Upload
kristopher-cain
View
214
Download
0
Tags:
Embed Size (px)
Citation preview
Institute of Biodiversity, Animal Health & Comparative Medicine
Clare Marsden, Hanny Verberkmoes, Rob Thomas and Barbara Mable
Pictus, Pedigrees and MHC: an integrated approach for genetic management of captive African wild dogs
• Lycaon pictus: one of most endangered canids• Threatened by: habitat loss, persecution, disease• Last 100 years: 98% reduction in population size;
95% reduction in range• Status: <5,000 individuals found in small,
fragmented populations• Captive population in Zoos: 632 (312 in Europe)
not genetically managed
African Wild Dogs
a) Have past bottlenecks reduced genetic diversity in the wild?
b) How much diversity is maintained in zoos and can management be improved?
c) Can genetic markers be used to trace extinction/recolonisation events?
PhD Project: Clare MarsdenComparing variation at adaptive and neutral genes:
• Lycaon pictus: one of most endangered canids• Threatened by: habitat loss, persecution, disease• Last 100 years: 98% reduction in population size;
95% reduction in range• Status: <5,000 individuals found in small,
fragmented populations• Captive population in Zoos: 632 (312 in Europe)
not genetically managed
African Wild Dogs
a) Have past bottlenecks reduced genetic diversity in the wild?
b) How much diversity is maintained in zoos and can management be improved?
c) Can genetic markers be used to trace extinction/recolonisation events?
PhD Project: Clare MarsdenComparing variation at adaptive and neutral genes:
How did this project come about?Brainstorming Session:
• Sarah Cleaveland (wildlife veterinarian)• Dan Haydon (theoretical ecologist/epidemiologist)• Rob Thomas (Conservation and Research Manager,
Royal Zoological Society of Scotland-Edinburgh Zoo)• me (Evolutionary Geneticist)• Lorna Kennedy (canid immune gene expert)
Why study genetics of wild and captive populations?•Severe bottlenecks could have meant reduction in genetic diversity in wild but hadn’t been studied•Unknown genetic variation in captive populations•Viral diseases problematic in wild populations but genetics unknown•Social structure means that low success rate of sharing of animals across zoos but unknown whether due to relatedness of individuals
How did this project come about?Brainstorming Session:
• Sarah Cleaveland (wildlife veterinarian)• Dan Haydon (theoretical ecologist/epidemiologist)• Rob Thomas (Conservation and Research Manager,
Royal Zoological Society of Scotland-Edinburgh Zoo)• me (Evolutionary Geneticist)• Lorna Kennedy (canid immune gene expert)
Innovation•Most studies only consider variation at DNA markers that have no effect on fitness (“neutral” markers)•We also used immune genes (Major Histocompatibility Complex, MHC) as proxy for adaptive variation
o Immune genes have been implicated in mate choiceo Immune genes might indicate whether wild of captive
populations at risk of disease due to low variation
Why did it work?
Outstanding student!!
Collaborative support from Studbook keeper
Collaborations with field researchers
EEP (European Endangered Species Programme):
~ 270 African wild dogs
~ 44 zoos holding groups of wild dogs
~ 10-12 successful breeding groups (max capacity)
Research aims:• Determine the ancestry and level of genetic
diversity conserved in the EEP• Assess how management could improve the
genetic status of the populationo inbreeding; risk of disease; breeding success
African wild dog EEP
• No records on breeding success tied to samples
• No samples kept from diseased animals• No pedigree• Lack of sample sharing between zoos• Incomplete records of original source of
animals
Initial Challenges
• No records on breeding success tied to samplesx Couldn’t assess breeding success in relation to
immune gene variation
• No samples kept from diseased animalsx Couldn’t assess risk of disease in relation to
immune gene variation
Initial Challenges
• No pedigree Clare and Hanny worked together to produce
pedigree based on studbook records
• Lack of sample sharing between zoos Clare and Hanny worked together to establish
system for collecting and sharing samples
• Incomplete records of original source of animals Genetics combined with pedigree to solveClare and Hanny implemented management plan
across zoos based on genetic variation
Initial Challenges
1) What is the genetic status of the EEP?o Pedigree based on existing records
2) Where did the EEP founders come from?o Genetic analysis of neutral markers compared to wild
populations
3) How much genetic diversity is found in the EEP?o Genetic analysis of neutral markers and immune genes
compared to wild populations
4) What impact will recent South African imports have on the EEP?
o Genetic analysis of source of new imports
Genetic questions
Pedigree analyses
What is the genetic status of the EEP?
Father Mother
Son Son Daughter Daughter
Father Mother
Son Daughter
Family 2Family 1
Son Daughter Son Daughter
Male
Female
Inbred
KEY
Generation 1
Generation 2
6009 T6004
3070
536453615365
T6001
3129WILDPRET
T6003
54455444 5442 54405443
30533054 3057
3036 3016
T6008 3124
1984WILDPRET
3083
T6049T6048T6046 T6026
T5927T5926T5925T5924T5923T5922T5921T5920
T6047
T6024
T6021 T6022
1983WILDPRET
913WILDPRET
T5976
T6005
3130WILDTRNS
T6035 T6034T6031
T5976
T6030 T6029T6032T6031 T6027 T6026T6033
3128WILDTRNS
5602
T6013
5454
T6011
1483
5323 5264
1574
896Wild
897WILD
695WILD
51515237
1289
813 812
694WILD
412 416
548
293UNK
291UNK
706
1741 1739
885
624Z00
984
5193
986
1509 1508
1847
15601753
5024 5180518351845028502750265025
T5949T5948T5947T5946T5945T5944T5941 T5942T5940 T5943
1565
T5859T5858T5857T5855T5854 T5856
UNK
15111637
1304
502250235019 5021
UNK
UNK715F
51435165
53335331 5332
5124Joberg
5158
715UNK
5203
UNK
5577
5452 53675375 53745373
56735672
56075605
567156695667566656585657
5606
5370536953665376 545354625461 54635460
T598157045701 5703569956985696 5700
54645459545754565455 5458
1333
766WILD
1702
52835282 5281 52875284 5204 5249
5346 53455341 5342
520652095207
T5959T5958T5957T5956T5955T5954T5953T5952T5951T5950
T5891T5890T5892T5888T5887T5886 T5889
895WILD
1463Zoo
767WILD
5093 5092
1544
T5960 T5961
1431
5523 55225520 5521
57265725 5727
56415640 563954515525 5450 558855865585 5524
56625617 5663
543554365433 5438 54345432 5437
5117
1046110460104591045810457104561045510454 T5937 T5939T5936T5935T5934T5933T5932T5931T5930T5929T5928 T5938
1029Wild
5474 56345602560156005599 5603
5215 5493521752185214
T5862
5213
559855975595559455935592550955035479547754765472 5596
1543
898WILD
5429
899WILD
T5829T5828T5827T5825T5824T5823T5822T5821T5820T581957095708
55165517 5514 55155512 55135467 5352546554685532 553655355534 5533553755315530552955275518
569556925691
T5830
56905689568856875686568555535552555155505549
57075705 5706
P20793P20791P20789 P20799P20790 P20796
5104
5575 55745572 5573
53285329532653255324 53275101
5395 5396
55795578 5580
53945393 5398
5107
5355 5353
FRIGUNK
T5853
FRIGUNK
T1350 T1353T1352
T6052T6051
T1357
3952PRET
3733PRET
T5985T5984T5983T5982 T5986
UNKHOED
T6053
UNKHOED
UNKHOED
T5991
T6061T6060T6059T6058T6057T6054T6055T6056
T5990T5993T5988T5987T5989
5723 572457205719 5721
UNKHOED
Born ~ April 2002. Guessed at parents
Born ~ June 2002. Guessed at parents
No information on parents
UNK
T6050
UNK
T5807T5806T5805 T5893 T5896T5895T58945651565056495648564756465645564456435642
T5839T5838T5837T5836T5835 T5840
51075101 5104
1982WILDPRET
1985WILDPRET
1986WILDPRET
1987WILDPRET
UNK
5014 5015
UNK
UNK
5097
UNK
Buy SmartDraw!- purchased copies print this document without a watermark .
Visit www.smartdraw.com or call 1-800-768-3729.
EEP African wild dog pedigree
6009 T6004
3070
536453615365
T6001
3129WILDPRET
T6003
54455444 5442 54405443
30533054 3057
3036 3016
T6008 3124
1984WILDPRET
3083
T6049T6048T6046 T6026
T5927T5926T5925T5924T5923T5922T5921T5920
T6047
T6024
T6021 T6022
1983WILDPRET
913WILDPRET
T5976
T6005
3130WILDTRNS
T6035 T6034T6031
T5976
T6030 T6029T6032T6031 T6027 T6026T6033
3128WILDTRNS
5602
T6013
5454
T6011
1483
5323 5264
1574
896Wild
897WILD
695WILD
51515237
1289
813 812
694WILD
412 416
548
293UNK
291UNK
706
1741 1739
885
624Z00
984
5193
986
1509 1508
1847
15601753
5024 5180518351845028502750265025
T5949T5948T5947T5946T5945T5944T5941 T5942T5940 T5943
1565
T5859T5858T5857T5855T5854 T5856
UNK
15111637
1304
502250235019 5021
UNK
UNK715F
51435165
53335331 5332
5124Joberg
5158
715UNK
5203
UNK
5577
5452 53675375 53745373
56735672
56075605
567156695667566656585657
5606
5370536953665376 545354625461 54635460
T598157045701 5703569956985696 5700
54645459545754565455 5458
1333
766WILD
1702
52835282 5281 52875284 5204 5249
5346 53455341 5342
520652095207
T5959T5958T5957T5956T5955T5954T5953T5952T5951T5950
T5891T5890T5892T5888T5887T5886 T5889
895WILD
1463Zoo
767WILD
5093 5092
1544
T5960 T5961
1431
5523 55225520 5521
57265725 5727
56415640 563954515525 5450 558855865585 5524
56625617 5663
543554365433 5438 54345432 5437
5117
1046110460104591045810457104561045510454 T5937 T5939T5936T5935T5934T5933T5932T5931T5930T5929T5928 T5938
1029Wild
5474 56345602560156005599 5603
5215 5493521752185214
T5862
5213
559855975595559455935592550955035479547754765472 5596
1543
898WILD
5429
899WILD
T5829T5828T5827T5825T5824T5823T5822T5821T5820T581957095708
55165517 5514 55155512 55135467 5352546554685532 553655355534 5533553755315530552955275518
569556925691
T5830
56905689568856875686568555535552555155505549
57075705 5706
P20793P20791P20789 P20799P20790 P20796
5104
5575 55745572 5573
53285329532653255324 53275101
5395 5396
55795578 5580
53945393 5398
5107
5355 5353
FRIGUNK
T5853
FRIGUNK
T1350 T1353T1352
T6052T6051
T1357
3952PRET
3733PRET
T5985T5984T5983T5982 T5986
UNKHOED
T6053
UNKHOED
UNKHOED
T5991
T6061T6060T6059T6058T6057T6054T6055T6056
T5990T5993T5988T5987T5989
5723 572457205719 5721
UNKHOED
Born ~ April 2002. Guessed at parents
Born ~ June 2002. Guessed at parents
No information on parents
UNK
T6050
UNK
T5807T5806T5805 T5893 T5896T5895T58945651565056495648564756465645564456435642
T5839T5838T5837T5836T5835 T5840
51075101 5104
1982WILDPRET
1985WILDPRET
1986WILDPRET
1987WILDPRET
UNK
5014 5015
UNK
UNK
5097
UNK
Buy SmartDraw!- purchased copies print this document without a watermark .
Visit www.smartdraw.com or call 1-800-768-3729.
Unequal founder contributions
EEP African wild dog pedigree
ONLY 18/80 wild founders have left descendents.
Very few descendentsVery few descendents
Many descendentsMany descendents
6009 T6004
3070
536453615365
T6001
3129WILDPRET
T6003
54455444 5442 54405443
30533054 3057
3036 3016
T6008 3124
1984WILDPRET
3083
T6049T6048T6046 T6026
T5927T5926T5925T5924T5923T5922T5921T5920
T6047
T6024
T6021 T6022
1983WILDPRET
913WILDPRET
T5976
T6005
3130WILDTRNS
T6035 T6034T6031
T5976
T6030 T6029T6032T6031 T6027 T6026T6033
3128WILDTRNS
5602
T6013
5454
T6011
1483
5323 5264
1574
896Wild
897WILD
695WILD
51515237
1289
813 812
694WILD
412 416
548
293UNK
291UNK
706
1741 1739
885
624Z00
984
5193
986
1509 1508
1847
15601753
5024 5180518351845028502750265025
T5949T5948T5947T5946T5945T5944T5941 T5942T5940 T5943
1565
T5859T5858T5857T5855T5854 T5856
UNK
15111637
1304
502250235019 5021
UNK
UNK715F
51435165
53335331 5332
5124Joberg
5158
715UNK
5203
UNK
5577
5452 53675375 53745373
56735672
56075605
567156695667566656585657
5606
5370536953665376 545354625461 54635460
T598157045701 5703569956985696 5700
54645459545754565455 5458
1333
766WILD
1702
52835282 5281 52875284 5204 5249
5346 53455341 5342
520652095207
T5959T5958T5957T5956T5955T5954T5953T5952T5951T5950
T5891T5890T5892T5888T5887T5886 T5889
895WILD
1463Zoo
767WILD
5093 5092
1544
T5960 T5961
1431
5523 55225520 5521
57265725 5727
56415640 563954515525 5450 558855865585 5524
56625617 5663
543554365433 5438 54345432 5437
5117
1046110460104591045810457104561045510454 T5937 T5939T5936T5935T5934T5933T5932T5931T5930T5929T5928 T5938
1029Wild
5474 56345602560156005599 5603
5215 5493521752185214
T5862
5213
559855975595559455935592550955035479547754765472 5596
1543
898WILD
5429
899WILD
T5829T5828T5827T5825T5824T5823T5822T5821T5820T581957095708
55165517 5514 55155512 55135467 5352546554685532 553655355534 5533553755315530552955275518
569556925691
T5830
56905689568856875686568555535552555155505549
57075705 5706
P20793P20791P20789 P20799P20790 P20796
5104
5575 55745572 5573
53285329532653255324 53275101
5395 5396
55795578 5580
53945393 5398
5107
5355 5353
FRIGUNK
T5853
FRIGUNK
T1350 T1353T1352
T6052T6051
T1357
3952PRET
3733PRET
T5985T5984T5983T5982 T5986
UNKHOED
T6053
UNKHOED
UNKHOED
T5991
T6061T6060T6059T6058T6057T6054T6055T6056
T5990T5993T5988T5987T5989
5723 572457205719 5721
UNKHOED
Born ~ April 2002. Guessed at parents
Born ~ June 2002. Guessed at parents
No information on parents
UNK
T6050
UNK
T5807T5806T5805 T5893 T5896T5895T58945651565056495648564756465645564456435642
T5839T5838T5837T5836T5835 T5840
51075101 5104
1982WILDPRET
1985WILDPRET
1986WILDPRET
1987WILDPRET
UNK
5014 5015
UNK
UNK
5097
UNK
Buy SmartDraw!- purchased copies print this document without a watermark .
Visit www.smartdraw.com or call 1-800-768-3729.
4 litters from 1 pair4 litters from 1 pair
Bred with 3 malesBred with 3 males
20 offspring20 offspring
1 offspring1 offspring
EEP African wild dog pedigree
Reproductive skew
80% of EEP wild dogs never breed
A large amount of genetic variation has been lost:• Only 18/80 WILD founders have left descendents• 80% of EEP wild dogs die before breeding.
Over- and under-representation of founder lineages
Wild dog social structure increases genetic risks:• Reproductive skew (Alpha pair monopolise breeding)
• Large litters
What is the genetic status of the EEP?
Stud book
Namibia, South Africa, Unknown
Mitochondrial DNA•Maternally inherited gene•“Neutral” genetic marker•Can be used to trace back to dead founders
Where do the founders of the EEP originate from in the wild?
Sampling from zoosZoo sampling kits
1. Pre-labelled sampling tubes
2. Sampling and sedation instructions
3. UK import licence
4. Pre-labelled envelopes
Clare
Mar
sden
Gla
sgow
Uni
vers
ity
#5572 ♀Date______
Sampling coordinated through stud book keeper
Sampling from zoosZoo sampling kits
1. Pre-labelled sampling tubes
2. Sampling and sedation instructions
3. UK import licence
4. Pre-labelled envelopes
Clare
Mar
sden
Gla
sgow
Uni
vers
ity
#5572 ♀Date______
Sampling coordinated through stud book keeper
75% response rate
Stud book
Namibia, South Africa, Unknown
Where do the founders of the EEP originate from in the wild?
Namibia
South Africa
EU zoos S. African zoos
Results
1)Founders have a diverse origin
2)Wider than S. Africa & Namibia
3) EU zoos have a more diverse origin than S. African zoos
4) Risk that some imports from wild populations
Expect
How much genetic diversity is found in the EEP?
Genetics: Assessed level of variation at a set of immunity genes involved with disease resistance
Major Histocompatibility Complex (MHC)
Variation at these genes is important because it determines the range of diseases you can fight
Genetics: Assessed level of variation at a set of immunity genes (Major Histocompatability Complex)
Southern African wild:14 genetic variants (alleles)
EU zoos:11/14 variants+ 1 variant not found in the wild
How much genetic diversity is found in the EEP?
Genetics: Assessed level of variation at a set of immunity genes (Major Histocompatibility Complex)
Genetics: Assessed level of variation at a set of immunity genes (Major Histocompatability Complex)
Southern African wild:14 genetic variants (alleles)
EU zoos:11/14 variants+ 1 variant not found in the wild
How much genetic diversity is found in the EEP?
The EU zoos contain a lot of the diversity found in the wild
Genetics: Assessed level of variation at a set of immunity genes (Major Histocompatability Complex)
How much genetic diversity is found in the EEP?
High diversity but concentration of alleles in some parts of pedigree suggests inbreeding and unequal reproduction
How much genetic diversity is found in the EEP?
Bias in MHC alleles in some families could suggest selection (diseases?) but sample sizes small and no disease records
Positive impact:•New genetic variationo3/11 variants introduced by South African animals•Reduce inbreeding
What impact will recent South African imports have on the EEP?
EU zoos have imported ~ 20 African wild dogs from South African captive facilities in the last 10 years
Cautions:•Unknown parentage/ancestryoinbreeding?ooutbreeding depression?•Genetics suggest some sampled from wild
o impacts on wild populationso encourages poaching?
1) What is the genetic status of the EEP?oLoss of variation in the past. Current over and under-representation of some lineages
2) Where did the EEP founders come from?oA range of countries in Southern Africa, not just Namibia & S. Africa. EEP is more diverse than S. African zoos
3) How much genetic diversity is found in the EEP?oA large proportion of the diversity found in wild populations in Southern Africa but could be managed better
4)What impact will recent South African imports have on the EEP?oIntroduce new genetic variation but risks might outweigh benefits
Genetic questions
• Try to limit reproduction to 2-3 litters/pair and 2-3 siblings per family
• Form breeding groups with animals from different lineages; bias under-represented lineages
• Integrate S. African imports into the EEP
Management implications?
SMALL CHANGES => BIG IMPACT
Lessons Learned• Value of coordinating samples, stud book records,
behavioural data and health records• Benefits of collaborative approach and networking• Value of genetics for “forensics” of imports• Genetics demonstrated more variation than expected
based on studbook records• 5 years on, management plan resulted in births with more
genetic variation in the EEP• Interest in genetic management from other zoo networks
(USA, Australia)
Remaining Challenges• Continuity and implementation • Sample and data storage • Biology of species/quality of zoo facilities
Acknowledgments
Aalborg zooAmneville zooArtis zooAttica zooBasel zooBelfast zooBoras zooColchester zooDortmund zooDublin zooDuisburg zooDvurkralv zooEbeltoft zooEdinburgh zooEskilstun zooFriguia zoo
Hilvarenbeek zooHowletts wild parkKerkrade zooKolmarden zooLa Palmyr zooLe Pal zooLisieux zooLondon zooLympne wild parkMunich zooPeaugres zooPont-Scorff zooRamat-Gan zooRoma zooRostock zooWest Midlands
Contributing zoosPhD supervisorsBarbara MableDan HaydonLorna Kennedy
Chief collaboratorsHanny VerberkmoesRosie WoodroffeGreg RasmussenSarah CleavelandRob Thomas
PhD fundingNatural Environment Research CouncilRoyal Zoological Society of Scotland