6 Jon E. Hess 1, Nathan R. Campbell 1, Margaret F. Docker 2,
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1 1 Use of genotyping-by-sequencing data to develop a highthroughput and multi-functional set of genetic markers for conservation applications in Pacific lamprey Jon E. Hess 1, Nathan R. Campbell 1, Margaret F. Docker 2, 7 Cyndi Baker 3, Matt Fox 3, Aaron Jackson 4, Ralph Lampman 5, Brian McIlraith 1, Mary L. Moser 6, Dave Statler 7, William P. Young 7, Andrew J. Wildbill 3, and Shawn R. Narum 1 Hess et al. (in review) Molecular Ecology Resources
2 Adults return to freshwater, overwinter, and construct redds for spawning. Adults spend 3 years in ocean feeding parasitically Pacific lamprey Life cycle NAIAD.org Jeremy Monroe Macrothalmia: migrate to sea Ammocoetes filter feed 7 years in the stream
3 Marker Development & Marker Versatility Objectives: Develop 96 multi-functional SNP assays from a total of 4,439 quality filtered RAD-seq loci: 1) Characterizing neutral and adaptive variation 2) Parentage analysis 3) Species identification A B C Who s your daddy??? 1 2 3
4 Demonstration of Marker Versatility Apply these 96 markers to address conservation directives: 1) link genotypes with phenotypes (i.e. adult migratory traits) 2) validate reproductive success of a translocation 3) identify species of early life stages of lamprey
5 Pacific lamprey study area 1096 Individuals 35 collections
6 Selection of a 96 panel of SNPs N = 4,439 SNPs Hess et al. (2013) Population genomics of Pacific lamprey. Molecular Ecology, 22, Quality-filtered SNPs: 4,439 Putatively neutral SNPs: 4,068 Adaptive SNPs: 162
7 Pacific lamprey: lack of natal homing No place like home No place like home No place like home Hmmm doesn t smell too bad here Yun SS, et al. (2011) Canadian Journal of Fisheries and Aquatic Sciences, 68,
8 Selection of a 96 panel of SNPs N = 4,439 SNPs N = 94 SNPs
9 Population structure (neutral) 85 putatively neutral SNPs Nei s (1972) genetic distance 1000 bootstraps
10 Dwarf Pacific lamprey Beamish, RJ (1980) Canadian Journal of Fisheries and Aquatic Sciences, 37: Kostow, K. (2002) Oregon Department of Fish and Wildlife.
11 Population structure (adaptive) 9 adaptive SNPs Nei s (1972) genetic distance 1000 bootstraps
12 Characterize adaptive variation Collections Adaptive SNP loci Etr_1806 Etr_5317
13 Characterize adaptive variation application: Link genotype with phenotype- adult length Adult body length (mm) # of big SNP Etr_1806
14 Parentage analysis g 4.4 g g Rearing study: Known parents and their offspring
15 Parentage analysis 01? g 4.4 g g Rearing study: Known parents and their offspring
16 Parentage analysis application part 1: validate reproductive success of a translocation Newsome Cr. Translocation: (~50 adults per year) Washington Parents genotyped adults adults adults Juvenile collections larvae (Electrofishing) larvae (Screw trap) Oregon Idaho
17 Parentage analysis application part 1: validate reproductive success of a translocation 25 Length distribution of Newsome Cr. lamprey from screw trap in 2012 Number of lamprey Total Length
18 Parentage analysis application part 1: validate reproductive success of a translocation 25 Length distribution of Newsome Cr. lamprey from screw trap in 2012 Number of lamprey Total 5-Year-old Length N=119 larvae genotyped N=118 Assigned to 2007 parents (5-year-olds)
19 12 08 * mm (87-111) 88mm (80-95) 98mm (90-105) 106mm (77-140) 07 98mm (85-109) mm ( ) 48 * 05 97mm (74-125) 107mm (98-116) 87mm mm ( ) mm (82-123) 97mm (96-98) 105mm 104mm ( ) 2012 Screw trap: 5-year-old 2009 Electrofishing: 2-year-old *radio-tagged * mm 90mm 27 of 50 (54%) translocated adults confirmed as spawners!
20 Species identification Entosphenus tridentatus N=1121, 100% Lampetra Sp. N=92, 100% Raw data from SNP diagnostic marker: LampSD_478
21 Species identification application: Document a recent natural reintroduction of Pacific lamprey from 0-yr larvae Hood R. Natural Reintroduction: 2012 (~60 0-year ammocoetes) Washington Oregon Above and below Powerdale Dam site (dam removed in 2010) 59 out of 60 identified as Pacific lamprey??
22 NAIAD.org Concluding remarks 1) Marker associated with adult length can differentiate Pacific lamprey from interior Columbia R. versus lower Columbia R. 2) Pacific lamprey translocation success verified! AND - multiple mating + outmigration initiated at age 5. 3) Natural reintroduction possible with improvement to habitat. 4) Large scale parentage analysis will be used to track translocations, and markers will be used to estimate effective # spawners. Jeremy Monroe
23 Acknowledgements Nick Hoffman; Lori Maxwell; Travis Jacobsen: laboratory experts Ben Hecht; Mike Miller: RAD-seq gurus Pacific lamprey collections: John Crandall, Elmer Crow, Joyce Faler, Leo Grandmontagne, Michael Hayes, Don Ignace, Patrick Luke, R.D. Nelle, Matt Powell, Bob Rose, Christian Smith, Greg Tamblyn, and Eric Taylor. BPA: Funding NAIAD.org Jeremy Monroe
24 Questions? NAIAD.org Jeremy Monroe
25 Parentage analysis application part 2: estimate effective number of spawners Juvenile lamprey impinged on turbine intake screen
26 Parentage analysis application part 2: estimate effective number of spawners Juvenile N=14 Juvenile lamprey impinged on turbine intake screen
27 Parentage analysis application part 2: estimate effective number of spawners Spawner N=8 Juvenile N=14 Juvenile lamprey impinged on turbine intake screen Wang J (2009) A new method for estimating population sizes from a single sample of multilocus genotypes. Molecular Ecology, 18,
28 Translocations begin in Snake River 1200 Lower Granite Dam- Pacific lamprey abundance Number of individuals TotalEstReturn Predicted Ne Translocation Year
29 Translocations begin in Snake River 1200 Lower Granite Dam- Pacific lamprey abundance 1000 Number of individuals TotalEstReturn Ne Predicted Ne Translocation 2012 Year
30 LampSD_478 Species diagnostic markers LampSD_802 Entosphenus tridentatus N=958, 100% Lampetra richardsoni N=103, 96% Lampetra Sp. N=132, 100% Lampetra pacifica N=30, 100%
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