The Origins of Life History Variation in Steelhead/Rainbow Trout from Coastal California John Carlos Garza, Alicia Abadía-Cardoso, Devon Pearse

Molecular Ecology & Genetic Analysis Team Southwest Fisheries Science Center and UC Santa Cruz

Life History Variation Age- 2.0 Sex- M Length-12 cm

Age- 1.1? Sex- M Length- 41cm

Age- 5.0?? Sex- M Length- 27 cm

Age- 1.3 Sex- M Length- 88 cm

Age- 2.2 Sex- M Length- 71cm

Age- 4.0 estuarine Sex- F Length- 32 cm

Age- 3.4 estuarine? Sex- F Length- 42 cm

Age- 2.1 Sex- M Length- 53 cm

Coastal CA Steelhead Population Structure •  “Snapshot” of population

structure from 60 sites, 40 basins in all five CA Coastal steelhead ESUs

•  ~4500 juvenile fish non-lethally sampled from 5 sections/location

•  Samples collected June-Oct. 2001 •  Avg. of 66 fish/site analyzed •  Data from 18 microsatellite loci •  ~132,000 allele copies, 540

unique alleles sampled.

100 replicates

Redwood-Prairie

BigCk

SanL-Bear!Waddell

Pescadero Scott

SanL-Boulder!

Corralitos SanL-Zayante!

SanPedro SanL-Carbonera

Chorro SanSimeon

Carmel

BigSur WillowCk!

Mont

507 656

Redwd!Marin

Walker Lagunitas

Blueline Olema

949 Miller!

LosTrancos

558

Big-Humb

Smith-Rowdy

Klamath-Hunter WilsonCk

794

767

Klamath-HLinto Klamath-Blue!

597

831

Redwood-Panther Redwood- LostMan!

Freshwater 891

719 702

Mattole-Bear BearHumb Eel-HTree Mad-Blue

Eel-Indian Eel-Willits Eel-Lawrence Mad-Canon

Mad-Sullivan

934

647 707

777

Ten-LNFk Ten-SFk

Ten-Smith Ten-Redwd

507

Wages Usal Elk

Gualala Garcia

652 Big

Noyo NoyoSfk

Albion Noyo-Kass Noyo-LNFk

912 BigSalmon

Pudding Navarro

Russian

Steelhead Bootstrap Consensus Tree

South Central California

Klamath Mountain Northern California Central California

ESU Assignment

Strict consensus of 1000 neighbor-joining trees

Isolation by distance Regression of genetic distance on geographic distance for 59 steelhead

populations in coastal California. Geographic distance explains about 30% of the variation in genetic distance

r2=0.31! r2=0.18!

All data!Full siblings excluded!

Model Based Clustering Assignment Tests

Coastal CA Steelhead Population Structure

Model Based Clustering Assignment Tests Coastal CA Steelhead Population Structure

DPS/ESU vs. Genetic Group Boundaries

Coastal CA Steelhead Population Structure

Humboldt Bay

Lost Coast

Russian Gulch

San Francisco Bay

Southern California Trout Population Structure

•  Extension of population structure study to South-Central & Southern California

•  Five basins with population sampling above and below dams

•  Small numbers from further south •  All strains of rainbow trout used in

stocking also sampled •  ~1900 juvenile fish non-lethally

sampled w/ standardized protocol •  Data from same 18 microsatellite

loci as previous study.

Consensus chord distance tree with bootstrap support (10,000 replicates)

Santa Clara River

Salinas River Arroyo Grande Santa Ynez River

Fillmore Hatchery Strains

Ventura River

100

S.Ynez-SalsB

S.Ynez-NFJuncalA S.Clara-SantaPaulaB

Fillmore-MtWhitLt

Fillmore-MtWhitEa

100

Fillmore-Coleman

Fillmore-Wyoming

Fillmore-Virginia03

Fillmore-Virginia02

100

91

76

99

S.Clara-LionCanB S.Clara-PiruFFA

S.Clara-LockwoodA

S.Clara-PiruGHA

100 90

76

51

S.Ynez-HiltonB

S.Ynez-S.CruzA A.Grande-LopezCanA

Ventura-NFMatilijaB

Ventura-BearB

100

Ventura-UpNFMatilijaA Ventura-MatilijaA

99

61

A.Grande- mainB

A.Grande- LosBerrosA

Salinas-NacimientoA Salinas-TassajeraB

Salinas-TassajaraB

Salinas-SanAntonioA 87

Fillmore Hatchery Southern Steelhead

Factorial Correspondence Analysis

Expeditions of John Otterbein Snyder -Prominent early California ichthyologist-Student of David Starr Jordan

-Zoology professor at Stanford. Organized the National Museum fish collections.

-Published “The Fishes of the Streams Tributary to Monterey Bay, California”-1912

-Population collections of steelhead in Central California from 1897 & 1909 described.

Historical ModernWatershed Location Year N Year NEel River South Fork 1897 30 2001, 03 24Lagunitas Creek 1909 10 2001, 03 20Coyote Creek 1909 15 1998-2000 40San Lorenzo River 1897, 1909 41 2002, 04 32Pajaro River Uvas Creek 1909 19 1997, 98 16

Llagas Creek 1897 13 1997, 98 32Salinas River Arroyo Seco 1897, 1909 33 2001 32

San Antonio River 1909 27 2003 22Nacimiento River 1909 24 2003 22

TOTAL: 212 240American River Hatchery-Mt. Shasta - 2002 24Santa Clara River Hatchery-Virginia - 2003 23

Sampling for Historical Steelhead Study

Mitochondrial DNA- ~200bp section of control region

-Lagunitas population coho!

-No significant difference in number of alleles/diversity

-Four new alleles detected: 3 historically, 1 contemporary

-Differences range from very minor to dramatic

-No major replacement with hatchery stocks, although poorly sampled

Eel River

San Lorenzo

Pajaro-Llagas

Pajaro-Uvas

Salinas-Nacimiento

Coyote Creek

Salinas-Arroyo Seco

Salinas-San Antonio

Mt Shasta Virginia

Results

Mitochondrial DNA- ~200bp section of control region

-Lagunitas population coho!

-No significant difference in number of alleles/diversity

-Four new alleles detected: 3 historically, 1 contemporary

-Differences range from very minor to dramatic

-No major replacement with hatchery stocks, although poorly sampled

Eel River

San Lorenzo

Pajaro-Llagas

Pajaro-Uvas

Salinas-Nacimiento

Coyote Creek

Salinas-Arroyo Seco

Salinas-San Antonio

Mt Shasta Virginia

Results

Modern samples, River distances

r 2 = 0.0673

0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9

1

0 50 100 150 200 250 300 350 400 450 500 Distance (Miles)

Fst/

(1-F

st)

Geographic versus genetic distance-mtDNA control region Modern

Historical samples, River distances

r 2 = 0.9038

-0.5

0

0.5

1

1.5

2

2.5

0 50 100 150 200 250 300 350 400 450 500

Distance (Miles)

Fst/

(1-F

st)

Geographic versus genetic distance-mtDNA control region Historical

BlKlaRi_M

Matto_M

Guala_M

AmRNF_M

UpYuL_M

McClC_M

Battl_M

DeerC_M

LosTran_M

Wadd_M

Carmel_M

Tassaja_M

BigSuRi_M

WilloCk_M

PenChor_M

Simeon_M

CuyRey_M

SisqMnz_M

Sisq_M

MnteCr_M

Quiota_M

SCrz_M

Hilt_M

Junc_M

Sals_M

VeSAnt_M

NFMati_M

BearVen_M

SPau_M

Piedra_M

LionCyn_M

Sespe_M

BuckCr_M

Piru_M

SAnita_M

NFSGab_M

SGaBear_M

DevSG_M

WFSGab_M

Cattle_M

FishFk_M

SFIronFk_M

IronFk_M

EFSGab_M

FishCyn_M

TrabCr_M

OraSnAn_M

StaAna_M

ColdCr_M

FulMil_M

NFSnJaB_M

NFSnJaE_M

Doane_M

PaumaR_M

PaumaO_M

WFSLuis_M

SDiego_M

SweetO_M

SweetR_M

nelsoni_M

FHCol_M

FHVirg_M

FHWhi_M

FHWyo_M

ARHEag_M

ARHShas_M

HCKm

lp_M

BlKlaRi_M

Matto_M

Guala_M

AmRNF_M

UpYuL_M

McClC_M

Battl_M

DeerC_M

LosTran_M

Wadd_M

Carmel_M

Tassaja_M

BigSuRi_M

WilloCk_M

PenChor_M

Simeon_M

CuyRey_M

SisqMnz_M

Sisq_M

MnteCr_M

Quiota_M

SCrz_M

Hilt_M

Junc_M

Sals_M

VeSAnt_M

NFMati_M

BearVen_M

SPau_M

Piedra_M

LionCyn_M

Sespe_M

BuckCr_M

Piru_M

SAnita_M

NFSGab_M

SGaBear_M

DevSG_M

WFSGab_M

Cattle_M

FishFk_M

SFIronFk_M

IronFk_M

EFSGab_M

FishCyn_M

TrabCr_M

OraSnAn_M

StaAna_M

ColdCr_M

FulMil_M

NFSnJaB_M

NFSnJaE_M

Doane_M

PaumaR_M

PaumaO_M

WFSLuis_M

SDiego_M

SweetO_M

SweetR_M

nelsoni_M

FHCol_M

FHVirg_M

FHWhi_M

FHWyo_M

ARHEag_M

ARHShas_M

HCKmlp_M

San  Gabriel  R.

The Deep South

Sta A

na-T

emas

cal-

Sn Ja

cint

o12

FH-V

irginia A

RH-Shasta

EF Sn Gabriel- Iron Fork

EF Sn Gabriel-Fish Fork NF Sn Gabriel WF Sn Gabriel-Bear

EF Sn Gabriel EF Sn Gabriel-Cattle

Klamath-Blue Santa Ana

Sta Ana-Temescal- Coldwater Canyon

O. m. nelsoni

Sta Clara-Sespe

Los Trancos

San Luis Rey

Sta Ynez-Hilton Sa

linas

-Tas

saja

ra

Sta Y

nez-

Junc

al

Waddell Chorro-Pennington Sta Ynez-Quiota

Sta Ynez-Sta Cruz Sta Ynez-Salsipuedes

93 100

69

88

75

100

67

100 67

96 92

100

62

76

Sta A

na-T

emes

cal-

Sn Ja

cint

o12

FH-V

irginia A

RH-Shasta

EF Sn Gabriel- Iron Fork

EF Sn Gabriel-Fish Fork NF Sn Gabriel WF Sn Gabriel-Bear

EF Sn Gabriel EF Sn Gabriel-Cattle

Klamath-Blue Santa Ana

Sta Ana-Temescal- Coldwater Canyon

O. m. nelsoni

Sta Clara-Sespe

Los Trancos

San Luis Rey

Sta Ynez-Hilton Sa

linas

-Tas

saja

ra

Sta Y

nez-

Junc

al

Waddell Chorro-Pennington Sta Ynez-Quiota

Sta Ynez-Sta Cruz Sta Ynez-Salsipuedes

93 100

69

88

75

100

67

100 67

96 92

100

62

76

The Deeper South

Big Creek Falls

>> Strong, continuing selection on above-falls fish not to move downstream.

Photos: Corey Phillis"

• O. Mykiss introduced above Big Creek Falls c. 1910

• Genetic analysis supports within-basin origin of the above-falls population

(Pearse et al. 2009)

• 1.8% emigration rate over the falls, based on PIT tag data. (Hayes et al. 2012)

•  24 individuals each from above and below falls.

•  298 microsatellite loci genotyped, many mapped. (Martinez et al. 2011)

•  96 un-mapped SNP loci. (Abadía-Cardoso et al. 2011)

~400 loci distributed over all 29 linkage groups with ~10 cM coverage of the genome.

Genome Screen

Fst Histogram Micros and SNPS

0

5

10

15

20

25

30

35

40

45

50

-0.1

-0.1

-0.1 -0 -0 0

0.02

0.04

0.06

0.08 0.1

0.12

0.14

0.16

0.18 0.2

0.22

0.24

0.26

0.28 0.3

0.32

0.34

0.36

0.38 0.4

0.42

0.44

0.46

0.48 0.5

0.52

0.54

Fst

Freq

uen

cy

SNPsMicros

SH114448 SH121006 SH127236 BHMS426

Fst(298)=0.034

(Martinez et al. 2011; Pearse et al. 2014)

Hatchery    Eagle    Hatchery    MtWhitney    Hatchery    Kamloops    Goose  Lake  Bauers    Upper  Klamath  Buckboard    McCloud    Butcherknife    Eel    CuCinger    

   Summer  SH        Willow        Winter  SH    

ScoE    Above        Below    

San  Lorenzo  San  Lorenzo    Carmel    Carmel    Salinas    Tassajera    

   Nacimiento    Santa  Ynez    Hilton    

   NF  Juncal        Salsipuedes        Santa  Cruz    

Santa  Clara  Lion  Canyon        Frenchmen        Santa  Paula        Gold  Hill   Pearse et al. 2014!

Populations

SNP loci

R19198R14511

SH121006R14383R34385R33562R28680R14589R40580R33010R24370R23330R18251R40252R30015

SH114448R00586R21561R40342R19633R40319R13730R30423R40152R30220R34662R24068R21285R21330

SH127236R30678R37560R33411R14225R35324R40094R34286R38346R19731R39365R12738R30589R37205R24273R38993R23044

OMS00169

OMS00143

OMS00116R37229R22570R23813

OMS00144

OMS00159R30355

ARHEagle

FHMtWhitney

Kamloops

GLBauers

UKBuckboard

McCloudBk

EelCutfinger

EelSummerSH

EelWillow

EelWinterSH

ScottAbove

ScottWeir

SanLorenzo

Carmel

Tassajera

Nacimiento

SYHilton

SYNFJuncal

SYSalsipuedes

SYSantaCruz

SCLionCan

SCFrenchmen

SCSantaPaula

SCGoldHill

0 20 40 60 80 100Pearse et al. 2014! Frequency of the allele most common in anadromous adults

Conclusions •  Historical population structure relatively “intact” north of Pt. Conception:

mostly concordant with geography, no detectable hatchery impact

•  Migration and drift represents natural state: corridors important

•  Between Pt. Conception and the Los Angeles basin, above and below dam populations recently derived from coastal steelhead

•  Deep south populations (LA, Orange and San Diego counties) highly variable, many with a strong signal of hatchery ancestry

•  Little support for current DPS boundaries. Primary structuring: Local (~90%) -> Drainage -> Region

•  A chromosomal region on Omy5 is strongly associated with life history variation in O. mykiss throughout its range.

Acknowledgements •  Eric Anderson •  Joe Anderson •  Andres Aguilar •  Russell Barabe •  David Boughton •  Anthony Clemento •  Heidi Fish •  Libby Gilbert-Horvath •  Derek Girman •  Steve Gough •  David Hamm

•  Terry Jackson •  Sandi Jacobson •  Mary Larson •  Chris Lima •  Jack Marshall •  Andy Martinez •  Edith Martinez •  Dennis McEwan •  Chris McKibbin •  Brian Spence •  Tommy Williams

Other collaborators who helped in sample collection. Funding: Fishery Restoration Grant Program, NOAA Fisheries