Admix u e and Gene Flow om Russia in he Reco e ing
No he n Eu opean B own Bea (
U sus a c os
)
Alexande Kopa z
1
*, Hans Gei Eiken
1
, Jouni Aspi
2
, Ilpo Kojola
3
, Camilla Tobiassen
1
,
Kons an in F. Ti onen
4
, Pjo I. Danilo
4
, Sno e B. Hagen
1
*
1Bio o sk - No wegian Ins i u e o Ag icul u al and En i onmen al Resea ch, S an ik, No way, 2Depa men o Biology, Uni e si y o Oulu, Oulu, Finland, 3Finnish Game
and Fishe ies Resea ch Ins i u e, Oulu, Finland, 4Ins i u e o Biology, Ka elian Resea ch Cen e o he Russian Academy o Science, Pe oza odsk, Russia
Abs ac
La ge ca ni o es we e pe secu ed o nea ex inc ion du ing he las cen u ies, bu ha e now eco e ed in some coun ies. I
has been p oposed ea lie ha he eco e y o he No he n Eu opean b own bea is suppo ed by mig a ion om Russia.
We es ed his hypo hesis by ob aining o he i s ime con inuous sampling o he whole Finnish bea popula ion, which is
loca ed cen ally be ween he Russian and Scandina ian bea popula ions. The Finnish popula ion is assumed o expe ience
high gene low om Russian Ka elia. I so, no o a low deg ee o gene ic di e en ia ion be ween Finnish and Russian bea s
could be expec ed. We ha e geno yped bea s ex ensi ely om all o e Finland using 12 alida ed mic osa elli e ma ke s
and compa ed hei gene ic composi ion o bea s om Russian Ka elia, Sweden, and No way. Ou ine masked in es iga ion
iden i ied wo o e lapping gene ic clus e s s uc u ed by isola ion-by-dis ance in Finland (pai wise F
ST
= 0.025). One clus e
included Russian bea s, and mig a ion analyses showed a high numbe o mig an s om Russia in o Finland, p o iding
e idence o eas e n gene low as an impo an d i e du ing eco e y. In compa ison, bo h clus e s excluded bea s om
Sweden and No way, and we ound no mig an s om Finland in ei he coun y, indica ing ha eas e n gene low was
p obably no impo an o he popula ion eco e y in Scandina ia. Ou analyses on di e en spa ial scales sugges a
con inuous bea popula ion in Finland and Russian Ka elia, sepa a ed om Scandina ia.
Ci a ion: Kopa z A, Eiken HG, Aspi J, Kojola I, Tobiassen C, e al. (2014) Admix u e and Gene Flow om Russia in he Reco e ing No he n Eu opean B own Bea
(U sus a c os). PLoS ONE 9(5): e97558. doi:10.1371/jou nal.pone.0097558
Edi o : Paul Hohenlohe, Uni e si y o Idaho, Uni ed S a es o Ame ica
Recei ed Decembe 19, 2013; Accep ed Ap il 21, 2014; Published May 19, 2014
Copy igh : ß2014 Kopa z e al. This is an open-access a icle dis ibu ed unde he e ms o he C ea i e Commons A ibu ion License, which pe mi s
un es ic ed use, dis ibu ion, and ep oduc ion in any medium, p o ided he o iginal au ho and sou ce a e c edi ed.
Funding: The s udy was unded by Bio o sk. The unde had no ole in s udy design, da a collec ion and analysis, decision o publish, o p epa a ion o he
manusc ip .
Compe ing In e es s: The au ho s ha e decla ed ha no compe ing in e es s exis .
* E-mail: alexande .kopa[email p o ec ed] (AK); sno e.hagen@bio o sk.no (SBH)
In oduc ion
Habi a agmen a ion and an h opogenic dis u bance is a
global h ea o wildli e, wi h impac s such as declining popula ion
sizes and educed gene low among popula ions. Bo h e ec s a e
widely epo ed o p omo e gene ic d i and oppose long- e m
popula ion iabili y [1]. Ce ain species a e pa icula ly sensi i e o
loss o in e -popula ion connec i i y [2–4]. Examples a e many
apex p eda o s, cha ac e ized by small popula ion size, long
gene a ion imes, la ge home anges, and high le els o human
pe secu ion [2,5–8].
Du ing he las cen u y, la ge e es ial ca ni o es declined
bo h in numbe s and geog aphic dis ibu ion (see e.g. [4,9]). E en
hough hey we e almos ex i pa ed in mos o Eu ope, la ge
ca ni o es ha e now eco e ed in some a eas and popula ions a e
expanding [2,4,9,10]. An impo an s ep owa ds unde s anding
he unde lying causes o eco e y is o de e mine he cu en
deg ee o gene low and gene ic di e en ia ion among la ge
ca ni o e popula ions ac oss na ional bo de s [10].
In Finland, he b own bea (U sus a c os) was dis ibu ed
h oughou he coun y un il he beginning o he 19 h cen u y
[11]. A he end o he 19 h cen u y, bea s seemed o be ex inc
om cen al, sou he n, and wes e n Finland, while obse a ions o
bea s we e s ill epo ed in he no h and eas [12]. His o ic
eco ds indica e ha he b own bea popula ion o Finland wen
h ough a demog aphic bo leneck, wi h a leas 9,000 indi iduals
killed be ween 1875 and 2000 [12]. I is assumed ha he
popula ion size eached i s minimum be ween 1920 and 1950. In
1963, he emaining numbe o bea s was es ima ed o be abou
150 indi iduals [13]. Es ima es based on bea obse a ions
sugges ed an inc ease om app oxima ely 300 o 800 indi iduals
be ween 1978 and 2003 [14,15]. Mig a ion om Russia in o
Finland has been assumed o ha e suppo ed he g ow h o he
Finnish popula ion [11,13,16–18]. The mos ecen es ima es
based on obse a ions o he numbe o li e s-o - he-yea a e
sugges i e o a numbe be ween 1,150 and 1,950 bea s in 2009,
wi h highes densi ies in he sou h along he Finnish-Russian
bo de [19]. In his a ea, eco ds o killed bea s also indica e a
pa icula ly high p opo ion o emale bea s [16,20,21].
The Finnish b own bea popula ion is loca ed cen ally be ween
he popula ions o Russia and Scandina ia. The Republic o
Ka elia and he Mu mansk Oblas in Russia a e he neighbo ing
dis ic s owa ds Finland. Based on hun ing eco ds, obse a ions,
and ack coun ing he es ima ed numbe s o bea s in hese
dis ic s in 1990 we e abou 3,500 and 500 bea s, espec i ely
[22,23]. Towa ds he no h, Finland sha es he bo de wi h
No way, whe e nonin asi e gene ic sampling o sca s and hai s has
documen ed small b own bea popula ions in he Pas ik Valley, in
he Ka asjok-Ana johka egion, and in he a ea o Di idalen in
T oms [24,25]. In Sweden, owa ds he wes , e o -co ec ed
PLOS ONE | www.plosone.o g 1 May 2014 | Volume 9 | Issue 5 | e97558
moose-hun e obse a ions combined wi h nonin asi e gene ic
cap u e- ecap u e s udies ha e been used o es ima e he
popula ion o be app oxima ely 3,300 bea s [26].
Recen s udies o b own bea s om No he n Eu ope sugges
bo h gene ic s uc u ing due o isola ion-by-dis ance (IBD) and he
exis ence o sepa a e gene ic popula ions [24,25,27–31]. P e ious-
ly, we ha e de ec ed bi-di ec ional mig a ion a es o abou 30%
be ween bea s in Eas e n Finland and bea s u he eas in
A khangelsk, Russia [28]. Ano he s udy applying au osomal
mic osa elli es o a es ic ed numbe o samples sugges ed ha
Finnish bea s a e di ided in o a no he n and a sou he n
subpopula ion [30]. A ecen mi ochond ial genome s udy o
bea s in No heas e n Eu ope also indica ed a no he n and a
sou he n clus e in luenced by mi ogene ic haplog oups om
Eu opean Russia [32]. Fu he mo e, we ha e ound indica ions
ha he connec i i y be ween he bea popula ions in Eas e n
Finland and Scandina ia o be limi ed [25].
Since he eco e y o b own bea s in Finland is assumed o be
explained by high gene low om Russian Ka elia, one should
expec a low deg ee o gene ic di e en ia ion be ween b own bea s
om hese a eas oday, which has no been su icien ly es ed. In
addi ion, he esul s o he p e ious s udies sugges ing mo e han
one subpopula ion o bea s in Finland [30], may be inaccu a e
because o IBD and selec i e sampling. In con as , in his s udy
we ha e sampled indi iduals ex ensi ely and con inuously all o e
Finland o answe he ques ion whe he o no he e is a no he n
and sou he n popula ion o bea s in Finland. We included samples
om Russia o sc u inize he in luence o eas e n gene low on he
composi ion o he Finnish bea popula ion. In a las s ep, we
included ou p e iously published gene ic da a on bea s om
Scandina ia (Sweden and No way) o in es iga e he connec i i y
u he wes wa ds. Compa ing esul s on he gene ic s uc u e
om h ee di e en geog aphic scales allowed us o de e mine
mo e p ecisely he unde lying gene ic admix u e and gene low in
No hwes e n Eu ope.
Ma e ials and Me hods
Sampling
All samples we e collec ed om dead animals, ha es ed legally
in Finland and Russia. Legal ha es o bea s in Finland in he
di e en hun ing dis ic s ollows an annual quo a co esponding
o he es ima ed abundance and dis ibu ion o b own bea s in
hose a eas [19], and he sampling in his s udy ollows his
dis ibu ion h oughou Finland. Tissue samples we e ob ained by
ou collabo a o s namely he Finnish Game and Fishe ies
Resea ch Ins i u e and he Ka elian Resea ch Cen e o he
Russian Academy o Science. No e hic pe mi was equi ed, as he
sample collec ion did no in ol e li e animals.
In ou s udy, we analyzed he da a o a o al o 517 bea s om
2006 o 2010 (Figu e 1, Table S1), including 286 issue samples
om indi iduals om Finland, collec ed annually om legally
ha es ed bea s (91 emales, 195 males). To in es iga e gene low
om Russia in o Finland and wes wa ds o Scandina ia, we
included p e iously geno yped indi iduals om No way (N= 97),
Sweden (N= 84) and Russia (N= 22); (see Kopa z e al. 2012 and
Figu e 1. Sampling loca ions o he b own bea s (
N
= 517) in No he n Eu ope. Samples we e collec ed om 2006 o 2010 and each
indi idual is ep esen ed by a ed do .
doi:10.1371/jou nal.pone.0097558.g001
Reco e ing No he n Eu opean B own Bea
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Sch egel e al. 2012) and 28 addi ional issue samples om
Russian Ka elia ( o al N= 50 bea s) om he same ime pe iod.
Molecula Analysis
Immedia ely a e collec ion, issue samples we e s o ed in 95%
e hanol un il ex ac ion. Samples we e ex ac ed wi h DNeasy
Tissue Ki (Qiagen), ollowing he manu ac u e ’s ins uc ions, and
geno yped using 12 di e en dinucleo ide ma ke s (sho - andem-
epea s, STRs) de eloped o bea s: G1A, G1D, G10B, G10L
[33,34]; Mu05, Mu09, Mu10, Mu15, Mu23, Mu50, Mu51 and
Mu59 [35]. We ha e p e iously alida ed hese STRs o hei
species sensi i i y, p ecision and p obabili y o iden i y [24,27].
The p o ocol o PCR and agmen analysis can be ound in
And eassen e al. [27]. Ou labo a o y p ocedu es ollow he
guidelines o he analysis o non-human o ensic DNA ma e ial
[36]. We e i ied he uniqueness o all geno ypes by calcula ing
hei p obabili y o iden i y using he so wa e Gimle e sion 1.3.3
[37]. Geno ypes we e es ed in Mic o-Checke e sion 2.2.3 o
possible allelic d opou , p esence o null alleles, and sco ing e o s
caused by s u e peaks [38].
Popula ion S uc u e
We es ed o gene ic s uc u e using wo Bayesian assignmen
algo i hms (S uc u e and Geneland) and ac o ial co espondence
analysis (FCA). Since ea lie s udies ha e indica ed a es ic ed
numbe o gene ic clus e s in No hwes e n Eu ope [25,28–30], we
se ou Bayesian analyses on gene ic clus e ing o a maximum o
K= 10. In S uc u e e sion 2.3.3 [39,40], we assumed popula ion
admix u e and co ela ed allele equencies wi hin he popula ion.
Ten independen uns o each K alue be ween one and en we e
pe o med. Fo each un, we se a bu n-in pe iod o 100,000
Ma ko Chain Mon e Ca lo (MCMC) i e a ions, ollowed by
sampling o 1,000,000 i e a ions. The esul s we e pos -p ocessed
wi h he ad-hoc app oach o E anno e al. [41] o es ima e he
numbe o gene ic clus e s using S uc u e Ha es e [42]. A
membe ship coe icien (q) abo e 0.6 has been conside ed as a
easible cu -o membe ship alue o assign indi iduals o a
popula ion wi h con idence, since mo e han 50% o he genome is
assigned o a g oup and he e o e sugges s in e ed ances y
[43,44]. P e ious s udies on bea s ha e used a membe ship
coe icien (q) o 0.7 [30,44]. Thus, we ha e applied a h eshold
alue o q.0.7 in his s udy.
In Geneland [45], we an i e independen uns, whe e he
pa ame e s o possible popula ions we e K= 1 o 10, and he
Figu e 2. Bayesian clus e ing esul s o Finnish and Russian Ka elian bea s wi h S uc u e (P i cha d e al. 2000). Ba plo s show he
assignmen p obabili ies o each bea o one o he iden i ied wo clus e s when only samples om Finland we e analyzed (a) and samples om
Finland and Russian Ka elia pooled oge he (d); no he n clus e (g een), sou he n clus e (blue). The y-axis shows he calcula ed membe ship
coe icien (q). Indi iduals a e a anged by la i ude om no h (le ) o sou h ( igh ). (b and e) The maps show he geno ypes in acco dance o hei
assignmen in S uc u e and geog aphical loca ion. Indi iduals which we e no assigned unambiguously (membe ship coe icien q,0.7) a e shown
on a sepa a e map as da k ed do s. (c and ) Maps on he bo om show he assignmen wi h he p og am Geneland (Guillo e al. 2005).
doi:10.1371/jou nal.pone.0097558.g002
Reco e ing No he n Eu opean B own Bea
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numbe o MCMC i e a ions was 1,000,000, wi h a hinning o
100. The maximum a e o Poisson p ocess was se o 100, and he
maximum numbe o nuclei was 300. Geog aphical loca ion o he
samples (longi ude, la i ude) was included in o he analysis. FCA
was pe o med wi h he p og am Gene ix 4.05.2 [46].
To de e mine he deg ee o di e en ia ion among gene ic
clus e s, AMOVA analyses and pai wise F
ST
alues we e
calcula ed wi h he p og am A lequin e sion 3.5.1.2 [47].
Isola ion-by-dis ance
We calcula ed IBD among pai s o b own bea s in Finland and
Russian Ka elia using he so wa e Spagedi e sion 1.3 [48] wi h
he kinship coe icien by Loiselle e al. [49].
Gene Flow
To u he es he eas -wes gene low hypo hesis we es ima ed
he amoun o mig a ion be ween he bea s in Finland and
Russian Ka elia as well as be ween Finland and Scandina ia using
wo di e en me hods. Fi s ly, he e ec i e numbe o mig an s
(Nm) was es ima ed using he p i a e allele me hod [50]
implemen ed in he p og am Genepop [51]. Secondly, o iden i y
possible ecen mig an s, we es ima ed he likelihood o a bea o
belong o he popula ion i was sampled using he indi idual
Bayesian assignmen me hod in he p og am Geneclass 2 [52]. We
used he algo i hm by Rannala and Moun ain [53] and
esampling as desc ibed in Pae kau e al. [54] o iden i y i s
gene a ion mig an s. The simula ion was se o 10,000 indi iduals
and he ype I e o (alpha) o 0.05.
Gene ic Di e si y
We calcula ed numbe o alleles, expec ed and obse ed
he e ozygosi y wi h he p og am A lequin e sion 3.5.1.2 [47].
Inb eeding coe icien s and es s o linkage disequilib ium
be ween pai s o loci we e pe o med wi h he p og am Gene ix
4.05.2 [46] using he me hod by Black and K a su [55].
De ia ions om Ha dy-Weinbe g equilib ium (HWE) we e es ed
wi h Fishe ’s me hod [56] o all loci and popula ions wi h he
p og am Genepop e sion 4.0 [51], wi h unbiased P alues by a
Ma ko chain me hod o 1000 bu n-in i e a ions, 500 ba ches and
1000 i e a ions pe ba ch.
Popula ion Bo lenecks
Fo he bea s om Finland and Russia, we es ed o la ge
obse ed he e ozygosi y han expec ed o de ec possible gene ic
bo lenecks in he ecen his o y o he bea popula ions wi h he
p og am Bo leneck 1.2.02 [57]. We applied he wo-phase
mu a ion model using 95% single s ep mu a ions o es ima e he
expec ed he e ozygosi ies (20,000 i e a ions) and es ed he
signi icance o he di e ences be ween obse ed and expec ed
he e ozygosi ies using he Wilcoxon es . Fu he , we applied he
M a io es o in es iga e i he e a e signs o gene ic bo lenecks
u he in he pas (.100 gene a ions) and he e o e we calcula ed
he modi ied Ga za-Williamson indices [58] o he clus e s ound
implemen ed in he p og am A lequin e sion 3.5.1.2 [47].
Resul s
Popula ion S uc u e in Finland and Russian Ka elia
The S uc u e clus e ing app oach sugges ed wo gene ic
clus e s in Finland wi h a high deg ee o admix u e and
geog aphical o e lap (Figu e 2a and b, Figu e S1a, and Figu e
S2a). While one clus e was sp ead almos h oughou wo- hi ds
o he coun y, he o he one was es ic ed o he sou he n pa o
Finland (Figu e 2b). A o al o 60 bea s (21%) we e no assigned
unambiguously o he iden i ied clus e s (membe ship coe icien
q,0.7), and hose we e mainly ound in he zone whe e he
clus e s o e lapped (Figu e 2b). All al e na i e models o
popula ion s uc u e using a la ge numbe o clus e s (K=3 o
5) had lowe likelihoods and showed subs an ially highe numbe s
o unassigned indi iduals up o 72% (Figu e S2a). Geneland
iden i ied also wo clus e s, i.e. a no he n and a sou he n one
(Figu e 2c). FCA suppo ed he esul s by S uc u e, showing wo,
o e lapping g oups o bea s (Figu e 3a). Bea s no unambiguously
Figu e 3. Fac o ial co espondence plo s o b own bea s sampled 2006–2010 in Finland, Russia, No way and Sweden. Di e en
colo s ep esen he clus e s iden i ied by he Bayesian clus e ing app oach. (a) FCA analysis o he Finnish samples only: no he n clus e (g een),
no he n clus e wi h a membe ship coe icien (q),0.7 (ligh g een), sou he n clus e (blue), sou he n clus e wi h assignmen membe ship
p obabili y ,0.7 (cyan). (b) FCA analysis o Finnish and Russian Ka elian samples: no he n clus e (g een), no he n clus e wi h an assignmen
membe ship p obabili y ,0.7 (ligh g een), sou he n clus e (blue), sou he n clus e wi h assignmen membe ship p obabili y ,0.7 (cyan). (c) FCA
analysis o Finnish, Russian Ka elian popula ions and bea s sampled in No he n No way and Sweden: no he n clus e (g een), no he n clus e wi h a
membe ship coe icien ,0.7 (ligh g een), sou he n clus e (blue), sou he n clus e wi h assignmen membe ship p obabili y ,0.7 (cyan), wes e n
(Scandina ian) clus e (o ange), wes e n clus e wi h an assignmen membe ship p obabili y ,0.7 (yellow).
doi:10.1371/jou nal.pone.0097558.g003
Reco e ing No he n Eu opean B own Bea
PLOS ONE | www.plosone.o g 4 May 2014 | Volume 9 | Issue 5 | e97558
assigned by S uc u e showed highes simila i y and occu ed on
he FCA plo be ween he wo clus e s (Figu e 3a).
Simila o he esul s in Finland alone, assigning geno ypes om
Finland and Russian Ka elia oge he also sugges ed wo gene ic
clus e s (Figu e 2d, Figu e S1b and Figu e S2b). One clus e
sp ead h oughou he dis ibu ion ange while he o he one was
concen a ed mainly o he sou he n pa o he s udy egion
(Figu e 2e). Admix u e and geog aphical o e lap as sugges ed by
he assignmen p obabili ies (Figu e 2d) could be as well obse ed
he e (Figu e 2e). Simila ly, mos o he unambiguously assigned
geno ypes, 79 indi iduals in o al (22.8%), we e ound in he
geog aphic o e lap zone (Figu e 2e). Geneland showed wo
gene ic clus e s: a no he n and sou he n clus e , wi h a dis inc i e
bo de in he middle o Finland (Figu e 2 ). FCA analyses
suppo ed he esul s by S uc u e o wo, o e lapping gene ic
g oups (Figu e 3b). Repea edly, bea s which we e no assigned
unambiguously seem o highligh an admix u e g oup be ween he
wo iden i ied clus e s (Figu e 3b).
Connec i i y wi h Scandina ia
A e pooling Finnish and Russian Ka elian bea s oge he wi h
bea s om he no he n ans-bo de a ea o Pas ik in No way
and Russia, T oms in No way, and Va¨s e bo en in Sweden, he
Bayesian clus e ing app oaches (S uc u e and Geneland) sugges -
ed h ee gene ic clus e s: a wes e n one, including mainly
geno ypes om Scandina ia, namely Va¨s e bo en and T oms, a
no he n one, including geno ypes om Pas ik and no he n
Finland and Mu mansk, and a sou he n clus e con aining
geno ypes om middle and sou he n Finland as well as Russian
Ka elia (Figu e 4a and b, Figu e S1c and Figu e S2c). In
compa ison o he analyses o popula ion s uc u e using samples
om Finland and Russian Ka elia only, he bo de be ween he
wo g oups in Finland and Ka elia was loca ed a bi u he no h
(Figu es 2 and 4). He e, we ound app oxima ely 20 indi iduals in
he no h assigned o he sou he n clus e , compa ed o he esul s
when using solely Finnish bea samples, whe e only one indi idual
in he no h has been assigned o he sou he n clus e .
Fu he mo e, only 18 (3.5%) o he indi iduals could no be
assigned unambiguously, sugges ing ha mos o he unassigned
geno ypes ound a smalle spa ial scales we e in e media e
geno ypes om he admix u e zone a he han indi iduals om
an unknown popula ion. Geno ype assignmen wi h S uc u e in
acco dance o he sampling loca ion is shown in Figu e 4b. FCA
Figu e 4. Assignmen o bea s sampled 2006–2010 in No hwes e n Eu ope wi h he p og am S uc u e (P i cha d e al. 2000). Ba
plo s show he assignmen p obabili ies o each bea o one o he h ee iden i ied clus e s (a). Geno ypes a e so ed ‘‘clockwise’’ in acco dance o
hei loca ion om sou h-wes in Sweden o sou h eas in Finland and Russia acco ding o om le o igh : in o ange Va
¨s e bo en (sou h-no h) and
T oms (wes -eas ), in g een No he n Finland (wes -eas ) and Pas ik (no h-sou h), in blue Sou he n Finland and Russian Ka elia (no h-sou h). They-
axis shows he calcula ed membe ship coe icien (q). (b) The maps show he geno ypes in acco dance o hei assignmen in S uc u e and
geog aphical loca ion: wes e n clus e in Scandina ia, namely Va
¨s e bo en and T oms, shown in o ange; no he n clus e in g een and sou he n
clus e in blue. (c) Maps on he bo om show he assignmen wi h he p og am Geneland (Guillo e al. 2005).
doi:10.1371/jou nal.pone.0097558.g004
Reco e ing No he n Eu opean B own Bea
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analysis was in line wi h he esul s by he Bayesian assignmen s
and isualized h ee dis inc i e g oups o bea s (Figu e 3c).
Popula ion Di e en ia ion in Finland and Russian Ka elia
The pai wise F
ST
alues be ween he wo subpopula ions we e
signi ican (P,0.001), wi h F
ST
= 0.025 be ween he no he n and
sou he n clus e ound in Finland and F
ST
= 0.026 be ween he wo
clus e s iden i ied when Finnish and Russian samples we e
analyzed oge he . AMOVA analysis wi hin Finland showed ha
2.54% o he a ia ion was be ween he clus e s and 97.46%
wi hin hem (P,0.01). Fo he no h-sou h di ision in Finland and
Russian Ka elia, 2.59% a ia ion was be ween he clus e s and
97.41% a ia ion wi hin he hem, espec i ely (P,0.01).
Isola ion-by-dis ance
We de ec ed a signi ican , nega i e ela ionship (P,0.001)
be ween kinship and spa ial dis ance be ween pai s o indi iduals
sampled con inuously in Finland and Russian Ka elia, p o iding
e idence o an in luence o IBD on he deg ee o gene ic
s uc u ing. All dis ance classes showed signi ican de ia ion o
kinship om he popula ion mean (Figu e 5).
Gene Flow
The es ima ed e ec i e numbe o mig an s was much highe
be ween Finland and Russian Ka elia han be ween Finland and
Scandina ia (Figu e 6, Table S2). Simila esul s we e ound using
he so wa e Geneclass 2, which de ec ed 18 mig an s be ween
Finland and Russian Ka elia. Ou o hese, 15 bea s we e
iden i ied as i s gene a ion mig an s om Russia in o Finland. In
compa ison only h ee indi iduals we e iden i ied as mig an s om
Finland in o Russia. Be ween Scandina ia and Finland 8
indi iduals we e de ec ed as mig an s. All o hem we e sampled in
Finland and o igina ed om Scandina ia.
Gene ic Di e si y
Mean obse ed and expec ed he e ozygosi y in Finland we e
highe in he no he n clus e han in he sou he n one. The
no he n clus e also showed highe numbe o alleles pe locus
han he sou he n one (Table 1). One locus (G10B) showed
de ia ion om HWE wi hin he sou he n popula ion, due o
excess o he e ozygo es. This locus as well as locus Mu05 showed
signi ican , nega i e alues o F
IS
(Table 1).
When all geno ypes om Finland we e pooled, i esul ed in he
whole popula ion de ia ing om HWE. One locus (Mu09)
de ia ed as well and showed an ele a ed, albei low, posi i e
alue o F
IS
due o excess o homozygo es (Table 1). This o e all
de ia ion om HWE may be mos p obably caused by he
Wahlund e ec , by pooling samples om wo di e en gene ic
clus e s in o one. F
IS
a locus Mu23 was ele a ed and signi ican
(Table 1).
We ound signi ican linkage disequilib ium (P,0.01) a e
sequen ial Bon e oni co ec ion in 40 ou o 66 ma ke pai s.
No able is ha ou o hese, 29 pai s we e solely ound in he
Scandina ian clus e (Va¨s e bo en and T oms). Signi ican LD
ound was no consis en ac oss all samples and all gene ic clus e s
iden i ied.
Popula ion Bo lenecks
We de ec ed a gene ic bo leneck (P= 0.034) o he gene ic
clus e iden i ied in Scandina ia (Va¨s e bo en and T oms). This
clus e showed also he lowes alue o he Ga za-Williamson
index wi h M= 0.64, which is jus below M
c i
o M,0.68
p oposed by Ga za and Williamson [58] o sugges he occu ence
o a gene ic bo leneck in he pas .
Discussion
We ha e es ed he hypo hesis ha he bea popula ion o
Russian Ka elia has ac ed as a sou ce popula ion du ing he
eco e y o he Finnish and Scandina ian bea popula ions. We
Figu e 5. Co ela ion be ween geog aphical dis ance and
kinship o he b own bea s in Finland and Russian Ka elia.
Samples we e collec ed om 2006 o 2010 (N= 346) and IBD was
analyzed wi h he p og am Spagedi 1.3 (Ha dy and Vekemans 2002). All
nine dis ance classes di e signi ican ly (P,0.001) om he mean
kinship o he popula ion.
doi:10.1371/jou nal.pone.0097558.g005
Figu e 6. The es ima ed numbe o e ec i e mig an s pe
gene a ion (
Nm
). Es ima ed mig an s be ween Finland and Russian
Ka elia (black squa es) as well as be ween Finland and Scandina ia (g ey
iangles) plo ed agains sample size (see Table S2).
doi:10.1371/jou nal.pone.0097558.g006
Reco e ing No he n Eu opean B own Bea
PLOS ONE | www.plosone.o g 6 May 2014 | Volume 9 | Issue 5 | e97558
Table 1. Gene ic di e si y o he Finnish b own bea popula ion.
B own bea s in Finland 2006–2010 - Gene ic di e si y
No h
(N = 164)
Sou h
(N = 122)
No h and sou h (
N = 286)
Locus
AH
E
H
O
F
IS
AH
E
H
O
F
IS
AH
E
H
O
F
IS
MU05 10 0.82 0.82 20.001 9 0.76 0.82 20.086* 10 0.81 0.82 20.017
MU09 13 0.89 0.90 20.014 9 0.86 0.84 0.014 13 0.88 0.88 0.006
MU10 10 0.82 0.84 20.021 9 0.75 0.78 20.037 10 0.81 0.81 20.007
MU15 7 0.78 0.76 0.019 7 0.81 0.85 20.047 7 0.80 0.80 0.001
MU23 13 0.89 0.84 0.050 11 0.81 0.80 0.013 13 0.87 0.83 0.056*
MU50 10 0.76 0.76 0.008 9 0.58 0.56 0.046 10 0.70 0.67 0.040
MU51 9 0.82 0.84 20.026 7 0.75 0.77 20.032 9 0.81 0.81 20.002
MU59 16 0.90 0.91 20.014 12 0.87 0.83 0.048 16 0.90 0.88 0.021
G1A 10 0.83 0.81 0.031 9 0.82 0.82 0.004 10 0.83 0.81 0.027
G1D 9 0.86 0.87 20.019 8 0.82 0.79 0.038 9 0.85 0.84 0.012
G10B 12 0.87 0.88 20.023 8 0.81 0.81 20.076* 12 0.84 0.88 20.040
G10L 11 0.77 0.76 0.004 8 0.73 0.75 20.027 11 0.75 0.76 20.006
Mean 10.8 0.83 0.83 20.001 8.8 0.78 0.79 20.012 10.8 0.82 0.82 0.008
*P,0.05
Expec ed, (H
E
) and obse ed (H
O
) he e ozygosi ies, numbe o di e en alleles (A) and inb eeding alues (F
IS
) calcula ed o he 12 sho andem epea s in he Finnish b own bea popula ion o 286 indi iduals, sampled om 2006
o 2010. Signi ican F
IS
alues a e ma ked wi h *. Loci de ia ing signi ican ly om Ha dy-Weinbe g equilib ium a e Bon e oni co ec ion a e highligh ed by bold F
IS
alues.
doi:10.1371/jou nal.pone.0097558. 001
Reco e ing No he n Eu opean B own Bea
PLOS ONE | www.plosone.o g 7 May 2014 | Volume 9 | Issue 5 | e97558
applied con inuous sampling co esponding o he es ima ed
dis ibu ion o bea s in he a ea and co e ed all possible mig a ion
ou es. Ou esul s showed ha he b own bea popula ion in
Finland and Russian Ka elia consis s o wo clus e s, a no he n
and a sou he n one. The clus e s showed subs an ial geog aphical
o e lap and he gene ic di e en ia ion be ween hem was modes ,
sugges ing a high deg ee o admix u e. Mig a ion analyses
suppo ed hese indings and showed ha gene low be ween
Finland and Russian Ka elia was high, especially in he eas -wes
di ec ion. In compa ison, gene low be ween Finland and
Scandina ia appea ed o be es ic ed, and was ound o be
absen om he eas owa ds Scandina ia.
The s uc u ing o he Finnish bea popula ion [30] was no as
expec ed, showing a subs an ial deg ee o o e lap be ween he
clus e s. This is mos p obably caused by he s ong in luence o
IBD on his popula ion. In he p e ious s udy by Tammeleh e al.
[30], 70 Finnish bea samples we e epo ed o show a pai wise
F
ST
be ween wo clus e s o F
ST
= 0.067. This esul is conside ably
highe han in ou s udy and may be an e ec o non-con inuous
sampling [59]. Howe e , i may also be explained in pa by
in oking he his o y o he b own bea s in he coun y. Wi h he
ecen demog aphic bo leneck o he Finnish bea popula ion in
mind, i may be possible ha he wo clus e s we e once a single
popula ion o bo h popula ions may ha e been connec ed be e in
he pas and migh ha e been di ided du ing ime o pe secu ion.
Acco ding o his o ical eco ds, he b own bea was i ually
ex inc om mos pa s o Finland, wi h excep ion o he a ea
sou h-eas and in he no h, nea he bo de o Russia [11]. Du ing
he ime o ex ensi e pe secu ion he numbe o indi iduals
plumme ed and he popula ion may ha e become subdi ided. The
demog aphic eco e y migh ha e connec ed he clus e s again. I
ha was he case, he di e en ia ion be ween he wo popula ions
was p obably ne e high. The signi ican , albei low F
ST
alues
could be explained by such a scena io [3]. Pe haps he no he n
and he sou he n clus e iden i ied ep esen wo lineages o
ecoloniza ion o Finland du ing he las decades: one lineage om
he sou h-eas and ano he om no h-eas . The occu ence o
his o ic mig a ion e en s has been s ongly indica ed by esul s o
analyses using he mi ochond ial genome [32]. Howe e , ecen
in o ma ion and da a om a eas u he eas emain ague and
e i ica ion he e o e is no possible a his poin .
No iceable is he high numbe o bea s which could no be
assigned unambiguously o any o he iden i ied clus e s when
gene ic s uc u e was analyzed on an in e media e scale (Finland
and Russian Ka elia). The ambiguously assigned indi iduals we e
mainly om he admix u e zone in he sou he n pa o Finland
along he bo de o Russia (and in Russian Ka elia) and aise he
ques ion on hei o igin. Howe e , no e ha o he clus e
assignmen analysis on he la ge scale (incl. Scandina ia), he
numbe o ambiguously assigned indi iduals was a he low
(3.5%). Hence, bea s ha could no be assigned unambiguously on
he in e media e scale we e assigned almos comple ely when
compa ed o a mo e dis an popula ion (i.e. Scandina ia). We
belie e ha hese esul s sugges he exis ence o a con inuous bea
popula ion s uc u ed by IBD in Finland and Russian Ka elia.
Consequen ly, we in e p e he low membe ship coe icien s as a
likely esul o admix u e be ween subpopula ions. This migh
ha e led o di icul ies in clea ly assigning indi idual geno ypes o
one o he iden i ied clus e s du ing he analyses. Howe e ,
in luence o o he bea popula ions o he eas and sou h, e.g.
owa ds S . Pe e sbu g and u he sou h o Es onia [30] may also
be possible. I he bea popula ions u he eas o sou h sha e
indeed he same his o y o pe secu ion, hei eco e y and
expansion may explain he g adual inc ease o immig a ing
indi iduals om o he popula ions in o Finland.
No gene ic bo leneck was de ec ed o he bea s in Finland and
Russian Ka elia, as p e iously indica ed o a small pa o he
popula ion [28], leading o he assump ion, ha a su icien
numbe o indi iduals may ha e su i ed du ing he ime o he
demog aphic bo leneck and/o he bo leneck was e y sho in
ime; oo sho o lead o a subs an ial loss in gene ic ma e ial. I
has been epo ed ea lie , ha Russian bo de ences loca ed along
he Finnish-Russian bo de may p e en o a ec wol es oaming
in eas -wes di ec ion [60]. Ou esul s showed ha he gene low
ac oss he Finnish-Russian bo de has been su icien and ha
hose ences may no cons i u e a se ious obs acle o b own bea s.
Connec i i y o he Finnish and Russian Ka elian b own bea s
wi h popula ions in he wes owa ds Scandina ia seemed mo e
es ic ed, as ou p e ious s udy has indica ed [25]. All de ec ed
i s gene a ion mig an s in he no h we e iden i ied as indi iduals
o igina ing om he Scandina ian popula ion, which mig a ed
owa ds eas , in o Finland, poin ing o unidi ec ional gene low.
The Scandina ian bea popula ion has i s main dis ibu ion in
Sweden wi h ou lie s in o No way. App oxima ely 30 yea s a e
he eco e y s a ed, he bea s in Sweden we e di ided in o h ee
gene ic clus e s, which co esponded o a eas wi h high concen-
a ion o emales [29]. These a eas a e assumed o ep esen
his o ic elic a eas, in which a ew bea s ha e su i ed he ime o
in ensi e hun [29,61,62]. Despi e o a gene ic bo leneck, he
Scandina ian bea s showed ela i ely high le els o he e ozygosi y
(H
O
= 0.66) [31], al hough conside able smalle han ound in
Finland and Russia in his s udy. This ema kable misma ch may
be he esul o he ex eme di e ences in gene low om Russia.
The Finnish bea popula ion is he only connec ion o he
Scandina ian bea popula ion o he Russian one. Al hough he
Finnish and he Scandina ian popula ions bo h s a ed o hei
eco e y om being hun ed down o nea ex inc ion in mos pa s,
hei mechanisms o eco e y mus ha e been qui e di e en and
his is e lec ed in oday’s gene ic composi ion. Ou esul s show
ha he Finnish popula ion p obably has always expe ienced gene
low om Russia in compa ison o he Scandina ian bea
popula ion, which eco e ed wi hou subs an ial suppo om
o he popula ions.
We p opose ha u u e s udies should analyze his o ical samples
o elucida e he his o y o he b own bea s in Finland, Russian
Ka elia and Scandina ia du ing he ime o pe secu ion and ini ial
phases o eco e y. Fu he , analyses on ecen mig a ion should
be moni o ed and ocus mo e in ensi ely on bea s in di e en
egions by applying nonin asi e gene ic sampling and es ima ion
o cap u e-ma k- ecap u e p obabili ies. This can esul in easible
es ima ions on possible demog aphical changes, such as ep o-
duc ion and u n-o e a es as well as he a io be ween e ec i e
and census popula ion sizes.
Suppo ing In o ma ion
Figu e S1 Bayesian clus e ing esul s o No he n
Eu opean bea s wi h he p og am S uc u e (P i cha d
e al. 2000). Samples we e collec ed om 2006 o 2010. (a)
Finnish samples only; (b) Finnish and Russian Ka elian b own
bea samples oge he as well as (c) b own bea samples om all
o e he sampling ange o no he n Scandina ia, Finland and
no h wes e n Russia o he. P esen ed a e he mean likelihoods
L(K) and s anda d de ia ions o K= 1 o 10 clus e s o e 10
independen uns (1,000,000 i e a ions and 100,000 bu n-in) and
he es ima e o DKusing he app oach desc ibed by E anno e al.
Reco e ing No he n Eu opean B own Bea
PLOS ONE | www.plosone.o g 8 May 2014 | Volume 9 | Issue 5 | e97558
(2006). G aphs we e plo ed using he web based analysis S uc u e
Ha es e (Ea l and onHold 2012).
(TIF)
Figu e S2 Bayesian clus e ing esul s o he No he n
Eu opean bea s wi h S uc u e (P i cha d e al. 2000).
Ba plo s showing he assignmen p obabili ies o each bea o he
iden i ied clus e s om K= 2 o 5 when only samples om Finland
we e analyzed (a) and samples om Finland and Russian Ka elia
pooled oge he (b). Indi iduals a e a anged by la i ude om
no h (le ) o sou h ( igh ). Ba plo s o K= 2 o 5 when all da a
(Finland, Russian Ka elia and Scandina ia) is analyzed oge he
(c). No able is he inc ease o unassigned indi iduals (q,0.7) wi h
inc easing K. Fo Finland, he numbe o K= 2 was 60 (20.98%),
while o K= 3 o 5 he numbe inc eased om 103 (36.01%) o
206 (72.03%).
(ZIP)
Table S1 B own bea geno ypes (N= 517) used in his
s udy.
(XLSX)
Table S2 The es ima ed numbe o e ec i e mig an s
pe gene a ion (Nm). Numbe o mig an s be ween Finland
and Russian Ka elia as well as be ween Finland and Scandina ia.
Nm esul s a e shown a e co ec ion o di e en sample sizes o
10, 25 and 50 as well as o he mean sample size.
(XLSX)
Acknowledgmen s
In memo y o he la e Minna Ruokonen who deceased p io o publica ion
o his s udy. We would like o hank Julia Sch egel and h ee anonymous
e iewe s o help ul commen s on his manusc ip . Fu he , we would like
o hank he Finnish Hun e s and Finnish Hun e s’ Associa ion, he
Swedish En i onmen al P o ec ion Agency and he No wegian S a e
Na u e Inspec o a e o collec ing he bea samples used in his s udy.
Financial suppo o his p ojec has been p o ided by he No wegian
Minis y o En i onmen .
Au ho Con ibu ions
Concei ed and designed he expe imen s: AK HGE JA IK SBH.
Pe o med he expe imen s: AK HGE SBH. Analyzed he da a: AK
HGE SBH. Con ibu ed eagen s/ma e ials/analysis ools: IK KFT PID
CT SBH. W o e he pape : AK HGE SBH. Commen ed on he
manusc ip d a s: JA IK KFT PID.
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PLOS ONE | www.plosone.o g 9 May 2014 | Volume 9 | Issue 5 | e97558