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Towards a strategy for the conservation of the genetic diversity of European cattleEU project ResGen CT98-118
UtrechtJ.A. LenstraI.J. NijmanMalleG. MommensBerneG. DolfRoslinJ.L. WilliamsP. WienerD. BurtonDublinD. BradleyD.E. MacHughR.A. FreemanJouy-en-JosasK. Moazami-GoudarziD. Laloë
GiessenG. ErhardtO. JannC. WeimannE. PrinzenbergHannoverB. HarliziusKielE. KalmC. LooftMunichI. MedugoracGrenobleP. TaberletG. LuikartC. Maudet
PiacenzaP. Ajmone-MarsanR. NegriniE. MilanesiViterboA. ValentiniM.C. SavareseC. MarchitelliMilanoM. ZanottiG. CeriottiCampo-bassoF. PillaA. BruzzoneD. Iamartino
MadridS. DunnerJ. CañónZaragozaP. ZaragozaC. RodellarI. Martín-BurrielBarcelonaA. SanchezJ. PiedrafitaPortoA. Beja-PereiraN. Ferrand
TjeleL.E. HolmOsloI. OlsakerJokioinenJ. KantanenReykjavikE. EythorsdottirUppsalaB. DanellVilnasI. MiceikieneJelgavaZ. GrislisTartuH. Viinalass
Sheep and goat genetic resources in marginal ruralareas sirs.epfl.ch/projets/econogene/
Geographical patterns ofcattle, sheep and goat diversity
Clines, clusters, introgression, and a conservation dilemma
� Reconstruct history of the genetic landscape migration, introgression, breed formation> partitioning of diversity, relationships of breeds,
geographic effects
� Compare cattle, sheep and goat
� Indicate priorities for conservation
Geographical patterns ofcattle, sheep and goat diversity
Clines, clusters, introgression, and a conservation dilemma
2
� Reconstruct history of the genetic landscape migration, introgression, breed formation> partitioning of diversity, relationships of breeds,
geographic effects
� Compare cattle, sheep and goat
� Indicate priorities for conservation
Geographical patterns ofcattle, sheep and goat diversity
Clines, clusters, introgression, and a conservation dilemma
� Microsatellites- cattle, core data set : 77 breeds, 25-50 animals/breed,
30 markers- cattle, previous data : 104 breeds, 25-50 animals/breeds,
15-26 markers- sheep : 56 sheep, 50 animals/breed, 31 markers (Giessen)- goat : 46 breeds, 50 animals/breeds, 30 markers (Berne, Madrid)
� AFLP (Utrecht, Piacenza )
� SNPs in candidate genes
� mtDNA variation in sheep and goat
� Y-chromosomal SNPs ( SNPs in 7.5 kbUtrecht, Hubrecht Laboratory )
Geographical patterns ofcattle, sheep and goat diversity
Clines, clusters, introgression, and a conservation dilemma
3
� Microsatellites- cattle, core data set : 77 breeds, 25-50 animals/breed,
30 markers- cattle, previous data : 104 breeds, 25-50 animals/breeds,
15-26 markers- sheep : 56 sheep, 50 animals/breed, 31 markers (Giessen)- goat : 46 breeds, 50 animals/breeds, 30 markers (Berne, Madrid)
� AFLP (Utrecht, Piacenza )
� SNPs in candidate genes
� mtDNA variation in sheep and goat
� Y-chromosomal SNPs ( 7.5 kb, 800 animals,Utrecht, Hubrecht Laboratory )
Geographical patterns ofcattle, sheep and goat diversity
Clines, clusters, introgression, and a conservation dilemma
� Microsatellites- cattle, core data set : 77 breeds, 25-50 animals/breed,
30 markers- cattle, previous data : 104 breeds, 25-50 animals/breeds,
15-26 markers- sheep : 56 sheep, 50 animals/breed, 31 markers (Giessen)- goat : 46 breeds, 50 animals/breeds, 30 markers (Berne, Madrid)
Geographical patterns ofcattle, sheep and goat diversity
Clines, clusters, introgression, and a conservation dilemma
� Y-chromosomal SNPs ( 7.5 kb, 800 animals,Utrecht, Hubrecht Laboratory )
Analysis- Model based-clustering of multilocus genotypes- Network representation of genetic distances
4
Model-based clusteringStructure, J. Pritchard (2000)
� Originally designed for detection of stratification in geneticassociation studies
� Finding subdivision by optimization of Hardy-Weinbergand linkage equilibria via Monte-Carlo procedure
� Bayesian assignment of individuals to k clusters
� Application to human genotypes(Rosenberg et al., 2002, Science 298, 2381-2385 ) praised by the Lancetas ‘ the most relevant biomedical publication in 2002’and already in textbooks
k
2
SwedishRed Polled
Bohemian RedPolish Red
Red Danish Angeln
MRYRed HF dual
Red HF dairyGroningen WH
Swiss HFBritish HF
Jutland 1950Dutch Belted
German BP-WFriesian-Holland
Belgian BlueGerm. Shorthorn
Maine-AnjouNormande
Bretonne BPCharolais
AyrshireHighland
HerefordDexter
Aberdeen AngusJersey
GuernseyBetizu A
Betizu BPirenaica
Blonde d'AquitaineLimousin
BazadaisGasconne
AubracSalers
MontbéliardPezzata Rossa Ital.
Germ. SimmentalSimmental
HinterwaelderGerman Yellow
EvoleneEringer
PiemonteseGrigio Alpina
RendenaCabannina
Swiss BrownGerm. Br. Württemberg
Germ. Br. BavariaGerm. Br. OrigBruna Pirineds
MenorquinaMallorquina
RetintaMorucha
Avilena
SayaguesaAlistano
Rubia GallegaAsturiana Valles
Asturiana MontanaTudanca
Tora de LidiaCasta Navarra
Hungarian Grey Istrian
PodolicaRomagnola
ChianinaN'Dama
SombaLagunaire
BorgouZebu Peul
3
North-West
ASVASM TUDALI
SAYAVIMOR
RET
PIR
BPI
GAS
AUB
SAL
LIMBAZ
BPN
NOR
CHAMBE
SIM
MAN
GW
H
FRH
MRY
BDA
SWB
JERGUE
DARANG
JUT
BOR
ERIEVORGA
DUB
MENMAL
SRP
HER
ABASHI
DEX
BWB
BPWRH2, RHD
GSHGSI
HIW
GYE
BRBGBO
BRW
BET
POR
IST
REN
CAB
CHI
ROM
POD
HGYGRA
TDL
CNA
AYR
HFR
PIM
Model-based clustering of cattle
AfricaEurope
5
SwedishRed Polled
Bohemian RedPolish Red
Red Danish Angeln
MRYRed HF dual
Red HF dairyGroningen WH
Swiss HFBritish HF
Jutland 1950Dutch Belted
German BP-WFriesian-Holland
Belgian BlueGerm. Shorthorn
Maine-AnjouNormande
Bretonne BPCharolais
AyrshireHighland
HerefordDexter
Aberdeen AngusJersey
GuernseyBetizu A
Betizu BPirenaica
Blonde d'AquitaineLimousin
BazadaisGasconne
AubracSalers
MontbéliardPezzata Rossa Ital.
Germ. SimmentalSimmental
HinterwaelderGerman Yellow
EvoleneEringer
PiemonteseGrigio Alpina
RendenaCabannina
Swiss BrownGerm. Br. Württemberg
Germ. Br. BavariaGerm. Br. OrigBruna Pirineds
MenorquinaMallorquina
RetintaMorucha
Avilena
SayaguesaAlistano
Rubia GallegaAsturiana Valles
Asturiana MontanaTudanca
Tora de LidiaCasta Navarra
Hungarian Grey Istrian
PodolicaRomagnola
ChianinaN'Dama
SombaLagunaire
BorgouZebu Peul
3
4
> 3 main groups of breeds- North-West- Central- Mediterranean
North-West Central Mediterranean
Model-based clustering of cattle
k
2
AfricaEurope
ASVASM TUDALI
SAYAVIMOR
RET
PIR
BPI
GAS
AUB
SAL
LIMBAZ
BPN
NOR
CHAMBE
SIM
MAN
GW
H
FRH
MRY
BDA
SWB
JERGUE
DARANG
JUT
BOR
ERIEVORGA
DUB
MENMAL
SRP
HER
ABASHI
DEX
BWB
BPWRH2, RHD
GSHGSI
HIW
GYE
BRBGBO
BRW
BET
POR
IST
REN
CAB
CHI
ROM
POD
HGYGRA
TDL
CNA
AYR
PIM
HFR
AfricaEurope3
AlpineIntermediates
AlpineBrown
AlpineWest
3 5
LowlandPied
BalticRed
NWIntermediates
Iberian PodolianFrenchBrown
British
4
Germanic Central Mediterranean
4
Model-based clustering of cattle
SwedishRed Polled
Bohemian RedPolish Red
Red Danish Angeln
MRYRed HF dual
Red HF dairyGroningen WH
Swiss HFBritish HF
Jutland 1950Dutch Belted
German BP-WFriesian-Holland
Belgian BlueGerm. Shorthorn
Maine-AnjouNormande
Bretonne BPCharolais
AyrshireHighland
HerefordDexter
Aberdeen AngusJersey
GuernseyBetizu A
Betizu BPirenaica
Blonde d'AquitaineLimousin
BazadaisGasconne
AubracSalers
MontbéliardPezzata Rossa Ital.
Germ. SimmentalSimmental
HinterwaelderGerman Yellow
EvoleneEringer
PiemonteseGrigio Alpina
RendenaCabannina
Swiss BrownGerm. Br. Württemberg
Germ. Br. BavariaGerm. Br. OrigBruna Pirineds
MenorquinaMallorquina
RetintaMorucha
Avilena
SayaguesaAlistano
Rubia GallegaAsturiana Valles
Asturiana MontanaTudanca
Tora de LidiaCasta Navarra
Hungarian Grey Istrian
PodolicaRomagnola
ChianinaN'Dama
SombaLagunaire
BorgouZebu Peul
k
2
� 8 clusters of breeds
� 2 intermediate zones
� New classification of breeds
ASVASM TUDALI
SAYAVIMOR
RET
PIR
BPI
GAS
AUB
SAL
LIMBAZ
BPN
NOR
CHAMBE
SIM
MAN
GW
H
FRH
MRY
BDA
SWB
JERGUE
DARANG
JUT
BOR
ERIEVORGA
DUB
MENMAL
SRP
HER
ABASHI
DEX
BWB
BPWRH2, RHD
GSHGSI
HIW
GYE
BRBGBO
BRW
BET
POR
IST
REN
CAB
CHI
ROM
POD
HGYGRA
TDL
CNA
AYR
PIMPRI
HFR
6
AfricaEurope3
AlpineIntermediates
AlpineBrown
AlpineWest
3 5
LowlandPied
BalticRed
NWIntermediates
Iberian PodolianFrenchBrown
British
4
Germanic Central Mediterranean
4
Model-based clustering of cattle
SwedishRed Polled
Bohemian RedPolish Red
Red Danish Angeln
MRYRed HF dual
Red HF dairyGroningen WH
Swiss HFBritish HF
Jutland 1950Dutch Belted
German BP-WFriesian-Holland
Belgian BlueGerm. Shorthorn
Maine-AnjouNormande
Bretonne BPCharolais
AyrshireHighland
HerefordDexter
Aberdeen AngusJersey
GuernseyBetizu A
Betizu BPirenaica
Blonde d'AquitaineLimousin
BazadaisGasconne
AubracSalers
MontbéliardPezzata Rossa Ital.
Germ. SimmentalSimmental
HinterwaelderGerman Yellow
EvoleneEringer
PiemonteseGrigio Alpina
RendenaCabannina
Swiss BrownGerm. Br. Württemberg
Germ. Br. BavariaGerm. Br. OrigBruna Pirineds
MenorquinaMallorquina
RetintaMorucha
Avilena
SayaguesaAlistano
Rubia GallegaAsturiana Valles
Asturiana MontanaTudanca
Tora de LidiaCasta Navarra
Hungarian Grey Istrian
PodolicaRomagnola
ChianinaN'Dama
SombaLagunaire
BorgouZebu Peul
k
2
� Genetic distances?ASVASM TUDALI
SAYAVIMOR
RET
PIR
BPI
GAS
AUB
SAL
LIMBAZ
BPN
NOR
CHAMBE
SIM
MAN
GW
H
FRH
MRY
BDA
SWB
JERGUE
DARANG
JUT
BOR
ERIEVORGA
DUB
MENMAL
SRP
HER
ABASHI
DEX
BWB
BPWRH2, RHD
GSHGSI
HIW
GYE
BRBGBO
BRW
BET
POR
IST
REN
CAB
CHI
ROM
POD
HGYGRA
TDL
CNA
AYR
PIMPRI
HFR
Visualization of distance analysis
� Trees (hierarchical clustering)confounded by reticulation(e.g., relationships of breeds from different clusters)
� Coordinate plots > geospatial gradientsdisplay part of the informationconfounded by inbred breeds
� Networks for more complex situations
7
Same distance
A
B
C
D
Distance analysisexample of reticulation
A
B
C
D
Distance analysisnetworks for reticulated data set
NeighborNet: networks via Neighbor-Joining
8
Danish Red
An
gler
Du
tch B
el ted
Friesian-Holland
GroningenWhite-headed
Meuse-Rhine-Yssel
Germ
an Black-P
ied West
Jutland
British H
olstein
Red Holstein Dual
Red Holstein Dairy
Swiss HolsteinBelgian blue
Maine-Anjou
Po
lish
Red
Bo
hem
ian
Red
CharolaisNormande
Breton Pie-Noire
Jersey
DexterGuernsey
AberdeenAngus Ayrshire
Hereford
ScottishHighland
Piemontese
Serrana de Teruel
Rende
na
Swis
s B
row
n
Ori
gin
al G
erm
an B
row
n
Ger
man
Bro
wn
Cab
ann
ina
Eringer
Evolenard
Germ
an Y
ellow
Sim
men
tal
Pezzata
Ro
ssaItal ian
a
Montbéliard
Hinterw
älder
Grigia
Alpina
Bazadaize
Limousin
Pirenaica
SalersAubracBlonde d’Aquitaine
Istrian
Toro di Lidia
Rub
iaG
alle
ga
Ast
uria
naM
onta
naA
vile
na
Moruch
a
Monchin
a
Betizu
Casta Navarra
RetintaPodolica
Chianina
Romagnola
African zebu
Gasconne
Sayaguesa
Betizu
Distance analysis of cattle breedsNeighbor networks
� Again 3 major groupsNorth-West
Central
Mediterranean
Danish Red
An
gler
Du
tch B
el ted
Friesian-Holland
GroningenWhite-headed
Meuse-Rhine-Yssel
Germ
an Black-P
ied West
Jutland
British H
olstein
Red Holstein Dual
Red Holstein Dairy
Swiss HolsteinBelgian blue
Maine-Anjou
Po
lish
Red
Bo
hem
ian
Red
CharolaisNormande
Breton Pie-Noire
Jersey
DexterGuernsey
AberdeenAngus Ayrshire
Hereford
ScottishHighland
Piemontese
Serrana de Teruel
Rende
na
Swis
s B
row
n
Ori
gin
al G
erm
an B
row
n
Ger
man
Bro
wn
Cab
ann
ina
Eringer
Evolenard
Germ
an Y
ellow
Sim
men
tal
Pezzata
Ro
ssaItal ian
a
Montbéliard
Hinterw
älder
Grigia
Alpina
Bazadaize
Limousin
Pirenaica
SalersAubracBlonde d’Aquitaine
Istrian
Toro di Lidia
Rub
iaG
alle
ga
Ast
uria
naM
onta
naA
vile
na
Moruch
a
Monchin
a
Betizu
Casta Navarra
RetintaPodolica
Chianina
Romagnola
African zebu
Gasconne
Sayaguesa
Betizu
Distance analysis of cattle breedsNeighbor networks
� Again 3 major groupsNorth-West
Central
Mediterranean
Baltic-HighlandRed
Lowland Pied
NW intermediates
British
Iberian
Podolian
French-Pyrenean
Central-WestCentral Brown
Central Intermediates
� Network reproduces clusters
� NW breeds more developed
� Visualization only incomplete
9
Distance analysis of cattle breedsNeighbor networks of clusters
Reduction of data
� African – Iberian relationshipBaltic-Highland
Red
Lowland Pied
NWintermediates
British
Central-West
Iberian
PodolianFrench-Pyrenean
Central Brown
African taurine
Africanzebu
� dairy NW clusters most distal
What about the Y-chromosomes?
Danish Red
An
gler
Du
tch B
el ted
Friesian-Holland
GroningenWhite-headed
Meuse-Rhine-Yssel
Germ
an Black-P
ied West
Jutland
British H
olstein
Red Holstein Dual
Red Holstein Dairy
Swiss HolsteinBelgian blue
Maine-Anjou
Po
lish
Red
Bo
hem
ian
Red
CharolaisNormande
Breton Pie-Noire
Jersey
DexterGuernsey
AberdeenAngus Ayrshire
Hereford
ScottishHighland
Piemontese
Serrana de Teruel
Rende
na
Swis
s B
row
n
Ori
gin
al G
erm
an B
row
n
Ger
man
Bro
wn
Cab
ann
ina
Eringer
Evolenard
Germ
an Y
ellow
Sim
men
tal
Pezzata
Ro
ssaItal ian
a
Montbéliard
Hinterw
älder
Grigia
Alpina
Bazadaize
Limousin
Pirenaica
SalersAubracBlonde d’Aquitaine
Istrian
Toro di Lidia
Rub
iaG
alle
ga
Ast
uria
naM
onta
naA
vile
na
Moruch
a
Monchin
a
Betizu
Casta Navarra
RetintaPodolica Chianina
Romagnola
African zebu
Baltic-HighlandRed
Lowland Pied
NW intermediates
British
Iberian
Podolian
French-Pyrenean
Gasconne
Central-WestCentral Brown
Sayaguesa
Central Intermediates
Alistana
Cattle Y-chromosomesresults also from Götherström et al., 2005 haplotype Y1
haplotype Y2
(3) Europeanaurochs bones!
� at least 2 independent aurochs introgressionevents
� Y2 original haplotype
� Y1 in (1) NW Europe(2) Northern Spain
10
BPWRH2RHD
BPE
SIM
NordicBaltic-Highland RedBritish
Ayrshire-likeLowland PiedNorth-West IntermediateFrench-PyreneanCentral WestCentral IntermediateCentral BrownIberianPodolian
Other colour of first letter(ASV): introgression
ASVASM TUDALIMAR
SAYAVIMOR
ALEMER
RET
PIR
BPI
GAS
AUB
SAL
LIMBAZ
BPN
NOR
CHAMBE
MAN
GW
H
FRH
MRY
BDA
SWB
JERGUE
DARANG
JUT
BOR
ERIEVORGA
DUB
MENM
WFC
EFC
NFCICL
TMK
DOL
WFJ
SRPORPWRP
DBP
HER
ABA
AYR
SHI
DEX
BWB
SIM
HIW
GYE
GBO
BRG
POR
IST
REN
CAB
CHI
ROM
MMA
POD
MOD
SYK
HGY
PRI
GRA
TDL
CNA
FJA
BOH
NVR
SRW
RIN
VANSBW
PBW
AYR
HFR
HFR
HFR
DJE
PIM
PUSPIG
TGV
ILR
BUS
BUS
BUS
ALL
ARQ
MAL
ICL
DOL
SFRBST
GSH
REN
SYK
SBW
ESN
ESR
LBL
LBRLIR LBW
LLGLWB
DAR
WFR VBE
HAR
VGT
GLA
LMP
BPWRH2RHD
2. Differentiation byadaptation, breeding
- divergence of oldBritish breeds
- divergence of dairyNW clusters ( Lowland Pied ,
Baltic-Highland Red , NW intermed. )with Y1 haplotype
Genetic history of European cattle
1. Neolithic migration routes- Mediterranean coast- Africa > Iberia
- Russia > Scandinavia- Danube > France, NW
and wild introgression?
Y1
Y1
BPWRH2RHD
BPE
SIM
NordicBaltic-Highland RedBritish
Ayrshire-likeLowland PiedNorth-West IntermediateFrench-PyreneanCentral WestCentral IntermediateCentral BrownIberianPodolian
Other colour of first letter(ASV): introgression
ASVASM TUDALIMAR
SAYAVIMOR
ALEMER
RET
PIR
BPI
GAS
AUB
SAL
LIMBAZ
BPN
NOR
CHAMBE
MAN
GW
H
FRH
MRY
BDA
SWB
JERGUE
DARANG
JUT
BOR
ERIEVORGA
DUB
MENM
WFC
EFC
NFCICL
TMK
DOL
WFJ
SRPORPWRP
DBP
HER
ABA
AYR
SHI
DEX
BWB
SIM
HIW
GYE
GBO
BRG
POR
IST
REN
CAB
CHI
ROM
MMA
POD
MOD
SYK
HGY
PRI
GRA
TDL
CNA
FJA
BOH
NVR
SRW
RIN
VANSBW
PBW
AYR
HFR
HFR
HFR
DJE
PIM
PUSPIG
TGV
ILR
BUS
BUS
BUS
ALL
ARQ
MAL
ICL
DOL
SFRBST
GSH
REN
SYK
SBW
ESN
ESR
LBL
LBRLIR LBW
LLGLWB
DAR
WFR VBE
HAR
VGT
GLA
LMP
BPWRH2RHD
2. Differentiation byadaptation, breeding,wild introgression
Genetic history of European cattle
3. Historic North-Southcontrasts maintained
- Langue d’oc - d’oïl- Hoch - Niederdeutsch- Catholic - Protestant
Landscape effect?
1. Neolithic migration routes- Mediterranean coast- Africa to Iberia- Danube > central, >NW- Russia > Scandinavia
Y1
Y1
11
� Reconstruct history of the genetic landscape migration, introgression, breed formation> partitioning of diversity, relationships of breeds,
geographic effects
� Compare cattle, goat and sheep
� Indicate priorities for conservation
Geographical patterns ofcattle, sheep and goat diversity
Clines, clusters, introgression, and a conservation dilemma
Central-Mediterranean
Western-Mediterranean
Central/Alpine
Middle-Eastern
Thuringianforest
GreekSkopelos
Albanian M
uzhake
Albanian Liqenasi
Albanian Capore
Albanian Hasi
Romanian Carpathian
Albanian Mati
Saudi-ArabianNajrani
Saudi-ArabianBeeshi
Turikish Abaza
Turkish GurcuTurkish AngoraTurkish Hair
Italian Girgentana
Italia
n Grig
ia
Molisana
Italia
n Arg
entata
dell'Etn
a
Cypriotic Machaeras
Hungarian Native
Greek goat
Albanian Dukati
AustrianTauernschecken
Orobica
Italian
Vald
ostan
a
Italian Camosciata
Polish fawn coloured
German AlpineAustrianPinzgauer
French Pyrenean
Portuguese Brava
Spanish FloridaSpanish Payoya
Spanish Verata
Spanish Guadarra
ma
Spanish Malaguena
Italia
n Sarda
French Rove
Swiss St. Gallenbooted
Sw
issPeaco
ckg
oat
Valais Black Neck
French Alpine
French Corsican
Swiss Grisons Striped
Swiss Alpine
It alian B
ion
da
dell’A
dam
ello
Goat microsatellites, Neighbor-Net graph
� Most differentiation inCentral, Western Europe
12
Central-Mediterranean
Western-Mediterranean
Central/Alpine
Middle-Eastern
Thuringianforest
GreekSkopelos
Albanian M
uzhake
Albanian Liqenasi
Albanian Capore
Albanian Hasi
Romanian Carpathian
Albanian Mati
Saudi-ArabianNajrani
Saudi-ArabianBeeshi
Turikish Abaza
Turkish GurcuTurkish AngoraTurkish Hair
Italian Girgentana
Italia
n Grig
ia
Molisana
Italia
n Arg
entata
dell'Etn
a
Cypriotic Machaeras
Hungarian Native
Greek goat
Albanian Dukati
AustrianTauernschecken
Orobica
Italian
Vald
ostan
a
Italian Camosciata
Polish fawn coloured
German AlpineAustrianPinzgauer
French Pyrenean
Portuguese Brava
Spanish FloridaSpanish Payoya
Spanish Verata
Spanish Guadarra
ma
Spanish Malaguena
Italia
n Sarda
French Rove
Swiss St. Gallenbooted
Sw
issPeaco
ckg
oat
Valais Black Neck
French Alpine
French Corsican
Swiss Grisons Striped
Swiss Alpine
It alian B
ion
da
dell’A
dam
ello
Goat microsatellites, Neighbor-Net graph
� Structure: 5 reproducible clusters
� Regions in graphscorrespond to clusters
� Clear correlation withgeography
BRA COR FLR GDR MLG PYR PYY ROV SAR VER
6.8GDR
6.3VER
6.9MLG
5.6BRA
PYY 6.2
6.5CORSAR
7.0
5.5PYR
5.8ROV
FrALP 6.4 5.4VAL
4.7ORO
6.2BIO
6.1PIZ
4.6TAS
TWZ
5.5BDE
6.3
PCG
5.5
VBN
4.4
6.8FLR
SGB
4.95.8GRS
6.0ALP 5.8CAM
6.4BUK
6.9GMO
5.3GIR
7.6ARG
HAS
7.3
7.5
MUZ
7.3 CAPDUK 7.3
6.4NAT
SKO
6.38.1 GRG
7.4ANG
7.5CAR
7.7HAI
7.5GUR
ABA
8.3
MAK
6.8
NAG
6.9BES
7.3
ALP BDEBIOBUKCAM FrALPGRS PCGPIRSGB
7.3MAT
7.4LIQ
BravaCorsicanFloridaCab. del GuadarranaMalaguenaPyrenaenPayoyaRove SardaVerata
Swiss AlpineGerman AlpineBionda dell’AdamelloPolish fawn-colouredCamosciata delle AlpiniFrench AlpineGrisons StripedPeacock GoatPinzgauerSt Gallen Booted
VALOROTASTWZ VBNNATARGCAPCARDUK
ValdostanaOrobicaTauernscheckenThuringian Forest Goat Valais Black NeckHungarian NativeArgentata dell’EtnaCaporeCarpathianDukati
GIRGRGGMOHASLIQMATMUZSKO
GirgentanaGreek GoatGrigia MolisanaHasiLiquenasiMatiMuzhakeSkopelos
ABAANGBALBESGURHAIMAKNAG
AbazaAngoraBaladiBeeshoGurcuHairMachaerasNajrani
• Allelic richness : Middle-Eastern, Central-Mediterranean >Western-Mediterranean > Northern/Alpine
• Loss of alleles during migration into Europe?
Goat, genetic clusters
13
Middle-Mediterranean
Western-Mediterranean
Central/Alpine
Middle-Eastern
Thuringianforest
GreekSkopelos
Albanian M
uzhake
Albanian Liqenasi
Albanian Capore
Albanian Hasi
Romanian Carpathian
Albanian Mati
Saudi-ArabianNajrani
Saudi-ArabianBeeshi
Turikish Abaza
Turkish GurcuTurkish AngoraTurkish Hair
Italian Girgentana
Italia
n Grig
ia
Molisana
Italia
n Arg
entata
dell'Etn
a
Cypriotic Machaeras
Hungarian Native
Greek goat
Albanian Dukati
AustrianTauernschecken
Orobica
Italian
Vald
ostan
a
Italian Camosciata
Polish fawn coloured
German AlpineAustrianPinzgauer
French Pyrenean
Portuguese Brava
Spanish FloridaSpanish Payoya
Spanish Verata
Spanish Guadarra
ma
Spanish Malaguena
Italia
n Sarda
French Rove
Swiss St. Gallenbooted
Sw
issPeaco
ckg
oat
Valais Black Neck
French Alpine
French Corsican
Swiss Grisons Striped
Swiss Alpine
It alian B
ion
da
dell’A
dam
ello
Goat Y-chromosomes
� Eastern origin ofY1A and Y2
� Founder effects in Europe
Haplotype Y1AHaplotype Y1BHaplotype Y2
� Reconstruct history of the genetic landscape migration, introgression, breed formation> partitioning of diversity, relationships of breeds,
geographic effects
� Compare cattle, goat and sheep
� Indicate priorities for conservation
Geographical patterns ofcattle, sheep and goat diversity
Clines, clusters, introgression, and a conservation dilemma
14
German White Mountain
British Exmoor
Italian delle Langhe
British SwaledaleScottish Black-faced
German Rhön
Polish Kamieniec
Polish PomeranianWelsh Mountain
Italian Bergam
asca
Polish HeathHungarian Cikta
GermanBrown Mountain
Polish Zelazna
Spanish Rubiadel Molar
German Merino
Spanish Colmenareña
Transy
lvanian
Mer
ino
Hungaria
n Mer
ino
Spanis
h M
erin
o
Portu
gue se
Chu
r ra
Braga
nçan
a
Spanis
h Seg
ureña
Spani
sh M
anch
ega
Italia
n Alta
mur
ana
Greek AnogeianoHungarian Tsikaia
Romanian Turcana
Polish Mountain
Turkish KarayakaHungarian Racka
Cypriote Fat-tailed
Turkish Akkaraman
Egyptian Ossimi
Saudi-Arabian HeriSaudi-Arabian Najdi
Romanian Karakul
Greek Kymi
Greek Orin
oGreek K
aragouiko
Alb
ania
n B
ard
hok
a
Greek Skopelos
Italia
n Gen
tile d
e Puglia
Itaia
nLa
ticau
da
Greek Sfakia
Greek Kefalleneas
Romanian Tsikaia
Turkish Morkaraman
Saudi-Arabian NaemiGreek Lesvos
Greek Kymi
Turkish DaglicGreek K
alarritik
o
Alb
ania
n R
ud
a
Alb
ania
n S
hko
dra
ne
Polish Merino
French Thone et Martod
Middle-East
Merinos
South-Eastern Europe
Central, NW Europe
Sheep microsatellites, Neighbor-Net graph
� Most differentiation againin Central, Western Europe
German White Mountain
British Exmoor
Italian delle Langhe
British SwaledaleScottish Black-faced
German Rhön
Polish Kamieniec
Polish PomeranianWelsh Mountain
Italian Bergam
asca
Polish HeathHungarian Cikta
GermanBrown Mountain
Polish Zelazna
Spanish Rubiadel Molar
German Merino
Spanish Colmenareña
Transy
lvanian
Mer
ino
Hungaria
n Mer
ino
Spanis
h M
erin
o
Portu
gue se
Chu
r ra
Braga
nçan
a
Spanis
h Seg
ureña
Spani
sh M
anch
ega
Italia
n Alta
mur
ana
Greek AnogeianoHungarian Tsikaia
Romanian Turcana
Polish Mountain
Turkish KarayakaHungarian Racka
Cypriote Fat-tailed
Turkish Akkaraman
Egyptian Ossimi
Saudi-Arabian HeriSaudi-Arabian Najdi
Romanian Karakul
Greek Kymi
Greek Orin
oGreek K
aragouiko
Alb
ania
n B
ard
hok
a
Greek Skopelos
Italia
n Gen
tile d
e Puglia
Itaia
nLa
ticau
da
Greek Sfakia
Greek Kefalleneas
Romanian Tsikaia
Turkish Morkaraman
Saudi-Arabian NaemiGreek Lesvos
Greek Kymi
Turkish DaglicGreek K
alarritik
o
Alb
ania
n R
ud
a
Alb
ania
n S
hko
dra
ne
Polish Merino
French Thone et Martod
Middle-East
Merinos
South-Eastern Europe
Central, Western Europe
Sheep microsatellites, Neighbor-Net graph
� Structure: 3 reproducible clusters
� North, West of Balkan nocorrelation with geneticdistances or geography
15
6.95.4SKO
7.0CHU
6.6MRS
7.0SGR
6.3MCG
6.0THM 5.2
LAN
6.2BER
LAT 6.1
WBS 5.4
MLS 6.1
RHO 5.4
GGH 5.0
POM 6.5
MPO 5.7 5.4ZEL
GOR
7.0
RAC
6.0
CIK
5.7
6.7TSI
RME
6.7
KKL
6.2
7.1TUR
RTS
7.5
5.2EXH
WMT
6.9
5.9SBF
SHK
6.8
7.1BAR
7.3RUD
ORI 7.1
KEF 6.87.2KAR
KAL
6.96.7
PIL
KYM
LES
6.96.2AKK
6.9MOR
OSS
7.0HER
6.9NAE
7.3NAJ
7.1
7.2DAG
6.9KRY
5.8CFT
CHUGDP KAM MLS MPO MRS POK RME UMEZELALTBER
CIKCLM EXHGGHGMSLANLATMCGRBMRHOSBFSDL
Churra BraganzanaGentile di PugliaKanieniecGerman MerinoPoish MerinoSpanish MerinoPomorskaTransylvanian MerinoHungarina MerinoZelaznaAltamuranaBergamasca
CiktaColmenareñaExmoor HornGerman Grey HeathGerman Brown/White MountainDelle LangheLaticaudaManchegaRubia del MolarRhönScottish Black FaceSwaledale
SGRTHMWMTWRZANOBARGORKALKARKEFKYMLES
SegureñaThone et MartodWelsh MountainPolish HeathAnogeianoBardhokaPolish MountainKalarritikoKaragounikoKefalleneasKymiLesvos
ORIPILRACRTSRUDSFASHKSKOTSITURAKKAWA
OrinoPilioritikoRackaRomanian MerinoRudaSfakiaShokodraneSkopelosTsigaiaTurcanaAkkamaranAwassi
CFTDAGHERKKLKRYMORNAENAJ
Cypriote Fat-TailedDaglicHeriKarakulKarayakaMorkaramanNaemiNajdi
6.1
CLM
5.7
RBM
6.8ANO
SFA
6.6
6.4UME
6.7
GDP
5.6 ALT
5.5SDL
� Allelic richness : again decrease SE > NW
6.4 KAM6.0
WRZ
Sheep genetic clusters� 2 clusters in the East, dispersal in the North and West
German White Mountain
British Exmoor
Italian delle Langhe
British SwaledaleScottish Black-faced
German Rhön
Polish Kamieniec
Polish PomeranianWelsh Mountain
Italian Bergam
asca
Polish HeathHungarian Cikta
GermanBrown Mountain
Polish Zelazna
Spanish Rubiadel Molar
German Merino
Spanish Colmenareña
Transy
lvanian
Mer
ino
Hungaria
n Mer
ino
Spanis
h M
erin
o
Portu
gue se
Chu
r ra
Braga
nçan
a
Spanis
h Seg
ureña
Spani
sh M
anch
ega
Italia
n Alta
mur
ana
Greek AnogeianoHungarian Tsikaia
Romanian Turcana
Polish Mountain
Turkish KarayakaHungarian Racka
Cypriote Fat-tailed
Turkish Akkaraman
Egyptian Ossimi
Saudi-Arabian HeriSaudi-Arabian Najdi
Romanian Karakul
Greek Kymi
Greek Orin
oGreek K
aragouiko
Alb
ania
n B
ard
hok
a
Greek Skopelos
Italia
n Gen
tile d
e Puglia
Itaia
nLa
ticau
da
Greek Sfakia
Greek Kefalleneas
Romanian Tsikaia
Turkish Morkaraman
Saudi-Arabian NaemiGreek Lesvos
Greek Kymi
Turkish DaglicGreek K
alarritik
o
Alb
ania
n R
ud
a
Alb
ania
nS
hko
dra
ne
Polish Merino
French Thone et Martod
Middle-East
Merinos
South-Eastern Europe
Central, Western Europe
Sheep Y-chromosomesG variantA variant
� European origin of A?
� Dispersal of A over Europeby long-distance upgrading
16
Comparison of cattle, sheep and goat
Expected effects of migration and breeding
- correlation geography and genetic distance
- decrease of allelic richness SE > NW- phenotypes of NW breeds more developed
Goat - prototype species
Sheep - more panmictic in NW Europe by upgrading with ramsfrom other regions
Cattle - less effect on allelic richness within continent- outstanding position of NW dairy breeds
explained by introgression of aurochs bulls
� Reconstruct history of the genetic landscape migration, introgression, breed formation> partitioning of diversity, relationships of breeds,
geographic effects
� Compare cattle, sheep and goat
� Indicate priorities for conservation
Geographical patterns ofcattle, sheep and goat diversity
Clines, clusters, introgression, and a conservation dilemma
17
Criteria for conservation
1. Genetic distancesmainly determined by geneticdrift of allele frequencies
0%
10%
20%
30%
40%
0.4 0.5 0.6 0.7 0.8Heterozygosity (exp)
Contributions of cattle breedsto diversity of safe set ofnon-endangered breeds
FST distances,via Weitzman algorithm
To be tested with realistic datasets. Correlation with kinship?
2. Low kinshipsMarker-Estimated Kinships(J. Windig, K. Engelsma, H. Eding, Lelystad) 1%
2%
3%
4%
0%> priority of Eastern breeds
BetizuA
Mallorquina
> priority of inbred breeds
3. Molecular diversitynumber of alleles
4. Diverse phenotypes
Criteria for conservation
> priority to Middle-Eastern breeds
GCAACAAACTACTCTCGGCTTTTAGGAAAGACTCTTGTGCACAGACAGT..G....................................T...........G..........G.........T...............T...........G..........A...............C.........T.........
4. Diverse phenotypes
> priority to Northern/Western/Central breeds
1. Genetic distances by random drift
2. Low kinship,3. Molecular diversity
18
> priority to Middle-Eastern breeds
GCAACAAACTACTCTCGGCTTTTAGGAAAGACTCTTGTGCACAGACAGT..G....................................T...........G..........G.........T...............T...........G..........A...............C.........T.........
4. Diverse phenotypes
> priority to Northern/Western/Central breeds
1. Genetic distances by random drift
2. Low kinship,3. Molecular diversity
Dilemma for conservation
Two obvious criteria lead to different choices
Recommendations for conservation
1. Forget genetic distances on the basis of genetic drift
2. Conserve molecular diversityprimitive breeds, hybrid species origin
GCAACAAACTACTCTCGGCTTTTAGGAAAGACTCTTGTGCACAGACAGT..G....................................T...........G..........G.........T...............T...........G..........A...............C.........T.........
3. Specify valuable phenotypes to be conserved
4. Breed management select on desired phenotypebut also protect the heterozygosity :
Genetic purity : > considerable sentimental appeal> direct threat of animal health> yet difficult to define on the DNA level
consider outcrossing
19
� History of the genetic landscape migration, introgression, breed formation> partitioning of diversity, relationships of breeds,
geographic effects
� Differences between cattle, sheep and goat
� Conservation : dilemma, considerations
Geographical patterns ofcattle, sheep and goat diversity
Clines, clusters, introgression, and a conservation dilemma
Recommended