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Conservation Genetics (chapter 11)

Conservation Genetics (chapter 11). Aims : 1. Molecular tools to assess factors affecting extinction risk. 2. Mitigation through management to preserve species as dynamic entities able to respond to environmental change. Fisher's Fundamental Theorem of Natural Selection states that:

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Conservation Genetics (chapter 11)

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  1. Conservation Genetics (chapter 11) Aims: 1. Molecular tools to assess factors affecting extinction risk. 2. Mitigation through management to preserve species as dynamic entities able to respond to environmental change Fisher's Fundamental Theorem of Natural Selection states that: 1) the rate of evolutionary change in a population is proportional to its genetic diversity, thus preserving genetic diversity is of paramount importance to long term survival of species 2) The level of heterozygosity within a population is sometimes related to fitness

  2. Why is genetics important in conservation? • Phenotypic traits influenced by genotypic variation • Different forms of a gene = alleles - two in most sexually reproducing species • Environment and allelic interactions during gene expression affect an individuals phenotype • When an individual has the same alleles for a gene it is said to be Homozygous; When they are different = Heterozygous

  3. Genetic diversity is measured at three levels: 1. Within Individual 2. Among individuals in a population (heterozygosity) 3. Among populations HT = HP + DPT where HT = total genetic diversity, HP is average within population diversity, and DPT is average divergence among populations within pop'n between pop'ns

  4. Heterozygosity = Mean proportion of heterozygous loci in a population Loss of genetic diversity may have both long and short-term effects A. Long-term: retards evolution Much of the genetic variation in a species or among populations has accumulated over long evolutionary time. Low genetic diversity = loss of adaptive response capability to changing environment compromised: Why? Genes can influence phenotypic variation on which natural selection acts

  5. B. Short-term: reproductive fitness • Loss of diversity can elevate the risk of inbreeding: i.e. matings in which parents are related due to common descent • Leads to increased homozygosity i.e. a greater probability of identical alleles across loci Consequences include inbreeding depression: low survival and reproduction. In worst case scenario, we get an accumulation of deleterious mutations in the homozygous state resulting in mutational meltdown and a continuous (downward spiral) loss of fitness • An individual’s inbreeding coefficient (F): Probability that alleles at a locus are identical by descent • F ranges from 0 (i.e. parents unrelated) to 1 with complete inbreeding. In a two allele system: brother-sister matings, F = 0.25, with self fertilization, F = 0.5 • Both short and long-term effects increase extinction probability

  6. Are species naturally genetically diverse? Mean total heterozygosity varies across taxa. Vagile (mobile) taxa have lower differences among populations, presumably due to increased gene flow

  7. Is genetic diversity related to fitness? vs growth rate in clams # Heterozygote loci vs condition factor in trout vs No. asymmetric traits in trout vs O2 consumption in Oysters

  8. By definition: Endangered species have poor survival & reproduction We would expect to see lower diversity in endangered species Microsatellite loci No Sampling effect

  9. Is genetic diversity related to demography? YES Red cockaded woodpecker r = 0.48 Halocarpus: N.Z. conifer r = 0.94

  10. For management purposes we need to know what causes genetic diversity to change in populations Allele distributions determines level of genetic diversity in a population, i.e. through changes in their frequency from generation to generation (= evolution) Causes 1) Mutation: primary cause of all evolution. Heritable mutations provide the raw material. However, rates of m from one allele to another are low (10-4 to 10-6 per locus, per generation). 2) Selection: will cause the frequency of a mutant alleleto increase if the phenotypic effect is adaptive

  11. 3. Genetic drift: chance loss of alleles in a population 4. Gene flow: dispersal among populations (immigration, emigration) 5. Non-random mating: unequal contributions to reproduction, may result from assortative mating or female choice 6. Changes in population size, especially losses

  12. Why is genetic diversity lower in small populations? 1. Genetic drift: random loss of alleles is proportional to population size. Small populations have a greater probability of having less genetic variation due either to a) Founder effects: new populations founded by few inds. b) Bottlenecks: e.g. mass mortality 2. Lower probability of new mutations in small pops. 3. Greater isolation (sometimes) = less gene flow among populations e.g. habitat fragmentation: genetic homogenisation

  13. Should an estimated population size be a good indicator of genetic diversity? We would base our population size estimate (Nc) on a random census sample of our population Yet this may yield a poor estimator of the true diversity since not al individuals may reproduce (old, young, infirm, dominant, subordinate) Effective population size (Ne): The population contributing to heritable genetic variation Ne: usually contributed effectively by few individuals, thus using actual or Nc may be a poor indicator of population endangerment Ne is important because it determines the rate of loss of H per generation

  14. Why should Ne < NC ? • Age structure: mature vs immature • Sex ratio: often uneven • Unequal family size • Non-random mating • Fluctuations in population size over time: environment and/or human induced

  15. The effect of sex ratio on Ne • where NM and NF are the number of breeding males and breeding females, respectively Ne = (4*NM * NF)/(NM + NF) 1) Assume 500 mature adults: 50:50 sex ratio, random mating, equal reproductive success: Ne = (4*250*250)/(250+250) = 500 But this may be unrealistic owing to dominance, social structures, sex-related mortality etc. So, consider an elephant seal harem as a population: 2) 1 male and 100 mature females, he mates with all of them Ne = (4*100*1)/(101) = 3.96

  16. Ne = 4Nc/(s+2) where s = variance in female reproduction Assume a stable population of mean family size = 2 with average of 1 M and 1 F to replace each parent. Assume s = 2, with some females producing 0 offspring, others 4 If Nc = 10, then Ne = (4*10)/(2+2) = 10 Again, this is unrealistic. The effect of variation in family size on Ne variance

  17. The effect of variation in population size on Ne Variation in the environment can cause major fluctuations in population size over time, e.g. predator-prey cycles • lynx/snowshoe hare: 80 fold change in abundance in last 100 yrs. • Recall, in small populations drift has a large influence on loss • Greater genetic diversity is lost through drift after population crashes • If numbers recover rapidly, the adverse effect of low population size and inbreeding may be mitigated

  18. The effect of population size fluctuation on Ne Estimated using the Harmonic mean and time over which fluctuation occurs: 1/Ne = 1/t * (1/N1+ 1/N2 + 1/N3 …1/Nt) wheret = number of generations, and N = population size at each time or generation Northern Elephant seals: hunted to 20-30 individuals, now recovered to 100,000 • Assume initial population 100,000 to 20 then 100,000, with 5 generations of loss and 5 generations of recovery • What is the effect of this crash and recovery on Ne? We need to know the Ne for each generation, then plug it into the equation

  19. Loss of genetically effective population over each generation depending on initial population size The influence of Ne on the level of diversity remaining in the next generation is estimated as: 1 - (1/(2Ne)) If Ne is large, terms subtracted from 1 will be low: and most of genetic variation will remain in next generation Populations with Ne > 100 lose less genetic diversity. General recommendation not to let population fall below 500

  20. The level of diversity remaining is also dependent on the number of generations Ne remains at a low level Diversity Remaining =(1-(1/2Ne))t Assume t = 10, Ne = 10 Then: (1-(1/2*10)) = 0.9510 = 0.6 after 10 years, only 60% of the original genetic diversity remains

  21. High population growth rate allows populations to escape deleterious effect of low population size (after disasters etc) r = intrinsic growth rate

  22. Effect of drift on the loss of rare alleles • By definition, rare alleles occur at low frequencies since they may not be adaptive. • But, this could be adaptive if selective pressure changes • Decreasing Ne elevates the rate of loss of rare alleles through drift • This may compromise response to environmental variation. loss of rare alleles in an endangered daisy in Australia

  23. The flightless Galapagos Island Cormorant: • N = 1000, distributed in 10 subpopulations • Long life-span, stable numbers, sex ratio, age structure. • Gene flow considerable • But reproductive success low and variable • Estimated Ne = 648 < Nc • Low Ne & Nc suggest a high risk of inbreeding depression Endemic and a species of high conservation priority.

  24. Valle (1995) estimated that a level of homozygosity of 0.997 would be achieved in 189,000 years. • 95% of expected heterozygosity lost in ~54,000 years. • Why so high? • No regional populations • Relatively small Ne, and low rate of new mutations • Lack of future evolutionary potential = high extinction probability • Immediate threats: • Predator introduction and habitat disturbance With estimates of Ne and the amount of genetic diversity lost per generation we can predict levels of inbreeding

  25. Inbreeding depression • Recall, inbreeding increases the probability of two identical alleles at a locus in the homozygous state • If they are recessive lethal or sub-lethal, they will may cause death or lower fitness • Fitness reductions appear dependent on the number of these ‘lethal equivalents' in a population

  26. Inbreeding causes a reduction in fitness (solid line) from the outbred case (dotted line). Slope of solid line is equivalent to the inbreeding load. Individual B is more inbred than individual A.

  27. Evidence that inbreeding compromises fitness in captive animals Juvenile mortality in inbred captive mammal populations far exceeds the same species in outbred situations

  28. Jimenez et al. (1994) Science Non-inbred F = 0 Survival of Inbred and Ourbred white-footed mice Inbred F = 0.25 • Inbred mice: weekly survival rate 56% of non-inbred lines • Inbred males: lost significantly more body mass • Non-inbred: no significant loss

  29. How can we rescue wild species in which low Ne and high inbreeding predict extinction? Appropriate Management: 1. Providing benign environments such as managed reserves with low predator prevalence, minimize disease through vaccinations, minimize natural and human disturbance, reduce habitat loss 2. Supplement genetic diversity through reintroductions 3. Transplant species to novel habitat: very controversial

  30. Genetic Rescue Inbreeding Depression: Reduction in fitness as a result of increased homozygosity. Solution: Outbreeding Outbreeding: reverse deleterious effects of inbreeding by mating with “rescue” populations BUT, if introduced populations are highly divergent, concern for outbreeding depression

  31. Outbreeding Depression Populations with different combinations of loci specially adapted to different environments Cold environment Hot environment a b A B a b A B 1. Loss of local adaptation Genotypes adapted to neither environment a b a b A B A B F1 Recombination a B A b 2. Loss of Co-adapted gene complexes Loci not paired with alleles of same source pop. = loss of co-adapted gene complexes F2

  32. IdentifyingESU (Evolutionary Significant Unit) • ESU= Distinct population segment of a species Criteria: • Must be substantially reproductively isolated from other population units of the same species • Must represent an important component in the evolutionary legacy of the species • Crandall et al. (2000) suggested that Ecological Exchangeability also be considered: - In populations where there has been historical or recent gene flow, there may be little genetic divergence, suggesting management as single ESU. - However, if populations differ phenotypically, in habitat use, or have particular gene loci under selection, then they should also be managed as distinct populations

  33. D E High gene flow High gene flow C A B Effective conservation relies on identifying appropriate managements units • Species are clearly separate ESUs • However, species exists as loosely connected populations with some dispersal and gene flow to others • Degree of isolation, coupled with environmental variation, may also lead to adaptive differences • Knowledge of how genetic variation is partitioned at different spatial scales can guide management No gene flow Most of the variation is partitioned between regional groups with a lesser variation among populations within regions (2 possible ESUs)

  34. Failure to identify ESUs may result in poor management decisions with profound consequences Out-breeding depression: Tatra mountain Ibex • Following extirpation in Czech., a population was successfully re-established by translocation of Austrian animals • Additional supplementation of desert adapted animals (unknown to be a different subspecies) introduced from Turkey & Sinai desert Adapted to different environmental conditions • Mountain species bred late in year, desert species earlier; hybridization disrupted the breeding cycle • Hybrids rutted too early: young born in Feb. and all died • Loss of local adaptive differences

  35. Genetic rescue of the Florida Panther • Putatively, 29 sub-species of panther (cougar, puma, mountain lion) in the Americas • Formerly widespread throughout SE USA, now restricted to Mid-west and west • In S. Florida only 60-70 individuals remained, due to road kills, hunting • Genetic analyses: some individuals introgressed from S. American puma genes after release by private breeders • Hybrids occurred in areas distant from ‘true’ population 1967: listed as federally endangered

  36. ‘True’ populations: low allozyme, mtDNA and microsatellite diversity compared to hybrids or puma populations in westEvidence of severe inbreeding depression 1. Kinked tails, 2. Cardiac defects 3. Poor semen quality 4. Cryptorchidism in all pure males: At least one undescended testis 5. High disease prevalence Mid-piece constricted Bent acrosome good

  37. Management intervention: Increase genetic variability via introductions from other populations In 1995, 8 females introduced from Texas (the nearest source) Controversial decision: Would it lead to outbreeding depression? Test (Culver et al. 2000): Estimated genetic population structure in panther populations used mtDNA, microsatellites Results1. mtDNA: 6 groupings = 6 subspecies, but all North American animals were similar: of 194 individuals, 190 had identical haplotypes and the remaining 4 individuals differed by a Single Nucleotide Polymorphism (SNP)

  38. 2. Microsatellite loci: Evolve quicker and provide finer population resolution: • 6 major sub-groups as inferred in mtDNA (not 29 subspecies) • Based on genetic divergence and estimated mutation rate: all groups diverged from a common ancestor ~400,000ya. • All North American populations occurred as a single ESU-evolved within 12,000yrs • Florida museum specimens were more diverse than extant Florida individuals but not differentiated from Texas Conclusion Out-breeding depression predicted to be low after re-introduction program

  39. Rescue had Immediate Measurable Fitness Benefits Pimm et al. (2006): • 5 of the released females produced 20 kittens lacking kinked tails • ‘Hybrids’ had 3 fold greater survival to adulthood than purebred • Adult Hybrid females have higher natural survivorship • ‘Hybrids’ are expanding their range to areas previously considered unsuitable

  40. Captive Breeding Captive breeding can be done to maximise genetic diversity: • select for fitness • maximise allozyme diversity • equalise family size • minimise kinship: i.e. maximise matings between distantly related individuals

  41. Guam Rail • Flightless: endemic to Pacific Island of Guam • Brown tree snake: Introduced WW II • Novel predator • Rail population • 1960s- 80,000 individuals • 1980s- very few individuals • 21 individuals taken into captivity • Wild population extinct by 1986

  42. To reduce Inbreeding: • DNA fingerprint profiles facilitate selection of unrelated individuals: • 6 chosen and placed into 2 different groups Offspring reared: • Contingency releases on nearby Rota island that lacked tree snakes • Until 2000, 384 Rails released on Rota • 1999: First successful reproduction from 3 pairs of previously captive-reared birds Problem: • In Guam, Brown tree snake is still present • In 1998: Snakes eliminated in a 60 acre site over 26 weeks • Predator fences erected to create enclosure: 16 Birds released • 9 rails produced 40 hatchlings

  43. Are Captive Breeding Programs the way forward? Balmford et al. (1995) est. value of in situ vs ex situ conservation programs Field-based programs cheaper, and as effective as captive breeding

  44. Forensics • Illegal hunting of protected species is difficult to police • Difficult to prosecute from sale of Illegal meat or body parts • Molecular genetics can resolve origins of biological material • Whales • Used mtDNA to monitor trade in dolphin/whale products by purchasing from retail markets in Korea & Japan • Some samples grouped with Minke • Many others grouped with protected species • Some were from dolphins and porpoises! • In response, Japan argued that the meat was from freezer stock piles collected before 1985 ban • No evidence for this and low supply of Minke on the market suggests when they come on the market they sell quickly

  45. Cloning of Extinct Species? • Until recently, it looked like cloning of endangered species was only science fiction. • However, early in 2009 a press report described successful cloning of the Pyrenean (Spanish) ibex Caprapyrenaica, from tissue skin cells in 2000 when the last living specimen died • DNA taken from these skin samples was put in place of the genetic material in eggs from domestic goats, to clone a female Pyrenean ibex • The animal died shortly after birth from lung problems, but it raises a promising method of preventing formal extinction www.telegraph.co.uk/

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