Population Genomics of Coastal California Resident and Anadromous Oncorhynchus mykiss in

Scott Creek, CA

Devon Pearse

Molecular Ecology and Genetic Analysis TeamNOAA/National Marine Fisheries Service, Southwest Fisheries Science

CenterSanta Cruz, CA

andUniversity of California, Santa Cruz

Dept. of Ocean Science and Dept. of Ecology and Evolutionary Biology

Pacific Coast Steelhead Meeting, March 9, 2010

Oncorhynchus mykiss: a highly variable species.

Steelhead: Anadromous, spend 1-2 years in freshwater and 1-4 years in salt water prior to spawning. Iteroparous.

Rainbow Trout: Stay in stream entire life (Resident).

“Variation... is one of the most marked characteristics of animal life. Andof the the vertebrates, the trouts are among the most variable of all.Further, of the trouts the steelhead is one of the most variable forms.”

----Shapovalov & Taft (1954)

Fitness trade-offs of Resident vs Anadromous life-history

-fecundity advantage for anadromous females (and males)

-low survival at sea

-competition in stream, low growth. (Hayes et al. 2008)

Vs.

S.F.

Santa Cruz

~60miles

~12 miles

Scott Creekwatershed

Over the Falls?

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

•Records indicate source waswithin same watershed

•Hatchery stocking may haveoccurred above other barriers.

•Regardless of source, there mustbe strong selection on above fallsfish not to move downstream.

Above Barrier, ~100%

Below Barrier, >90%

Over the Falls?

•Surveyed 18 microsatellite lociin fish throughout watershed.

•Pairwise Fst at Big Creek Fallswas low, 0.018, supportingwithin basin origin.

•Although above barrier habit islimited, bottleneck/founder effectsdo not appear to be significant. (Anderson & Slatkin 2007)

•Other above-barrier populationsmore divergent (0.05-0.23)

Above-Barrier populations Anadromous Adults

from Pearse et al. 2009

Over the Falls?

Below Big Creek Falls

Photo: Morgan Bond

Above barrier fish phenotypically and genetically distinct:=>drift due to small population sizes=>adaptation to residency.

Hybridization with anadromous fish below is possible.=> one-way gene flow.=> better markers will help here...

When above-barrier fish move below the barrier, they maintain a resident life-history.

=>strong above-barrier selection not to go downstream.

from Pearse et al. 2009

Genome Scan

• Microsatellite loci: Rexroad et al. (2001); Rexroad et al. (2001); Coulibaly et al. (2005)….

• EST-linked microsatellite loci; Rexroad et al. (2005)

• Linkage maps: Nichols et al. (2003); Danzmann et al. 2005; Rexroad et al. (2008)-- >1,000 microsatellites, ~2.6cM resolution.

X a

X a

b

X a

X a

a

b

Positive selection onnew mutation

Gene region Genetic marker

time

traitfrequency

linkage to specific marker allele

0

1

Recombination and mutation selection

Recombination and mutation break down the associationbetween the selected locus and specific marker alleles...

X b

X c

X bX c

X a

X a

X a

X a

recombinational distance (cM)

Of course,situation in Scott Creek is much more complicated!

=>residency as a trait is complex, controlled by many lociso selection is not acting on a single gene.

=>genetic variation for residency likely existed prior totransfer above the falls, so was not a new mutation event.

Genome Scan

• 24 individuals each from above and below falls

• 298 loci successfully genotyped using 363 published primers, 188 anonymous and 110 EST-linked microsatellites

• Loci distributed over all 29 linkage groups with ~10 cM coverage of the O. mykiss genome.

0

5

10

15

20

25

30

35

40

45

50

-0.10-0.08-0.06-0.04-0.020.00 0.02 0.04 0.06 0.08 0.10 0.12 0.14 0.16 0.18 0.20 0.22 0.24 0.26 0.28 0.30 0.32 0.34 0.36 0.38 0.40

Fst

Frequency

Fst(298)=0.034

DifferentiationFdist; Beaumont & Nichols 1996.DetSel; Vitalis et al. 2003.

Variationln(RV), ln(RH); Schlötterer 2002; Kauer et al. 2002.

Genome Scan: methods of outlier detection

Fdist, Beaumont & Nichols 1996

OMM5166

OMM5136

OMM1009

OMM1120

OMM5117

OMM5014

CA361411

OMM5038

OMM5011

CA054538

OMM3090_MHC1

OMM1756

OMM1213

OMM1000 OMM5229

OMM5060

BX310634

BHMS426

OMM1386

OMM5195

OMM3097

OMM1231

OMM1289

OMM3024_MHC2

OMM3067

OMM1409

BX873238

OMM1292

OMM1581

F2

F1

DetSel, Vitalis et al. 2001, 2003

Standardized ln (RH) vs FST

-0.05

0

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

-5 -4 -3 -2 -1 0 1 2 3 4 5

ln(RH)

FST

OMM1289

OMM5011

OMM1009

OMM1241

BX076085OMM5124

OMM5109

OMM1036

OMM1762

Oki23

OMM3024

OMM1409

OMM3067

Schlötterer 2002; Kauer et al. 2002

Locus DetSel Fdist ln (RH) Linkage group PositionOMM1120 X X X* 10 80.5OMM1009 X X X 5 76.7OMM1289 X X X 21 32.4OMM1409 X X X 15 93.4OMM3067 X X X 19 39.3

OMM5011 X X X 23 24.2BHMS426 X X 5 76.7BX873238 X X 18 110.2OMM1213 X X 6 74.4OMM1292 X X 22 26.4

OMM3090_MHC1 X X 18 62.7OMM5195 X X 10 104.4OMM5229 X X sex 48.3

OMM5136 X X* sex 35.6OMM3024_MHC2 X X 17 0

BX310634 X 9 106.4CA054538 X 6 51.9CA361411 X 22 45.4OMM1000 X sex 21.1OMM1231 X 1 96.8OMM1386 X 22 19.8OMM1581 X 11 22.8OMM1756 X 24 9.6OMM3097 X 11 51.6

OMM5014 X 9 61.9OMM5038 X 20 43OMM5060 X 5 60.5

OMM5117 XOMM5166 XOMM5008 X 12 30.1

OKI23 XOMM1036 X 21 52.4OMM1762 X 28 5.3OMM5109 X 3 120.4OMM5124 X 18 76

•Total of 37 outliers.

•20 anonymous•17 EST-linked --elevated proportion of

EST-linked loci

•9 with two methods.

•6 outlier loci (2%) with all methods

Summary

from Martinez et al. In Prep

QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.

from Leder et al. 2006

OMM1009 (3) & BHMS426 (2) map to same region identified as a QTL of 20-50% for spawn timing, as well as the Clock gene.

(O’Malley et al. 2003; Leder at al. 2006)

Conclusions:

Loci identified as outliers are candidate markers ofgenomic regions under selection.

Concordant signals from multiple analyses provide the strongest evidence for selection. 6 loci =>OMM1009, OMM1120, OMM1289,

OMM1409, OMM3067, OMM5011

OMM1009 and BHMS426, which had the highest overall Fst value, are located in a genomic region identified as a QTL for spawn timing and containing the Clock gene.

In addition to being potential markers for selected gene regions, these loci will be fantastic indicators of hybridization and ancestry.

from Martinez et al. In Prep

Now What?

Now What?

Screen putative outlier loci with more above/below individuals.

Development of SNP loci.

Breeding experiments among genotypic and phenotypic classes.

Use of high-Fst loci to evaluate hbridization below the falls.

AcknowledgementsMolecular Ecology Team:Alicia Abadia, Eric Anderson, Anthony Clemento,Gregory Charrier, Carlos Garza, Libby Gilbert-Horvath,Andres Martinez, and Edith Martinez.

Scott Creek Ecology group:Morgan Bond, Chad Hanson, Sean Hayes, Bruce MacFarlane.

FundingNOAA FisheriesCA Dept. Fish & Game Fisheries Restoration Grant ProgramSociety for Advancment of Chicanos and Native Americans in Science

QUESTIONS?