RESEARCH ARTICLE Open Access
Mic osa elli e-based gene ic di e si y and
popula ion s uc u e o domes ic sheep in
no he n Eu asia
Miika Tapio
1
, Mikhail Oze o
1
, Ilma Tapio
1
, Miguel A To o
2
, Nu biy Ma zano
3
, Mi jana Ćinkulo
4
,
Galina Goncha enko
5
, Ta yana Kiselyo a
6
, Maziek Mu awski
7
, Juha Kan anen
1*
Abs ac
Backg ound: Iden i ica ion o global li es ock di e si y ho spo s and hei impo ance in di e si y main enance is
essen ial o making global conse a ion e o s. We sc eened 52 sheep b eeds om he Eu asian subcon inen wi h
20 mic osa elli e ma ke s. By es ima ing and weigh ing di e en ly wi hin- and be ween-b eed gene ic a ia ion ou
aims we e o iden i y gene ic di e si y ho spo s and p io i ize he impo ance o each b eed o conse a ion,
espec i ely. In addi ion we es ima ed how impo an wi hin-species di e si y ho spo s a e in li es ock
conse a ion.
Resul s: Bayesian clus e ing analysis e ealed h ee gene ic clus e s, e med No dic, Composi e and Fa - ailed.
Sou he n b eeds om close o he egion o sheep domes ica ion we e mo e a iable, bu less gene ically
di e en ia ed compa ed wi h mo e no he n popula ions. Dec easing weigh o wi hin-b eed di e si y componen
led o e y high ep esen a ion o gene ic clus e s o egions con aining mo e di e ged b eeds, bu did no
inc ease pheno ypic di e si y among he high anked b eeds. Sampling popula ions h oughou 14 egional g oups
was sugges ed o maximized o al gene ic di e si y.
Conclusions: Du ing ini ial s eps o es ablishing a li es ock conse a ion p og am popula ions om he di e si y
ho -spo a ea a e he mos impo an ones, bu o he ull design ou esul s sugges ed ha app oxima ely equal
popula ion p esen a ion ac oss en i onmen s should be conside ed. E en in his case, highe pe popula ion
emphasis in a eas o high di e si y is app op ia e. The analysis was based on neu al da a, bu we ha e no eason
o hink he gene al end is limi ed o his ype o da a. Howe e , a comp ehensi e alua ion o popula ions
should balance p oduc ion sys ems, pheno ypic ai s and a ailable gene ic in o ma ion, and include conside a ion
o p obabili y o success.
Backg ound
The domes ic sheep (O is a ies) has been an economic-
ally and cul u ally impo an a m animal species since
i s domes ica ion in he Nea Eas app oxima ely 9,000
yea s B.P. [1]. A no he n Eu asian sheep s ock o med
some 6,000 yea s ago as sheep we e b ough o he B i -
ish Isles, no he n Eu ope and Russia a e he expan-
sion o he Eu opean con inen ia Danubian and
Medi e anean ou es [2], and a possible ou e h ough
Russia [3]. Sheep dispe sed ac oss Eu ope in empo ally
sepa a e mig a o y episodes: he mos o iginal and a
mo e p imi i e ype o domes ic sheep was la e
eplaced by a mo e de eloped wool ype o sheep.
Ances y om he i s immig an wa e seems o ha e
su i ed only in no h-wes e n and no he n pe iphe ies
o Eu ope [4].
A simila eplacemen p ocess is occu ing in mode n
days. Global s anda diza ion o p oduc ion en i onmen s
and b eed compe i ion ha e led o he disappea ance o
many na i e b eeds. Food and Ag icul u e O ganiza ion
o he Uni ed Na ions (FAO) has es ima ed ha 36% o
he sheep b eeds o known census size a e ei he ex inc
o endange ed [5]. Fu he mo e, he use o a ew high-
quali y males o in ense ma ing has esul ed in he
* Co espondence: [email p o ec ed]
1
Bio echnology and Food Resea ch, MTT Ag i ood Resea ch Finland, 31600
Jokioinen, Finland
Full lis o au ho in o ma ion is a ailable a he end o he a icle
Tapio e al.BMC Gene ics 2010, 11:76
h p://www.biomedcen al.com/1471-2156/11/76
© 2010 Tapio e al; licensee BioMed Cen al L d. 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 (h p://c ea i ecommons.o g/licenses/by/2.0), 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 wo k is p ope ly ci ed.
educ ion o e ec i e popula ion size (N
e
) o e ime and
educed gene ic di e si y wi hin b eeds [6]. These p o-
cesses will lead o he dec ease o e ec i e popula ion
sizeo heen i especies.Thiscould es ic b eeding
op ions and gene ic gain o b eeding p og ams o he
ex en ha unp edic able u u e equi emen s migh no
be me [6-8]. B eed conse a ion aims o main ain hese
op ions, bu limi ed esou ces, e.g. inancial limi a ion,
migh no allow conse a ion o all he b eeds.
One can a gue ha he b eeds o igina ing om o
close o he domes ica ion cen e s, such as he Nea
Eas e n egion, should be pa icula ly p io i ized in con-
se a ion p og ams. Mic osa elli e s udies in ca le (Bos
au us) [9-11], goa (Cap a hi cus) [12] and sheep (O is
a ies) [13] sugges ed ha he b eeds loca ed close o he
pu a i e domes ica ion cen e s a e he mos a iable.
These b eeds migh possess allelic a ia ions e ained
om he wild ances o s ha ne e eached a eas u he
om he cen e o o igin. Al hough one canno easily
di e en ia e hese p ima y di e si y ho spo s om he
seconda y ho spo s c ea ed by a mo e ecen c oss-
b eeding, con inen -wide mapping o he egions o
excep ional li es ock di e si y (gene ic di e si y ho -
spo s) has been sugges ed as a means o a ge ing con-
se a ion e o s o li es ock species [10,14]. DNA
ma ke da a can be used o calcula e molecula coances-
ies wi hin and be ween b eeds and de e mine con i-
bu ions o each b eed o a pool o animals ha would
maximize gene ic di e si y o he pool, i.e. minimize
a e age molecula coances y [15]. These calcula ions
can p o ide c i ical in o ma ion when he p io i iza ion
o b eeds needs o be done o conse a ion o di e si y
o domes ic animal species. Using his conse a ion
app oach, i would be possible o maximize N
e
o he
subdi ided species and hus minimize he deple ing
e ec o gene ic d i on gene ic a ia ion.
The e ha e been a ew qui e comp ehensi e gene
di e si y s udies in sheep [13,16-18]. Howe e , none o
hese ocused on b eed p io i iza ion o desc ibe gene al
ends in he conse a ion o gene ic di e si y in sheep.
Though genome-wide Single Nucleo ide Polymo phisms
(SNP) da a a e becoming he s anda d o li es ock
gene ics [18], hey can ha e a p oblem o asce ainmen
bias o igina ing om SNP disco e y p o ocols [19].
Though he p oblem can be alle ia ed h ough using
haplo ypic measu es [20] o h ough bias co ec ions
[21], he es ablished baseline end using low bias ma -
ke s such as mic osa elli es emains an impo an
benchma k. We used a ep esen a i e se o sheep ypes
ac oss he No he n Eu asia o explo e he di e si y pa -
e ns and in e ed conse a ion p io i ies based on
mic osa elli es. Fo b eed anking we applied he
me hod based on he minimiza ion o molecula coan-
ces y in a subdi ided popula ion by Caballe o and To o
[15]. We es ed he e ec by weigh ing di e en ly he
wo componen s o maximum gene ic di e si y, wi hin-
b eed and be ween-b eed a ia ion, when doing p io i y
se ings o b eeds. Based on he common s a emen ha
popula ions om di e si y ho spo egions a e mo e
impo an [9,14,10], we expec ed la ge numbe o b eeds
om a ho spo egion o be highly p io i ized.
Resul s
Gene ic di e si y
In o al, 342 alleles we e de ec ed a he 20 mic osa el-
li e loci analyzed (Addi ional ile 1: Table S1). A sum-
ma y o he gene ic di e si y pa ame e s compu ed o
16 egional g oups is p esen ed in Table 1 and he
b eed-wise alues based, on an a e age, on 32 sheep pe
b eed a e gi en in Addi ional ile 2: Table S2. The o al
gene ic di e si y (H
T
) a ied om 0.651 o 0.807 in he
Danish and he Uk ainian egional g oups, espec i ely.
The a ea ha ing egional g oups wi h H
T
alues abo e
0.8 (Uk aine, sou heas Eu ope, Kazakhs an and eas o
he Caspian Sea, Bu ya ia and he sou he n Caucasus),
was e med a di e si y ho spo . Among b eeds, he
unbiased expec ed he e ozygosi y (H
S
) anged om
0.613 ( he No wegian Che io ) o 0.806 ( he Russian
Ka akul), wi h an a e age alue o 0.759. Allelic ichness
a ied in he simila pa e n as o he wi hin-popula ion
di e si y measu es (e.g. H
T
and H
S
)ac oss heb eeds
(Table 1). The o e all es ima e o [22] was 0.011. The
b eed-wise es ima es we e signi ican ly (P<0.05)
g ea e han ze o only o he No wegian Rygja Sheep
and he Swedish Rya Sheep sugges ing ha mos b eeds
a e qui e uni o m (Addi ional ile 2: Table S2).
Gene ic clus e analysis
A model-based clus e ing was applied o esol e he
popula ion gene ic s uc u e. A K=3,oneclus e was
cons i u ed by he b eeds descending mainly om he
no he nmos edge o he s udied dis ibu ion ( e med
he ‘No dic clus e ’), while he a - ailed b eeds, o igina -
ing mainly om he Caucasus and Caspian basin a eas,
geog aphically close o he Nea Eas e n domes ica ion
cen e , o med he second clus e ( e med he ‘Fa - ailed
clus e ’). A hi d clus e mainly con ained he composi e
sheep b eeds om cen al Eu asia ( e med he ‘Compo-
si e clus e ’) (Figu e 1). The mean simila i y coe icien
(SC) ac oss 10 uns was 0.984 a K=3.A K= 4, a spli
wi hin he No dic clus e was obse ed, bu he d op o
SC o 0.534 indica ed a iable assignmen s o b eeds
ac oss uns and lack o addi ional s ong high-le el sub-
s uc u e among he popula ions. The e o e, sepa a ing
he en i e da ase in o h ee clus e s was chosen as he
inal global con igu a ion.
To dissec he gene ic s uc u e wi hin he h ee clus-
e s, STRUCTURE analysis was u he applied o each
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o hem sepa a ely. In he No dic clus e , he mos con-
sis en g ouping o 11 no h Eu opean sheep b eeds was
achie ed a K= 7 (SC = 0.641), wi h he mean SC an-
ging om 0.250 o 0.314 a Ko he han se en. B eeds
o igina ing om he same coun y (e.g. Finnsheep and
Finnish G ey Land ace) o om he neighbo ing egions
(e.g. he Icelandic Sheep and he Fae oe Island Sheep)
ended o clus e oge he (Figu e 1).
The Fa - ailed sheep clus e was composed mainly o he
coa se-wool na i e b eeds om he Caucasus and s eppes
o he Caspian basin and Kazakhs an. Su p isingly, he
no he n sho - ailed coa se-wool Romano Sheep was
Table 1 Gene ic di e si y wi hin 16 egional g oups
Geog aphical egion Regional g oup N H
T
R
Caucasus Sou h Caucasus* 6 0.802 0.020 6.57
No h Caucasus 5 0.795 0.017 6.24
S a opol 3 0.792 -0.005 6.04
Caspian dep ession 3 0.795 0.023 6.19
Asia Kazakhs an and eas o Caspian Sea* 6 0.804 0.037 6.45
Al ai 2 0.795 0.004 6.41
Bu ya ia* 2 0.802 -0.008 6.42
Eas e n inge o Eu ope Volga egion 2 0.779 0.015 5.88
Wes Russia 3 0.794 -0.041 5.45
Uk aine* 2 0.807 -0.004 6.43
Sou heas Eu ope* 4 0.806 -0.006 6.14
Poland 3 0.759 -0.015 6.24
Finland 2 0.758 0.007 5.35
Scandina ia 6 0.774 0.030 4.59
Denma k 1 0.651 0.028 4.41
Iceland and Fae oe Islands 2 0.746 -0.001 4.95
Numbe o b eeds (N), o al gene di e si y (H
T
), depa u es om Ha dy-Weinbe g equilib ium ( ), and mean allelic ichness (R).
* Regional g oups iden i ied as di e si y ho spo s.
Figu e 1 Clus e ing o 52 sheep b eeds. Indi iduals a e p esen ed as e ical lines di ided in o Kcolo s, ep esen ing cons uc ed popula ions.
The lowes ow ep esen s u he clus e ing o 3 g oups, iden i ied a K= 3, sepa a ely. The No dic g oup is di ided in o 7 subclus e s, while
he Composi e (in he middle) and he Fa - ailed g oups each spli in o 3 subclus e s.
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also assigned in o his clus e . The b eed’s es ima ed ac-
ion o he Fa - ailed clus e was 0.59. Howe e , he mos
consis en subclus e ing o he Fa - ailed clus e was
ob ained a K= 3 (SC = 0.865), wi h he Romano sheep
o ming a dis inc subclus e (Figu e 1). The Andi and he
Ka akul ype sheep b eeds ancho ed he emaining wo
subclus e s. Eigh ou o 14 b eeds showed pa ial and
a ying membe ships o he wo subclus e s, indica ing
hei admixed o igin (Figu e 1).
The Composi e clus e hos ed he emaining 26 syn-
he ic semi- and ine-wool sheep b eeds ha we e spli
in o h ee gene ic subclus e s (SC = 0.932). The h ee
subclus e s iden i ied ollowed a pa e n o geog aphical
sepa a ion: long-wool Ma sh and Texel ype b eeds om
he no h g ouped in o subclus e I (ligh blue); ine-wool
b eeds om he Caucasus, Kazakhs an and Bu ya ia
o med subclus e II (ligh g een) and he sou he n Eu -
opean Zackel ype b eeds g ouped in o subclus e III
(pink, Figu e 1). O he nine Eu opean, Caucasian and
Asian sheep b eeds had pa ial membe ship o mul iple
clus e s, which ep esen s mo e di e se ances ies in he
p ocess o b eed de elopmen (Figu e 1).
The PCoA esul s we e qui e in acco dance wi h he
STRUCTURE esul s. The b eeds om he abo e men-
ioned No dic clus e we e sepa a ed om he o he
b eeds on Axis I, which explained 48% o he dis ance
ma ix (Figu e 2). On Axis II, b eeds om he Fa - ailed
clus e we e sepa a ed om he Composi e clus e
b eeds, which explained an addi ional 7%. A no able
excep ion was he Romano Sheep whose yellow ci cle
in Figu e 2 (a -0.085,-0.004) sugges ed he b eed’sclus-
e ing wi h he No dic a he han he Fa - ailed b eeds
(Figu e 2). This ma ched ou p io expec a ions on he
basis o pheno ypic cha ac e s be e han he STUC-
TURE esul .
The p opo ions o No dic, Fa - ailed and Composi e
gene ic ances ies wi hin each o he egional g oups
s udied a e p esen ed in Figu e 3. The highes p opo -
ion o Fa - ailed ances y was eco ded a he sou he n
pe iphe y o he s udied dis ibu ion, which g adually
dec eased no hwa ds and was he smalles in he no h-
e n egional g oups. The p opo ion o No dic ype
ances y mi o ed his pa e n and was he la ges in he
no he n egional g oups and dec eased sou hwa ds.
The 16 egional g oups had simila p opo ions o Com-
posi e ances y, wi h he excep ion o S a opol and
Caspian dep ession egional g oups, whe e he p opo -
ion o Composi e ances y was highes , and he no h-
e nmos and sou he nmos egional g oups, whe e he
Composi e ances y p opo ion was leas .
Geog aphical pa e ns in gene ic di e si y
To educe he e ec o possible ecen b eed-speci ic
ac o s on he o e all geog aphical dis ibu ion o
gene ic di e si y, a syn he ic map o gene ic di e si y
was based on he o al gene di e si y (H
T
) o iple so
neighbo ing b eeds (Figu e 4). The highes di e si y was
ound in he sou he n egion o he s udied a ea: Bu ya-
ia (sou h Sibe ia), Caspian Sea and Black Sea basins. I
dec eased g adually in Cen al and no he n Eu ope and
he lowes H
T
alues we e eco ded o sou he n Scandi-
na ia (Figu e 4). The end can be obse ed also based
on wi hin b eed es ima es (Addi ional ile 3: Figu e S1).
A signi ican bu weak posi i e co ela ion ( =0.382,P
< 0.05) was calcula ed be ween he expec ed he e ozyg-
osi y and he le el o admix u e based on global
STRUCTURE esul s (K= 3) o he 52 sheep b eeds
s udied, sugges ing ha admix u e does no explain he
p esence o di e si y ho spo s, hough i can con ibu e
o i in some a eas.
Analysis o molecula a iance (AMOVA)
We es ed he ex en o popula ion di e en ia ion using
AMOVA in he whole da ase , as well as g ouping
Figu e 2 P incipal coo dina e plo o b eeds based on Cho d dis ance. Axis I explains 48% o he a ia ion, axis II explains 7% o he
a ia ion. B eeds om No dic clus e (based on STRUCTURE) a e ma ked wi h ed, b eeds om Fa - ailed clus e a e ma ke wi h yellow and
b eeds om he Composi e clus e a e ma ked wi h black ci cles.
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b eeds acco ding o geog aphical egions ( he Caucasus,
Asia, o he eas e n inge o Eu ope), and acco ding o
he 15 egional g oups (excluding he Danish g oup
ep esen ed by a single b eed) (Table 2). As expec ed,
mos gene ic a ia ion (> 86%) was e ained wi hin he
b eeds, whe eas only 0.41% o 0.95% (P<0.001)o he
a ia ion could be explained by geog aphical pa i ioning
(Table 2). The be ween-b eed a ia ion wi hin each o
he h ee gene ic subclus e s was signi ican (P<0.001),
anging om 2.48% (Fa - ailed subclus e ) o 13.71%
(No dic subclus e ) (Table 2). In ou da a, using gene ic
clus e ing in AMOVA gi es highe be ween g oups a -
iance han using geog aphical ca ego iza ions.
Co e-se analysis
O he 52 sheep b eeds 24 had con ibu ions o he
co e-se when he 4 weigh ings (l=0,0.2,0.5,1)o
wi hin-b eed di e si y we e conside ed. The 24 b eeds
ep esen ed all he 16 egional g oups, excep hose o
he Al ai and Bu ya ia egions. The dis ibu ion o
b eeds was ela i ely e en, wi h 1 o 2 sheep b eeds pe
egion, he excep ion being he Scandina ian egional
g oup, which con ibu ed 5 sheep b eeds o his accu-
mula ed co e-se (Addi ional ile 4: Table S3). Looking
a he ou co e-se s sepa a ely, he numbe o con i-
bu ing b eeds inc eased om 8 o 17 when weigh o
wi hin-b eed a iabili y inc eased om 0 o 1 (Table 3).
Resul s o analysis based on gene ic clus e ing a e com-
pa able o hose based on geog aphic egions (Addi-
ional ile 5: Table S4).
E e y es ed scena io wi h educed weigh o wi hin-
b eed a ia ion (l< 1) ga e a signi ican ly highe num-
be o b eeds wi h non-ze o con ibu ion om he a eas
ou side he ho spo egions (all he wo- ailed P alues <
0.02 using Fishe ’s exac es o independence; Table 3,
Addi ional ile 4: Table S3). Looking a he con ibu ion
o he co e-se , hese non-ho spo egion popula ions
comp ised o > 90% o he se . Howe e , op imizing o
global di e si y (l= 1), he e is no signi ican di e ence
( he wo ailed P= 0.77) in he p opo ion o b eeds
included be ween ho spo and non-ho spo egions.
Ve y dis inc i ely, now he co e-se consis s o 65% o
he b eeds om he ho spo egions because he
included ho spo egion b eeds make a signi ican ly la -
ge mean con ibu ion (each ~11%) han he included
b eeds om he non-ho spo egions (each ~3%) (Welch
wo sample - es P= 0.009). Thus he di e si y ho spo
a eas we e impo an o conse ing o al gene ic
Figu e 3 Dis ibu ion o h ee in e ed gene ic clus e s in he s udy egions. Slices in he pie diag ams ep esen Fa - ailed (yellow),
Composi e (black) and No dic ( ed) clus e s. The Caucasus a ea is ep esen ed by ou egions: Sou h Caucasus (1), No h Caucasus (2), S a opol
(3) and he Caspian dep ession (4). The Asian egion is ep esen ed by h ee egions: Kazakhs an and eas o he Caspian Sea egion (5), he Al ai
egion (6) and he Bu ya ia egion (7). The emaining g oups belong o eas e n inge o Eu ope: he Volga egion (8), Wes Russia (9), Uk aine
(10), Sou heas Eu ope (11) Poland (12), Finland (13), Scandina ia (14), Denma k (15) and Iceland and he Fae oe Islands (16).
Figu e 4 Con ou syn he ic map o o al gene ic di e si y (H
T
) calcula ed o iple s o neighbo ing b eeds. Da ke shading indica es
highe le els o di e si y.
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di e si y in e ms o he e o pe conse ed popula ion
a he han p opo ion o numbe o b eeds o be
conse ed.
Conse a ion p og ams migh be ini ia ed wi h limi ed
in o ma ion. In cases whe e esou ces allow keeping
only a small numbe o b eeds and when he e is no
aim o di e en ia e be ween hei con ibu ions o he
co e-se (assuming equal con ibu ions), he maximum
amoun o gene ic di e si y would be main ained by gi -
ing p io i y o b eeds om he di e si y ho spo egions.
In he scena io o 5 b eeds, ou o hem a e om he
ho spo a eas (Addi ional ile 6: Table S5). The p opo -
ion o ho spo b eeds was educed om 80% o 45%
when assuming esou ces o keep 20 b eeds. This la e
se is simila o 17 b eeds iden i ied as con ibu o s o
he co e-se when l= 1 (Addi ional ile 4: Table S3),
bu includes also h ee a - ailed popula ions om he
Caucasus (Bozakh, Tushin and Lezian). These esul s
ag ee wi h he idea o ha ing he ini ial conse a ion
ocus on ho spo egions.
Discussion
We p esen he e a comp ehensi e gene ic analysis o
sheep popula ions o igina ing om a b oad geog aphical
a ea o he Eu asian subcon inen . Ou esul s de ec ed
he p esence o a sheep gene ic di e si y ho spo loca ed
close o he Nea Eas , he assumed sheep domes ica ion
cen e , and highligh he impo ance o such an a ea in
conse a ion planning. The esul s co espond well wi h
he geog aphical pa e n o gene ic di e si y dis ibu ion
epo ed o ca le (B. au us) [23] and goa (Cap a hi -
cus) [12] as well as a p e ious s udy o Eu opean sheep
Table 2 Analysis o molecula a iance
Sample Numbe o b eeds Numbe o b eed g oups Pe cen age o a iance and signi icance (P)
Wi hin b eeds Among b eeds wi hin g oups Among g oups
Whole da a 52 1 93.56 (< 0.001) 6.44 (< 0.001)
Th ee geog aphical egions* 52 3 93.43 (< 0.05) 6.17 (< 0.001) 0.41 (< 0.001)
15 egional g oups* 51 15 93.68 (< 0.001) 5.38 (< 0.001) 0.95 (< 0.001)
Th ee s uc u e clus e s: 52 3 93.13 (< 0.001) 5.63 (< 0.001) 1.24 (< 0.001)
No dic subclus e 11 1 86.29 (< 0.001) 13.71 (< 0.001)
Composi e subclus e 26 1 95.45 (< 0.001) 4.55 (< 0.001)
Fa - ailed subclus e 15 1 97.52 (< 0.001) 2.48 (< 0.001)
* See Table 1 and suppo ing in o ma ion o de ails.
Table 3 Dis ibu ion o co e-se con ibu ions
Geog aphical Regional g oup l=0 l= 0.2 l= 0.5 l=1
egion B eeds Con B eeds Con B eeds Con B eeds Con
Caucasus Sou h Caucasus* 00000020.17
No h Caucasus 000010.04 1 0.01
S a opol 00000020.04
Caspian dep ession 00000010
Asia Kazakhs an and* eas o Caspian Sea 00000010.14
Al ai 00000000
Bu ya ia* 00000000
Eas e n inge Volga egion 00000010.06
o Eu ope Wes Russia 1 0.04 2 0.11 2 0.20 1 0.03
Uk aine* 00000020.24
Sou heas Eu ope* 000010.04 1 0.10
Poland 1 0.11 1 0.09 1 0.05 1 0.02
Finland 00000010.03
Scandina ia 4 0.56 4 0.51 5 0.42 2 0.10
Denma k 1 0.19 1 0.17 1 0.13 0 0
Iceland and Fae oe Islands 1 0.10 1 0.11 2 0.13 1 0.06
Sum 8191131171
SD 1.03 0.14 1.09 0.13 1.33 0.11 0.68 0.07
Numbe o b eeds (B eeds) and he sum o hei op imal con ibu ions (Con ) o he co e se o each egional g oup using ou di e en weigh ings (l) o he
wi hin-b eed a ia ion.
* Regional g oups in di e si y ho spo .
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[13] which ocused on mo e sou he n b eeds. The con-
g uence ac oss s udies sugges s he pa e n o be genu-
ine, hough la ge numbe o ma ke s could be
desi able. Based on obse ed allele numbe , we can
expec he eliabili y o be app oxima ely simila as in a
s udy o 300-400 unbiased bi-allelic SNPs [24]. Howe e ,
since s udies o humans do no sugges g ea disc epan-
cies ac oss nuclea ma ke ypes as long as asce ain-
men bias can be a oided [19,20,25], we expec he
p esen ed gene al di e si y pa e ns o be obus . Since
in ou analysis conse a ion op imiza ion was based on
hesameda aused ode ine hedi e si yho spo ,ou
gene al ecommenda ion o conside ing ho spo egions
ough o be sound.
Li es ock gene ic di e si y ho spo s ha e been sug-
ges ed o be e y impo an o conse a ion because
he domes ic animal s ocks associa ed wi h hem migh
possess allelic a ia ion om wild ances o s, which, due
o a sequence o ounding e en s, was los du ing he
dispe sion o animals owa ds he no he n pa s o he
con inen [14]. Howe e , o he bes o ou knowledge
his ques ion has no been di ec ly add essed p e iously.
Ou esul s p o ide addi ional e idence o he impo -
ance o hese egions, while indica ing an impo an
e inemen o he conse a ion goal. Ou esul s do no
sugges ha a la ge p opo ion o popula ions om
hese a eas needs o be conse ed, bu a he sugges
mo e emphasis be placed on each conse ed di e si y
ho spo popula ion. This dis inc ion, howe e , is highly
ele an o domes ic species, whe e managemen uni s
a e in mos cases clea ly de inable as b eeds. Fu he he
esul s suppo o di ec ing he i s conse a ion
esou ces o wo k on ho spo egions.
O he h ee iden i ied No he n Eu asian gene ic clus-
e s, he No dic clus e was ep esen ed by na i e and
old comme cial sheep b eeds adap ed o li e unde cold
and we no he n Eu opean clima ic condi ions. This
g oup includes b eeds such as Gu e, Icelandic Sheep
and Finnsheep, which descended om he sheep s ock
in he i s dispe sion e en o Eu ope [4]. S ic b eed
bounda ies o e a long pe iod and geog aphical isola-
ion, pa icula ly o insula b eeds ( he Icelandic Sheep
and he Fae oe Island Sheep), a e cha ac e is ic o he
g oup and ha e esul ed in a unique and gene ically
highly he e ogeneous pool o No dic sheep popula ions
(Table 2).
The la ge Composi e clus e wi h pa ial ances y om
imp o ed wes e n b eeds con ains gene ically a iable
ine- and semi- ine-wool sheep b eeds o admixed o igin
wi h mode a e di e en ia ion be ween he b eeds. The
p esence o subs uc u e wi hin he clus e e lec s he
di e ences in he b eeding ends wi hin he o me
So ie Union ha ook place in he middle o he las
cen u y. The sheep in he wes e n pa o Russia and
Volga egions ha e Ma sh-Texel ype composi e ances-
y esul ing om c ossing local popula ions wi h B i ish
ype long-wool sheep (Figu e 1). The second subclus e
wi hin he Composi e g oup includes he b eeds p e a-
len in he Caucasus, he S a opol egion and he Cas-
pian basin, ano he geog aphical cen e o pu pose ul
c ossb eeding, wi h a signi ican gene ic componen o
he Me ino ype sheep. The hi d subclus e wi hin he
Composi e clus e is ancho ed by wo Zackel ype
moun ain sheep popula ions, P amenka and Kuchugu ,
and e lec s a common ances y o he majo i y o
b eeds wi hin he subclus e . The g ouping o Tsigai in
he same subclus e con i ms he assump ion ha his
b eed was s ongly in luenced by Zackel (e.g. see [17]).
Mos o he popula ions o he Composi e clus e also
ep esen gene ic di e si y o local o igins as he upg ad-
ing was pe o med on he basis o local sheep popula-
ions, mixing hem wi h a numbe o imp o ed b eeds
o o eign ances y o combine desi ed p oduc ion and
obus ness cha ac e is ics.
The Fa - ailed clus e hos ed e y a iable na i e
coa se-wool popula ions, li ing unde a a ie y o cli-
ma ic condi ions, anging om semi-dese and s eppe
egions a ound he Caspian Sea and Cen al Asia o
Caucasian moun ain e ains. The di e en ia ion o a -
ailed sheep om he o he s indica es es ic ed gene
low be ween s eppe o moun ain en i onmen s in cen-
al Eu asia and coole and mois e no he n a eas o
he con inen . The gene pool o he a - ailed sheep
di ided in o he moun ain ype sheep (e.g. Andi and
Lezgian) and s eppe-dese ypes (e.g. Gala and Ka akul).
Howe e , he majo i y o a - ailed b eeds ha e hei
ances ies in bo h o hese subclus e s (Figu e 1), which
oge he wi h low di e en ia ion es ima es indica es sub-
s an ial gene low be ween hem. This ag ees wi h he
adi ional sheep b eeding p ac ices in he Caucasus,
which p omo e gene low h ough he long-dis ance
nomadic pas u ing o animals. G ouping o Romano
sheep wi hin he Fa - ailed clus e (Figu e 1) should be
ega ded cau iously.
Decisions on adap a ion conse a ion should la gely
be based on eliable pheno ypic e alua ions. In humans,
gene ic and pheno ypic di e si y ag ee [26], bu selec ion
migh a ec pheno ypes educing co ela ion be ween
pheno ypic di e gence and gene al genomic ela edness
[27,28]. This is pa icula ly ue o li es ock which
would imply need o es ing (ecological) exchangeabili y
(as in [29]). Un o una ely his is e y di icul . A la ge
p opo ion o he necessa y pheno ypic in o ma ion
exis s only as in o mal knowledge o local b eede s.
E en he mo e igidly collec ed da a is a ely compa -
able be ween en i onmen s.
Molecula da a can ha e a ole in poin ing ou po en-
ial conse a ion gaps when pheno ypic knowledge is
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limi ed. The usabili y o app oaches based on molecula
ma ke da a in se ing conse a ion p io i ies can be
g ea ly imp o ed by genome-wide su eys o molecula
a ia ion [30]. Fo example, scanning ens o housands
o SNP ma ke s has he po en ial o iden i y selec ed
loci [31] and allow compa ison o he conse a ion
alues o se e al popula ions, bo h in he neu al and
non-neu al con ex [30]. Howe e , e en wi h ull gen-
ome sequences, alua ion o popula ions can p o e o
be di icul due o incomple e unde s anding o he biol-
ogy o he o ganisms and poo ly de inable conse a ion
goals.
We used neu al molecula da a o a speci ic se o
popula ions and applied he me hod o Caballe o and
To o [15] o calcula e op imal con ibu ions o Eu asian
sheep b eeds o he co e se , which would minimize he
mean kinship in he se and maximize N
e
and gene ic
di e si y o he species. While gi ing mo e emphasis o
di e gence has heo e ical appeal, i did no inc ease
ecological o pheno ypic he e ogenei y in he p e e ed
se o b eeds compa ed wi h he maximiza ion o global
di e si y (and N
e
). Maximiza ion o global di e si y
p io i ized a mo e di e se se o b eeds o igina ing om
a ange o biogeog aphic en i onmen s and ha ing di -
e en gene ic his o ies. Though he se looks easonable,
we acknowledge ha i is based on incomple e da a and
we a e hesi an o conclude ha his pa icula design is
op imal.
Conclusions
Neu al a ia ion sugges ed a gene al ule o humb o
a ou b eeds om he di e si y ho spo egions in he
i s phase o in si u and ex si u conse a ion ac ions. In
he inal design, howe e , app oxima ely equal popula-
ion p esen a ion ac oss en i onmen s is ecommended,
bu s ill highe pe popula ion emphasis in a eas o high
di e si y is sugges ed. A comp ehensi e alua ion o
b eeds, pa icula ly wi hin each physical en i onmen ,
should conside p oduc ion sys ems, impo an biologi-
cal cha ac e is ics and a ailable gene ic in o ma ion, as
well as conside a ion o he p obabili y o success and
he ex inc ion isk o b eeds.
Me hods
Biological samples
In o al, 1675 animals ep esen ing 52 sheep b eeds
we e s udied (Addi ional ile 2: Table S2). Sheep we e
sampled om h ee geog aphical egions: The Caucasus,
Asia, and he eas e n inge o Eu ope, including cen al
and wes e n Russia. Each geog aphical egion was
u he subdi ided in o egional g oups. The Caucasian
a ea was composed o he sou he n Caucasus ( he ol-
lowing b eeds we e sampled: Aze baijan Moun ain Me -
ino, Bozakh, Gala, Ka abakh, Mazekh, Tushin), no he n
Caucasus (Andi, Dages an local, Dages an Moun ain
Me ino, Ka achai, Lezgian), S a opol (Caucasian, No h
Caucasian Mu on-Wool, S a opol), and he Caspian
dep ession (Aksa aisk ype o So ie Mu on-Wool,
G ozny, Volgog ad). The Asian a ea was subdi ided in o
he Kazakhs an and eas o he Caspian Sea g oup
(Dege es Mu on-Wool, Kazakh A kha -Me ino, Kazakh
Edilbai, Kazakh Finewool, Russian Edilbai, Russian Ka a-
kul), Al ay (Go no-Al ay local, Kulunda), and he Bu ya-
ia g oup (Baida ak, T ansbaikal Finewool). The
emaining nine g oups co e ed he eas e n inge o
Eu ope: he Volga egion (Kuibyshe , Opa in), wes e n
Russia (Kuchugu , Romano , Russian Romney Ma sh),
Uk aine (Ca pa hian Moun ain, Sokolsk), sou heas Eu -
ope (Molda ial Ka akul, Molda ial Tsigai, P amenka,
Russian Tsigai), Poland (Olkuska, Swinia ka, W zo-
sowka), Finland (Finnsheep, Finnish G ey Land ace),
Scandina ia (Swedish Rya Sheep, Swedish Go land
Sheep, Swedish Gu e Sheep, No wegian Rygja Sheep,
No wegian Che io , No wegian Fe al Sheep), Denma k
(Danish Texel), and Iceland and he Fae oe Islands (Ice-
landic Sheep, Fae oe Island Sheep). Un ela ed animals
we e sampled based on pedig ee eco ds ( wo p e ious
gene a ions) o a me s’knowledge.
Genomic DNA was ex ac ed om blood as desc ibed
in [32], o om skin samples using DNeasy Tissue Ki
(Qiagen, C awley, Wes Sussex, UK). P io o DNA
ex ac ion, skin samples s o ed in e hanol we e washed
wice wi h phospha e bu e ed saline o emo e ixa i es.
Gene ic loci
The polyme ase chain eac ions (PCR) o 20 mic osa-
elli es (Addi ional ile 1: Table S1) we e pe o med as
desc ibed in [33] and geno yped using he MegaBACE™
500 DNA Sequence (Ame sham Biosciences). F agmen
sizing was pe o med using he MegaBaceTM Gene ic
P o ile 2.2 o F agmen P o ile 1.2 (Ame sham Bios-
ciences). Geno ypes o 20 mic osa elli es we e a ailable
in he ea lie s udies o he Romano sheep [34] and
o he 11 b eeds om Finland, Scandina ia, Denma k,
Iceland and he Fae oe Islands [16].
S a is ical analysis
The mic osa elli e loci we e cha ac e ized by he o al
numbe o alleles, expec ed he e ozygosi y o o al gene
di e si y [35], sample-size-co ec ed allelic ichness [36]
co esponding he e expec ed allele numbe in a sample
o nine diploid indi iduals, and F-s a is ics using FSTAT
2.93 [37]. F-s a is ics we e es ima ed using Wei and
Cocke ham [22] me hod whe e and θco espond o
W igh ’s coe icien s F
IS
and F
ST
, espec i ely. The
gene ic ela ionships among b eeds we e analyzed using
p incipal coo dina e analysis (PCoA) as implemen ed in
PAST 1.73 [38] using he Cho d dis ance [39].
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A model-based Bayesian clus e ing analysis was used
o in e popula ion s uc u e and he le el o admix u e
in he sheep b eeds implemen ed in STRUCTURE 2.2
[40]. The STRUCTURE algo i hm assumes Kpopula-
ions, each o which is in Ha dy-Weinbe g and linkage
equilib ium and cha ac e ized by a se o allele equen-
cies a each locus. Analysis was pe o med wi h a bu n-
in leng h o 20,000 ollowed by 100,000 Ma ko chain
Mon e Ca lo i e a ions o each o K= 1 o 10, wi h en
eplica e uns o each Kusing independen allele e-
quencies and an admix u e model. Resul s ac oss en
uns a each Kwe e compa ed based on simila i y coe -
icien s (SC) as p e iously desc ibed in [41]. The b eeds
we e assigned o wide clus e s based on majo ances y
and submi ed o a second ound o STRUCTURE ana-
lysis pe o med wi hin each wide clus e .
A linea eg ession analysis was pe o med o s udy
he in luence o b eed ances y di e si y (admix u e)
on he le el o gene ic di e si y. Ances y di e si y o
each b eed was calcula ed as 1-Σ(q
k
)
2
,whe eq
k
is an
a e age ac ion o he b eed’s gene ic ances y om
he ksepa a e gene ic clus e s a he op imal K,iden i-
ied in STRUCTURE analysis. To examine he signi i-
cance o mixed ances ies as sou ces o wi hin-b eed
di e si y, he ob ained ances y di e si y alues we e
compa ed wi h he unbiased expec ed he e ozygozi y
es ima es.
Fo he geog aphical plo ing o gene ic di e si y pa a-
me e s, la i ude and longi ude alues o each b eed
we e ob ained om he cen e o he sample dis ibu-
ion. The A cView GIS 9.1 (En i onmen al Sys ems
Resea ch Ins i u e, ESRI, Redlands, CA, USA) was used
o map he allelic ichness andexpec edhe e ozygosi y
o each b eed and he su ace was ex apola ed o a ull
ec angle. This was based on he In e se Dis ance
Weigh ed in e pola ion me hod [42], which assumes
each inpu poin o ha e a local in luence ha
diminishes wi h dis ance. A syn he ic map o he dis i-
bu ion o local o al gene di e si y (H
T
) and θcalcula ed
o he geog aphically neighbo ing iple s o popula-
ions was done simila ly. Popula ion iple s we e
o med using Delaunay iangula ion me hod implemen-
ed in he p og am T iangle [43].
Componen s o wi hin- and be ween-b eed gene ic
di e si y we e calcula ed based on he molecula coan-
ces y o popula ions ollowing he me hod desc ibed
by Caballe o and To o [15]. The molecula coances y
be ween wo indi iduals is he p obabili y ha wo
alleles a he locus aken a andom om each indi i-
dual a e alike in s a e. In a s uc u ed popula ion wi h n
b eeds he molecula coances y be ween b eeds iand j
(
ij
) is he a e age ac oss loci and ac oss indi iduals.
De ining he wi hin-b eed a e age coances y as
n
ij
ij
=∑,
2, he o al popula ion coances y as
n
ij
ij
=∑,
2,Nei’s minimum dis ance as
D
ij
ii jj
ij
=+−
2and he a e age Nei’s minimum dis-
ance as D
D
n
ij
ij
=∑,
2, hen he o al gene di e si y o
expec ed he e ozygosi y ()GD
T=−1is pa i ioned
in o componen s wi hin b eeds ()GD
WS =−1and
ano he be ween b eeds ()GD D
BS =−=
.
The impo ance o di e en b eeds has been calcula ed
based on he con ibu ion o each b eed o a pool o ani-
mals o a co e se ha would maximize i s gene ic di e -
si y (e.g. [15,44]). In he p esen s udy, he co e se e e s
o he smalles se o sheep b eeds ha s ill encompasses
he neu al gene ic di e si y in he species using he co-
ances y measu e de ailed abo e. These op imal con i-
bu ions can also be applied wi h a weigh ed (l) combina-
ion o wi hin- and be ween-b eed componen s o gene
di e si y

()1−+

D
. Maximizing global di e si y is
achie ed by gi ing equal weigh s o wi hin- and be ween-
b eed di e si y (l= 1), while maximizing be ween-b eed
a ia ion is achie ed by igno ing wi hin-b eed di e si y
(l= 0). Two in e media e l alues we e ecommended
in ea lie s udies. Piyasa ian and Kingho n [45] sugges ed
gi ing i e imes weigh o he be ween b eed a ia ion as
o he wi hin-b eed a ia ion (l= 0.2), e lec ing he
speed by which gene ic change can be made ac oss popu-
la ions compa ed wi h selec ion wi hin one la ge mixed
popula ion. Bennewi z and Meuwissen [46] p oposed a
weigh ing based on maximizing he o al gene ic a iance
o a hypo he ical quan i a i e ai , which is equi alen by
using a weigh ing ac o o l=0.5.These ou l alues
we e applied in es ima ing he op imal con ibu ions
using a simula ed annealing algo i hm [47].
Addi ional ma e ial
Addi ional ile 1: Table S1 - Ma ke di e si y pa ame e s. PDF ile
wi h lis o mic osa elli es and hei ch omosomal loca ion, o al numbe
o alleles, expec ed unbiased he e ozygosi y, and es ima es o wi hin-
popula ion ( ) and among-popula ion (θ) ixa ion indices.
Addi ional ile 2: Table S2 - Table o he name o sheep b eeds,
hei o igin, demog aphic s a us and di e si y pa ame e s. PDF ile
wi h da a on pe popula ion sample size, expec ed he e ozygosi y,
wi hin-b eed ixa ion index ( ), allelic ichness, and numbe o p i a e
alleles.
Addi ional ile 3: Figu e S1 - Addi ional syn he ic maps. PDF ile
syn he ic maps o wi hin-b eed di e si y and b eed di e en ia ion.
Addi ional ile 4: Table S3 - B eed-wise op imal con ibu ions o a
co e-se o di e en weigh ings o he wi hin-b eed a ia ion.PDF
ile wi h de ailed da a summa ized in Table 3.
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