Population genetic structure and ancestry of steelhead/rainbow trout

15 Pages·2016·1.11 MB·English

ConservGenet
DOI10.1007/s10592-016-0814-9
RESEARCH ARTICLE
Population genetic structure and ancestry of steelhead/rainbow
trout (Oncorhynchus mykiss) at the extreme southern edge of their
range in North America
Alicia Abad´ıa-Cardoso1,2,5 • Devon E. Pearse1,2 • Sandra Jacobson3,6 •
Jack Marshall3 • Dale Dalrymple3 • Frank Kawasaki3 •
Gorgonio Ruiz-Campos4 • John Carlos Garza1,2
Received:31July2015/Accepted:21January2016
(cid:2)SpringerScience+BusinessMediaDordrecht(outsidetheUSA)2016
Abstract Steelhead (Oncorhynchus mykiss) populations USA and Baja California, Mexico. In the northern part of
have declined dramatically in many parts of their range in thisregion,nearlyallpopulationsappearedtobeprimarily
North America, most critically in Southern California, descendants of native coastal steelhead. However, in the
where these anadromous trout are now classified as ‘En- southern, more urbanized part of this region, the majority
dangered’undertheUnitedStatesEndangeredSpeciesAct. of the sampled populations were derived primarily from
Thewidespreadintroductionofhatcheryrainbowtrout,the hatchery trout, indicating either complete replacement of
domesticated freshwater resident form of the species O. native fish or a strong signal of introgression overlaying
mykiss, is one factor threatening the long-term persistence native ancestry. Nevertheless, these genetically intro-
ofnativesteelheadandothertroutpopulations.Toidentify gressed populations represent potentially critical genetic
wherenativefishofcoastalsteelheadlineageremained,we resources for the continued persistence of viable networks
performed a population genetic analysis of microsatellite ofO.mykisspopulations,giventhelimitednativeancestry
and SNP genotypes from O. mykiss populations at the uncovered in this region and the importance of genetic
extremesouthernendoftheirrangeinSouthernCalifornia, variation in adaptation. This study elucidates the geo-
graphic distribution of native trout populations in this
region, and serves as a baseline for evaluating the impacts
ThispapercarriesforwardthememoryofthelateSkipPricewho of hatchery trout on native O. mykiss populations and the
participatedinthissamplingeffortandwasanactivememberand success of steelhead conservation and recovery efforts.
leaderinGSFandTU-Chapter920.Heishonoredforhismany
contributionstoconservationeffortsthroughouttheregionin
Keywords Oncorhynchus mykiss (cid:2) Rainbow trout (cid:2)
fieldworkandeducationalprograms.
Steelhead (cid:2) SNPs (cid:2) Microsatellites (cid:2) Introgression
& JohnCarlosGarza
[email protected]
Introduction
1 FisheriesEcologyDivision,SouthwestFisheriesScience
Center,NationalMarineFisheriesService,110ShafferRoad,
SantaCruz,CA95060,USA ThenativedistributionofthespeciesOncorhynchusmykiss,
2 InstituteofMarineSciences,UniversityofCalifornia, commonly known as rainbow trout, redband trout, or steel-
SantaCruz,CA,USA head,extendsfromtheKamchatkaPeninsulainnortheastern
3 TroutUnlimited–Chapter920andaffiliatedGoldenState Eurasia, across to North America, and south into northern
Flycasters,SanDiego,CA,USA BajaCalifornia,Mexico.Whilebothtroutandsteelheadlife-
4 FacultaddeCiencias,UniversidadAuto´nomadeBaja history forms reproduce in fresh water, steelhead are
California,Ensenada,BajaCalifornia,Mexico anadromous, while resident trout live entirely in freshwater
5 PresentAddress:FacultaddeCienciasMarinas,Universidad (Busby et al. 1996). Steelhead numbers have declined dra-
Auto´nomadeBajaCalifornia,Ensenada,BajaCalifornia, matically in the past hundred years, especially at the
Mexico southern end of the species’ distribution and in heavily
6 PresentAddress:CaliforniaTrout,SanDiego,CA,USA urbanized areas such as Southern California (Swift et al.
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1993;Behnke2002).Amajorcontributortothisdeclinehas and maladaptation (Araki et al. 2007). Stocked trout may
been the creation of barriers to migration by dam con- also compete with or predate upon native fish, potentially
struction and large-scale water development. This has iso- leading to complete replacement of the native population.
lated manyO.mykisspopulationsintheremote headwaters Hence, genetic characterization of O. mykiss populations
of their native basins without access to the ocean, creating where stocking has occurred is needed to determine the
fragmented populations of native coastal steelhead ancestry extent of introgression by hatchery rainbow trout and
that are forced to adopt a completely resident life history identify extant natural-origin populations. Clemento et al.
(Clemento et al. 2009). However, despite their native (2009)undertooksuchanevaluationinthenorthernpartof
ancestry,allpopulationsabovecompletenaturalorartificial the Southern California DPS, but ancestry of trout popu-
barriers to anadromy are excluded from the steelhead Dis- lations in the remainder of Southern California and Baja
tinct Population Segments (DPSs) that are protected under California has not been comprehensively examined.
the U.S. Endangered Species Act (ESA; NOAA 2006). Yet Berg and Gall (1988) surveyed O. mykiss populations
below-barrier spawning and rearing habitat accessible to throughoutCalifornia,includingpopulationsintheSouthern
anadromous steelhead has been extremely degraded, par- CaliforniaDPS,andfoundevidenceofhighgeneticvariability
ticularly in Southern California, leading to intensive efforts at24allozymeloci.Asubsequentstatusreview(Busbyetal.
by federal and state agencies to restore habitat and protect 1996)alsopresentedevidenceforhighgeneticvariabilitywith
them from extinction (NMFS 2012). Accordingly, the allozymes in Southern California O. mykiss populations.
Southern California Coast Steelhead DPS, which extends Similar analyses with mitochondrial DNA control region
from just north of Point Conception southward to the U.S.- sequencesandnuclearmicrosatellitegenotypes(Nielsenetal.
Mexico border, is the only steelhead DPS listed as ‘endan- 1994) again found higher variability than expected in these
gered’, at the highest risk of extinction, under the U.S. smallpopulations.Furthermoleculargeneticstudiestodefine
Endangered Species Act (ESA; Good et al. 2005; NOAA populationstructureofO.mykissintheregionhaveidentified
2006).WithinthisDPS,populationsarefurthermanagedas significantdifferentiationthroughoutSouthernCaliforniaand
fiveBiogeographicPopulationGroups(BPGs;NMFS2012). Mexico (Nielsen 1996; Nielsen et al. 1997b; Nielsen et al.
Similarly, O. mykiss inhabiting the R´ıo Santo Domingo 1998). However, none of this previous work attempted to
basin in the Sierra de San Pedro Ma´rtir in Baja California distinguish native and hatchery-derived populations, and
areconsideredofSpecialConcernandprotectedbyMexican therefore could not determine whether the higher genetic
laws (SEMARNAT 2010; Ruiz-Campos et al. 2014). diversityintheregionwasduetoanalysisofacombinationof
Although the species O. mykiss is native to the North nativeand hatchery trout comingfromdiverseevolutionary
Pacific and its tributaries, it has been introduced to every lineages.
continent of the world, except Antarctica, due to intense Inrecentyears,afinerresolutionviewofO.mykisspop-
demand for trout angling opportunities. This stocking of ulation genetic structure in California has been developed
hatchery-produced rainbow trout has also occurred within throughextensiveanalysisofbothmicrosatelliteandsingle
the species native range, primarily in reservoirs above nucleotide polymorphism (SNP) data (Abad´ıa-Cardoso
dams and in other locations where it was believed that 2014;AguilarandGarza2006;Clementoetal.2009;Garza
anthropogenic disturbance would otherwise preclude trout et al. 2014; Pearse et al. 2007; Pearse and Garza 2015).
angling (Clemento et al. 2009). This introduction of Notably,intheSouthernCaliforniaandSouthCentralCal-
hatchery rainbow trout of diverse, but uniformly alien, iforniaCoaststeelheadDPSs,populationsofO.mykisshave
ancestry into most Southern California streams and reser- been found to have greater genetic similarity within a
voirs presents an additional threat to the survival of native watershed than between proximate watersheds, even when
O.mykisspopulations.Mosthatcheryrainbowtroutstrains separated by physical barriers (Clemento et al. 2009). In
used in California were domesticated from populations in addition,thesignalofhighdiversityinsouthernpopulations
the inland Sacramento River (Central Valley) basin (Bu- foundbypreviousworkhasnotbeenfoundwhenonlynative
sackandGall1980),aregioninwhichthephylogenetically ancestry populations are analyzed. Also of relevance is a
distinct steelhead are recognized as a separate DPS (Niel- study of museum specimens from steelhead populations
sen 1996, Nielsen et al. 1997b; NOAA 2006; Pearse and sampledin1897and1909(Pearseetal.2011)thatfounda
Garza 2015). From a conservation perspective, stocking much stronger association between genetic distance and
hatchery trout can negatively impact native O. mykiss geographicdistanceseparatingpopulationshistoricallythan
populations, because most hatchery rainbow trout strains inthecontemporarypopulations,presumablyreduceddueto
are genetically depauperate and have experienced strong anthropogenicinfluencessuchasconstructionofmigration
domestication selection (Busack and Gall 1980; Clemento barriers,degradationofhabitatandrainbowtroutstocking.
et al. 2009; Pearse and Garza 2015). Thus, interbreeding Here, we conduct a large-scale population genetic
with natural-origin populations can cause reduced fitness analysis of O. mykiss at the extreme southern end of their
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range,extendingsouthwardfromthegeographicfocusarea Steelhead DPS (for details see Jacobson et al. 2014). A
of Clemento et al. (2009). We used statistical analysis of similar capture effort using hook and line was undertaken
data from more than 100 microsatellite and SNP loci to in 1994 in the R´ıo Santo Domingo in the Sierra de San
provide insight into the origins and ancestry of O. mykiss Pedro Ma´rtir mountain range in Baja California, Mexico,
populations in the remaining aquatic habitatin this region. the southernmost known population of O. mykiss in its
In addition, we evaluated data from two SNP loci located nativerange.U.S.captureeffortsoccurredin30creeksand
in a genomic region of O. mykiss chromosome Omy5 that rivers spanning 10 watersheds extending south from the
has been shown to be associated with the anadromous and Santa Maria River to the Sweetwater River watershed
resident life-history strategies in the species (Pearse et al. immediately north of the U.S./Mexico international
2014). These loci are in strong linkage disequilibrium in boundary (Fig. 1; Table 1). Approximately 600 fish total
many coastal California O. mykiss populations, and show werecapturedandsmallcaudalfinclipsexcisedforgenetic
parallel changes in allele frequency in coastal O. mykiss analysis before the fish were released in the location of
populations isolated above natural and artificial barriers capture. Tissue samples were also obtained from collec-
(Pearse et al. 2014). Our analysis provides greater insight tions more than a decade before the current effort in three
into the adaptive landscape inhabited by Southern Cali- basins:SespeCreek(N = 40),PaumaCreek(N = 47),and
forniaO.mykissandwillbecriticalforinformingrecovery Sweetwater River (N = 26). These basins were resampled
planning efforts for Southern California and Baja Califor- as part of the current study, providing temporal compar-
nia O. mykiss populations. isons of genetic variation in these locations (Tables 1, 2).
DNA extraction and genotyping
Materials and Methods
Genomic DNA was extracted from dried fin clips using
Tissue sample collection DNeasy 96 Tissue Kits (Qiagen Inc.) with a protocol
modifiedforuseonaBioRobot3000workstation(Qiagen).
From 2009 to 2013, fish were captured by fly-fishing and DNA was eluted in 200 lL Tris buffer for subsequent
netting in basins for which the waters with anadromous analyses. A total of 19 microsatellite loci used to study O.
access are considered habitat of the Southern California mykissthroughout California (Clementoet al. 2009;Garza
Fig.1 Geographiclocationof
thesteelheadDistinct
PopulationSegmentsin
California.Theinsetshowsthe
SouthernCaliforniaSteelhead
DPSandthemajorwatersheds
analyzedinthisstudy.Stars
representmajorcities:from
northtosouth—SantaBarbara,
LosAngeles,SanDiego,
Tijuana,andEnsenada.KMP
KlamathMountainProvince,
NCANorthernCaliforniaCoast,
CVCaliforniaCentralValley,
CCCCentralCaliforniaCoast,
SCCSouth-CentralCalifornia
Coast,SCASouthernCalifornia
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a
aba es zan
PopulationID aKlamath-Blue aMattole-BearaGualala-Fuller aMcCloud-ClaiborneaSacramento-BattleaSacramento-Deer Sacramento-Feather-YuaAmericanNF aLosTrancosaWaddell aCarmelbSalinas-TassajaracBigSurcWillowaChorro-PenningtoncSnSimeon StaMaria-Cuyama-Rey StaMaria-Sisquoc-MandStaMaria-Sisquoc Montecito StaYnez-QuiotabStaYnez-StaCruzbStaYnez-HiltonbStaYnez-JuncalbStaYnez-Salsipuedes Ventura-SnAntonioeVentura-MatilijabVentura-Matilija-BearbStaClara-StaPaula
6 4 6 1 3 6 9 3 3 7 9 1 9 5 0 5 6 3 9 0 4 6 2 1 2 7 4 7 7
s 0 2 2 2 4 6 1 1 9 6 7 8 8 5 3 6 0 7 8 4 9 6 8 0 9 0 8 6 6
e 9 0 3 1 1 9 7 6 1 2 6 6 7 4 7 0 3 8 2 6 0 7 9 5 3 3 3 2 0
at 3. 4. 3. 2. 2. 1. 0. 0. 2. 2. 1. 0. 1. 1. 0. 1. 9. 9. 0. 9. 0. 9. 9. 9. 0. 9. 9. 9. 9.
n 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 2 1 2 1 1 1 2 1 1 1 1
ordi -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
co 42, 33, 98, 57, 84, 00, 70, 03, 07, 16, 06, 86, 45, 94, 42, 18, 68, 35, 77, 27, 67, 33, 80, 17, 22, 81, 06, 15, 47,
S 4 0 6 0 3 0 5 2 4 1 4 3 2 8 3 6 6 7 8 4 5 6 5 5 6 3 5 5 4
GP 41. 40. 38. 41. 40. 40. 39. 39. 37. 37. 36. 35. 36. 35. 35. 35. 34. 34. 34. 34. 34. 34. 34. 34. 34. 34. 34. 34. 34.
Site BlueCreek SFBearCreek FullerCreek ClaiborneCreek BattleCreek DeerCreek YubaRiver NFAmericanRiver LosTrancosCreek WaddellCreek CarmelRiver TassajaraCreek BigSurRiver WillowCreek PenningtonCreek SanSimeonCreek ReyesCreek ManzanaCreek SisquocRiver MontecitoCreek QuiotaCreek SantaCruzCreek HiltonCreek NFJuncalCreek SalsipuedesCreek SanAntonioCreek NFMatilijaCreek BearCreek SantaPaulaCreek
k
Tributary BearCreek SFGualalaRiver McCloudRiver FeatherRiver AmericanRiver ArroyoSecoCree CuyamaRiver SisquocRiver QuiotaCreek MatilijaCreek NFMatilijaCreek
k
e
e
Watershed KlamathRiver MattoleRiver GualalaRiver SacramentoRiver SacramentoRiver SacramentoRiver SacramentoRiver SacramentoRiver SanFrancisquitoCr WaddellCreek CarmelRiver SalinasRiver BigSurRiver WillowCreek ChorroCreek SanSimeonCreek SantaMariaRiver SantaMariaRiver SantaMariaRiver MontecitoCreek SantaYnezRiver SantaYnezRiver SantaYnezRiver SantaYnezRiver SantaYnezRiver VenturaRiver VenturaRiver VenturaRiver SantaClaraRiver
o o o o o
st p p p p p
Table1Samplelocations DPSCounty KlamathMountainsProvince DelNorte NorthernCalifornia Humboldt Sonoma CentralValley SanFrancisco SanFrancisco SanFrancisco SanFrancisco SanFrancisco CentralCaliforniaCoast SanMateo SantaCruz South-CentralCaliforniaCoa Monterey Monterey Monterey Monterey SanLuisObis SanLuisObis SouthernCalifornia SanLuisObis SanLuisObis SanLuisObis SantaBarbara SantaBarbara SantaBarbara SantaBarbara SantaBarbara SantaBarbara Ventura Ventura Ventura Ventura
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n
o
y
n
a
PopulationID StaClara-Piru StaClara-Piru-BuckdStaClara-Sespe StaClara-Sespe-PiedraBlancaeStaClara-Sespe-LionCanyon LosAngeles-Hondo-StaAnita NFSnGabriel WFSnGabriel-Bear WFSnGabriel-Devil’sCanyon WFSnGabriel EFSnGabriel-Cattle EFSnGabriel-FishFork EFSnGabriel-SFIronFork EFSnGabriel-IronFork EFSnGabriel SnGabriel-FishCanyon StaAna-Chino-SnAntonio StaAna-Bear StaAna-Temescal-ColdwaterC StaAna-Temescal-FullerMill StaAna-Temescal-SnJacinto09 StaAna-Temescal-SnJacinto12 SnJuan-ArroyoTrabuco SnLuisRey-Doane PaumaR(recent2009–2011) WFSnLuisRey SnDiego-BouldereSweetwater(old1997) Sweetwater(recent2010/2013) dO.m.nelsoni bFH-ColemanbFH-VirginiafFH-Whitney
d
7) 9
6 6 5 7 5 8 0 4 3 9 1 7 5 2 5 9 5 9 5 9 7 9 6 3 9 5 1 7 0 7 5
coordinates 06,-118.94 62,-118.82 95,-118.94 79,-119.16 80,-118.95 01,-118.01 91,-117.84 52,-117.88 63,-117.97 46,-118.04 30,-117.75 08,-117.72 11,-117.76 98,-117.75 84,-117.74 77,-117.92 38,-117.65 54,-117.01 54,-117.49 93,-116.74 93,-116.74 93,-116.74 74,-117.52 49,-116.91 maO(old19 47,-116.92 28,-116.80 72,-116.63 13,-116.57 080,-116.5 20,-115.62
GPS 34.7 34.6 34.4 34.5 34.3 34.2 34.2 34.2 34.2 34.2 34.2 34.3 34.3 34.2 34.2 34.1 34.2 34.1 33.7 33.7 33.7 33.7 33.6 33.3 Pau 33.3 33.3 32.9 32.9 32.9 30.8 N/A N/A N/A
3
9 2 1
0 1 0
k 0 0 1 2
Site PiruCreek BuckCreek SespeCreek1997 PiedraBlancaCreek LionCanyonCreek SantaAnitaCreek NFSanGabrielRiver BearCreek Devil’sCanyonCreek WFSanGabrielRiver CattleCreek FishFork IronFork EFIronFork EFSanGabrielRiver FishCanyonCreek SanAntonioCreek BearCreek ColdwaterCanyonCree FullerMillCreek NFSanJacintoCreek2 NFSanJacintoCreek2 ArroyoTrabucoCreek DoaneCreek 33.331,-116.974 PaumaCreek2009-1 WFSanLuisRey BoulderCreek SweetwaterRiver1997 SweetwaterRiver2010/ SanAntonio/LaGrulla FillmoreHatchery FillmoreHatchery FillmoreHatchery
River River River River River River 97
Tributary PiruCreek SespeCreek SespeCreek RioHondo WFSanGabriel WFSanGabriel EFSanGabriel EFSanGabriel EFSanGabriel EFSanGabriel ChinoCreek TemescalWash TemescalWash TemescalWash TemescalWash PaumaCreek19 ´RıoSanAntonio
Watershed SantaClaraRiver SantaClaraRiver SantaClaraRiver SantaClaraRiver SantaClaraRiver LosAngelesRiver SanGabrielRiver SanGabrielRiver SanGabrielRiver SanGabrielRiver SanGabrielRiver SanGabrielRiver SanGabrielRiver SanGabrielRiver SanGabrielRiver SanGabrielRiver SantaAnaRiver SantaAnaRiver SantaAnaRiver SantaAnaRiver SantaAnaRiver SantaAnaRiver SanJuanCreek SanLuisReyRiver SanLuisReyRiver SanLuisReyRiver SanDiegoRiver SweetwaterRiver SweetwaterRiver ´RıoSantoDomingo
er
v
Ri a
y ni
continued County Ventura Ventura Ventura Ventura Ventura LosAngeles LosAngeles LosAngeles LosAngeles LosAngeles LosAngeles LosAngeles LosAngeles LosAngeles LosAngeles LosAngeles Orange Orange Orange Orange Orange Orange Orange SanDiego SanLuisRe SanDiego SanDiego SanDiego SanDiego SanDiego nelsoni BajaCalifor strains
1 kiss ery
e y h
Tabl DPS O.m Hatc
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PopulationID bFH-WyomingfARH-EagledARH-ShastagHC-Kamloops signationistheEF=EastFork, ccep3hotr7oan3adid0lnu.iXtci2rLtoes0na1Dscw4tN)iaeosrAwnereAee(rPpelneoCacgrRltteyre)onzdpoeahtrbmyoy(prpAeelCdsipfiepldecolmainetadienaondlnBtloisdwoaeesamttysespcatlptelee.emsdr.(fs2o,oP0rnoIm0nl9ycea)m.dn.)ePwwArCaiiBsttRhheI
dek,
S)For the use of fluorescently labeled primers. Genotypes were
P
Dh called using GeneMapper (Applied Biosystems) and all
(ut
ntSo allele calls checked for consistency with previously geno-
meF= typed reference samples. To reduce error rate and control
gS
e
es Sk, forbiasincallingalleles,allgenotypeswerederivedtwice
oordinat pulationorthFor ibnedtwepeeenndefinrstltyanadndsetcwoondpecoaplllse.resolved any discrepancies
Sc A A A A Po=N A total of 93 SNP loci were also genotyped on all
GP N/ N/ N/ N/ nctNF samplesevaluatedinthecurrentstudy.TheseSNPmarkers
Distibers include loci from Aguilar and Garza (2008), Campbell
arly,mem getenaol.ty(p2e0d09w),itahnd50A-nbuacdl´ıeaa-sCearcdhoesmoisettryal.(T(2a0q1M1a)naTnMd,wLeirfee
Similered Technologies, Inc.) on an EP1 system (Fluidigm Corpo-
d
y y d.si ration).SeeAbad´ıa-Cardosoet al. (2013) for details of the
Site FillmoreHatchery AmericanRiverHatcher AmericanRiverHatcher HotCreekHatchery ocationwithinthewatershesamplinglocationarecon 4) 2009) 2009) etal.(2015) shaptoyolartlphemtTc-eesaehsroimxeaOfrpponyC.rlraoiralmfivatylhciiiysfndeaekobetsirisosona(sawniTmapabateorbsrnotpoldmeeuuaestdlgilachse1etrtrenioroaaaospnnditanhysdt,syepD2lli(iloPnn)Ni.gtgSceels=ucoaodg(n3Nnirdna3dgp1=iSth)irN,oi1ecwnPp1ser5c.emro2esn)eatinrneaktxncaeltdtru,isvdsgeefeesrdvnoeoominn-f
ary ecificcollectinglfromthespecific Garzaetal.(201 Clementoetal.( Clementoetal.( ´Abadıa-Cardoso POdeobvpsieuartlviaoetnidosn(fHrgoeOmn)eHtainacrdddyiev–xeWprseeicittnyebdaenrg(dH(sEHt)rWuhc)ettueeqrrueoizlyibgroiusimtywaenrde
Tribut theocean,notthespdlessofwhetherfish microsatellitesfrom oetal.(2015) microsatellitesfrom microsatellitesfrom microsatellitesfrom maeq(nBgsueeteseeinsmlnktoce(ahfydAtieprRlidoe)nelvtyucHeamsalPilslnc.o-ugwRr1pl9aAaGhs9tiReE6cedE–NsS2tuEi(N0msKP0iPnaOa4stgl)ePi,(ndPtaoh(n)wRwedaoistrtkuhmais0riset.2che9f0rate5o0c2ss5taaio0)notf0.ednt8wll)0im.at.er9eTe9tahhGleoaleEldpllNeiecilrmEecrTipefcrnlIheeXt----
Table1continued DPSCountyWatershed Countyindicateslocationwhereagivenwatershedentersoneappliedwherethewatershedenterstheocean,regarWF=WestFork N/Anotapplicablea´SNPgenotypesfromAbadıa-Cardosoetal.(2015)andbMicrosatellitegenotypesfromClementoetal.(2009)cMicrosatellitegenotypesfromGarzaetal.(2014)d´SNPandmicrosatellitegenotypesfromAbadıa-Cardose´SNPgenotypesfromAbadıa-Cardosoetal.(2015)andf´SNPgenotypesfromAbadıa-Cardosoetal.(2011)andg´SNPgenotypesfromAbadıa-Cardosoetal.(2011)and pCitrlsupbhlmaithoineanesoayenaefcemerscppreerTtatiadeellhauohroptoehdtseigeltoidlvoteahnoteerdroetnenycssesoisclos.oeo)p.sofoe,oinfnFefnrVmswtKfott5swivtiorraia0,ehtbeansiaiblr,neritsoneut0rean,oetedenvdep0inpeturigspahso0ybdvrtiS.aleeenpriuttTTrdoesghsuepmafeietufReheolntrendaianoieprdpUnnottKilmedeainisgurroCtvedtegiemt=nlicamsTedpi-dbwnnubbraoUudyunfdl2feafipatoalostfiRsr–sttlhutrrehi1l7aoEmil-wfiiode5anlaefofsw0taetawcdc(iahictr,coPloelaian0.euueuhonrnrtnd0rTssaeisnrect0tKtosehbsceeeaeoftiherarsgirMntsirvtsanatubnedwartnaBrvcon(oyagledleyeyeturoauru.imeskzetytgienoertynoendeie,.ftefp,gdtvesgthwtapaeahiraahreauntslcolooineae.nltdshpdudhndigc2aunpaOcvaeeoi0alnhgsennimoaan.0sasidwntgsbsust0lipmMrdttryoeuai)oiylatvtsnolryrhpuouiinwfieksiayzsonhesc-rineevoeaniusaiatidnddeecssssrltlt
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Table2 Summarystatisticsofallpopulationsanalyzed
PopulationID N H H Ar P(0.95) P(0.99) r2
O E
Klamath-Blue 32 0.38 0.40 5.32 0.90 0.97 0.930
Mattole-Bear 31 0.41 0.40 4.57 0.88 0.97 0.999
Gualala-Fuller 61 0.45 0.44 4.78 0.98 0.99 0.999
McCloud-Claiborne 33 0.38 0.38 4.29 0.79 0.92 –
Sacramento-Battle 92 0.41 0.42 5.04 0.97 1.00 0.240
Sacramento-Deer 43 0.44 0.43 5.26 0.98 1.00 0.369
Sacramento-Feather-Yuba 27 0.44 0.44 4.78 0.94 1.00 0.996
AmericanNF 48 0.39 0.39 4.36 0.91 0.98 0.672
LosTrancos 24 0.41 0.40 3.98 0.89 0.93 0.999
Waddell 31 0.41 0.41 3.96 0.95 0.96 0.997
Carmel 32 0.43 0.43 4.59 0.95 0.98 0.675
Salinas-Tassajara 46 0.42 0.42 4.16 0.95 0.99 0.877
BigSur 31 0.43 0.43 4.77 0.98 0.99 0.999
Willow 27 0.39 0.41 4.80 0.94 1.00 1.000
Chorro-Pennington 30 0.40 0.37 3.67 0.86 0.90 0.999
SnSimeon 31 0.44 0.42 4.58 0.95 0.98 0.942
StaMaria-Cuyama-Reyes 47 0.41 0.41 4.08 0.94 0.99 1.000
StaMaria-Sisquoc-Manzana 47 0.36 0.34 3.30 0.79 0.88 0.585
StaMaria-Sisquoc 47 0.37 0.37 3.76 0.91 0.96 0.790
Montecito 5 0.37 0.32 – – – –
StaYnez-Quiota 35 0.40 0.39 3.77 0.91 0.98 0.887
StaYnez-StaCruz 35 0.38 0.38 4.08 0.88 0.93 0.999
StaYnez-Hilton 42 0.40 0.40 3.93 0.90 0.98 0.379
StaYnez-Juncal 81 0.38 0.37 3.53 0.81 0.95 0.990
StaYnez-Salsipuedes 47 0.36 0.38 3.79 0.90 0.95 0.999
Ventura-SnAntonio 5 0.37 0.37 – – – –
Ventura-Matilija 46 0.38 0.37 3.70 0.86 0.96 0.732
Ventura-Matilija-Bear 14 0.37 0.35 3.47 0.79 0.86 0.882
StaClara-StaPaula 45 0.41 0.42 4.34 0.93 0.97 1.000
StaClara-Piru 26 0.34 0.35 3.82 0.83 0.94 0.999
StaClara-Piru-Buck 16 0.36 0.37 3.61 0.88 0.93 0.997
StaClara-Sespe 39 0.36 0.37 4.13 0.90 0.98 0.999
StaClara-Sespe-PiedraBlanca 10 0.32 0.33 3.35 0.89 0.89 0.999
StaClara-Sespe-LionCanyon 47 0.36 0.36 3.95 0.88 0.98 0.909
LosAngeles-Hondo-StaAnita 23 0.25 0.33 2.83 0.79 0.90 0.890
NFSnGabriel 16 0.37 0.39 4.18 0.91 0.97 0.802
WFSnGabriel-Bear 22 0.38 0.38 4.06 0.89 0.98 0.832
WFSnGabriel-Devil’sCanyon 13 0.33 0.31 2.65 0.69 0.71 –
WFSnGabriel 22 0.32 0.34 3.32 0.80 0.90 1.000
EFSnGabriel-Cattle 16 0.38 0.40 4.19 0.93 0.96 0.999
EFSnGabriel-FishFork 11 0.40 0.40 3.89 0.82 0.88 0.998
EFSnGabriel-SFIronFork 15 0.37 0.35 2.91 0.80 0.82 0.000
EFSnGabriel-IronFork 28 0.37 0.37 3.52 0.91 0.97 0.350
EFSnGabriel 18 0.38 0.39 4.13 0.90 0.98 0.724
SnGabriel-FishCanyon 5 0.36 0.35 – – – 0.999
StaAna-Chino-SnAntonio 36 0.39 0.40 3.84 0.89 0.93 0.052
StaAna-Bear 22 0.38 0.40 4.57 0.83 0.94 0.645
StaAna-Temescal-ColdwaterCanyon 19 0.13 0.12 1.76 0.30 0.32 0.485
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ConservGenet
Table2 continued
PopulationID N H H Ar P(0.95) P(0.99) r2
O E
StaAna-Temescal-FullerMill 16 0.34 0.27 2.50 0.57 0.71 –
StaAna-Temescal-SnJacinto09 12 0.36 0.35 3.01 0.78 0.84 0.996
StaAna-Temescal-SnJacinto12 24 0.31 0.34 3.04 0.85 0.90 0.428
SnJuan-ArroyoTrabuco 14 0.39 0.41 4.12 0.94 0.98 0.532
SnLuisRey-Doane 3 0.28 0.27 – – – 0.999
PaumaO(old1997) 39 0.38 0.38 3.92 0.87 0.97 0.813
PaumaR(recent2009–2011) 26 0.31 0.32 2.93 0.78 0.82 0.828
WFSnLuisRey 12 0.26 0.26 2.53 0.59 0.66 0.999
SnDiego-Boulder 11 0.37 0.34 3.09 0.80 0.83 0.353
Sweetwater(old1997) 26 0.36 0.37 3.58 0.86 0.94 0.229
Sweetwater(recent2010/2013) 37 0.38 0.37 3.69 0.83 0.92 0.409
O.m.nelsoni 39 0.16 0.19 2.27 0.43 0.55 0.999
FH-Coleman 47 0.38 0.38 4.04 0.91 0.98 0.220
FH-Virginia 48 0.31 0.33 3.82 0.79 0.89 0.070
FH-Whitney 48 0.37 0.37 3.64 0.83 0.94 0.563
FH-Wyoming 47 0.39 0.39 3.96 0.89 0.94 0.100
ARH-Eagle 47 0.30 0.30 3.38 0.76 0.94 0.997
ARH-Shasta 47 0.35 0.36 3.32 0.81 0.92 0.121
HC-Kamloops 47 0.29 0.29 3.84 0.72 0.79 –
N number of samples genotyped for the genetic analysis, H Observed heterozygosity, H Expected heterozygosity, Ar Microsatellite allelic
O E
richness,PPercentageofpolymorphicSNPs,r2linkagedisequilibriumbetweenthetwoOmy5loci.–indicatesthatr2couldnotbecalculated
using the software CLUMPP (Jakobsson and Rosenberg history traits in coastal California O. mykiss populations
2007)andDISTRUCT(Rosenberg2004). (Pearse et al. 2014). Analysis of these two SNPs in Central
Phylogeographic dendrograms were constructed using Valley O. mykiss populations, from which the majority of
Cavalli-Sforza and Edwards (1967) chord distances and the hatchery rainbow trout strains used in California were
neighbor-joiningmethod(TakezakiandNei1996),withthe derived, has shown similar patterns of allele frequency
software PHYLIP (Felsenstein 2005). Markers for which variation but with significantly reduced linkage disequilib-
genotypes were lacking for any entire population were riumrelativetocoastalpopulations(PearseandGarza2015).
excluded,leaving13microsatelliteand90SNPloci.Forthis We examined patterns of variation in these two markers to
analysis,populationsampleswithmixedancestryevidentin (1) explore the association between adaptive variation at
the STRUCTURE results were first sub-divided to reflect Omy5 and migratory life history patterns in Southern and
differences detected among sampling sub-locations and BajaCaliforniaO.mykissand(2)furtherevaluatetheextent
times. Allele frequencies were bootstrapped 10,000 times of genetic introgression by hatchery trout in these popula-
and the resulting datasets used to construct dendrograms to tions, as inferred from linkage disequilibrium between the
evaluate statistical support for branching patterns. two markers using the allelic correlation coefficient (r2)
Finally,aprincipalcomponentanalysis(PCA)wasused calculatedintheRpackagegenetics(Warnes2003).
to graphically explore differentiation and relationships
among all populations and individuals using the R-based
package adegenet 1.3-4 (Jombart 2008). Populations were Results
plotted to indicate four groups (northern coastal steelhead,
hatchery/Central Valley, O. m. nelsoni, and Southern Cal- Genotypesof577individualfishwere combinedwith data
ifornia DPS basin populations). from previously genotyped O. mykiss from throughout
California, including seven hatchery rainbow trout strains,
Life history adaptation for a total of genotypes from 2109 fish (Table 2). These
genotypes consisted of 106–110 loci per population, and
TwooftheSNPlocigenotypedinallindividualsarelocated genotypesof25fishwereremovedfromallanalysesdueto
on chromosome Omy5 in a genomic region strongly asso- missing data (C10 microsatellite or SNP loci missing).
ciated with the prevalence of resident or anadromous life This combined dataset provided increased resolution
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ConservGenet
relative to single marker-type datasets or those based on CoastBPG,comprisedofpopulationsfromOrangeandSan
fewer loci (Narum et al. 2008). Diego counties, had H that ranged from 0.26 to 0.39. In
O
contrast, H in coastal populations from the northern DPSs
O
Genetic diversity statistics ranged from 0.38 to 0.45.
Consistent with the above observations, Northern Cali-
NoneofthemicrosatelliteorSNPlocideviatedsignificantly forniapopulationshadhighermicrosatelliteallelerichness,
from HW equilibrium after correction for multiple com- and a higher proportion of polymorphic SNPs (Table 2).
parisons.SouthernCaliforniaDPSpopulationsgenerallyhad Microsatellite Ar was highest in the Klamath-Blue (5.32)
lower heterozygosity than northern populations, and had and lowest in the Sta Ana-Temescal-Coldwater Canyon
variation similar to the hatchery rainbow trout strains. The population (1.76). Gualala-Fuller, Sacramento-Deer and
northernmostoftheBPGs,theMonteAridoHighlandsBPG, BigSurhadthehighestproportionofpolymorphicSNPsat
containingtheSantaMaria,SantaYnez,Ventura,andSanta 0.95 (0.98), while Sacramento-Feather-Yuba, Sacramento-
Clara rivers, had H values that ranged from 0.32 to 0.41. Battle, Sacramento-Deer, and Willow were highest at 0.99
O
Further south, the Mojave Rim BPG, containing the Los (1.00).StaAna-Temescal-ColdwaterCanyonagainhadthe
Angeles, San Gabriel, and Santa Ana rivers, had H values lowest variation, with SNP polymorphism of
O
withawiderrange(0.13–0.40),butthemajorityofsamples P(0.95) = 0.30 and P(0.99) = 0.32.
came from tributaries of the San Gabriel River and values
for those populations were generally high (0.33–0.40). Of Population genetics
note is that the southernmost sampled population in this
BPG is in a small currently land-locked tributary of the Model-based clustering at low K values (Fig. 2a) gave an
Santa Ana River (Sta Ana-Temescal-Coldwater Canyon), initial indication of whether populations and individuals
and had strikingly low heterozygosity (H = 0.13 and were primarily of native coastal steelhead or hatchery
O
H = 0.12;Table 2).ThesouthernmostSantaCatalinaGulf rainbowtroutancestry.Populationsofnorthernandcentral
E
ni
o
(a) els
Northern/CV Central/South-Central n Hatchery
Steelhead CA Steelhead Southern CA O. mykiss m. rainbow trout
O.
n
(b) nyo
Klamath-Blue Mattole-Bear Gualala-Fuller McCloud-Claiborn Sacramento-Battle Sacramento-Deer Sacramento-Feather-Yuba American NF Los Trancos Waddell Carmel Salinas-Tassajara Big Sur Willow Chorro-Pennington Sn Simeon Sta Maria-Cuyama-Reyes Sta Maria-Sisquoc-Manzana Sta Maria-Sisquoc Montecito Sta Ynez-Quiota Sta Ynez-Sta Cruz Sta Ynez-Hilton Sta Ynez-Juncal Sta Ynez-Salsipuedes Ventura-Sn Antonio Ventura-Matilija Ventura-Matilija-Bear Sta Clara-Sta Paula Sta Clara-Piru Sta Clara-Piru-Buck Sta Clara-Sespe-Piedra Blanca Sta Clara-Sespe-Lion Canyon Sta Clara-Sespe Los Angeles-Hondo-Sta Anita NF Sn Gabriel WF Sn Gabriel-Bear WF Sn Gabriel-Devil’s Canyon WF Sn Gabriel EF Sn Gabriel-Cattle EF Sn Gabriel-Fish Fork EF Sn Gabriel- SFIron Fork EF Sn Gabriel- Iron Fork EF Sn Gabriel Sn Gabriel-Fish Canyon Sta Ana-Chino-Sn Antonio Sta Ana-Bear Sta Ana-Temescal-Coldwater CaSta Ana-Temescal-Fuller Mill Sta Ana-Temescal-Sn Jacinto09 Sta Ana-Temescal-Sn Jacinto12 Sn Juan-Arroyo Trabuco Sn Luis Rey-Doane PaumaO (old 1997) PaumaR (recent 2009-11) WF Sn Luis Rey Sn Diego-Boulder Sweetwater (old 1997) Sweetwater (recent 2010/13) O. m. nelsoni FH-Coleman FH-Virginia FH-Whitney FH-Wyoming ARH-Eagle ARH-Shasta HC-Kamloops
SantaMMaorinateRc.itoSantaYnezR.VenturaR.SantaClarLaoRs.AngeSleasnRG.abrielRS.antaASnaanSRJua.annSLauRni.sSDRwieeeygeOotRw.R.am.te.rnRel.sroaniHinabtocwh etrryo ut
Fig.2 Results from STRUCTURE showing individual fractional fromSouthernCAarederivedprimarilyfromhatcheryrainbowtrout
ancestry and genetic relationships. Each vertical line represents an lineages. Individuals with more light grey represent ancestry of
individual’s fractional assignment to each of K genetic lineages. coastal steelhead lineage, while intermediate values indicate intro-
Samplinglocationsareseparatedwithblacklines,orderedfromnorth gression and shared ancestry from both lineages. b K=7 genetic
to south. a K=2 genetic clusters in the data (five out of five clusters,showingconcordanceandvariabilityamongfiveruns
replicateshadthesamepattern).Individualsrepresentedindarkgrey
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ConservGenet
California coastal steelhead were clearly differentiated groups of contemporary fish contained significant native
fromhatcheryrainbowtroutandCentralValleyO.mykiss. coastal steelhead ancestry: 1) populations from the San
The predominance of native coastal O. mykiss ancestry Gabriel River system, 2) Coldwater Canyon Creek in the
(light grey in Fig. 2a) in Southern California decreased in SantaAnaRiver,3)theWestForkSanLuisReyRiver,and
themoresouthernregions,withmanypopulationsofmixed 4)O.mykissnelsonifromtheSantoDomingoRiverinBaja
or completely hatchery ancestry (dark grey in Fig. 2a). California. Differences among some hatchery trout strains
At higher values of K, population structure within and were also discernible, with apparent widespread stocking
between basins became evident, as did the distinctiveness of the Mount Whitney strain (Fig. 2b). Moreover, O.
of many of the populations. Examination of individual mykiss nelsoni was consistently identified as distinct from
fractional ancestry at K = 7 clearly identified both native all other population samples (Fig. 2b).
and hatchery origin/introgressed fish among the Southern Population-level phylogeographic relationships, recon-
CaliforniaDPS(Fig. 2b).IndividualsfromtheSantaClara structed with a neighbor-joining tree (Fig. 3), were consis-
Rivertributaries(Piru,SantaPaulaandSespecreeks)were tentwiththeclusteringresults.Thedivisionbetweennative
of native coastal steelhead descent, consistent with the coastal steelhead lineage populations and hatchery trout/
results of Clemento et al. (2009). Further south, only four CentralValleypopulations was clear and issummarized on
Fig.3 Neighbor-joining tree of all populations included in the significant hatchery rainbow trout/Central Valley ancestry (upper
analysis, with bootstrap support for internal branches of[60 % section). The Southern California DPS populations are indicated in
shown. Note that the dashed line almost perfectly divides coastal bold,andthosethatclusterwiththehatcheryrainbowtroutstrainsare
steelhead lineage populations (lower section) from those with underlined
123