations in W alleye Pollock Gadus chalcogrammus grow th rates have been attributed to regional differences in zooplankton species com position (W ilson et al. 2013).
In addition to reproductive success, grow th may also influence survival due to size- selective m ortality, w ith large-bodied fish exhibiting higher survivorship w hen facing predators,
extrem e environm ental conditions, or periods o f low food availability (Sogard 1997; H urst 2007). Large body size reduces the risk o f predation in tw o ways. First, large size physically prevents predation due to gape lim itations o f predators. Second, swim m ing ability is positively related to body size; therefore, larger fish can swim faster to escape potential predators than sm aller individuals (Sogard 1997). Large-bodied fish also have a survival advantage over smaller conspecifics during periods o f low food availability due to the allom etric scaling o f m etabolic requirem ents; larger individuals need to expend less energy per unit body m ass on basal processes than sm aller fish (Thom pson et al. 1991; Sogard 1997; W ootton 1998; Schultz and Conover 1999; B iro et al. 2004; H urst 2007). Finally, larger fish have a low er gill surface area relative to body mass, w hich may increase survival w hen experiencing extrem e environm ental conditions (Sogard 1997; B jerknes et al. 1992). For example, Bjerknes et al. (1992) found that small A tlantic Salm on parr Salmo salar had low er osm oregulatory abilities and higher rates o f mortality than larger individuals w hen exposed to stepw ise increases in salinity levels. Therefore, grow th may regulate survival o f fish groups that experience high rates of predation and extrem e environm ental conditions.
Salm on are susceptible to size-selective m ortality throughout their freshw ater and m arine residence. In freshwater, predation is thought to be an im portant cause of m ortality in Pacific salmon, w ith juveniles being exposed to a suite o f potential predator groups, such as mammals, birds, and other fishes (Peterson 1982; W ood 1987; Q uinn 2005). In addition, the physiological stress associated w ith overw intering in freshw ater may result in high rates of size-m ediated mortality (H urst 2007; B row n et al. 2011). F or exam ple, pre-w inter body size and condition w ere positively related to overw inter survival in several species o f salm onids (Sm ith and Griffith
m ediate salm on m ortality w hile in the ocean. The critical size, critical period hypothesis proposes that salm on m ortality in the ocean is concentrated in tw o distinct periods during early m arine residence (Beam ish and M ahnken 2001). The first period o f high m ortality is size- m ediated and occurs shortly after smolts enter the ocean. Smolting is an osm otically stressful process that may lead to reduced predator avoidance and high m ortality w hen entering predator- rich coastal environm ents (H andeland et al. 1996; D ieperink et al. 2002). R ecent studies indicate that sm olt body size at ocean entry is positively related to m arine survival for A tlantic and Pacific salm on (K allio-N yberg et al. 2004; Jutila et al. 2006; A ntonsson et al. 2010; M urphy et al. 2013). Therefore, smolts that do not reach a “critical size” are m ore likely to suffer predation- based m ortality soon after entering the ocean than sm aller individuals. The second period of high m ortality for Pacific salm on in the ocean occurs during the first m arine w inter (Beam ish and M ahnken 2001; B eam ish et al. 2004). Similar to freshwater, the overw intering period in the m arine environm ent is physiologically stressful; as a result, individuals that fail to store sufficient energy reserves during their first m arine sum m er and fall may deplete their energy stores and suffer starvation-induced m ortality during their first m arine w inter (Beam ish and M ahnken 2001; B eam ish et al. 2004). Therefore, if conditions are poor for grow th and size- selective m ortality is high, size-m ediated m ortality in freshw ater and m arine environm ents may regulate brood year-class strength o f Pacific salm on (Bradford 1995; Sogard 1997; B eam ish and M ahnken 2001).
Clim ate plays an im portant role in shaping m arine ecosystem s, w hich in turn, may affect Pacific salm on production directly through changes in w ater tem perature and indirectly through changes in bottom -up processes (M ueter et al. 2002; Edw ards and Richardson 2004; Seo et al. 2006; N oakes and B eam ish 2009; Petrosky and Schaller 2010; D oney et al. 2012). M ultiple
studies indicate significant relationships betw een sea-surface tem peratures (SST) and Pacific and A tlantic salm on survival (K oslow et al. 2002; M ueter et al. 2002, 2005; Logerw ell et al. 2003; K allio-N yberg et al. 2004; Stachura et al. 2014; M iller et al. 2014). F or instance, regional SSTs influenced survival rates for both northern (i.e., A laska) and southern stocks (i.e., B ritish Colum bia and W ashington) o f Pacific salm on (M ueter et al. 2002). Clim ate may also affect the survival o f Pacific salm on indirectly through changes in the tim ing and availability o f prim ary and secondary production (Edw ards and R ichardson 2004; Petrosky and Schaller 2010). Climate is dynam ic and can change directionally or oscillate betw een varying regim es, both o f w hich may alter trophic relationships (Francis et al. 1998; H are and M antua 2000; M antua and H are 2002). V ariations in long-term abundance trends of Pacific salm on from large regions in the N orth Pacific O cean have tracked changes in large-scale clim ate indices such as the Pacific D ecadal O scillation (PDO; M antua et al. 1997; H are and M antua 2000) and the A leutian Low Pressure Index (ALPI; B eam ish and B ouillon 1993). Thus, the non-static nature o f clim ate and its regulation of the processes that influence recruitm ent success may explain long-term
fluctuations in the abundance o f highly valued species such as Chinook Salm on Oncorhynchus
tshawytscha.
Chinook Salm on is the largest and least abundant species o f Pacific salm on and has a spaw ning distribution that ranges from south-central C alifornia to K otzebue Sound, Alaska, in N orth A m erica and H okkaido, Japan, to the A nadyr River, R ussia (Healey 1991; Q uinn 2005). Certain traits, such as anadrom y and semelparity, are com m on to C hinook Salm on throughout their range (Quinn 2005). H ow ever, C hinook Salm on stocks exhibit diverse life-history strategies due to specialized adaptations to local environm ents, but in general can be classified into tw o life-history types based on extent o f freshw ater rearing (Healey 1991; Q uinn 2005).
O cean-type C hinook Salmon do not rear in freshw ater for extended periods, and instead m igrate to the ocean soon after em erging from the gravel. This life-history strategy is only found at the southern end o f their spawning distribution (i.e., south o f 56o latitude). In contrast, stream -type Chinook Salm on rear in freshw ater for 1-2 years prior to m igrating to the ocean. W hile stream- type C hinook Salm on are found throughout their spaw ning range, they are m ore com m on in northern extent o f their distribution (i.e., Alaska).
In Alaska, C hinook Salm on spaw ning m igrations occur in the spring and summer, w hile spaw ning takes place in the late sum m er or fall (Quinn 2005; H endrich et al. 2008; M cPherson et al. 2010). C hinook Salm on spawn in a w ide range o f habitats, but in general prefer areas w ith high subgravel flow (H ealey 1991; Q uinn 2005). Fem ale spaw ners deposit eggs into redds w here, after being fertilized by males, the em bryos incubate in the gravel overwinter. Em bryos hatch the follow ing spring, and the m ajority o f parr spend one year in freshw ater prior to im m igrating to the ocean betw een April and July as age-1 smolts (H endrich et al. 2008;
M cPherson et al. 2010). A fter entering the m arine environm ent, A laska Chinook Salmon m ake extensive, seasonal offshore m igrations (M yers et al. 2009). In Southeast A laska (SEAK), the extent o f oceanic m igrations varies by stock, w ith some rearing w ithin the w aters o f SEAK and B ritish C olum bia and others m igrating into the G u lf o f A laska and the B ering Sea (D er
H ovanisian et al. 2011). C hinook Salm on spend 2-5 years feeding in the m arine environm ent prior to returning to their natal stream to spawn (H endrich et al. 2008; M cPherson et al. 2010). V ariations in life-history strategies exhibited by stocks across the state may explain regional differences in the recruitm ent success o f C hinook Salmon.
The productivity (return per spaw ner) o f C hinook Salmon stocks has long displayed considerable tem poral and regional variability w ithin Alaska. Recently, declines in productivity
have been w idespread across the state, w hich have prom pted researchers to identify the cause of these declines (A D F& G C hinook Salm on Research Team 2013; Schindler et al. 2013). D ue to the im portance of size-m ediated processes in determ ining recruitm ent success, the factors driving recruitm ent failure may be uncovered by studying long-term variations in grow th and their relation to productivity. One useful w ay to study long-term changes in abundance and recruitm ent is scale-based retrospective analyses.
Scale-based retrospective analyses have been used to study long-term trends in growth and their relationship to climate, survival, and productivity in salm on (Healey 1982; H oltby et al. 1990; C rozier and K ennedy 1999; Friedland et al. 2000; B eam ish et al. 2004; Farley et al. 2007; Ruggerone et al. 2007, 2009; Cross et al. 2008). Scale form ation (i.e., circulus spacing and form ation rate) is positively related to som atic grow th rate (Fisher and Pearcy 2005; W alker and Sutton 2016) and can be used as an index o f grow th in salm on (R uggerone et al. 2007; M cCarthy et al. 2008; H ogan and Friedland 2010). Further, scale form ation can be correlated to recruitm ent benchm arks (e.g., total return, productivity, etc.) to determ ine how grow th rates influence
survival throughout the life cycle o f Pacific salm on (Fisher and Pearcy 2005; M cCarthy et al. 2008; H ogan and Friedland 2010). For example, circulus spacing indicates that early m arine grow th influences survival in A tlantic Salmon Salmo salar (Friedland et al. 2000), Sockeye
Salm on O. nerka (Ruggerone et al. 2007), Coho Salm on O. kisutch (Beam ish et al. 2004), and Pink Salm on O. gorbuscha (M oss et al. 2005; Cross et al. 2008). Ruggerone et al. (2007) found a positive correlation betw een the run sizes o f Sockeye Salm on from w estern and central A laska and scale grow th during the first tw o years at sea. Scale-based retrospective analyses have also been used to exam ine the influence o f freshw ater grow th on productivity o f C hinook Salmon from tributaries o f the Y ukon and K uskokw im rivers (Leon 2013) and on the pre-fishery
abundance o f A tlantic Salm on from the D ram m en River, N orw ay (M cCarthy et al. 2008). N either study found a significant effect o f freshw ater grow th on recruitm ent, but previous research indicates freshw ater grow th may be im portant because it positively correlated w ith first year m arine grow th in Chinook Salm on (Ruggerone et al. 2009; Leon 2013). Therefore,
exam ining tim e series of scale grow th patterns may lend insights into the factors that influence survival, productivity, and abundance o f C hinook Salmon.
W hile size-selective processes are thought to influence the brood-year recruitm ent success o f Pacific salmon, there role in current recruitm ent declines o f C hinook Salmon in SEAK is unknown. Chapter one o f this thesis characterizes the influence o f freshw ater and m arine annual grow th in determ ining the recruitm ent success o f Taku and U nuk R iver Chinook
Salmon. The second chapter exam ines the relative influence o f biotic and abiotic factors on the freshw ater overw inter survival and sm olt production o f U nuk R iver Chinook Salmon. C hapter 3 investigates the influence of early m arine conditions and sm olt body size on the m arine survival o f U nuk R iver C hinook Salmon. Overall, this research provides insights into the factors
potentially responsible for the reduced runs sizes and survival of stocks across the region and can be used to guide future research in this area.
Literature Cited
A D F& G C hinook Salm on R esearch Team. 2013. C hinook Salm on assessm ent and research plan, 2013. A laska D epartm ent o f Fish and Game, Special Publication No. 13-01, Anchorage. A ntonsson, T., T. H eidarsson, and S. S. Snorrason. 2010. Smolt em igration and survival to
adulthood in tw o Icelandic stocks o f A tlantic Salmon. Transactions o f the A m erican Fisheries Society 139:1688-1698.
Beacham , T. D., F. C. W ithler, and R. B. M orley. 1985. Effect o f egg size on incubation-tim e and alevin and fry size in Chum Salm on (Oncorhynchus keta) and Coho Salmon
(Oncorhynchus kisutch). Canadian Journal o f Zoology 63:847-850.
Beam ish, R. J., and D. R. Bouillon. 1993. Pacific salm on production trends in relation to climate. Canadian Journal o f Fisheries and A quatic Sciences 50:1002-1016.
Beam ish, R. J., and C. M ahnken. 2001. A critical size and period hypothesis to explain natural regulation o f salm on abundance and the linkage to clim ate and clim ate change. Progress in O ceanography 49:423-437.
Beam ish, R. J., C. M ahnken, and C. M. Neville. 2004. Evidence that reduced early m arine grow th is associated w ith low er m arine survival o f Coho Salmon. Transactions o f the A m erican Fisheries Society 133:26-33.
Biro, P. A., A. E. M orton, J. R. Post, and E. A. Parkinson. 2004. O ver-w inter lipid depletion and mortality o f age-0 R ainbow Trout (Oncorhynchus mykiss). Canadian Journal o f Fisheries and A quatic Sciences 61:1513-1519.
Bjerknes, V., J. Duston, D. K nox, and P. Harm on. 1992. Im portance o f body size for acclim ation o f underyearling A tlantic Salm on parr (Salmo salar L.) to seawater. A quaculture
104:357-366.
Bradford, M. J. 1995. Com parative review o f Pacific salm on survival rates. Canadian Journal o f Fisheries and A quatic Sciences 52:1327-1338.
Brown, R. S., W. A. H ubert, and S. F. Daly. 2011. A prim er on w inter ice, and fish: w hat fisheries biologists should know about w inter ice processes and stream -dw elling fish. Fisheries 36:8-26.
Candolin, U., and H. R. Voigt. 2001. Correlation betw een m ale size and territory quality: consequence o f m ale com petition or predation susceptibility? Oikos 95:225-230. Cross, A. D., D. A. Beaucham p, K. W. M yers, and J. H. M oss. 2008. Early m arine grow th o f
Pink Salm on in Prince W illiam Sound and the coastal G ulf o f A laska during years o f low and high survival. Transactions o f the A m erican Fisheries Society 137:927-939.
Crozier, W. W ., and G. J. A. Kennedy. 1999. R elationships betw een m arine grow th and m arine survival o f one sea w inter A tlantic Salmon, Salmo salar L., from the R iver Bush, N orthern Ireland. Fisheries M anagem ent and Ecology 6:89-96.
D er H ovanisian, J., S. M cPherson, E. Jones, P. Richards, R. Chapell, B. Elliott, T. Johnson, and S. Fleischm an. 2011. C hinook Salm on status and escapem ent goals for stocks in
Southeast Alaska. A laska D epartm ent o f Fish and Game, Special Publication No. 11-19, Anchorage.
D ickerson, B. R., T. P. Quinn, and M. F. W illson. 2002. Body size, arrival date, and reproductive success o f Pink Salmon, Oncorhynchus gorbuscha. Ethology Ecology & Evolution 14:29-44.
D ieperink, C., B. D. Bak, L. F. Pedersen, M. I. Pedersen, and S. Pedersen. 2002. Predation on A tlantic Salmon and Sea Trout during their first days as postsmolts. Journal o f Fish Biology 61:848-852.
Doney, S. C., and coauthors. 2012. Clim ate change im pacts on m arine ecosystem s. A nnual R eview o f M arine Science 4:11-37.
Edw ards, M ., and A. J. R ichardson. 2004. Im pact o f clim ate change on m arine pelagic phenology and trophic m ism atch. N ature 430:881-884.
Farley, E. V., J. H. M oss, and R. J. Beam ish. 2007. A review o f the critical size, critical period hypothesis for juvenile Pacific salmon. N orth Pacific A nadrom ous Fish Com m ission B ulletin 4:311-317.
Fisher, J. P., and W. G. Pearcy. 2005. Seasonal changes in grow th o f Coho Salmon
(Oncorhynchus kisutch) off O regon and W ashington and concurrent changes in the
spacing o f scale circuli. Fishery B ulletin 103:34-51.
Francis, R. C., S. R. Hare, A. B. H ollow ed, and W. S. W ooster. 1998. Effects o f interdecadal clim ate variability on the oceanic ecosystem s of the N E Pacific. Fisheries O ceanography 7:1-21.
Friedland, K. D., L. P. Hansen, D. A. D unkley, and J. C. M acLean. 2000. Linkage betw een ocean climate, post-sm olt growth, and survival o f A tlantic Salm on (Salmo salar L.) in the N orth Sea area. ICES Journal o f M arine Science 57:419-429.
Groot, C., L. M argolis, and W. C. Clarke. 1995. Physiological ecology o f Pacific salmon. U niversity of B ritish C olum bia Press, Vancouver.
H andeland, S. O., T. Jarvi, A. Ferno, and S. O. Stefansson. 1996. O sm otic stress, antipredator behaviour, and m ortality o f A tlantic Salm on (Salmo salar) smolts. Canadian Journal o f Fisheries and A quatic Sciences 53:2673-2680.
Hare, S. R., and N. J. M antua. 2000. Em pirical evidence for N orth Pacific regim e shifts in 1977 and 1989. Progress in O ceanography 47:103-145.
H ealey, M. C. 1982. Tim ing and relative intensity o f size-selective m ortality o f juvenile Chum Salm on (Oncorhynchus keta) during early sea life. Canadian Journal o f Fisheries and A quatic Sciences 39:952-957.
H ealey, M ., C. Groot, and L. M argolis. 1991. Life history o f C hinook Salm on (Oncorhynchus
tshawytscha). Pages 311-393 in C. G root and L. M argolis, editors. Pacific salm on life
histories. U niversity o f B ritish C olum bia Press, Vancouver.
H endrich, C. F., J. L. W eller, S. A. M cPherson, D. R. Bernard. 2008. Optim al production o f Chinook Salm on from the U nuk River. A laska D epartm ent o f Fish and Game, Fishery M anuscript No. 08-03 , A nchorage.
Hogan, F., and K. D. Friedland. 2010. R etrospective grow th analysis o f A tlantic Salm on Salmo
salar and im plications for abundance trends. Journal o f Fish B iology 76:2502-2520.
H oltby, L. B., B. C. Andersen, and R. K. K adow aki. 1990. Im portance o f sm olt size and early ocean grow th to interannual variability in m arine survival o f Coho Salmon
(Oncorhynchus kisutch). Canadian Journal o f Fisheries and A quatic Sciences 47:2181
2194.
Hurst, T. P. 2007. Causes and consequences o f w inter m ortality in fishes. Journal o f Fish Biology 71:315-345.
H uusko, A., L. Greenberg, M. Stickler, T. Linnansaari, M. N ykanen, T. V ehanen, S. K oljonen, P. Louhi, and K. Alfredsen. 2007. L ife in the ice lane: the w inter ecology o f stream
salmonids. R iver R esearch and A pplications 23:469-491.
Jutila, E., E. Jokikokko, and M. Julkunen. 2006. Long-term changes in the sm olt size and age o f A tlantic Salmon, Salmo salar L., in a northern B altic river related to parr density, grow th opportunity and postsm olt survival. Ecology o f Freshw ater Fish 15:321-330.
K allio-N yberg, I., E. Jutila, I. Saloniemi, and E. Jokikokko. 2004. A ssociation betw een environm ental factors, sm olt size and the survival o f w ild and reared A tlantic Salmon from the Simojoki R iver in the B altic Sea. Journal o f Fish B iology 65:122-134.
K oslow, J. A., A. J. H obday, and G. W. Boehlert. 2002. Clim ate variability and m arine survival o f Coho Salm on (Oncorhynchus kisutch) in the O regon production area. Fisheries O ceanography 11:65-77.
Leon, J. M. 2013. Freshw ater grow th and recruitm ent o f Y ukon and K uskokw im river C hinook Salmon: a retrospective grow th analysis. M aster’s thesis, U niversity o f Alaska,
Fairbanks.
Logerw ell, E. A., N. M antua, P. W. Law son, R. C. Francis, and V. N. Agostini. 2003. Tracking environm ental processes in the coastal zone for understanding and predicting Oregon Coho (Oncorhynchus kisutch) m arine survival. Fisheries O ceanography 12:554-568. M antua, N. J., and S. R. Hare. 2002. The Pacific D ecadal Oscillation. Journal o f Oceanography
58:35-44.
M antua, N. J., S. R. Hare, Y. Zhang, J. M. W allace, and R. C. Francis. 1997. A Pacific interdecadal clim ate oscillation w ith im pacts on salm on production. B ulletin o f the A m erican M eteorological Society 78:1069-1079.
M anzer, J. I., and I. M iki. 1986. Fecundity and egg retention o f some Sockeye Salmon
(Oncorhynchus nerka) stocks in British-Colum bia. Canadian Journal o f Fisheries and
A quatic Sciences 43:1643-1655.
M cCarthy, J. L., K. D. Friedland, and L. P. Hansen. 2008. M onthly indices o f the post-sm olt grow th o f A tlantic Salm on from the D ram m en River, N orway. Journal o f Fish Biology 72:1572-1588.
M cPherson, S. A., E. L. Jones III, S. J. Fleischm an, and I. M. Boyce. 2010. Optim al production o f C hinook Salm on from the Taku R iver through the 2001 year class. A laska D epartm ent o f Fish and Game, Fishery M anuscript Series No. 10-03, A nchorage.
M eyer, K. A., and J. S. Griffith. 1997. First-w inter survival o f R ainbow Trout and B rook Trout in the H enrys Fork o f the Snake River, Idaho. Canadian Journal o f Zoology 75:59-63. M iller J. A., D. J. Teel, W. T. Peterson, and A. M. Baptista. 2014. A ssessing the relative
im portance o f local and regional processes on the survival o f a threatened salmon population. PLoS One 9(6):e99814.
M oss, J. H., D. A. Beaucham p, A. D. Cross, K. W. M yers, E. V. Farley Jr. J. M. M urphy, and J. H. Helle. 2005. Evidence for size-selective m ortality after the first sum m er o f ocean grow th by Pink Salmon. Transactions o f the A m erican Fisheries Society 134:1313-1322. M ueter, F. J., R. M. Peterm an, and B. J. Pyper. 2002. O pposite effects o f ocean tem perature on
survival rates o f 120 stocks o f Pacific salm on (Oncorhynchus spp.) in northern and southern areas. Canadian Journal o f Fisheries and A quatic Sciences 59:456-463. M ueter, F. J., B. J. Pyper, and R. M. Peterm an. 2005. R elationships betw een coastal ocean
conditions and survival rates o f northeast Pacific salm on at m ultiple lags. Transactions o f the A m erican Fisheries Society 134:105-119.
M urphy, J., K. H oward, L. Eisner, A. A ndrews, W. Tem plin, C. Guthrie, K. Cox, and E. Farley. 2013. Linking abundance, distribution, and size o f juvenile Y ukon R iver Chinook Salm on to survival in the northern Bering Sea. N orth Pacific A nadrom ous Fish Com m ission Technical R eport No. 9:25-30.
M yers, K. W ., R. V. W alker, N. D. D avis, J. L. A rm strong, and M. K aeriyam a. 2009. H igh seas distribution, biology and ecology of A rctic-Y ukon-K uskokw im salmon: direct
inform ation from high seas tagging experim ents, 1954-2006. A m erican Fisheries Society Symposium Series 70:201-239.
N oakes, D. J., and R. J. Beam ish. 2009. Synchrony o f m arine fish catches and clim ate and ocean regim e shifts in the N orth Pacific Ocean. M arine and Coastal Fisheries 1:155-168.
Peterson, N. P. 1982. Population characteristics o f juvenile Coho Salm on (Oncorhynchus
kisutch) overw intering in riverine ponds. Canadian Journal o f Fisheries and A quatic
Sciences 39:1303-1307.
Petrosky, C. E., and H. A. Schaller. 2010. Influence o f river conditions during seaw ard m igration and ocean conditions on survival rates o f Snake R iver Chinook Salm on and Steelhead. Ecology o f Freshw ater Fish 19:520-536.
Quinn, T. P. 2005. The behavior and ecology o f Pacific salm on and trout. U niversity o f W ashington Press, Seattle.
Rosenfeld, J. S., T. Leiter, G. Lindner, and L. Rothm an. 2005. Food abundance and fish density alters habitat selection, growth, and habitat suitability curves for juvenile Coho Salmon
(Oncorhynchus kisutch). Canadian Journal o f Fisheries and A quatic Sciences 62:1691
Ruggerone, G. T., J. L. N ielsen, and B. A. Agler. 2009. L inking m arine and freshw ater grow th in w estern A laska Chinook Salm on Oncorhynchus tshawytscha. Journal o f Fish Biology 75:1287-1301.
Ruggerone, G. T., J. L. N ielsen, and J. Bum garner. 2007. Linkages betw een A laskan Sockeye Salm on abundance, grow th at sea, and climate, 1955-2002. D eep-Sea Research Part II 54:2776-2793.
Schindler, D., and coauthors. 2013. A rctic-Y ukon-K uskokw im C hinook Salm on research action plan: Evidence o f decline o f C hinook Salm on populations and recom m endations for future research. A Y K Sustainable Salm on Initiative, Anchorage, Alaska.
Schultz, E. T., and D. O. Conover. 1999. The allom etry o f energy reserve depletion: test o f a m echanism for size-dependent w inter mortality. O ecologia 119:474-483.
Seo, H., S. Kim, K. Seong, and S. Y. Kang. 2006. V ariability in scale grow th rates o f Chum Salm on (Oncorhynchus keta) in relation to clim ate changes in the late 1980s. Progress in O ceanography 68:205-216.
Smith, R. W ., and J. S. Griffith. 1994. Survival o f R ainbow Trout during their 1st w inter in the H enrys Fork o f the Snake River, Idaho. Transactions o f the A m erican Fisheries Society
123:747-756.
Sogard, S. M. 1997. Size-selective m ortality in the juvenile stage o f teleost fishes: a review. B ulletin o f M arine Science 60:1129-1157.
Stachura, M. M ., N. J. M antua, and M. D. Scheuerell. 2014. O ceanographic influences on patterns in N orth Pacific salm on abundance. C anadian Journal of Fisheries and A quatic Sciences 71:226-235.
Thom pson, J. M ., E. P. Bergersen, C. A. Carlson, and L. R. K aeding. 1991. R ole o f size, condition, and lipid content in the overw inter survival o f age-0 Colorado Squawfish. Transactions o f the A m erican Fisheries Society 120:346-353.
W acker, S., K. de Jong, E. Forsgren, and T. Amundsen. 2012. Large m ales fight and court m ore across a range o f social environm ents: an experim ent on the tw o Spotted Goby
G obiusculusflavescens. Journal o f Fish B iology 81:21-34.
W alker, B. M ., and T. M. Sutton. 2016. G row th-increm ent form ation using otoliths and scales for age-0 C hinook Salmon. N orth A m erican Journal o f Fisheries M anagem ent 36:995 999.
W ilson, M. T., K. L. M ier, and C. M. Jump. 2013. Effect o f region on the food-related benefits to age-0 W alleye Pollock (Theragra chalcogramma) in association w ith m idw ater habitat characteristics in the G ulf o f Alaska. ICES Journal o f M arine Science 70:1396-1407. W ood, C. C. 1987. Predation o f juvenile Pacific salm on by the Com m on M erganser (Mergus
merganser) on E aster V ancouver Island. II: predation of stream -resident juvenile salm on
by M erganser broods. Canadian Journal o f Fisheries and A quatic Sciences 44:950-959. W ootton, R. J. 1998. Ecology o f teleost fishes, second edition. K luw er A cadem ic Publishers,
C hapter 1: E valuation o f grow th, survival, and recruitm ent o f C hinook Salm on in Southeast A laska rivers1
A bstract
Chinook Salm on Oncorhynchus tshawytscha brood-year (BY) strength may be determ ined by size-selective processes that occur during early m arine residence; however, the relative
im portance o f freshw ater versus m arine grow th in determ ining recruitm ent success is unknown. A scale-based retrospective analysis w as conducted to exam ine the relative effects o f freshw ater and m arine grow th on survival to the age o f reproduction, determ ine if grow th dependency betw een adjacent grow th zones w as present, and analyze the influence of sm olt body size on survival to reproductive m aturity for fem ale C hinook Salm on by B Y in the Taku (BYs 1979 - 1985, 1990 - 1999, 2002 - 2004) and U nuk (BY s 1981 - 1983, 1986 - 1988, 1994 - 2003, 2005 - 2006) rivers. First-year m arine grow th (SW 1) w as positively related to survival and total return for C hinook Salmon stocks from both systems. In the Taku River, grow th during the third year at sea w as positively related to m arine survival. Growth during freshw ater residence (i.e., size-at- ocean entry; FW 1) w as not related to the survival or total return o f either stock. A nnual grow th o f Taku R iver C hinook Salm on w as correlated w ith previous grow th through the second year at sea (SW 2; F W 1 versus S W 1 [r = 0.11]; S W 1 versus SW2 [r = 0.10]); however, no correlations w ere detected betw een adjacent grow th zones o f U nuk R iver fish (FW1 versus SW1 [r = -0.01]; SW1 versus SW2 [r = 0.01]). Positive skew and low variability o f freshw ater grow th
distributions suggested that smolts experienced size-selective m ortality during early m arine residence. These findings suggest that current regional declines in Chinook Salm on abundance are likely attributed to changes in grow th conditions during the first year at sea.
1 Graham, C. J., T. M. Sutton, M. V. McPhee, M. D. Adkison, and P. J. Richards. 2016. Evaluation of Growth survival and recruitment o f Chinook Salmon in Southeast Alaska. Prepared for submission to Transactions o f the
Introduction
Chinook Salm on Oncorhynchus tshawytscha are valued as social, cultural, and econom ic resources in Southeast A laska (SEAK; D er H ovanisian et al. 2011). For example, Chinook Salm on are harvested in com m ercial, sport, and subsistence fisheries throughout the region (D er H ovanisian et al. 2011). Com m ercial fisheries target C hinook Salm on w ith a variety o f gear types (e.g., drift gill nets, purse seines, etc.), but the troll fishery harvests the m ajority o f the com m ercial catch o f this species. M ultiple Chinook Salm on stocks in SEAK are also harvested via in-river com m ercial fisheries in Canada (e.g., Taku and Stikine rivers). H owever, recent declines in stock abundances have led to harvest restrictions and, consequently, regional reductions in sport fish landings and com m ercial harvests (A D F& G C hinook Salmon Research Team 2013). B ecause reduced harvests may cause social and econom ic hardships for m ultiple user groups, it is im portant to understand the factors contributing to the current declines in Chinook Salm on stocks across SEAK.
Previous research indicates that salm on abundance is m ediated by size-dependent m ortality, w ith the tim e period during freshw ater and early m arine residence being critical for influencing survival patterns and, ultim ately, recruitm ent to the spaw ning stock (Beam ish and M ahnken 2001; Farley et al. 2007). The critical size, critical period hypothesis proposes that Pacific salm on year-class strength is determ ined during tw o distinct periods of high m ortality during the first year o f m arine residence (Beam ish and M ahnken 2001). The first period o f high m ortality is driven by size-dependent predation shortly after smolts enter the m arine environm ent (Pearcy 1992). Sm oltification is an osm otically stressful process that may lead to reduced
(H andeland et al. 1996; D ieperink et al. 2002). Large sm olt body size may reduce the risk o f predation in tw o w ays (Sogard 1997). First, large body size may physically prevent predation due to gape lim itations o f predators (Sogard 1997; Juanes et al. 2002; D orner and W agner 2003). Second, sw im m ing ability increases w ith body size; therefore, large smolts can swim faster to escape potential predators than sm aller-bodied m em bers of their cohort (Juanes 1994). Because body size at ocean entry has been found to influence the m arine survival o f A tlantic Salmon
Salmo salar (Jutila et al. 2006) and Pacific salm on (W oodson et al. 2013), high grow th during
freshw ater residence may increase survival during the first period o f high mortality. The second period o f high m ortality is m ediated by physiological processes and occurs during the first fall and w inter at sea. The overw inter period in the m arine environm ent is physiologically stressful; as a result, individuals that fail to store sufficient energy reserves during their first m arine sum m er may deplete their energy stores and suffer m ortality during their first fall and m arine w inter at sea (Beam ish and M ahnken 2001; B eam ish et al. 2004). L arge-bodied fish are also thought to have a survival advantage during this period due to the allom etric scaling o f m etabolic requirem ents w hich requires that large fish expend less energy per unit biom ass on basal
processes than sm aller fish (Thom pson et al. 1991; Sogard 1997; Schultz and C onover 1999; B iro et al. 2004). B ecause m ortality is m ediated by size-dependent processes during the first year at sea, rapid grow th during freshw ater and early m arine residence may increase the survival of Pacific salmon. Therefore, if conditions are poor for grow th and size-selective m ortality is high, size-m ediated m ortality during the first m arine year m ay reduce the brood year strength of Pacific salm on (Sogard 1997; B eam ish and M ahnken 2001).
Clim ate plays a profound role in shaping the structure and function of m arine ecosystem s, w hich in turn, may affect Pacific salm on grow th and survival directly through changes in w ater
tem perature and indirectly through changes in bottom -up processes (M ueter et al. 2002; Edw ards and Richardson 2004; Seo et al. 2006; N oakes and B eam ish 2009; Petrosky and Schaller 2010; D oney et al. 2012). The survival o f Pacific salm on has been linked to variations in sea-surface tem peratures at regional and basin-w ide scales (M ueter et al. 2002, 2005; B urke et al. 2013). For instance, regional sea-surface tem peratures influenced the survival rates o f northern (i.e., Alaska) and southern stocks (i.e., B ritish C olum bia and W ashington) o f Pacific salm on (M ueter et al. 2002). Clim ate m ay also affect the survival o f Pacific salm on indirectly through changes in the tim ing and availability o f prim ary and secondary production (Edw ards and R ichardson 2004; Petrosky and Schaller 2010). F or example, the m atch-m ism atch hypothesis proposes that variability in the recruitm ent success o f fishes may be related to spatial and temporal overlap of the availability o f biological production and key life-history events (e.g., tim ing o f outm igration; Cushing 1990; Tom aro et al. 2012). D ue to the im portance o f grow th and clim ate in influencing the survival patterns of Pacific salmon, the factors driving the current recruitm ent failures of Chinook Salm on in SEAK m ay be uncovered by studying long-term variations in grow th and their relation to productivity and survival. One useful w ay to study long-term changes in grow th o f fishes is scale-based retrospective analysis.
Scale-based retrospective analyses have been used to study long-term trends in growth and their relationship to climate, survival, and productivity in both Pacific and A tlantic salmon (Healey 1982; H oltby et al. 1990; Crozier and K ennedy 1999; Friedland et al. 2000; B eam ish et al. 2004; Farley et al. 2007). Scale form ation (i.e., circulus spacing and form ation rate) is proportionally related to som atic grow th and therefore can be used as an index of grow th in salm on (Fisher and Pearcy 2005; R uggerone et al. 2007; M cCarthy et al. 2008; H ogan and Friedland 2010; W alker and Sutton 2016). Further, scale form ation can be correlated to
recruitm ent benchm arks (e.g., total return, productivity, etc.) to determ ine how grow th rates influence survival throughout the life cycle o f Pacific salm on (Fisher and Pearcy 2005; Ruggerone et al. 2007; M cC arthy et al. 2008; H ogan and Friedland 2010; Leon 2013). For example, R uggerone et al. (2007) used scale- form ation rate to determ ine that variability in the abundance o f B ristol Bay and C hignik Sockeye Salm on O. nerka stocks w as influenced by grow th during the first tw o years at sea. Therefore, exam ining tim e series o f scale-growth patterns may lend insights into the factors influencing the survival, productivity, and abundance o f C hinook Salm on in SEAK.
The goal o f the current study w as to determ ine how annual grow th influences the recruitm ent success o f Chinook Salm on in SEAK. To accom plish this goal, tim e series o f freshw ater and m arine grow th patterns w ere constructed and correlated to a series o f recruitm ent benchm arks (i.e., total return, productivity, m arine survival) for tw o regionally im portant
Chinook Salm on stocks in SEAK (i.e., Taku and U nuk river C hinook Salm on stocks). The specific objectives o f this study w ere to: 1) characterize the im portance of freshw ater and annual m arine grow th in determ ining the recruitm ent success o f C hinook Salm on in SEAK; 2)
determ ine if grow th dependency w as present in Chinook Salm on in SEAK; and 3) investigate the relationship betw een sm olt body size and survival to reproductive m aturity by brood year (BY). This study provides a region-w ide perspective on potential linkages betw een grow th and survival patterns, relationships in fresh and m arine w aters, and trends in abundance relative to recruitm ent for C hinook Salmon in SEAK.
M ethods
Study sites
This study w as conducted on C hinook Salmon captured in the Taku and U nuk rivers in SEAK (Figure 1.1). The Taku R iver is a large, glacially influenced river system originating in the Stikine Plateau o f northw estern B ritish Colum bia (D er H ovanisian et al. 2011). This river flows approxim ately 300 km through m ountainous terrain before draining into Taku Inlet 30 km east o f Juneau, Alaska. The glacial nature o f the Taku R iver results in highly turbid m ainstem waters. In contrast, m ost tributaries o f the Taku R iver are clear w ater w ith little glacial till. This pristine w atershed is large, encom passing an area over 17,000 km 2, and is an im portant producer o f all five N orth A m erican species o f Pacific salmon. The U nuk R iver is a large, glacially fed river that originates in northern B ritish C olum bia and flow s through the glacially forged M isty Fjords N ational M onum ent, w hich has been designated a federally protected w ilderness area, before draining into Behm Canal northeast o f K etchikan, A laska (D er H ovanisian et al. 2011). Similar to the Taku River, the U nuk R iver is characterized by highly turbid m ainstem w aters and clear w ater tributaries. The U nuk R iver is approxim ately 129 km in length, and drains an area that is approxim ately 3,885 km 2. In addition, the U nuk R iver supports healthy runs o f all five species o f N orth A m erican Pacific salmon.
The Taku and U nuk rivers w ere chosen for this study for m ultiple reasons. B oth rivers are im portant salm on producers w ithin SEAK. On average, the Taku R iver has the largest Chinook
Salm on run in the region, w ith m ean run sizes o f 50,000 large (> 660 mm) fish per year (D er H ovanisian et al. 2011). The U nuk R iver is the fourth largest producer o f C hinook Salm on in SEAK, w ith annual runs o f approxim ately 5,500 large fish (D er H ovanisian et al. 2011). Taku
and U nuk river Chinook Salm on stocks exhibit diverse ecological and genetic characteristics, such as distinct m arine-rearing locations (D er H ovanisian et al. 2011; A D F& G C hinook Salmon Research Team 2013). A fter em igrating to the ocean, juvenile C hinook Salmon from the Taku R iver are thought to reside in coastal w aters prior to m igrating offshore, w here they m ake seasonal m igrations in the G u lf o f A laska and the B ering Sea for the rem ainder o f their ocean residence (M cPherson et al. 2010). In contrast, Chinook Salm on from the U nuk R iver rear prim arily in nearshore w aters o f SEAK and B ritish Colum bia, and m ost do not m ake extensive offshore m igrations to the B ering Sea (D er H ovanisian et al. 2011). Finally, the U nuk R iver was selected for this study due to the proposed developm ent o f K err-Sulphurets-M itchell mine (KSM ), w hich is a proposed transboundary, open-pit m ine located on Sulphurets Creek in northern B ritish Colum bia, a tributary o f the U nuk River. As planned, K SM will be sim ilar in scale to the proposed Pebble M ine (Canadian Environm ental A ssessm ent A gency 2014). The location o f the proposed K SM dam and the long-term storage o f w aste threatens spaw ning and rearing habitat for C hinook Salm on and other Pacific salm on stocks. It is estim ated that
approxim ately 83% o f Chinook Salm on from the U nuk R iver spawn dow nstream from the Canadian border (Pahlke et al. 1995). The inclusion o f these rivers in this evaluation will allow for the characterization o f the relationship betw een annual grow th and recruitm ent success for regionally im portant salm on stocks that experience distinct freshw ater and m arine rearing locations.
Scale samples
A tim e series o f freshw ater- and m arine-grow th patterns for fem ale C hinook Salm on from the Taku (BYs 1979 1986, 1990 2000, 2002 2008) and U nuk (BYs 1976, 1978 1989, 1993
-2006) rivers w as constructed by brood year using scales collected by the A laska D epartm ent of Fish and G am e (ADF&G). C hinook Salm on in both systems w ere sampled during spawning migrations using a variety o f gear types (e.g., set gill nets, fish w heels, weirs, hook and line,) that varied by system and year. The A D F& G em ploys a m ulti-gear sam pling m ethod because
experience has shown that the use a variety of gear types produces unbiased estim ates of age, sex, and length com position for Taku and U nuk river C hinook Salm on (M cPherson et al. 1997; Jones et al. 1998). In both systems, scales w ere collected from the preferred area: tw o rows above the lateral line betw een the posterior end o f the dorsal fin and the anterior end o f the anal fin (H agen et al. 2001). Five scales w ere taken from each sam pled fish and m ounted on gum m ed scale cards for long-term storage. These scale samples w ere used to create acetate im pressions, w hich w ere later analyzed in this study.
O f the fish sam pled by A DF& G, only scales from fem ale Chinook Salm on w ere analyzed, w hich is justified for several reasons (Leon 2013). First, fem ale fish determ ine the m axim um possible num ber o f offspring through the num ber o f eggs produced. Second, there is a strong linear relationship betw een fem ale body size and reproductive potential (i.e., fecundity) in salm onids (Q uinn 2005). In contrast, the relationship betw een body size and reproductive
success in m ales is com plicated by pronounced sexual dim orphism (e.g., kype, hum ped dorsal surface) that is form ed during their spaw ning m igration (K innison et al. 2003; Q uinn 2005). Finally, fem ale returns have a sim pler age structure than males, resulting in few er returning age classes and a sim plified set o f analyses. For example, m ale C hinook Salm on from both systems may return at ages 1.1 through 1.5, w hile fem ale C hinook Salm on predom inately return as age
1.3 and 1.4 fish (M cPherson et al. 2010). Therefore, the inclusion o f only fem ale Chinook Salm on in this study reduced the num ber o f age classes for analysis.
Scale reading
Scales had to m eet the follow ing criteria to be selected for analysis: 1) the scale’s circuli, annuli, and focus w ere clearly defined; and 2) the scale w as sam pled from preferred area o f the fish. Scales selected for analysis w ere digitized according to the sem i-autom ated im age analysis procedure outlined by H agen et al. (2001). Scale im ages w ere captured using a high-resolution line cam era (Screenscan® M icrofiche Scanner, Salem W isconsin) attached to an Indus 4601 m icrofiche reader and stored as Tagged Im age File Form at (TIFF) files w ith a resolution o f 3352 x 4425 pixels. H igh-resolution im ages allow ed the entire scale to be view ed and insured the accurate representation and m easurem ent o f intercirculi spacing. D igitized scale im ages w ere uploaded into ImagePro® 7.0 Im age A nalysis Program (Im age-Pro Plus, Acton, M assachusetts), w here the m acro O tolithA nalysis w as used to sem i-autom atically define annuli and m easure circuli spacing for each scale. O nce the digitized im age w as loaded into Im age-Pro Plus, a reference line w as established along the longest scale axis from the focus to the scale’s edge. The scale reader m arked all annuli along the reference line and O tolithA nlaysis flagged all circuli using edge detection algorithm s. Because the accuracy o f the edge detection algorithm s varied w ith scale quality, the scale reader m anually review ed and edited each circuli placement. W hen all annuli and circuli w ere correctly m arked, O tolithA nlaysis enum erated all annuli and circuli and m easured intercriculi widths. The count and m easurem ent data w ere then exported as a text file, w hich w as subsequently exported and saved into M icrosoft Excel.
G rowth zones extracted from scales w ere defined using the follow ing criteria. Freshw ater grow th (FW 1) w as the m easured distance (m m ) from the focus to the outerm ost edge o f the first annulus (Figure 1.2). The first year o f m arine grow th (SW 1) w as the m easured distance betw een the last freshw ater circuli and the annulus separating SW 1 and the second year o f m arine growth
(SW2). Subsequent years o f m arine grow th (i.e., SW3, SW4) w ere defined as the m easured distance from the previous to the next annulus (Figure 1.2).
Recruitment benchmarks
Estim ates relating to the recruitm ent success (e.g., abundance, total return, m arine survival, productivity) o f C hinook Salm on stocks from the Taku and U nuk rivers w ere obtained from ADF&G. In both systems, biological data such as age, sex, and length (ASL) data w ere collected during their annual stock assessm ent programs, w hich allow ed escapem ent, survival, and m arine harvest to be estim ated (H endrich et al. 2008; M cPherson et al. 2010).
Currently, the spaw ning abundance o f large (> 660 mm m id-eye to tail fork [M EF]) and small (< 660 mm) adult Chinook Salm on has been estim ated using tw o-event m ark-recapture experim ents in both the Taku (1995 - present) and U nuk (1997 - present) rivers. In the Taku River, fish w heels and set gill nets (13.7-cm or 18.4-cm stretch mesh) w ere used to capture Chinook Salm on during the first event ju s t below the Canadian border. All captured fish w ere sam pled to determ ine the A SL com position o f the in-river run. All fish that w ere not m issing their adipose fin and determ ined to be in good condition w ere m arked using solid-core spaghetti tags. A left upper operculum punch (0.63 cm in diam eter) w as also used as a secondary m ark to assess tag retention rates. D uring the second event, Taku R iver C hinook Salm on w ere captured on the spaw ning grounds w ith a variety o f gear types. Each captured fish w as inspected for presence o f a spaghetti tag, left upper operculum punch, and m issing adipose fin. A fter m ark inspection, ASL data w ere collected and a low er left operculum punch w as used to prevent double sampling.
In the U nuk River, C hinook Salm on w ere m arked after being captured w ith set gill nets (37 m long x 4 m deep, w ith 1.8-mm stretch m esh) in the low er portion o f the river below the Canadian border for the first event. M ethods for sam pling and m arking fish follow ed the same procedures as in the Taku River. In the second event, fish w ere visually exam ined for m arks on the spawning grounds or after being caught w ith rod and reel, dip nets, and gill nets. In both systems, the abundance o f large and small adult C hinook Salmon w as estim ated separately by the A D F& G using a m odified Chapm an-Petersen estim ator (Seber 1982).
Prior to the onset o f the tw o-event m ark-recapture experim ents, relative abundance was estim ated suing aerial surveys during periods o f peak spaw ning in m ajor tributaries o f the Taku and U nuk rivers. In both systems, relative abundance estim ates from aerial surveys w ere converted into estim ated spaw ning abundances, w ith expansion factors calculated from years w hen both aerial surveys and m ark-recapture experim ents w ere conducted (U nuk R iver [N = 7], Taku R iver [N = 13]).
Total return w as calculated as the sum of estim ated in-river run and m arine harvest for 1.2 to 1.5 age fish w ithin a given BY. A bundance by age class w as estim ated using the estim ated abundance o f small and large fish and size-com position data from the spawning ground surveys. The m arine harvest o f C hinook Salm on in regional com m ercial and sport fisheries w as estim ated follow ing the m ethods described by B ernard and Clark (1996).
M arine survival w as calculated as the ratio of B Y total return and the estim ated B Y sm olt abundance. The B Y abundance o f U nuk and Taku river smolts w as estim ated by the A D F& G using a tw o-event m ark-recapture experim ent using a m odified Chapm an-Petersen form ula (Seber 1982; W eller and Evans 2012). In the first event, C hinook Salmon smolts w ere captured using m innow traps (420 mm long x 191 mm diameter, w ith 6-mm m esh) baited w ith salm on roe
in back eddies and m ajor sloughs o f the low er potions o f the Taku and U nuk rivers during smolt outm igration from late M arch through early M ay (H endrich et al. 2008; W eller and Evans 2012). All captured smolts > 50 mm fork length (FL) that w ere not m issing an adipose fin w ere
im planted w ith a coded w ire tag (CW T) and m arked by excising their adipose fin for future identification. In the second event, adults w ere sam pled on the spaw ning grounds w hen estim ating the in-river abundance o f m ature C hinook Salmon.
Relationship between annual grow th zones a n d recruitm ent benchmarks
To determ ine the influence o f annual grow th on survival to the age o f reproduction, scale-growth patterns for the Taku and U nuk rivers w ere related to C hinook Salm on recruitm ent benchm arks (i.e., total return, productivity) using m ultiple regression analyses. O ver the tim e series o f scale grow th patterns for the Taku River, the m ajority o f BY s w ere sam pled using set gill nets or fish wheels. G ear types may select for fish o f different sizes (W ells et al. 2008); therefore, a
H otelling’s T2 test (M anly 1994) w as used to com pare the average grow th zone distance for each annual grow th zone (i.e., FW 1, SW1, SW2, SW3, and SW4) for Taku R iver C hinook Salm on o f the same age (i.e., age-1.3 or age-1.4 fish) and BY, collected w ith set gill nets and fish wheels. Results indicated that there w ere no statistically significant (P < 0.05) differences betw een any o f the annual grow th zones for either age-1.3 fish (BY 2003 [P = 0.11], 2004 [P = 0.50], and 2006 [P = 0.42]) or age-1.4 fish (BY 2003 [P = 0.21], 2004 [P = 0.46], and 2006 [P = 0.82]). B ecause there w as no difference in average grow th zone distance for fish collected w ith either gear type, Taku R iver C hinook Salmon sampled using fish w heels or set nets w ere pooled into a single tim e series (BYs 1979 - 1985, 1990 - 1999, 2002 - 2004), w hich w as used to determ ine the effect o f annual grow th on recruitm ent success. The BY s included in the U nuk R iver tim e series w ere also
collected using m ultiple gear types (weir, dip net, hook and line, handpicked, and set gill net). H otellings T2 tests indicated there w ere no statistically significant differences betw een any o f the annual grow th zones for fish captured using set gill nets and hook and line fishing for age-1.3 (BY 1994 [P = 0.72] and 2006 [P = 0.96]) or age-1.4 fish (BY 1994 [P = 0.09], 2005 [P = 0.38], and 2006 [P = 0.91]). In addition, no significant differences in m ean annual grow th w ere found for w eir or handpicked fish (age-1.3 fish from B Y 1981, P = 0.77) or for fish collected w ith set gill nets or dip nets (age-1.4 fish from B Y 1988, P = 0.51). B ecause annual grow th rates w ere sim ilar for fish collected w ith each gear type in the U nuk River, fish that w ere collected using m ultiple gear types (weir, dip net, hook and line, handpicked, and set gill net) w ere com bined to form a subset o f the original tim e series (BYs 1981 - 1983, 1986 - 1988, 1994 - 2003, 2005 - 2006), w hich w as used in subsequent analyses.
M ultiple regression m odels w ere constructed separately for each system due to their distinct freshw ater and m arine rearing locations. Prior to analyzing the data, w eighted averages that accounted for differences in the B Y abundances o f age-1.3 and 1.4 fish w ere calculated for each annual grow th zone and each B Y class. The w eighted averages for each system w ere then used to explain the variability in log-transform ed B Y recruitm ent benchm arks.
The influence of annual grow th on m arine survival of stocks from both systems was assessed using w eighted simple linear regression. M odels w ere fitted using w eighted averages o f annual grow th zones as explanatory variables and log-transform ed m arine survival as the
response variable. Only annual grow th zones that explained high am ounts o f variation in BY total return and productivity w ere included in the model due to the few er num ber o f BY s w ith m arine survival estim ates relative to BY s w ith total return and productivity estimates. The current literature has dem onstrated the im portance o f large body size in determ ining the survival
and recruitm ent success o f m ultiple species o f Pacific salm on (M ortensen et al. 2000; B eam ish et al. 2004; M oss et al. 2005; Farley et al. 2007; M urphy et al. 2013); therefore, statistical
significance (P < 0.05) o f explanatory variables w as determ ined using a one-tailed t-test. All param eters in the m ultiple regression and simple linear regression m odels w ere estim ated using w eighted-least-squares regression, w ith each B Y in the m odel being w eighted by the num ber o f scale sam ples in that BY. R esiduals obtained from fitting m odels w ere used to test the assum ptions o f m ultiple and simple regression analyses (i.e., normality, constant variance, and independence of errors; Q uinn and K eough 2002). The assum ption o f norm ality w as assessed visually by exam ining norm al probability plots for one-to-one relationships betw een residuals and their theoretical values. The assum ption of constant variance w as also visually assessed by looking for an even distribution of residuals across the range o f fitted values. B ecause tim e-series data may lack independence, the presence o f tem poral autocorrelation w as assessed by plotting estim ated autocorrelation versus lag distance to determ ine the m agnitude and significance o f autocorrelations (Cryer and Chan 2008). M ultiple regression m odels also assum ed linear relationships betw een predictor and response variables. B ivariate scatterplots constructed and exam ined to determ ine the nature of the relationships betw een response and predictor variables. In all m odels that w ere fitted, no violations o f the previously m entioned assum ptions w ere found. All statistical analyses w ere perform ed using R (R Core Team 2014).
Relationship between growth zones
The relationships betw een adjacent grow th zones w ere exam ined using m ixed-effects modeling. To determ ine if the grow th o f individual C hinook Salm on from each system w as dependent on their previous growth, random intercept m ixed-effects m odels w ere fitted by regressing each
individual’s annual grow th zone on that individual’s subsequent annual grow th zone (e.g., FW1 versus SW1, SW1 versus SW2, etc.). The relationship betw een grow th zones and B Y
represented the fixed effect and random effect, respectively. The assum ptions of m ixed-effects m odeling (i.e., normality, constant variance, and independence o f errors) w ere tested using the previously described m ethods and no violations o f these assum ptions w ere found.
Size-selective m ortality a t ocean entry
The relationship betw een sm olt body size and survival to reproductive m aturity w as investigated by exam ining the skew o f FW1 by B Y freshw ater scale grow th distributions. Previous research has shown that the length distribution o f age-0 C hinook Salm on from the Taku R iver was norm ally distributed, and that size-selective m ortality o f small individuals results in positively skewed w eight and length distributions o f Chinook Salmon stocks (M urphy et al. 1989; M urphy et al. 2013; W oodson et al. 2013). B ecause the m easured distance o f the freshw ater grow th zone has been used as an index o f size at m arine entry for both Pacific and A tlantic salm on (Hogan and Friedland 2010; Leon 2013), the freshw ater grow th distribution w as used to represent the length-frequency distribution at ocean entry. Therefore, evidence for size-selective m ortality at ocean entry w as identified by exam ining the skew o f FW1 distributions by BY. To determ ine the presence and nature o f skew o f the F W 1 distribution, g1 w as calculated as:
g1 = k3/s3,
w here s3 and k3 represent the second and third m om ents around the mean, respectively (Zar 1999). Positive g1 values indicated skewed right (positively skewed) distributions and, therefore, g1 values that w ere significantly greater than zero im plied size-selective m ortality during early m arine residence. To determ ine if g1 values w ere significantly greater than zero, one-tailed 95%
