Population Genomics of Coastal California Resident and Anadromous Oncorhynchus mykiss in Scott Creek, CA Devon Pearse Molecular Ecology and Genetic Analysis Team NOAA/National Marine Fisheries Service, Southwest Fisheries Science Center Santa Cruz, CA and University 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. And of 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 ~60 miles ~12 miles Scott Creek watershed

Over the Falls? O. Mykiss introduced above Big Creek Falls c Records indicate source was within same watershed Hatchery stocking may have occurred above other barriers. Regardless of source, there must be strong selection on above falls fish not to move downstream.

Above Barrier, ~100% Below Barrier, >90%

Over the Falls? Surveyed 18 microsatellite loci in fish throughout watershed. Pairwise Fst at Big Creek Falls was low, 0.018, supporting within basin origin. Although above barrier habit is limited, bottleneck/founder effects do not appear to be significant. (Anderson & Slatkin 2007) Other above-barrier populations more divergent ( )

Above-Barrier populations Anadromous Adults from Pearse et al 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 ab X a X aab Positive selection on new mutation Gene region Genetic marker

time trait frequency linkage to specific marker allele 0 1 Recombination and mutationselection Recombination and mutation break down the association between the selected locus and specific marker alleles...

X b X c X b X 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 loci so selection is not acting on a single gene. =>genetic variation for residency likely existed prior to transfer 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.

Fst (298) =0.034

 Differentiation Fdist; Beaumont & Nichols DetSel; Vitalis et al  Variation ln(RV), ln(RH); Schlötterer 2002; Kauer et al Genome Scan: methods of outlier detection

Fdist, Beaumont & Nichols 1996

OMM5166 OMM5136 OMM1009 OMM1120 OMM5117 OMM5014 CA OMM5038 OMM5011 CA OMM3090_MHC1 OMM1756 OMM1213 OMM1000 OMM5229 OMM5060 BX BHMS426 OMM1386 OMM5195 OMM3097 OMM1231 OMM1289 OMM3024_MHC2 OMM3067 OMM1409 BX OMM1292 OMM1581 F2F2 F1F1 DetSel, Vitalis et al. 2001, 2003

Schlötterer 2002; Kauer et al. 2002

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

from Leder et al 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 of genomic 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?

 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.

Acknowledgements Molecular 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. Funding NOAA Fisheries CA Dept. Fish & Game Fisheries Restoration Grant Program Society for Advancment of Chicanos and Native Americans in Science

QUESTIONS?