Historical Population Structure of Central Valley Steelhead and Its Alteration by Dams

Home , Chowchilla River, Golden Trout Creek, Kaweah River, Little Kern River, Mariposa Creek, North Yuba River

UC Davis San Francisco Estuary and Watershed Science

Title Historical Population Structure of Central Valley Steelhead and Its Alteration by Dams

Permalink https://escholarship.org/uc/item/1ss794fc

Journal San Francisco Estuary and Watershed Science, 4(1)

ISSN 1546-2366

Authors Lindley, Steven T. Schick, Robert S. Agrawal, Aditya et al.

Publication Date 2006

DOI 10.15447/sfews.2006v4iss1art3

License https://creativecommons.org/licenses/by/4.0/ 4.0

Peer reviewed

eScholarship.org Powered by the California Digital Library University of California Historical Population Structure of Central Valley Steelhead and its Alteration by Dams

STEVEN T. LINDLEY1, ROBERT S. SCHICK1, ADITYA AGRAWAL2, MATTHEW GOSLIN2, THOMAS E. PEARSON2, ETHAN MORA2, JAMES J. ANDERSON3, BERNARD MAY4, SHEILA GREENE5, CHARLES HANSON6, ALICE LOW7, DENNIS MCEWAN7, R. BRUCE MACFARLANE1, CHRISTINA SWANSON8 AND JOHN G. WILLIAMS9

ABSTRACT

Effective conservation and recovery planning for Central Valley steelhead requires an understanding of historical population structure. We describe the historical structure of the Central Valley steelhead evolutionarily significant unit using a multi-phase modeling approach. In the first phase, we identify stream reaches possibly suitable for steelhead spawning and rearing using a habitat model based on environmental envelopes (stream discharge, gradient, and temperature) that takes a digital elevation model and climate data as inputs. We identified 151 patches of potentially suitable habitat with more than 10 km of stream habitat, with a total of 25,500 km of suitable habitat. We then measured the distances among habitat patches, and clustered together patches within 35 km of each other into 81 distinct habitat patches. Groups of fish using these 81 patches are hypothesized to be (or to have been) independent populations for recovery planning purposes. Consideration of climate and elevation differences among the 81 habitat areas suggests that there are at least four major subdivisions within the Central Valley steelhead ESU that correspond to geographic regions defined by the Sacramento River basin, Suisun Bay area tributaries, San Joaquin tributaries draining the Sierra Nevada, and lower-elevation streams draining to the Buena Vista and Tulare basins, upstream of the San Joaquin River. Of these, it appears that the Sacramento River basin was the main source of steelhead production. Pres- ently, impassable dams block access to 80% of historically available habitat, and block access to all historical spawning habitat for about 38% of the historical populations of steelhead.

KEYWORDS

Steelhead, O. mykiss, endangered species, population structure, dispersal, habitat model, dams, Central Valley.

1. National Oceanic and Atmospheric Adminis- tration 2. University of California, Santa Cruz 3. University of Washington 4. University of California, Davis 5. California Department of Water Resources 6. Hanson Environmental, Inc. 7. California Department of Fish and Game 8. The Bay Institute 9. 875 Linden Lane, Davis, CA Lindley et al.: Historical population structure of Central Valley steelhead and its alteration by dams

INTRODUCTION

Steelhead (O. mykiss) in California’s probably were extirpated from time to time. Central Valley were identified as an Following recovery from disturbance, evolutionarily significant unit (ESU) and listed catastrophically disturbed areas likely were in 1998 as a threatened species under the U.S. recolonized by neighboring populations whose Endangered Species Act (1973). Myriad members were adapted to similar problems afflict steelhead in the Central Valley: environmental conditions. Understanding the impassable dams block access to much of the historical distribution of populations within an historically available spawning and rearing ESU is therefore important to understanding habitat (Yoshiyama and others 1996), and how the ESU persisted in the past and how an water diversions and withdrawals, conversion altered ESU might or might not persist in the of riparian zones to agriculture, introduced future. species, water pollution, disruption of gravel supply, and other factors have degraded much To the extent that environmental conditions of the habitat below the dams (McEwan 2001). vary across the range of an ESU, population Recovering Central Valley O. mykiss structure could influence the ability of the ESU presumably will require some mix of improved to respond to climate or other sources of access to historically available habitat and ecological change, as well as its resilience to restoration of degraded habitat. A better catastrophic disturbances. McEwan (2001) understanding of the current and historical concluded that steelhead were widely distribution and population structure of distributed in the Central Valley, ranging from O. mykiss in the Central Valley will be critical the Pit River in the north to perhaps the Kings for guiding such restoration actions, but River in the south, a distribution spanning currently available information deals with multiple ecoregions and climate zones. This changes in distribution at a fairly coarse level wide distribution across diverse ecological and does not address population structure. conditions should have provided Central Valley O. mykiss with substantial opportunities for Detailed distribution data at the population adaptation to local conditions, creating the level are fundamental to planning effective genetic variation required for adaptation to restoration and protection activities. In the changing conditions (Darwin 1859). While short term, one must know where a species such variation would be important for ESU occurs in order to efficiently safeguard its persistence, it also limits the ability of some existence. In the longer term, an populations to rescue others because the understanding of historical distribution is fitness of a locally adapted population would be important because it gives insight into how the expected to be lower in other environments species might have survived catastrophic (Taylor 1991). Knowing which populations disturbances. Prior to the era of intensive might have members that are ecologically anthropogenic impacts, the Central Valley exchangeable would help guide steelhead ESU apparently survived prolonged reintroductions, should currently empty and droughts (Ingram and others 1996), degraded habitats be restored, and help to catastrophic volcanic eruptions (Kerr 1984), prioritize populations for conservation. landslides triggered by fires, floods and earthquakes (Keefer 1994), and other Habitat modeling is often used to devastating events, although individual extrapolate from and interpolate between populations of Central Valley steelhead observations of species occurrence to provide

Produced by eScholarship Repository 2 San Francisco Estuary and Watershed Science Vol. 4, Iss. 1 [February 2006], Art. 3

the comprehensive picture of the distribution of isolated from other clusters. These isolated species that is needed to guide conservation clusters of stream reaches are presumed to and restoration. Ideally, habitat units are have supported independent populations of sampled randomly for the presence of the O. mykiss. We assess the degree to which species and various qualities of the habitat are populations may be exchangeable by measured, allowing resource selection quantifying differences in climatic conditions functions to be estimated (Manly and others experienced by the populations. Finally, we 2002). These resource selection functions can assess how man-made impassable barriers then be used to characterize the suitability of have reduced the amount of habitat available habitat units that were not sampled for the to steelhead, and how this reduction in habitat occurrence of the species but for which the has altered the structure of the ESU. habitat information is available. A related but simpler approach is to characterize METHODS environmental attributes associated with specimen collections in terms of envelopes Modeling the Distribution of O. mykiss that characterize habitat as either suitable or O. mykiss habitat was predicted using two unsuitable. The edges of these envelopes are models. The first model predicts the spatial defined by the most extreme conditions under location of stream reaches, along with their which the organism has been commonly mean annual discharge and gradient, using a observed. Once defined, the envelopes can be digital elevation model (DEM) and used with appropriate environmental data to precipitation (the PRISM data set (Daly and predict the distributional limits of the species. others 2002)) as inputs (Burnett and others Within these distributional limits, the species 2003). Where available, we used the USGS may or may not be found, depending on the 10-m DEM; where this was not available, we effects of other factors not characterized by the created a 10-m DEM by interpolating the envelopes, but the species is not expected to USGS 30-m DEM to 10 m using a regularized be found outside of this distribution. Originally spline procedure (SPLINE function, ArcGIS developed for predicting the distribution of Ver. 9, ESRI, Redlands, CA). We recalibrated agricultural pests (Cook 1929), such models the precipitation-discharge equations in are increasingly used in conservation planning Burnett and others’ (2003) model with data for many species (e.g., Johnson and others from the Central Valley (Appendix A). 2004; Argáez and others 2005; Chefaoui and others 2005), including fish (Burnett and others The second model is a set of simple rules, 2003; Valavanis and others 2004; Wall and or environmental envelopes, that define others 2004; Quist and others 2005). whether a given stream segment is suitable for steelhead. The envelopes include mean In this paper, we use habitat models to annual discharge (suitable if >0.028 m3s-1), describe the historical structure of the Central gradient (suitable if <12%), and mean August Valley O. mykiss ESU and assess how air temperature (suitable if <24°C), and impassable dams have altered this structure. whether the area was considered by Knapp We start with a model of steelhead habitat to (1996) to be fishless prior to anthropogenic identify stream reaches within the Central introductions. We are aware of no published Valley that were likely to have supported data suitable for identifying a lower discharge O. mykiss during summer months. We then limit for steelhead, but Harvey and others analyze the spatial distribution of these stream (2002) found that the density of age one-year- reaches to identify clusters of reaches that are old-or-older steelhead was lower in streams http://repositories.cdlib.org/jmie/sfews/vol4/iss1/art3 3 Lindley et al.: Historical population structure of Central Valley steelhead and its alteration by dams

with lower discharge in tributaries to the Eel whose population dynamics or extinction risk River. A discharge of 0.028 m3 s-1 (or 1 cubic over a 100-year time period is not substantially foot per second) was taken as a lower bound, altered by exchanges of individuals with other although data of Harvey and others (2002) populations.” Within a basin such as the suggest that steelhead occasionally occur in Central Valley, high summer temperatures at streams with somewhat lower discharge. lower elevations fragment otherwise Steelhead are commonly found in stream acceptable and continuous habitat into reaches with gradients less than 6% (Burnett enclaves of interconnected habitats isolated 2001; Harvey and others 2002; Hicks and Hall from one another by downstream regions of 2003), but in some systems they are not thermally unsuitable habitat (Rahel and others uncommon in reaches with gradients of up to 1996). If these enclaves are far enough apart, 12% (and occasionally higher) (Engle 2002). we expect that the enclaves will function as Stream temperature is linearly related to air independent populations. We therefore temperature between 0 and 24°C (Mohseni intersected the 24°C mean August air and others 1998). Steelhead in southern temperature isotherm with the stream network California are almost never found in areas to identify downstream boundaries of habitat where mean August air temperatures exceed patches. We assume implicitly that while 24°C (D. Boughton, NOAA Fisheries Santa discharge, gradient, and temperature all affect Cruz Lab, in preparation). Schmidt and others the suitability of a habitat, only temperature (1979) reviewed available information on restricts movement between habitat patches. thermal tolerance of O. mykiss, and found that We computed the distance along the stream 24°C was the highest reported maximum network among these downstream edges with temperature for O. mykiss rearing. More the NODEDISTANCE function in the Network recently, Nielsen and others (1994) found that Module of ArcInfo, creating a matrix of 24°C was the upper lethal temperature for distances among habitat patches. We used juvenile steelhead in northern California. In the hierarchical clustering with a simple distance- Eel River, steelhead were not found in streams based rule to group nearby patches into with maximum weekly average summer independent populations using the LINKAGE temperatures greater than 22°C (Harvey and function (with the single linkage algorithm) in others 2002). Knapp (1996) developed a GIS Matlab (Version 6.5.1, The Mathworks, Natick, coverage of historical fish distributions through MA). Following the Interior Columbia Basin a survey of published papers and unpublished Technical Recovery Team (2003), who reports. Most areas of the western Sierra reviewed available information on straying of Nevada above 1500-m elevation were Pacific salmonids, we chose 35 km as the historically fishless due to Pleistocene critical dispersal distance: patches that link at glaciation and numerous migration barriers 35 km were grouped together as independent (Moyle and Randall 1998). The final output of populations. The sensitivity of the population this stage of the analysis was a GIS dataset delineation to the distance criterion was describing a collection of stream segments examined by calculating how the number of suitable for O. mykiss, connected by clusters declines with increasing linkage unsuitable stream segments. distance. If the total length of suitable stream habitat was less than 10 km, we ignored these Identification of Independent Populations small areas in subsequent analyses, on the Following McElhany and others (2000), we assumption that isolated populations with less define independent populations as “any than 10 km of habitat would be unlikely to collection of one or more local breeding units

Produced by eScholarship Repository 4 San Francisco Estuary and Watershed Science Vol. 4, Iss. 1 [February 2006], Art. 3

persist for long periods without immigration tree (with the DENDROGRAM function in (Bjorkstedt and others 2005). Matlab).

Quantification of Habitat Similarities Quantification of Habitat Loss to Dams In most basins, spawning by salmonids can Goslin (2005) prepared a nearly be successful only if it occurs at certain times, comprehensive database of dams for such that development and migration can California, using data from the Coastal occur before temperature or flow conditions Conservancy, McEwan (2001), USGS and the become unsuitable (Montgomery and others U.S. Army Corps of Engineers. We intersected 1996; Beer and Anderson 2001). Thus, these dams with our stream layer, and climate, through its effects on stream computed the amount of suitable habitat within temperature and flow regime, is thought to be each watershed that was above and below the an important selective force leading to local lower-most dam that was impassable to adaptation in salmonids (Burger and others anadromous fish, using the TRACE function in 1985; Konecki and others 1995; Brannon and the network module of ArcInfo. others 2004; Lytle and Poff 2004). As proxies for water temperature and flow, we RESULTS characterized mean elevation (from the USGS DEM), mean annual precipitation and the Distribution of O. mykiss Habitat temperature regime (annual mean, maximum Our model identifies 25,500 km of stream monthly mean, minimum monthly mean and habitat suitable for O. mykiss, broken up into range of air temperature (all from PRISM)) over 151 discrete habitat patches, each having at the watersheds containing the spawning and least 10 km of stream habitat (Figure 1). Rivers rearing habitats of each of the independent and streams on the valley floor are largely populations identified with the procedure rated as unsuitable for spawning and rearing above. Watershed boundaries were based on because of high summer temperatures. The 1 the CalWater 2.2 watershed map of 1999, but exception to this are tributaries around Suisun in cases where CalWater boundaries follow Bay, where summer temperatures are political rather than geomorphic boundaries, moderated by the marine influence of the we delineated boundaries by hand, following nearby San Francisco Bay and Pacific Ocean. the DEM. We characterized the similarity of Large portions of the upper watersheds watersheds by calculating the Mahalanobis draining the central Sierra are ruled out (1936) distance among the centroids of because they were historically fishless watersheds using the PDIST function in according to Moyle and Randall (1998). At Matlab. The Mahalanobis distance reduces the intermediate elevations, many small tributaries effect of variables that are highly correlated to the major San Joaquin River tributaries are with each other, and is equal to the normalized of too high gradient or too low flow to support Euclidean distance between the centroids if O. mykiss, and O. mykiss are restricted to the variables are uncorrelated. We then used mainstems and larger tributaries. Streams in hierarchical clustering based on the average the southern Cascades, coast range and distance to join groups (using the LINKAGE northern Sierra, in contrast, appear to have function in Matlab), and plotted the results as a much more O. mykiss habitat due to their lower elevation and more moderate stream

1. The CalWater data can be obtained from the gradients. California Spatial Information Library, 900 N Street, Sacramento, CA 95814. http://repositories.cdlib.org/jmie/sfews/vol4/iss1/art3 5 Lindley et al.: Historical population structure of Central Valley steelhead and its alteration by dams

h Russ

o l e S l lSl

a ou

o gh

o Pi u n e C t r hF eek

As rk k

hCr ee Pi r

t lC R l e i

ek i ve k M e A e s r r h C C t Bear Creek s er re a v e E i W k il Fal lo oR iver l R wC Cedar C reek R iver ent ud re m lo r e C k ra c r ve c M e a Ri Creek iv S it R P it k Hor P e s e e C re Squaw yCr ek e H n at

Bur C

r eek e Little Cow Cr ek

Clear Creek k eek w Cree r South Co over C Cl ek Manzanita C Bear Cre reek Creek K Clear ingsCre DiggerCreek ek

Cow Creek Creek Battle k Cree Pa um ynesCreek Beeg Dry Creek

neoeCreekAntelope k ee Cr eek k Co ill Cr e ldFork M Butt e L ek ast C re Cr ha k C nceC eek n re Ban Cr a ek ed ry k R gD ree di Bi C n reek er I R lder C De e E r dC e v lo ek i ve k e r ree r Cr C Bu er R e s h ek ma r k t o c ree k h h co C a T ineC i e er C P h v G eek ree ee F i rin n Cr C k rR dst or k Cr r e eh St g o h S i at on o e F ny B t t Fe e C h k C ree u t r r r o k e k B o F ek Creek le e ek N d er e e d id iv r u M R Cr W ll yC M te n i Fa o ls ek la St on e S Cold Cr S yCr tr eek River eam Dr North Yuba le tn CreekStony tt i k L e Log e an Creek Cr ver t a Ri u Yub c dle n Mid o iver H YubaR h th t ou Sacramento River S r o r

Willow Creek e N iv N reek R River o F rt r DeerC ar ican h e ive er F B R e Am o a a B k r ear Yub For kC k t h e h Nort a re Colusa T e Sco ch C Creek r eC Glenn-Colusa Canal lt r re Sa R tts C ek i Ru ke River v ive e b R k ico r na e r r e S r n eek ek o ek ar C R Cre u e g iv d g Be n e eek Cr o r an h y ek L S r e iver D r R onC on Co ic ub R C Ravine Cortina Cr a rn r c ubu ive h A R Kelsey Creek ican P eC mer uta rk A hCre r Fo e uth e ek Creek So ek k Dry eek C lesCre WeberCr amp Cap W Cree illow k Sloug h ek re r C r ve Putah Creek ee i k D ek ee ry C re rR r rk D a r outh Fo C ve S nd Be a rk U Ri eek hl Fo la s Cr ig t ark is ne utter ek H Cl C S re r re sum C ve ek K ek o on Ri k re en C s e e C ne C aguna Jack umn re er d ac L k el C av y ree ok o Cr h C M ni Be e e o ek Dry t Sl iver An o R n ug e a mn S ek h kelu er ek Mo v e Cre Rose Cre i r k ek s e ll e eek a ar Cr er ey R F Be iv k v teCr R k e a u r l herry C i s e re P ra e C C ve e C i av al n Tuolumne River C kCr va c li le R ek o l iver r Cre e R Rive L R n ne y dd ns Su lum m i u joh Tuo uol ell ittle ddle T M L Mi Fo Ol To r r dR m ive k Pa us R ive in isla r e Sl Stan oug h er Merced Riv TuolumneRiver S a ek n y Cre J Dr oaquin R Ch

ek i L qu ek re k e n e r o e C y wi i o n e k t n a i r e o Mo v sC oC e s rt e er C r Cre e r rn Riv r C F u lPu ed sa o B e De rc o rk e k M Bea rip a M Orestimba Cre k ek L B Cree W os ear ens Cree Ow i k ll ow Cr k Ba e e no r Cr Mud S er e y s iv R ive ek C la ke l R n re wchi ho o Di ek l C n ough s e San Fr Lu isC re ek Kings River South Fork Kin gs River er iv sR g n Ki

C Fre iver s no S hR

nwood ea K

lou o w er t a K

g ot n h

C R

k er

Los Gato ss

o ² s r Cr e eek Cr v r i eek e iv R Cr R e n ver Tul r ino eRi Tul kKe r oCh o

F Legend pat h a reek t Z u

Deer C So Hydrography

California State Boundary ree

Suitable O. mykiss Habitat Pos Not Suitable O. mykiss Habitat Due to High Temperature Not Suitable O. mykiss Habitat Due to r ve Ri Caliente Creek Natural Historical Barriers to Anadromy rn Ke Area of Habitat Modeling

025 50 100 Kilometers

Figure 1. Predicted historical distribution of summer rearing habitat for anadromous O. mykiss (green). Stream reaches that would be suitable if not for high summer temperatures are shown in orange, and suitable stream reaches that were historically fishless due to natural migration barriers are shown in magenta. For legibility, streams with unsuitable gradient or discharge are not shown. Hydrography is USGS 1:1,000,000; other data are 1:24,000. (Click here for PDF file of larger image).

Produced by eScholarship Repository 6 San Francisco Estuary and Watershed Science Vol. 4, Iss. 1 [February 2006], Art. 3

Independent Populations and Tulare lakes, and a large group of Most subbasins of the Central Valley contain Sacramento River tributaries. Within the large multiple discrete habitat patches, because high group of Sacramento tributaries are a few temperatures make the lower reaches of small tributaries that ultimately drain to the San tributaries unsuitable in summer months. At a Joaquin, including most notably the Calaveras dispersal distance of 35 km, there are 81 River, but also smaller tributaries to the clusters of habitat patches, suggesting 81 Merced, Kings and Mokelumne rivers. Some of independent populations of steelhead in the the groupings shown in Figure 4 may be Central Valley (Figure 2, Table 1). The artifacts of representing the multidimensional geometry of a watershed and its relationship environmental data as a neighbor-joining tree: tothe 24°C August isotherm has a strong effect the cophenetic coefficient (Sokal and Rohlf on the number of clusters within it: Cottonwood 1962) relating the tree to the underlying matrix Creek, with its highly dendritic form and low of Mahalanobis distances is only 0.73 (an elevation, has 6 isolated clusters, while the accurate representation would have a larger but more pinnate Tuolumne River cophenetic coefficient close to 1.0). contains a single cluster, as does the Pit River, which is entirely above the 24°C isotherm. The Habitat Loss to Dams sizes of clusters are highly variable, with a few About 80% of habitat identified by our large clusters and many small ones (Table 1). model that was historically available to anadromous O. mykiss is now behind The choice of dispersal distance criterion impassable dams, and 38% of the populations has a strong effect on the number of identified by the model have lost all of their independent populations identified by the habitat (Figure 5). Anadromous O. mykiss clustering algorithm. There are only a few populations may have been extirpated from obvious breaks in the relationship between the their entire historical range in the San Joaquin number of clusters and the along-stream Valley and most of the larger basins of the distance between them, occurring around 140, Sacramento River. The roughly 52% of 225 and 280 km (Figure 3), corresponding watersheds with at least half of their historical roughly to the distance among the major area below impassable dams are all small, low subbasins of the Central Valley. elevation systems. Of the eight population clusters that form at a Mahalanobis distance of Similarity of Habitats 2 (Figure 4), for example, only two clusters Figure 4 shows the similarity of the habitats contain watersheds with habitat that remains occupied by the 81 independent populations of accessible to anadromous O. mykiss, O. mykiss as a neighbor-joining tree based on suggesting that there has been a significant Mahalanobis distance. As expected, nearby reduction in the diversity of habitats available streams with similar mean elevations clustered to Central Valley O. mykiss. together, although some San Joaquin tributaries clustered with Sacramento tributaries. Well-resolved clusters include the tributaries near Suisun Bay (including Sweany and Marsh creeks), the upper San Joaquin and its major tributaries draining the Sierra Nevada, the small west-side tributaries to the San Joaquin, tributaries to the now-dry Buena Vista

http://repositories.cdlib.org/jmie/sfews/vol4/iss1/art3 7 Lindley et al.: Historical population structure of Central Valley steelhead and its alteration by dams

h Ru

u s s lo e l lS

a lou

o gh

outh Pine C reek

ork A s eek hC Pi r

t r lC e Riv l e Mi k 58 As e ek r hC Cre t Bear Cree s k re e ver 67 k Ea Ri r e Fa o iv ll t R Rive Cedar Creek d r u o Wi men l k r ll ow ee ive cra McC r C a ver R ree C i t S R k t Pi Hor ek Pi e se quaw Cr Cr S eek 23 78 ey Ha t Burn C 66 re e

eek 51 0 k Cr 49 23 Clear 52 29 50 Manzanita Creek

30 reek reek Ki ClearC C 7 ngs C r eek ow Digger Cre k 4 ek 30 C e BattleCre k 3 Cree gum ek Bee Dry Creek 65 27 es Cre yn a A P ek n 2 re t C k 31 28 e l t Creek e l Mil But ope e r La ek 61 st C Cre C hanc k n e an Cr Creek B a d i 32 Re e d ek n eek k I ElderCr 76 e Red C er 39 ek lo Cre ve 36 k 34 Riv rCr Cre ee tte r eek 75 B u sCr ur he ma B o ch at Th C 8 e er G k r Pine Cr Chico F v rin Cree eek d rn er Ri s Seho S ork tone Cre tony C Big 9 F eath r h rk F ee eek rt o e k o eF r k 10 eek 11 N iddl r 71 12 M Rive ll W a eC ils F at ek on Sl C oldS Cr Cre tre y ee r am k r le D Nor ve th Yuba Ri i River itt ver a 71 L b Log u a Y k n C to R e re e n ddle re k e 37 i l M C m on Creek a

Creek ana cr er 81 Stony w 38 v any a C lo S aRi b 72 Wil ver N 80 Yu ek Ri iver o Fe Cre r an R rt Colusa C eer eric h - D Fo B ea Am ather k n r B or r e F k n k rth C ar Cr No ve a e ee Co r i S che C R co Gl lt C lusa R 6 re e Sa e t ive t ek R s e 5 ubi k Creek r con R T nak ek rough S Be re k ek ek ar Ri 13 re e ive Cr v ng C r k e o r ree and C y r L e e S r iv D R n aC o Coon Creek 25 ic tin b yCre u e R or C

ls ache Cr C ine r Auburn Rav Rive Ke Pu 24 ican tah Amer Fork Cr e ee ek Creek South eek k Dry 1 reek Ca es Cr Weber C mp Cr Capl Wil eek low Slo u 69 gh r e v Putah Cree 26 k k Ri e r re k a C ee e B and k U Cr 62 For la r ighl ark tis 74 ee H Cl C D ree Sutter Creek 63 ek K k e enn Ca guna erCr ed La ek v y ch e a C Be re eSlough ek Dry Cr r 17 ive e R 73 mn 15 k ee okelu r M 16 Cr eek RoseCreek ive r k ls e 14 C l ek y Cre r Fa Cre ar r Be ver k vey R te e a sRi 70 e iu ra Cl Che P Cr ave l Creek mneRiver Ca an Tuolu k iv ek c l er Cre ul eRiv Ly hns Ro S lumn 73 lejo Tuo ell For 57 Litt 77 Middle O l To er d m Riv k Ri Pa laus ver ine anis Sloug St h er 59 Merced R iv Tuolumne River 60 S an J ek r y Cre Dr ive oa q k u 53 Le i ee n r reek ek quin R C R C wi e k 21 a ono iv e o M e e s r er Cr r iv Fo nJ R urns ar a ed sC c B e 22 rk S B 35 Mer en w ek 40 O re Orestim C 79 baCreek L ek W Be sCre a o ar en Cre Ow i s ek os llow C rip k B a a M ee n Cr o r r M r e y s ek u Rive ve e Cr la k dS chil n e ow Di e lo Ch no Ri k s ug S e a h Fr n L uisC 47 reek

South 48 Fork Kin gs River r e iv R 54 s ing K

eek

F r r ve e i K sno ood C R h e 64 a r nRi Legend nw Sl

o we o t a ug t K h ve

Co 41 r

Hydrography e

Cr 46 56 s s 42 California State Boundary o Cr r k ve tos Cree Ri 55 LosGa r le Rive Tu Modeled Areas with No Historical Potential Tule 43 45

Candidate Steelhead Populations Deer Creek 33 2 Habitat Density: (Stream Km / Population Area Km )*100 68 0.00 - 20.00

ek 46 so Cre 20.01 - 40.00 Po 40.01 - 60.00 44 20 iver rnR 60.01 - 80.00 Ke 18 80.01 - 100.00 19

025 50 100 Kilometers

Figure 2. Spawning and rearing habitat areas of independent O. mykiss populations. Green polygons indicate habitat boundaries; color intensity indicates the density of habitat (km stream habitat km-2 x 100). (Click here for PDF file of larger image).

Produced by eScholarship Repository 8 San Francisco Estuary and Watershed Science Vol. 4, Iss. 1 [February 2006], Art. 3

Table 1. Proposed historical independent populations of steelhead in the Central Valley Independent Population Basin Total Stream (km) Streams 1 American R. 1357.1 Auburn Ravine, NF 2 Antelope Cr 176.5 Cold Fork 3 Battle Cr 122.8 MF, SF 4 Battle Cr 349.1 Knob Gulch, NF, Rock Cr 5 Bear R (Feather trib) 58.5 NF 6 Bear R (Feather trib) 356.1 Long Valley Cr 7 Bear R (Sac trib) 51.5 Digger Cr, SF Bear Cr 8 Big Chico Cr 30.9 SF 9 Big Chico Cr 46.8 Rock Cr, mainstem 10 Big Chico Cr 114.9 East Branch Mud Cr 11 Butte Cr 29.2 MF 12 Butte Cr 269.4 mainstem 13 Cache Cr 1100.0 Deer Cr, Dry Cr, Wolf Cr, mainstem 14 Calaveras R 14.5 Woods Cr 15 Calaveras R 22.8 mainstem 16 Calaveras R 34.6 San Antonio Cr, San Domingo Cr 17 Calaveras R 71.9 McKinney Cr, O’Neil Cr 18 Caliente Cr 12.4 Indian Cr 19 Caliente Cr 60.5 Tehachapi Cr 20 Caliente Cr 75.8 Walker Basin 21 Chowchilla R 12.9 mainstem 22 Chowchilla R 61.3 Willow Cr, mainstem 23 Clear Cr 255.7 Crystal Cr, mainstem 24 Coon Cr 15.6 mainstem 25 Coon Cr 38.9 mainstem Cosumnes R 587.8 Cedar Cr, MF, NF, SF 27 Cottonwood Cr 16.8 mainstem 28 Cottonwood Cr 44.2 SF 29 Cottonwood Cr 55.2 Jerusalem Cr, Moon Fork, NF Bear Cr 30 Cottonwood Cr 62.4 Duncan Cr, Soap Cr, mainstem 31 Cottonwood Cr 96.8 Wells Cr 32 Cottonwood Cr 121.2 mainstem 33 Deer Cr (Kaweah trib) 46.2 Bull Run Cr, Chimney Cr, SF 34 Deer Cr (Sac trib) 299.4 Little Dry Cr 35 Del Puerto Cr 33.8 Whisky Cr 36 Elder Cr 59.3 NF, mainstem 37 Feather R 14.4 Briscoe Cr 38 Feather R 41.7 Rocky Honcut Cr Canyon Cr, Concow Cr, Little Butte Cr, MF, NF 39 Feather R 5193.5 Elk Cr, WB 40 Fresno R 38.6 Big Cr, NF 41 Kaweah R 11.6 SF Tule R http://repositories.cdlib.org/jmie/sfews/vol4/iss1/art3 9 Lindley et al.: Historical population structure of Central Valley steelhead and its alteration by dams

Table 1. Proposed historical independent populations of steelhead in the Central Valley (Continued) Independent Population Basin Total Stream (km) Streams 42 Kaweah R 20.9 Tyler Cr 43 Kaweah R 42.9 mainstem 44 Kern R 35.1 NF 45 Kern R 532.2 French Gulch, Little Poso Cr, Tillie Cr 46 Kern R 693.0 Fay Cr, Kelso Cr, Marsh Cr, 47 Kings R 20.6 SF 48 Kings R 123.3 Bitterwater Cyn, SF, mainstem 49 Little Cow Cr 33.3 Clover Cr 50 Little Cow Cr 59.4 South Cow Cr 51 Little Cow Cr 83.5 Cedar Cr, mainstem 52 Little Cow Cr 88.5 Gelndenning Cr, Old Cow Cr 53 Lone Tree Cr 28.5 EF 54 Los Banos Cr 10.2 MF Tule R 55 Los Gatos Cr 19.5 mainstem 56 Los Gatos Cr 20.1 Rube Cr 57 Marsh Cr 82.9 SF 58 McCloud R 1201.2 Nosoni Cr, mainstem 59 Merced R 18.1 Snow Cr 60 Merced R 227.9 MF, Miami Cr, mainstem 61 Mill Cr 158.7 NF Willow Cr 62 Mokelumne R 53.3 Sutter Cr, mainstem 63 Mokelumne R 276.8 NF 64 Panoche Cr 11.4 Warthan Cr 65 Paynes Cr 29.9 Beegum Cr 66 Pit R 146.5 Squaw Cr 67 Pit R 3948.0 Potem Cr, mainstem 68 Poso Cr 168.5 Alamo Cr, Indian Cr 69 Putah Cr 982.2 Scott Cr 70 Stanislaus R 218.3 Curtis Cr 71 Stony Cr 184.6 Grindstone Cr, NF, SF, Salt Cr 72 Stony Cr 237.2 Little Stony Cr, Salt Cr, South Honcut Cr Suisun Bay tribs, 73 northern Kelso Cr 573.1 Sullivan Cr, mainstem 74 Sweany Cr 127.6 Jesus Maria Cr 75 Thomes Cr 179.1 Maple Branch Mud Cr 76 Toomes Cr 34.4 Big Dry Cr, mainstem Bear Cr, Corral Hollow Cr, Maxwell Cr, Moccasin 77 Tuolumne R 323.8 Cr, mainstem Backbone Cr, Middle Salt Cr, Salt Cr, Squaw Cr, 78 Upper Sacramento R 766.6 Sugarloaf Cr, mainstem 79 Upper San Joaquin R 205.8 Clear Cr, Erskine Cr, Mill Flat Cr, mainstem 80 Yuba R 138.4 mainstem 81 Yuba R 1077.1 Dry Cr, mainstem

Produced by eScholarship Repository 10 San Francisco Estuary and Watershed Science Vol. 4, Iss. 1 [February 2006], Art. 3

150

100 Number of Clusters

0 0 50 100 150 200 250 300 350 400 Distance C riterion (km)

Figure 3. Linkage of habitat patches as a function of distance along the stream network. At a distance of 35 km, there are 81 discrete patches.

http://repositories.cdlib.org/jmie/sfews/vol4/iss1/art3 11 Lindley et al.: Historical population structure of Central Valley steelhead and its alteration by dams

Suisun Bay tribs(80) Sweany Cr (73) Marsh Cr (57) Merced R (60) Kern R (44) Caliente Cr (18) upper San Joaquin R (81) Kern R (46) Kern R (45) Stanislaus R (70) Tuolumne R (76) Mokelumne R (63) Kaweah R (42) Pit R (67) Kings R (48) Kaweah R (41) Panoche Cr (64) Los Gatos Cr (56) Los Banos Cr (54) Lone Tree Cr (53) Los Gatos Cr (55) Del Puerto Cr (35) Kaweah R (43) Deer Cr (Kaweah trib) (33) Poso Cr (68) Caliente Cr (20) Caliente Cr (19) Cottonwood Cr (29) Pit R (66) Clear Cr (23) Butte Cr (12) Big Chico Cr (10) Feather R (39) Mill Cr (61) Deer Cr (Sac trib) (34) Battle Cr (4) Battle Cr (3) McCloud R (58) Little Cow Cr (52) Little Cow Cr (50) Antelope Cr (2) Upper Sacramento R (77) Little Cow Cr (51) Yuba R (79) Little Cow Cr (49) Cottonwood Cr (32) Thomes Cr (74) American R (1) Big Chico Cr (9) Yuba R (78) Butte Cr (11) Big Chico Cr (8) Feather R (38) Feather R (37) Toomes Cr (75) Bear R (Feather trb) (6) Putah Cr (69) Coon Cr (24) Coon Cr (25) Cache Cr (13) Bear R (Feather trb) (5) Kings R (47) Fresno R (40) Mokelumne R (62) Cottonwood Cr (30) Cottonwood Cr (31) Cottonwood Cr (27) Elder Cr (36) Cottonwood Cr (28) Cosumnes R (26) Bear R (Sac trib) (7) Chowchilla R (22) Chowchilla R (21) Calaveras R (17) Stony Cr (72) Stony Cr (71) Paynes Cr (65) Calaveras R (15) Merced R (59) Calaveras R (16) Calaveras R (14)

.5 3 2.5 2 1.5 1 0.5 0 Normalized Distance

Figure 4. Neighbor-joining tree based on average Mahalanobis distances, calculated from normalized climatic variables and mean elevation. Colored backgrounds envelope clusters of basins that are largely from the same geographic region: orange—tributaries to the Sacramento below the delta; green—the upper San Joaquin and tributaries draining the southern Sierra Nevada; blue—other tributaries to the San Joaquin draining lower elevation areas; yellow—mostly tributaries to the Sacramento River. The numbers in parentheses after the basin name correspond to the population numbers in Table 1. (Click here for PDF file of larger image).

Produced by eScholarship Repository 12 San Francisco Estuary and Watershed Science Vol. 4, Iss. 1 [February 2006], Art. 3

h Ru

u sse

o l

l l

nS S

a l ou g

o g L h

S ou Pine C th re ek

r Pork As ek h

Cree i t

R ill Cre

i v M k 58 e A eek sh C r r C B t ear Creek re s er a ek iv 67 E R r e F o iv all t R Riv Cedar Creek n er Wil loud r C e low ra me c eek v c M r er Cr tRi e Sa ek t Riv Pi Ho Pi rseC quaw C Creek re S y ek 23 78 Ha urne tC B

k r eek e 66 e ! 51 0 rCr 49 ea l ! 23 C ! 52!! ! ! 29 ! ! k 50

e Manzanita Creek

e 30 reek r K Clear C C 7 ings C

! w r ! eek o 4 Digge r Creek 30 C reek BattleC ! 3 reek ! ! ek Beegum C re Dry Creek C 65 27 es yn Pa A n 2 reek t C ek 31 28 el ill re M Butt C p C ope ! k 61 reek Last Ch ree an k C ce an nC Cre a e B i k d r ! 32 Re e d ek n reek I R ! Elder C 76 ed Clove k r e 39 v ree 36 k eCreek Ri r 34 t C ee C r e re Cr ut 75 Bu o e as h k r B t c ic hom h a ! T C 8 r G k reek P Fe ive e i R r re ne Cr k indst gCh r Sehorn C S r ! ton Bi o Fo eathe ne ! y C 9 ! Cr reek e th rk F r Fo k ee e r e k k e e 10 11 No ddl v re 71 12 Mi Ri C ll W a il k F ate s e on Cr Sl C e oldSt Cr y re ee !r am r r k D ! e e ! v tl North Y ive ubaR Ri 71 ! iver a Lo Lit ! ub ga oR Y n Cr ! le ek eek 37 dd e l Mi Cr

ment a n reek n a yo Stony C 38 81 an Ca ver acr i C low Creek

S a aR s

Wil

lu ! 72 Yub iver N o 80 reek R iver o Feath C anR rth F C eer - D ear meric B kA o n r ! B For r ear ! kC n ek ! e North v e e a l C e r i S c C he C o rR c ! G lt Cree r lu 6 o eek Sa eR t sa Tr i Ru t k k ve s 5 ! !!a k b C r ic ! n o re ee S n o k Bea Ri k e e ! ! reek u rR v k 13 e C re g C ! iv er k h er r re and Long Cr e e S ! Dry iv ! ! nR !!Coon Creek 25 co tina C ! ! yCre ubi e R ! or C s l a C avine e R che Auburn ! K ! P ! 24 ican River uta ! Amer h C Cr r Fork eek outh eek Creek ! S eek Dry 1 ek C Cr eberCre amp Caples W W ! ! Creek il low ! Sl oug ! 69 h ! ! ! ! er Putah Cree 26 v k Ri ek !! re C ! ! ear reek B and Ul rC 62 k Fork ati 74 e Highl Clar sCr De ! ! Sutter Cr eek k ee ! ! 63 ee Ken k ! Cr n ! Cac na ! r e Lagu ! k ! dyC ee eave re ! ! h Cr ! B ek ! eSl r 17 ! Dry ve o e Ri ugh 15 k 73 e ! lumn ! ke r k e e Mo 16 v Cre e ! Rose Cre i r ek s 14 R C ll eek eek r Cr Fa C ! k rry e ! Bear iver vey e t k la h iu asR 70 P r ee C C ! ve r Cree ala C n lumne River C a Tuo k iv ek oc r Cre ull Rive Ly hns R S mne 73 ttlejo ! 77 le Tuolu el 57 Li Midd lFo ! ! ! O Tom r ld ve rk Ri Pa us!Ri v in isla er e S Stan loug ! h er 59 MercedRiv Tuo!lumne River! 60 S a eek r n yCr J Dr ive o a q u nR 53 L k i ! eek ui e k e n r ! e Cr

wis o R C 21 aq on i ree M ve s eek r r C r ive r F R C nJo urn ed o a rc ! B ea 22 rk S e B ns 35 M e k 40 Ow ree Orestim ! C 79 baCreek L ek Will Bear ! sCre a ! o Cre Owen s s ek o ip o k B ! ! ar w a ee M ! Cre r n C o r Mu r y s ve e Ri v ! e e Cre k dSl lla chi ink how oRi! D e n o C k s u e g r S ! F an h Lu 47 is Cre ! ek !

South 48 ForkKin ! gs River er iv R 54 gs Kin !

Fr dCr r

o ve es i K o R n e

w h 64 o rn S n ea

Legend o w l Riv ou t a gh ! K

Cot 41 r

! ek Dams e r

C 46 56 s s 42 o r Hydrography C Creek ver atos i 55 s G r Lo ive ule R e R T California State Boundary Tul ! 43 45

ek re r C Percent of Steelhead Habitat Dee 33 Inaccessible to Anadromy due to Dams 68 0.0 - 10.0 k ee 46 Cr so 10.01 - 50.0 Po ! 44 50.01 - 75.0 er 20 Riv rn 75.01 - 99.0 Ke 18 99.01 - 100.0 ! 19

025 50 100 Kilometers

Figure 5. Percentage of historically accessible habitat behind impassable dams. Numbers indicate populations (see Table 1). (Click here for PDF file of larger image). http://repositories.cdlib.org/jmie/sfews/vol4/iss1/art3 13 Lindley et al.: Historical population structure of Central Valley steelhead and its alteration by dams

DISCUSSION of 35 km as a threshold for delineating populations. While we believe that 35 km is a We used a simple habitat model and reasonable value, 25 or 50 km might also be readily available environmental information to reasonable, and the number of independent predict the historical distribution of O. mykiss populations identified by our model changes spawning and rearing habitat in the Central significantly if these alternatives are used Valley. In agreement with the suggestions of (Figure 3). Users of our model results should McEwan (2001) and Yoshiyama and others bear in mind that specific population (1996), our results suggest that O. mykiss was boundaries are uncertain, and consider how widespread throughout the Central Valley, but different but still plausible delineations might indicate that O. mykiss was relatively less influence their results. abundant in San Joaquin tributaries than Sacramento River tributaries due to natural The distribution of many discrete migration barriers. Due largely to high summer populations across a wide variety of temperatures on the valley floor, O. mykiss environmental conditions implies that the habitat is patchily distributed, with 81 discrete Central Valley steelhead ESU contained patches isolated by >35 km of unsuitable biologically significant amounts of spatially stream habitat. The posited existence of 81 structured genetic diversity. This hypothesis is independent populations is likely to be an bolstered by the presence of distinct underestimate because large watersheds that subspecies of non-anadromous O. mykiss in span a variety of hydrological and several regions of the basin (Behnke 2002). environmental conditions, such as the Pit According to Behnke’s map (his p. 78), coastal River, probably contained multiple populations. rainbow trout (which include Central Valley steelhead) are distributed throughout the High summer temperature on the valley Central Valley, with the exception of the Pit and floor is one important driver of habitat upper Kern rivers. Golden trout were fragmentation, and thus population structure, historically found in the mainstem Kern River in our model. At cooler times of the year, (O. mykiss gilberti), the South Fork Kern and O. mykiss could potentially move freely among Golden Trout Creek (O. mykiss aquabonita), habitat patches. If fish commonly moved from and the Little Kern River (O. mykiss whitei ). where they were born to distant habitat Similarly, redband trout (O. mykiss stonei ) patches for spawning, then the real population inhabit the upper Sacramento, including the structure could be much simpler than that McCloud, Pit, North and Middle Fork Feather predicted by our model. It is well known that rivers, and Butte Creek. Another implication of adult anadromous salmonids are capable of these observations is that not all of the dispersing long distances, but this occurs at a O. mykiss habitat identified by our model may low rate under natural conditions (Quinn 2005). have been used by Central Valley steelhead, Resident O. mykiss in the Kern River basin because coastal O. mykiss can interbreed with (Matthews 1996) and other systems (Bartrand golden and redband trout, yet introgression and others 1994; Young and others 1997; appears to be a recent phenomenon. Meka and others 2003) have small home ranges, on order of a few kilometers or less, It appears that much of the historical suggesting that few juveniles regularly move diversity within Central Valley O. mykiss has more than a few kilometers except during their been lost or is threatened by dams. Figure 5 migration to sea. The other main driver of shows that dams have heavily altered the population structure in our model is our choice distribution and population structure of

Produced by eScholarship Repository 14 San Francisco Estuary and Watershed Science Vol. 4, Iss. 1 [February 2006], Art. 3

steelhead in the Central Valley. Our estimate of Tailwater areas below dams with hypolimnetic steelhead habitat loss is somewhat larger than releases, while not identified by our model, the 70% habitat loss of Chinook salmon may also produce steelhead. Natural areas reported by Yoshiyama and others (2001), but that continue to produce steelhead should be a quite similar to the 80% loss reported by Clark top priority for conservation. Tailwater and (1929). The loss is not spread evenly among above-barrier populations in the San Joaquin populations, however. About 38% of the basin could also be important targets for discrete habitat patches are no longer conservation, because any such populations accessible to anadromous O. mykiss. For most could be the only representatives of a anadromous fish, such an impact would presumably ecologically distinct segment of generally mean extirpation of the affected the ESU, assuming that they are descended population, but the life-history flexibility of from native anadromous populations. The O. mykiss means that formerly anadromous value of these populations for recovering O. mykiss populations may persist as resident anadromous runs may be reduced due to the trout above the dams. Rainbow trout are selective effects of the dams. Obviously, for indeed common in streams above reservoirs in populations above dams, reproductive effort the Central Valley (Knapp 1996; Moyle and devoted to producing anadromous offspring is others 1996). It is not at all clear, however, completely lost to that population. More subtly, whether these populations are the residualized water releases from dams like Shasta change descendants of native anadromous the thermal regime and food web structure of populations, or are the descendants of rainbow the river below (Lieberman and others 2001) in trout that have been widely planted throughout ways that may provide fitness advantages to California to enhance recreational trout resident forms. Clearly, the current state of the fisheries. Nielsen and others (2005) found that Central Valley landscape presents a very fish from areas above barriers were more different selective regime than any faced by similar to other above-barrier populations than O. mykiss before, posing thorny issues for to fish from the same river downstream of the conservation of Central Valley steelhead. barrier. This could indicate a separate phylogenetic origin for these above-barrier ACKNOWLEDGMENTS populations (in particular, derivation from a common hatchery strain), or may be a case of STL appreciates useful discussions with B. long-branch attraction (Felsenstein 1978), an Spence, T. Williams, E. Bjorskstedt, and D. artifact of tree construction where widely Boughton. D. Boughton, K. Burnett, M. Mohr, divergent populations cluster together, away and R. Yoshiyama provided critical reviews of from the more closely-related populations. the manuscript. B. Swart assisted with GIS analyses. JJA, BPM and JGW were supported The extensive loss of habitat historically by the CALFED Science Program through available to anadromous O. mykiss supports Association of Bay Area Governments contract the status of O. mykiss as a species threatened CALFED/DWR 4600001642. with extinction. An important next step is to identify and secure the sources of current natural production of steelhead, limited as they may be. Our model identifies those few streams where historical habitat may still be accessible (e.g., Mill, Deer, Butte and Cottonwood creeks) as likely candidates. http://repositories.cdlib.org/jmie/sfews/vol4/iss1/art3 15 Lindley et al.: Historical population structure of Central Valley steelhead and its alteration by dams

REFERENCES Burger CV, Wilmot RL, Wangaard DB. 1985. Comparison of spawning areas and times Agajanian J, Rockwell GL, Anderson SW, for two runs of chinook salmon Pope GL. 2002. Water resources data (Oncorhynchus tshawytscha) in the Kenai California water year 2001. Volume 1. River, Alaska. Canadian Journal of Southern Great Basin from Mexican Fisheries and Aquatic Sciences 42:693– Border to Mono Lake Basin, and Pacific 700. Slope Basins from Tijuana River to Santa Maria River. Water-Data Report CA-01-1, Burnett KM. 2001. Relationships among U.S. Geological Survey. juvenile anadromous salmonids, their freshwater habitat, and landscape Argáez JA, Christen JA, Nakamura M, characteristics over multiple years and Soberon J. 2005. Prediction of potential spatial scales in Elk River, Oregon [PhD areas of species distributions based on dissertation]. Available from: Oregon State presence-only data. Environmental and University. Ecological Statistics 12:27–44. Burnett KM, Reeves GH, Miller D, Clark SE, Bartrand EL, Pearsons TN, Martin SW. 1994. Christiansen KC, Vance-Borland K. 2003. Movement of rainbow trout in the upper A first step towards broad-scale Yakima River basin. Northwest Science identification of freshwater protected areas 68:114. for Pacific salmon and trout. In: Beumer J, editor. Proceedings of the World Congress Beer WN, Anderson JJ. 2001. Effects of on Aquatic Protected Areas. Cairns, spawning behavior and temperature Australia: Australian Society for Fish profiles on salmon emergence: Biology. interpretations of a growth model for Methow River chinook. Canadian Journal Chefaoui RM, Hortal J, Lobo JM. 2005. of Fisheries and Aquatic Sciences 58:943– Potential distribution modelling, niche 949. characterization and conservation status assessment using GIS tools: a case study Behnke RJ. 2002. Trout and salmon of North of Iberian Copris species. Biological America. New York: The Free Press. Conservation 122:327–338.

Bjorkstedt EP, Spence B, Garza JC, Hankin Clark GH. 1929. Sacramento-San Joaquin DG, Fuller D, Jones W, Smith J, Macedo salmon (Oncorhynchus tshawytscha) R. 2005. An analysis of historical fishery of California. Fish Bulletin 17:1–73. population structure of Evolutionarily Significant Units of Chinook salmon, coho Cook WC. 1929. A bioclimatic zonation for salmon, and steelhead in the North- studying the economic distribution of Central California Coast Recovery injurious insects. Ecology 10:282–293. Domain. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-SWFSC-382, La Daly C, Neilson RP, Philips DL. 1994. A Jolla, CA. statistical-topographic model for mapping climatological precipitation over Brannon EL, Powell MS, Quinn TP, Talbot A. mountainous terrain. Journal of Applied 2004. Population structure of Columbia Meterology 33:140–158. River basin chinook salmon and steelhead trout. Reviews in Fisheries Science 12:99– 232.

Produced by eScholarship Repository 16 San Francisco Estuary and Watershed Science Vol. 4, Iss. 1 [February 2006], Art. 3

Daly C, Taylor G, Kittel T, Schimel D, McNab Hicks BJ, Hall JD. 2003. Rock type and A. 2002. Development of a 103-year high- channel gradient structure salmonid resolution climate data set for the populations in the Oregon Coast Range. conterminous United States. Transactions of the American Fisheries Comprehensive Final Report for 9/1/97 - 5/ Society 132:468–482. 31/02. NOAA Climate Change Data and Detection Program. Ingram BL, Ingle JC, Conrad ME. 1996. A 2000-yr record of Sacramento-San Darwin C. 1859. On the origin of species by Joaquin River inflow to San Francisco Bay means of natural selection, or the estuary, California. Geology 24:331–334. preservation of favoured races in the struggle for life. London: John Murray. Interior Columbia Basin Technical Recovery Team. 2003. Independent populations of Engle RO. 2002. Distribution and summer chinook, steelhead, and sockeye for listed survival of juvenile steelhead trout Evolutionary Significant Units within the (Oncorhynchus mykiss) in two streams interior Columbia River domain. Working within the King Range National draft, NOAA Fisheries, Seattle, WA. Conservation Area, California. [MS thesis]. Available from: Humboldt State University. Johnson CJ, Seip DR, Boyce MS. 2004. A quantitative approach to conservation Felsenstein J. 1978. Cases in which planning: using resource selection parsimony or compatibility methods will be functions to map the distribution of positively misleading. Systematic Zoology mountain caribou at multiple spatial 27:401–410. scales. Journal of Applied Ecology 41:238–251. Friebel MF, Freeman LA, Smithson JR, Webster MD, Anderson SW, Pope GL. Keefer DK. 1994. The importance of 2002. Water resources data California earthquake-induced landslides to long- water year 2001. Volume 2. Pacific Slope term slope erosion and slope-failure basins from Arroyo Grande to Oregon hazards in seismically active regions. state line except Central Valley. Water- Geomorphology 10:265–284. Data Report CA-01-2, U. S. Geological Survey. Kerr RA. 1984. Landslides from volcanos seen as common. Science (Washington DC) Goslin M. 2005. Creating a comprehensive 224:275–276. dam dataset for assessing anadromous fish passage in California. U.S. Dept. Knapp RA. 1996. Non-native trout in natural Commer., NOAA Tech. Memo. NMFS- lakes of the Sierra Nevada: an analysis of SWFSC-376, La Jolla, CA. their distribution and impacts on native aquatic biota. Sierra Nevada Ecosystem Harvey BC, White JL, Nakamoto RJ. 2002. Project: final report to Congress. Vol. III. Habitat relationships and larval drift of Davis (CA): Centers for Water and native and nonindigenous fishes in Wildland Resources, University of neighboring tributaries of a coastal California, Davis. California river. Transactions of the American Fisheries Society 131:159–170. Konecki JT, Woody CA, Quinn TP. 1995. Influence of temperature on incubation rates of coho salmon (Oncorhynchus kisutch) from ten Washington populations. Northwest Science 69:126–132. http://repositories.cdlib.org/jmie/sfews/vol4/iss1/art3 17 Lindley et al.: Historical population structure of Central Valley steelhead and its alteration by dams

Lieberman DM, Horn MJ, Duffy S. 2001. Mohseni O, Stefan HG, Erickson TR. 1998. A Effects of a temperature control device on nonlinear regression model for weekly nutrients, POM and plankton in the stream temperatures. Water Resources tailwaters below Shasta Lake, California. Research 34:2684–2692. Hydrobiologia 452:191–202. Montgomery DR, Buffington JM, Peterson NP, Lytle DA, Poff NL. 2004. Adaptation to natural Schuett-Hames D, Quinn TP. 1996. flow regimes. Trends in Ecology and Stream-bed scour, egg burial depths, and Evolution 19:96–100. the influence of salmonid spawning on bed surface mobility and embryo survival. Mahalanobis PC. 1936. On the generalized Canadian Journal of Fisheries and Aquatic distance in statistics. Proceedings of the Sciences 53:1061–1070. National Institute of Sciences in India 12:49–55. Moyle PB, Randall PJ. 1998. Evaluating the biotic integrity of watersheds in the Sierra Manly BFJ, McDonald LL, Thomas DL, Nevada, California. Conservation Biology McDonald TL, Erickson WP. 2002. 12:1318–1326. Resource selection by animals: statistical design and analysis for field studies. 2nd Moyle PB, Yoshiyama RM, Knapp RA. 1996. edition. Dordrecht/Boston/London: Kluwer Status of fish and fisheries. Sierra Nevada Academic Publishers. Ecosystem Project: final report to Congress. Vol II. Davis (CA): Centers for Matthews KR. 1996. Diel movement and Water and Wildland Resources, University habitat use of California golden trout in the of California, Davis. Golden Trout Wilderness, California. Transactions of the American Fisheries Nielsen JL, Lisle TE, Ozaki V. 1994. Thermally Society 125:78–86. stratified pools and their use by steelhead in Northern California streams. McElhany P, Ruckelshaus MH, Ford MJ, Transactions of the American Fisheries Wainwright TC, Bjorkstedt EP. 2000. Society 123:613–626. Viable salmonid populations and the conservation of evolutionarily significant Nielsen JL, Pavey SA, Wiacek T, Williams I. units. U.S. Dept. Commer., NOAA Tech. 2005. Genetics of Central Valley O. mykiss Memo. NMFS-NWFSC-42, Seattle, WA. populations: drainage and watershed scale analyses. San Francisco Estuary McEwan DR. 2001. Central Valley steelhead. and Watershed Science [online]. Vol. 3, In: Brown RL, editor. Fish Bulletin 179. Issue 2, Article 3. Available at: http:// Contributions to the biology of Central www.estuaryandwatershedscience.org/ Valley salmonids. Vol. 1. Sacramento vol3/iss2/art3. (CA): California Department of Fish and Game. p 1–43. Quinn TP. 2005. The behavioral ecology of Pacific salmon and trout. Seattle: Meka JM, Knudsen EE, Douglas DC, Benter University of Washington Press. RB. 2003. Variable migratory patterns of different adult rainbow trout life history Quist MC, Rahel FJ, Hubert WA. 2005. types in a southwest Alaska watershed. Hierarchical faunal filters: an approach to Transactions of the American Fisheries assessing effects of habitat and nonnative Society 132:717–732. species on native fishes. Ecology of Freshwater Fish 14:24–39.

Produced by eScholarship Repository 18 San Francisco Estuary and Watershed Science Vol. 4, Iss. 1 [February 2006], Art. 3

Rahel FJ, Keleher CJ, Anderson JL. 1996. Valavanis VD, Georgakarakos S, Potential habitat loss and population Kapantagakis A, Palialexis A, Katara I. fragmentation for cold water fish in the 2004. A GIS environmental modelling North Platt River drainage of the Rocky approach to essential fish habitat Mountains: response to climate warming. designation. Ecological Modelling Limnology and Oceanography 41:1116– 178:417–427. 1123. Wall SS, Berry CR, Blausey CM, Jenks JA, Rockwell GL, Smithson JR, Friebel MF, Kopplin CJ. 2004. Fish-habitat modeling Webster MD. 2002. Water resources data for gap analysis to conserve the California water year 2001. Volume 4. endangered Topeka shiner (Notropis Northern Central Valley basins and the topeka). Canadian Journal of Fisheries Great Basin from Honey Lake basin to and Aquatic Sciences 61:954–973. Oregon state line. Water-Data Report CA- 01-4, U.S. Geological Survey. Yoshiyama RM, Gerstung ER, Fisher FW, Moyle PB. 1996. Historical and present Schmidt AH, Graham CC, McDonald JE. distribution of chinook salmon in the 1979. Summary of literature on four factors Central Valley drainage of California. associated with salmon and trout fresh Sierra Nevada Ecosystem Project, Final water life history. Fisheries and Marine Report to Congress, vol III. Centers for Service Manuscript Report 1487, Water and Wildland Resources, University Vancouver B.C.: Fisheries and Marine of California, Davis. Service. Yoshiyama RM, Gerstung ER, Fisher FW, Smithson JR, Freeman LA, Rockwell GL, Moyle PB. 2001. Historic and present Anderson SW, Pope GL. 2002. Water distribution of chinook salmon in the resources data California water year 2001. Central Valley drainage of California. In: Volume 3. Southern Central Valley basins Brown RL, editor. Fish Bulletin 179. and the Great Basin from Walker River to Contributions to the biology of Central Truckee River. Water-Data Report CA-01- Valley salmonids. Vol. 1. Sacramento 3, U.S. Geological Survey. (CA): California Department of Fish and Game. p 71–176. Sokal RR, Rohlf FJ. 1962. The comparisons of dendrograms by objective methods. Taxon Young MK, Wilkison RA, Phelps IJM, Griffith 11:33–40. JS. 1997. Contrasting movement and activity of large brown trout and rainbow Solley WB, Pierce RR, Perlman HA. 1998. trout in Silver Creek, Idaho. Great Basin Estimated use of water in the United Naturalist 57:238–244. States in 1995. Circular 1200. U.S. Geological Survey.

Taylor EB. 1991. A review of local adaptation in Salmonidae, with particular reference to Pacific and Atlantic salmon. Aquaculture 98:185–207.

http://repositories.cdlib.org/jmie/sfews/vol4/iss1/art3 19