1 Towards a strategy for the conservation of the genetic diversity of European cattle EU project ResGen CT98-118 Utrecht J.A. Lenstra I.J. Nijman Malle G. Mommens Berne G. Dolf Roslin J.L. Williams P. Wiener D. Burton Dublin D. Bradley D.E. MacHugh R.A. Freeman Jouy-en- Josas K. Moazami- Goudarzi D. Laloë Giessen G. Erhardt O. Jann C. Weimann E. Prinzenberg Hannover B. Harlizius Kiel E. Kalm C. Looft Munich I. Medugorac Grenoble P. Taberlet G. Luikart C. Maudet Piacenza P. Ajmone- Marsan R. Negrini E. Milanesi Viterbo A. Valentini M.C. Savarese C. Marchitelli Milano M. Zanotti G. Ceriotti Campo- basso F. Pilla A. Bruzzone D. Iamartino Madrid S. Dunner J. Cañón Zaragoza P. Zaragoza C. Rodellar I. Martín- Burriel Barcelona A. Sanchez J. Piedrafita Porto A. Beja- Pereira N. Ferrand Tjele L.E. Holm Oslo I. Olsaker Jokioinen J. Kantanen Reykjavik E. Eythorsdottir Uppsala B. Danell Vilnas I. Miceikiene Jelgava Z. Grislis Tartu H. Viinalass Sheep and goat genetic resources in marginal rural areas sirs.epfl.ch/projets/econogene/ Geographical patterns of cattle, 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 of cattle, sheep and goat diversity Clines, clusters, introgression, and a conservation dilemma
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Geographical patterns of cattle, sheep and goat diversity
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Towards a strategy for the conservation of the genetic diversity of European cattleEU project ResGen CT98-118
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