Conservation genetics and captive breeding

1. Conservation geneticsand captive breeding Tim King, USGS Meredith Bartron, USFWS

3. Captive breeding: critiques If used for population or species decline� Population maintenance Genetic diversity maintenance Temporary fix Doesn�t address cause for population decline

4. �Captive breeding should be viewed as a last resort in species recovery and not a prophylactic or long term solution because of the inexorable genetic and phenotypic changes that occur in captive environments. Captive breeding can play a crucial role in the recovery of some species for which effective alternatives are not available in the short term.� -Snyder et al. Conservation Biology 1996

5. �Thus, our results suggest that the apparent short term demographic advantages of a supplementation program can be quite deceiving. Unless the selective pressures of the captive environment are closely managed to resemble those in the wild, long-term supplementation programs are expected to result in genetic transformations that can eventually lead to natural populations that are no longer capable of sustaining themselves.� -Lynch and O�Hely, Con. Gen. 1991

6. �Many endangered species require captive breeding to save them from extinction, as they are incapable of surviving in inhospitable natural environments due to direct or indirect human impacts in the form of habitat loss, overexploitation, pollution, or introduced predators, competitors or diseases�� -Frankham, Molecular Ecology 2007

7. Captive breeding ~2000-3000 terrestrial vertebrates ~2000 amphibians 245 vertebrate species being bred in captivity in zoos (1989) Royal Botanic Gardens: 2700 sp. (of 25,000 threatened sp.) US Center for Plant Conservation: >600 endangered US plants Frankham 2007

8. Prerequisites and assumptions Phylogeographic and phylogenetic relationships within and among close relatives is known Sufficient genetic diversity to realize unique multilocus genotypes Preserving maximum levels of genetic diversity within and among populations will increase fitness

9. Captive breeding: genetic concerns Loss of genetic diversity Inbreeding depression Accumulation of deleterious mutation Genetic adaptation to captivity Reduced fitness in the wild

10. Captive breeding: genetic concerns

14. Captive breeding Program goals vs. genetic concerns Restoration and recovery Supplementation Gene-banking

15. Interaction between captive and wild The program is run as an integrated hatchery program, however the number of wild fish in some populations is very low so the number of wild actually integrated might be very low. In these cases, the goal is to provide some �natural� experience and selection to the hatchery programThe program is run as an integrated hatchery program, however the number of wild fish in some populations is very low so the number of wild actually integrated might be very low. In these cases, the goal is to provide some �natural� experience and selection to the hatchery program

16. Captive breeding Founders Size and diversity of source population Selection pressure Artificial selection: Changes to genetic and phenotypic diversity while in captivity Gene flow Interaction with wild population when returned to natural environment (Ryman and Laikre 1991) Reproduction Mating strategies

17. Captive breeding Mating strategies Random Use of pedigrees Genetically-aided pairings Single paired-matings vs. splitting of egg lots Cryopreservation Equalize reproductive contribution Family size Number times reproducing

18. Pairwise relatedness values Rxy Females Males 257C63CFE8 421B716624 257C63EF98 0.197 0.456 257C63D9CE -0.185 0.135 486850414D -0.084 -0.284 48512B7222 0.023 -0.566 4870464E2D -0.329 -0.078 422E5C432B -0.075 0.053 422E6E717E -0.013 -0.466

19. Captive breeding and effective population size Size of total population (wild + captive) Size of captive population Size of number individuals reproducing in captive Fecundity/reproductive contribution Contribution of captive reproduction to total population

20. Effective population size and stocking effects

22. Parentage assignment

23. Captive breeding: Atlantic salmon

24. Atlantic salmon : Maine adult returns Due to the declining stocks and endangered status, a conservation hatchery program was established, building on an existing program to aid in recovery and restoration.Due to the declining stocks and endangered status, a conservation hatchery program was established, building on an existing program to aid in recovery and restoration.

26. Some Maine populations listed as endangered-distinct population segment Captive populations maintained at: Craig Brook NFH Green Lake NFH Restoration programs also in southern range: Merrimack River Connecticut River

27. Atlantic salmon: CBNFH captive populations Parr collection Adult collection Dennys Penobscot East Machias Machias Narraguagus Pleasant Sheepscot Reason for different broodstock strategies is due to the differences in number of returning adults. DPS population returns are so low that a broodstock couldn�t be sustained & production goals couldn�t be achieved (along with many genetic concerns due to low numbers).Reason for different broodstock strategies is due to the differences in number of returning adults. DPS population returns are so low that a broodstock couldn�t be sustained & production goals couldn�t be achieved (along with many genetic concerns due to low numbers).

28. Program types: parr collection

29. Program types: adult collection Some parr are also stocked as grading by productSome parr are also stocked as grading by product

30. Data management

31. Maine Atlantic salmon broodstock program: broodstock screening

32. Genetic parentage assignment Evaluate % recapture as hatchery origin Individual and family fitness From stocking stage to recapture Evaluate stocking practices Segregated versus mixed

33. Genetic parentage analysis: parr Capture # # assigned % Broodstock year screened parents assignment Dennys 2001 101 25 24.8 2002 270 42 15.6 2003 142 32 22.5 2004 148 40 27.0 East Machias 2001 135 41 30.4 2002 168 78 46.4 2003 156 95 60.9 2004 154 71 46.1 Machias 2001 244 23 9.42 2002 336 133 39.6 2003 248 152 61.3 2004 247 100 40.5 Narraguagus 2001 248 52 21.0 2002 243 80 32.9 2003 252 145 57.5 2004 234 114 48.7 Sheepscot 2001 300 44 14.7 2002 157 98 62.4 2003 160 82 51.3 2004 149 82 55.0 Low % assignment could be due to: incorporation of wild parr, incorrect assignments, errors during spawning, not having all parental genotypesLow % assignment could be due to: incorporation of wild parr, incorrect assignments, errors during spawning, not having all parental genotypes

34. Genetic parentage assignment

36. Monitoring estimates of genetic diversity Number Sample alleles Heterozygosity Broodstock size per locus (exp.) (obs.) mean rxy Dennys 138.7 8.90 0.552 0.555 -0.021 East Machias 135.0 8.44 0.559 0.569 -0.005 Machias 229.9 8.68 0.564 0.563 -0.002 Narraguagus 261.3 9.23 0.568 0.567 -0.001 Penobscot 460.9 9.24 0.571 0.571 0.003 Pleasant 155.7 8.06 0.571 0.571 -0.007 Sheepscot 138.6 8.08 0.569 0.577 -0.005 DPS population averages between 1994 and 2004, except Pleasant River (1995-2004) Estimates for Penobscot populations are averaged from 2002 to 2006 Rxy estimates from Queller and Goodnight (1989), 2000-2004

37. Spawning practices All fish PIT tagged & genotyped Natural cycle of maturation followed Multiple spawning dates throughout season based on maturation Adults are spawned within river-specific broodstocks Spawn �first time spawners� All individuals have an opportunity to pass genes 2nd (and 3rd) - time spawners used when needed 1:1 spawning sex ratio Production drives effective population size Tagging and genotyping all individuals allows for tracking 3 & 4. Natural maturation means no use of hormones or artificial means to speed up/slow down or change timing of spawning 5. Rivers are not crossed within the hatchery-natural straying and reproduction is allowed through incorporation of parr (and genetic screening processes allow for straying)Production drives effective population size Tagging and genotyping all individuals allows for tracking 3 & 4. Natural maturation means no use of hormones or artificial means to speed up/slow down or change timing of spawning 5. Rivers are not crossed within the hatchery-natural straying and reproduction is allowed through incorporation of parr (and genetic screening processes allow for straying)

40. Other program components Improving parentage assignment Aquaculture screening/mass marking Continued evaluation for pedigree lines Evaluation of specific traits to family and individuals for fitness Quantitative trait monitoring Evaluation of alternate rearing stocking practices Continued evaluation to reduce artificial selection