Geographical patterns of cattle, sheep and goat diversity

1

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



2


geographic effects





� 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 )



3




� AFLP (Utrecht, Piacenza )

� SNPs in candidate genes

� mtDNA variation in sheep and goat

� Y-chromosomal SNPs ( 7.5 kb, 800 animals,Utrecht, Hubrecht Laboratory )








� 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


Red Danish Angeln

MRYRed HF dual


Swiss HFBritish HF




Maine-AnjouNormande


AyrshireHighland

HerefordDexter


GuernseyBetizu A

Betizu BPirenaica


BazadaisGasconne

AubracSalers




EvoleneEringer


RendenaCabannina




RetintaMorucha

Avilena

SayaguesaAlistano





PodolicaRomagnola

ChianinaN'Dama

SombaLagunaire

BorgouZebu Peul

3

4

> 3 main groups of breeds- North-West- Central- Mediterranean

North-West Central Mediterranean


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


SwedishRed Polled


Red Danish Angeln

MRYRed HF dual


Swiss HFBritish HF




Maine-AnjouNormande


AyrshireHighland

HerefordDexter


GuernseyBetizu A

Betizu BPirenaica


BazadaisGasconne

AubracSalers




EvoleneEringer


RendenaCabannina




RetintaMorucha

Avilena

SayaguesaAlistano





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


SwedishRed Polled


Red Danish Angeln

MRYRed HF dual


Swiss HFBritish HF




Maine-AnjouNormande


AyrshireHighland

HerefordDexter


GuernseyBetizu A

Betizu BPirenaica


BazadaisGasconne

AubracSalers




EvoleneEringer


RendenaCabannina




RetintaMorucha

Avilena

SayaguesaAlistano





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


Meuse-Rhine-Yssel

Germ

an Black-P

ied West

Jutland

British H

olstein

Red Holstein Dual

Red Holstein Dairy


Maine-Anjou

Po

lish

Red

Bo

hem

ian

Red

CharolaisNormande

Breton Pie-Noire

Jersey

DexterGuernsey


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


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


Meuse-Rhine-Yssel

Germ

an Black-P

ied West

Jutland

British H

olstein

Red Holstein Dual

Red Holstein Dairy


Maine-Anjou

Po

lish

Red

Bo

hem

ian

Red

CharolaisNormande

Breton Pie-Noire

Jersey

DexterGuernsey


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


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


geographic effects

� Compare cattle, goat and sheep




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


Central/Alpine

Middle-Eastern

Thuringianforest

GreekSkopelos

Albanian M

uzhake

Albanian Liqenasi

Albanian Capore

Albanian Hasi

Romanian Carpathian

Albanian Mati


Saudi-ArabianBeeshi

Turikish Abaza


Italian Girgentana

Italia

n Grig

ia

Molisana

Italia

n Arg

entata

dell'Etn

a

Cypriotic Machaeras

Hungarian Native

Greek goat

Albanian Dukati


Orobica

Italian

Vald

ostan

a

Italian Camosciata



French Pyrenean

Portuguese Brava


Spanish Verata

Spanish Guadarra

ma

Spanish Malaguena

Italia

n Sarda

French Rove


Sw

issPeaco

ckg

oat

Valais Black Neck

French Alpine

French Corsican


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


Central/Alpine

Middle-Eastern

Thuringianforest

GreekSkopelos

Albanian M

uzhake

Albanian Liqenasi

Albanian Capore

Albanian Hasi

Romanian Carpathian

Albanian Mati


Saudi-ArabianBeeshi

Turikish Abaza


Italian Girgentana

Italia

n Grig

ia

Molisana

Italia

n Arg

entata

dell'Etn

a

Cypriotic Machaeras

Hungarian Native

Greek goat

Albanian Dukati


Orobica

Italian

Vald

ostan

a

Italian Camosciata



French Pyrenean

Portuguese Brava


Spanish Verata

Spanish Guadarra

ma

Spanish Malaguena

Italia

n Sarda

French Rove


Sw

issPeaco

ckg

oat

Valais Black Neck

French Alpine

French Corsican


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


geographic effects

� Compare cattle, goat and sheep




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


British Exmoor



German Rhön

Polish Kamieniec


Italian Bergam

asca



Polish Zelazna


German Merino


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


Romanian Turcana

Polish Mountain


Cypriote Fat-tailed

Turkish Akkaraman

Egyptian Ossimi


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


Greek Kymi


alarritik

o

Alb

ania

n R

ud

a

Alb

ania

n S

hko

dra

ne

Polish Merino


Middle-East

Merinos


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


British Exmoor



German Rhön

Polish Kamieniec


Italian Bergam

asca



Polish Zelazna


German Merino


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


Romanian Turcana

Polish Mountain


Cypriote Fat-tailed

Turkish Akkaraman

Egyptian Ossimi


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


Greek Kymi


alarritik

o

Alb

ania

n R

ud

a

Alb

ania

nS

hko

dra

ne

Polish Merino


Middle-East

Merinos


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


geographic effects





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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.........


> priority to Northern/Western/Central breeds

1. Genetic distances by random drift

2. Low kinship,3. Molecular diversity

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> priority to Middle-Eastern breeds



> 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


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

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� 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 of cattle, sheep and goat diversity

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