Tiger population genetics
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Talk given at the Canadian Society for the Ecology and Evolution at UBC Vancouver BC.
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Tiger population genetics
- 1. In situ and ex situ conservation genetics of the endangered Amur tiger P. Henry *, T. Sugimoto, D. Miquelle °, A. Caccone ‡ & M. Russello * * ° ‡
- 2. The Amur Tiger: Background • Panthera tigris altaica • Population decline to 30 individuals in the 1940’s • Critically endangered (IUCN red list) • In situ conservation strategies • Captive breeding program
- 3. The Amur Tiger: Background • Panthera tigris altaica • Population decline to 30 individuals in the 1940’s • Critically endangered (IUCN red list) • In situ conservation strategies • Captive breeding program
- 4. The Amur Tiger: Background • Panthera tigris altaica • Population decline to 30 individuals in the 1940’s • Critically endangered (IUCN red list) • In situ conservation strategies • Captive breeding program
- 5. The Amur Tiger: Background • Panthera tigris altaica • Population decline to 30 individuals in the 1940’s • Critically endangered (IUCN red list) • In situ conservation strategies • Captive breeding program
- 6. The Amur Tiger: Background • Panthera tigris altaica • Population decline to 30 individuals in the 1940’s • Critically endangered (IUCN red list) • In situ conservation strategies • Captive breeding program
- 7. Historic distribution Previously found in: • Eastern China (Manchuria) • The Korean Peninsula • Russian Far East (RFE)
- 8. Present distribution •Now mainly found in: - RFE - Small areas of China & North Korea • Estimated 490 individuals left in the wild
- 9. Samples • Wild samples: 112 scat samples collected throughout current range representing 95 individuals • Captive samples: 12 individuals from captive population (North American Zoos)
- 10. Samples • Wild samples: 112 scat samples collected throughout current range representing 95 individual • Captive samples: 12 individuals from captive population (North American Zoos)
- 11. Molecular data collection • 8 nuclear microsatellite loci • Mitochondrial DNA control region sequences
- 12. Molecular data collection • 8 nuclear microsatellite loci • Mitochondrial DNA control region sequences
- 13. Objectives • Investigate population genetic structure and demography of in situ population • Assess the genetic representation of the in situ population in captivity
- 14. Objectives • Investigate population genetic structure and demography of in situ population • Assess the genetic representation of the in situ population in captivity
- 15. Population genetic structure • Two hypothesized subpopulations separated by a development corridor • All test of differentiation were not significant (FST=0.0491, RST=0.0272) Sikhote Alin SW Primorye
- 16. Population genetic structure • Two hypothesized subpopulations separated by a development corridor • All test of differentiation were not significant (FST=0.0491, RST=0.0272) Sikhote Alin SW Primorye
- 17. • There is no evidence for recent bottleneck on three commonly used tests for bottleneck. (Luikart et al. 1998 + Garza & Williamson 2001) • Tests for population expansion indicate significant expansion. (Reich et al. 1999) • Estimates of effective population vary from 22 to 57 individuals with a mean estimate of 35 individuals (Tallmon et al. 2008) Demography in the wild
- 18. • There is no evidence for recent bottleneck on three commonly used tests for bottleneck. (Luikart et al. 1998 + Garza & Williamson 2001) • Tests for population expansion indicate significant expansion. (Reich et al. 1999) • Estimates of effective population vary from 22 to 57 individuals with a mean estimate of 35 individuals (Tallmon et al. 2008) Demography in the wild
- 19. • There is no evidence for recent bottleneck on three commonly used tests for bottleneck. (Luikart et al. 1998 + Garza & Williamson 2001) • Tests for population expansion indicate significant expansion. (Reich et al. 1999) • Estimates of effective population vary from 22 to 57 individuals with a mean estimate of 35 individuals (Tallmon et al. 2008) Demography in the wild
- 20. • Genetic diversity not significantly different • No significant differentiation (FST= 0.0496, RST= 0.0235) • 3 private alleles detected ex situ Genetic representation ex situ
- 21. • Genetic diversity not significantly different • No significant differentiation (FST= 0.0496, RST= 0.0235) • 3 private alleles detected ex situ Genetic representation ex situ Axe 1 (10.51%)
- 22. • Genetic diversity not significantly different • No significant differentiation (FST= 0.0496, RST= 0.0235) • 3 private alleles detected ex situ Genetic representation ex situ
- 23. • Population structure and demography in situ: - The development corridor does not represent a barrier to gene flow between the Sikhote Alin and SW Primorye - Population expansion may be responsible for the lack of genetic signature of a bottleneck - Effective population size is 10 X smaller than Significance of results
- 24. • Population structure and demography in situ: - The development corridor does not represent a barrier to gene flow between the Sikhote Alin and SW Primorye - Population expansion may be responsible for the lack of genetic signature of a bottleneck - Effective population size is 10 X smaller than Significance of results
- 25. • Population structure and demography in situ: - The development corridor does not represent a barrier to gene flow between the Sikhote Alin and SW Primorye - Population expansion may be responsible for the lack of genetic signature of a bottleneck - Effective population size is 10 X smaller than Significance of results
- 26. • Genetic representation ex situ - Ex situ sample is representative of the genetic variation found in situ - Some genetic resources (3 alleles) found ex situ were absent in situ Significance of results
- 27. • Genetic representation ex situ - Ex situ sample is representative of the genetic variation found in situ - Some genetic resources (3 alleles) found ex situ were absent in situ Significance of results
- 28. • The captive breeding program was successful in maintaining a representative sample of the wild population • Conservation measures in situ will need to be continued to ensure the survival of the species as it may be vulnerable to continued human-mediated stresses as well as environmental stochasticity Concluding remarks
- 29. • The captive breeding program was successful in maintaining a representative sample of the wild population • Conservation measures in situ will need to be continued to ensure the survival of the species as it may be vulnerable to continued human-mediated stresses as well as environmental stochasticity Concluding remarks
- 30. • Students: Rebecca Catapano-Friedman (YALE) Lisa Young (YALE) • Helpful discussions: Anders Gonçalves da Silva (UBC | O) Jérôme Goudet (UNIL) • Photo credit: Elvis Payne Tobi British Ashley Darby • Collaborators: A. A. Astafiev (Sihkote-Alin Zapovednik) Y. M. Dunishenko, E. N. Smirnov, G. Alkina, V. G. Abramov, D. G. Pikuno (Amur Tiger Monitoring program) John Goodrich (WCS) Kathy Traylor-Holzer (CBSG) Acknowledgements • Funding: WCS Species Survival Fund Conservation Award (MR) American Philosophical Society (MR) Christensen Fund (DM)
- 31. Thank you for your attention!
Editor's Notes
- Good morning to you all. I am Philippe Henry and my talk today will be on the conservation genetics of the Amur tiger of both the insitu and exsitu populations. This study constitute a side project of my PhD at the University of British Columbia Okanagan with Prof. Michael Russello and is done in collaboration with Dr. Taro Sugimoto, Dr. Dale Miquelle of the Wildlife Conservation Society and Prof. Adalgisa Caccone at Yale University.
- The amur tiger (PTA) is the largest of all tiger subspecies. Five out of eight subspecies of tigers are still extant. (bengal-tigris, sumatran-sumarae, indichinese- corbetti, amur-altaica & malay- jacksoni) Extinct: Javan-sondaica, bali- balica& caspian-virgata / south-china-amoyensis--only in zoos
- The wild population of amur tigers declined to about 30 individuals in the 1940’s due to poaching for asian medicine market and habitat destruction: due to logging and increased pressure from human populations
- The subspecies is still critically endangered as pressures from logging persist and poaching for chinese medicine is still happening.
- Conservation action in the the Russian Far east and China such as anti-poaching, human-tiger conflict mitigation, education and habitat management work has enabled the wild population to rebound toan estimated 490 individuals at present.
- This was supplemented by a captive breeding program that was initiated in 1950’s from 57 wild caught amur tigers. The captive population is now represented by 420 individuals in zoos and farms in china, europe and north america.
- The amur tiger was previously sistributed in large areas in eastern chine, the korean peninsula as well as the russian far east.
- Due to the pressures i mentionned before (Loggin, poaching for chinese medicinal practices, expansion of human population) it is now restricted to temperate forests of the RFE as well as small areas in neigboring china and north korea. The estimated individuals left in the wild is 490…
- Inthe present study we collected scat samples from the entire current range of the amur tiger. That is from two hypothesized subpopulations: a small subpopulation in The South-West Primorye (40 individuals) & the main subpopulation in the Sikhote Alin mountains in the east (450 individuals) i.e. a total of 490 individuals.
- and we also had a sample of 12 captive individuals representing the remaining matriline from the 57 founders of the captive breeeding program (29 females and 28 males!!!) from Omaha, Bronx, Minnesota, Philadelphia, WCS (New York?) , Louisville Based on the tiger studbooks.
- We genotyped all individuals at 8 Microsatellite loci initially developped for sumatran tiger. (Williamson et al 2002 mol ecol notes)
- And this was supplemented by mtDNA control region sequences. Haplotypes 3 in the wild one in captivity
- With the samples available, we investigated the population genetic structure and demography in the wild
- And we assessed how well the captive population was a genetic representation of the wild population
- It has been hypothesized that a development corridor between the cities of Vladivostok and Ussurisk that has been ongoing for the past 20 years may limit geneflow between SW primorye and the Sikhote Alin moutains. We tested this using several approaches: including standard Fst Rst measures of population differentiation as well a log-likelyhood test statistic G (Goudet e al 1996). And the bayesian approach implemented in the software structure.
- All lines of evidence, ie low values of Fst and Rst and the log-likelyhood test statistic G were all non significant, Here i have given you a structure plot also suggests that there is no evidence for population differentiation accross the corridor. Q- HWE assumption._2 out of 8 loci deviated from HWE after sequential bonferroni corrections (Rice 1989). Those were removed for the structure analyses. The log-likelyhood G-test was undertaken not assuming the HWE with all loci.
- Although a severe bottleneck event (20-30 individuals remaining) is well documented (Kaplanov 1948) there is no genetic evidence for a population crash based pn 3 commonly used tests: BOTTLENECK: heterozygote excess test (based on the wilkoxon sign rank test- most powerful for a small number of loci), mode-shift (no distortion in allele frequencies) & M-RATIO (large and never fell bellow the critical value Mc!) Q_ Spong, G. and L. Hellborg. 2002. A near-extinction event in lynx: do microsatellite data tell the tale? Conservation Ecology 6(1): 15. Suggest, low number of loci, undetected migration event, short, relatively narrow botlleneck may not leave any genetic signal,
- Based on the intralocus k- test. suggest population expansion , on the other hand another test proposed, the interlocus variance g- tests described in Reich et al 1999 does not follow this evidence Q_Based on the intralocus kurtosis k-tests (one-t ailed binomial test to deter mine whether fewer loci were associated with a positive k than would be expected for a constant-sized population- p<0.05) Because the expectation of k decreases with increasing kurtosis, such a reduction in the number of positive k values can be interpreted as a sign of population expansion. ---kurtosis=peakedness, interlocus variance g test - the variance of the variance of the allele length distributions Third, the within locus kurtosis test is designed to detect population expansions (Reich & Goldstein 1998; Reich et al. 1999) based on the distribution of allele sizes. The test is based on the observation that the allele distributions of an expanding population and that of a population that has been stable for a long time differ. In an expanding population the kurtosis (k), or rather a combination of the variance and kurtosis (Reich et al. 1999), of the allele size distribution is positive. The method uses a binomial test of the number of positive k-values based on the expectation of an almost (P = 0.515) equal probability of negative and positive k-values. Fourth, the variance test is an interlocus test which tests the observation that in stable populations the variance of the allele sizes is highly variable among loci, whereas in an expanding population this variance is more even. Thus, sufficiently low variances in allele sizes may be taken as evidence for an expansion, and we used cut-off values given in Reich et al. (1999). Q_ Spong, G. and L. Hellborg. 2002. A near-extinction event in lynx: do microsatellite data tell the tale? Conservation Ecology 6(1): 15. Suggest, low number of loci, undetected migration event, short, relatively narrow botlleneck may not leave any genetic signal,
- Onesamp 95% confidence interval (lower and upper bounds) with a mean at 35 inds… this value is backed up by the method of Guo and Waples based on Linkage disequilibrium with a estimates ranging from 20 to 61 individuals. Q _Onesamp, which uses summary statistics and approximate Bayesian computation to estimate Ne from a single sample. 8 summary stats with established a relationship with Ne: 1. number of alleles divided by allele length range, 2. the difference of the natural logarithms of variance in allele length and heterozygosity, 3. expected heterozygosity, 4. number of alleles per locus, 5. Wrightﾕs F Is, 6&7. mean and variance of multilocus homozygosity, 8. square of the correlation of alleles at different loci. note the test of Robin Wapples LDNe was also used and yielded 61 individuals (i.e. ) Q_ Spong, G. and L. Hellborg. 2002. A near-extinction event in lynx: do microsatellite data tell the tale? Conservation Ecology 6(1): 15. Suggest, low number of loci, undetected migration event, short, relatively narrow botlleneck may not leave any genetic signal,
- Genetic diversity were relatively low, but in accordance to previously published work on captive and wild amur tiger (Luo et al 2008) measured as Hs- expected heterozygosity (0.3-0.4) and Rs (about 3)- Allelic Richness (el mousadik & petit 1996) were no significantly different in ex situ and in situ samples. (the same applies to Fis!!! Although it is a bit higher in situ) I gave you the example of Hs: one can see the exsitu sample has a similar range
- Based on Fst, Rst and the loglikelyhood Gtest, the in situ and ex situ are not significantly differentiated I have illustrated this by showing you the results of a factorial correspondans analysis, where the blue squares represent the captive individuals and the yellow represnt the wild individuals.
- Three alleles found in captivity were absent from the wild: two at locus 6HDZ64 and one at locus 610
- The development corridor does not barrier to gene flow but as it has this corridor is only about 20 years old, it may be too recent for its effect to be detected at the genetic level yet.
- Popualtion expansion after the bottleneck may be responssible for the lack of genetic signature of bottleneck… Other reason could include; the low number of loci used in this study… undetected migration (unlikely…) the fact that the 1940s bottleneck was short in time and the population was able to rebound quickly and attain equilibrium.
- The effective population is more than ten times smaller the census size. This is important to take into consideration for future conservation action
- Based on our sample of 12 individuals
- Based on our sampling: (fairly low 12 individuals = 12 matrilines)
- Due to a low effective population size identified here, it is waranted to continue in situ conservation strategies that are already in palce and: Ultimately may benefit from an interactive ex situ-in situ management stratergie that could supplement genetic variability from the captive into the wild population by means of assisted reproductive technologies and/or transplanto f candidate individuals.
- We are grateful to the following: Students for conducting labwork. insightful discussions Teams on the field for collection of scats Photo credit collaborators Funding sources