Lec8a_Feb8-1020_Stephens_Hybrid

Lec8a_Feb8-1020_Stephens_Hybrid - Hybridization and...

Info iconThis preview shows page 1. Sign up to view the full content.

View Full Document Right Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: Hybridization and wildlife conservation Molly Stephens Genomic Variation Laboratory University of California, Davis http://genome-lab.ucdavis.edu Feb 8, 2010 PHR242 / ECL242 Lec 8a Acknowledgements Project Funding: California Department of Fish and Game (CDFG) US Fish and Wildlife Service Graduate Student Funding: UC Davis Dept. of Animal Science UC Davis Graduate Group in Ecology, Block Grant UC Davis John Muir Institute For the Environment Fellowship California Dept. of Fish and Game Golden West Women Flyfishers Sample Collection and Sharing: CDFG USFS Laboratory and Project Assistance Genomic Variation Laboratory John Pedroia Amy Sprowles Neil Clipperton Mandi Finger Emily Rastelo Rachel Simmons CDFG Christy McGuire Stan Stephens Threatened Trout Committee Collaborators Jan Cordes Dissertation Committee Dr. Bernie May, Advisor Dr. Peter Moyle Dr. Holly Ernest Hybridization… • What is it? • Why does it matter for conservation? Hybridization • What is it? – Defined: interbreeding of parental individuals from genetically distinct populations (regardless of the taxonomic status of populations) • intraspecific hybridization - parental individuals from different populations or subspecies • interspecific hybridization – parental individuals from different species – Compare with introgression - gene flow between populations whose individuals hybridize. Hybridization Categories (when is hybridization bad for species conservation?) Hybridization Natural Type 1 Natural hybrid taxon Anthropogenic Type 3 Natural Hybrid Zone Type 2 Natural Introgression F1s only Hybrid Swarm Type 4 Hybridization w/o introgression Type 5 Widespread Introgression Type 6 Complete Admixture Adapted from Allendorf et al., 2001 figure 1. The problems with hybrids: setting conservation guidelines. TRENDS in Ecology & Evolution Vol.16 No.11 November 2001 Conservation of threatened native trout species Human-induced hybridization through introduction of nonnative species • California golden trout - Oncorhynchus mykiss aguabonita • Little Kern golden trout - Oncorhynchus mykiss whitei • Both evolved from rainbow trout Conservation Importance • CA State Fish • CA Species of Special Concern • CAGT ESA petitioned • LKGT ESA listed Societal Valuation: Eureka! Gold in our roots California, “The Golden State” Threats Habitat Loss/alteration – Sheep and cattle grazing, horse pack trains, off-highway vehicles, backpackers Angling Pressure Competition and PredationIntroduced salmonids Hybridization- Hatchery rainbow trout Hybridization alters fish…forever • What makes a golden trout a golden trout? – ESU/DPS concepts: • What happens when golden trout interbreed with rainbow trout? – Changes in phenotype – Changes in genetic composition – Genomic extinction (aka genetic swamping): Loss of a lineage due to loss of genes and disruption of usual interactions (coadapted gene complexes) + ? = From genotype to phenotype • Hybridization “dilutes” native genotype and phenotype illustrations by Joe Tomelleri How might selection affect these two fish differently? Once you change evolutionary trajectories, can you go back? Genetic effects of hybridization: -Outbreeding depression -Hybrid vigor -loss of genetic diversity Genetic techniques can be used to address management questions for threatened populations 1. 2. Assess relationships among species and/or among populations Identify and quantify hybridization/introgression Molecular Genetics: Work Flow 1 Obtain samples 5 Check DNA quantity Extract DNA 3 2 Preserve samples 4 check DNA quality Single Nucleotide Polymorphisms (SNPs) A single nucleotide change in a DNA sequence Compare with microsats: Alleles based on number of repeats (e.g. GATA) Individual #1 Individual #2 TAATGCCC TAAAGCCC Individual# 1 2 3 136bp 132bp 128bp 120bp G6PD_103 Introduction of rainbow trout California golden trout •Historic movement of CGT •Rainbow trout stocking in headwater lakes on GTC and in lower SFK •Undocumented movements •Golden Trout Creek 2001 study – hybridization localized •South Fork Kern study – hybridization throughout pure golden rainbow Population 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 Volcano Creek (VC) Four Canyons Creek (FCC) Upper Mulkey Creek (UMC) Upper S. Fork Kern (USFK) Above Ramshaw Barrier (ARB) Below Ramshaw Barrier (BRB) Below Movie Stringer (BMS) Kern Peak Left Stringer (KPLS) Above Templeton Barrier (ATB) Below Templeton Barrier (BTB) Above Shaffer Barrier (ASB) Monache Meadows (MM) Middle Fish Creek (MFC) Upper Trout Creek (UTC) Kennedy Meadows RT (AKMRT) Rockhouse Basin (RHB) N. Fork Navarro (LNF) N. Fork American (NFAR) Hot Creek Strain (HCS) Mount Whitney Strain (MWS) Mount Shasta Strain (MSS) N 39 30 30 42 30 30 30 30 30 30 30 30 40 30 8 10 31 20 30 30 31 STRUCTURE analysis of South Fork Kern using SNPs rainbow golden • determine K, q • values comparable to microsats Little Kern golden trout Listed, Threatened, 1978 Allozyme studies Gall et al. Need to re-examine with more current genetic techniques Evaluate status of LKGT and update management plan with new genetic data Little Kern Golden Trout Genetic Status Genetic history Chemical Treatment Little Kern Golden Trout Restoration stocking Methods • Microsatellite Data Collection: – 18 Microsatellite Loci – Multiplex PCR with fluorescently labeled primers – Samples run on MJ (BioRad) Basestation 48-well polyacrylamide gels (Mandi Finger) – Scored in Cartographer software • SNP Data Collection – 10 SNP Loci – qPCR using fluorescent probes for each allele – Compiled genotypes Microsatellite data analysis -FCA Upper Coyote Rainbow Trout Little Kern golden Genetic structure of LKGT reflects restoration Deadman/ Soda Spring DDM95 UM DDM96 U USSC01 DDM97 964 USSC02 1000 995 Fish Creek UFC FC SSC95 1000 954 899 712 694 749 1000 891 UMC CLN SC UWC 494 Willow/ Sheep 997 996 1000 1000 LWC RC CLK 461 895 628 733 971 UCC SL Rifle 450 1000 526 954 NFAR MWS WMC95 BCB NFNR MSS Wet Meadow Little Kern golden trout microsatellite data – 15 loci UPGMA, unrooted phylogram, DCSE, Bootstrap values, 1000 reps WMC UWMC MWMC HCS Wild RT Hatchery RT Hybridization: Little Kern golden trout Pop 2 3 5 6 8 10 11 14 15 16 17 18 19 20 22 23 27 28 29 30 32 35 36 37 40 41 Population Deadman96 Deadman97 WetMdw95 LKBroder's Cabin MidWetMdw Silver Lake Shotgun06 Rifle06 Rifle99 Tamarack06 Upper Willow Lower Willow Sheep Lion Up.Soda Spring01 Soda Spring Pk Bdy Alpine Up. Mountaineer S. Mountaineer 06 S. Mountaineer Jacobsen 06 LK Burnt Corral 06 LK Burnt Corral Upp. Fish Upp. Coyote Low. Coyote SNP qRT 5% 1% 2% 2% 2% 2% 12% 3% 1% 3% 3% 2% 3% 3% 2% 2% 7% 6% 10% 4% 8% 30% 14% 3% 17% 2% Structure analysis of introgression – SNP data rainbow golden 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 Population Mode Shift? Deadman Creek Stock 1995 Deadman Creek Stock 1996 Deadman Creek 1997 Soda Springs Creek Stock 1995 Wet Meadow Creek Stock 1995 Clicks Creek, upper Upper North Fork Clicks Fish Creek Little Kern River above Broder’s Cabin Willow Creek, Lower (below Sheep Creek) Wet Meadow Creek, middle Rifle Creek Sheep Creek * Silver Lake Coyote Creek, Upper Fish Creek, Upper Upper Maggie Mountaineer Creek, Upper USSC 2001 Soda Spring Creek, Upper Willow Creek, Upper * Wet Meadow Creek, upper Wet Meadow Creek, upper (9) and lower (11) Hot Creek Strain North Fork Navarro River Mount Shasta Strain Mount Whitney Strain North Fork American River Genetic Diversity N 38 27 8 9 29 39 39 39 32 19 33 30 39 40 28 10 13 30 22 33 37 32 20 30 28 29 24 19 • Bottleneck genetic analysis of microsatellite data • allelic diversity reduced faster than heterozygosity (mode shift) • Evidence for genetic bottlenecks in several LKGT populations Question: • How can this information on introgression levels be applied to species conservation? 1) Influence Management Activities CA golden trout • Gill-net removal of introduced fish in lakes • Electrofishing removal of rainbows • Cessation of stocking/stocking (even triploids) • Protect GTC golden trout • Protect upper reaches of the SFK, and upper tributaries • Retain OBT populations as potential donor populations Little Kern golden trout • Evaluate whether restoration worked • chemical treatment of streams w/ hybrid fish? • Captive breeding native LKGT, KRRT? – Problems/potential consequences? – discuss… Adaptive Management –Genetic Monitoring over time – evaluate hybridization threat 2) Influence policy • Establish hybridization as a threat – Pattern of introgression • Increasing, stable, decreasing – Levels required to qualify as “threat” • Establish threatened throughout “Significant Portion of Its Range” • What to include as “protected” – Westslope cutthroat trout example Hybridization/Hatchery analogy ...
View Full Document

Ask a homework question - tutors are online