1. Conservation Genetics

2. Conservation Genetics
5 major extinction events
Rate of extinction today is of concern

3. Rate of Extinction
Many species in the past have gone extinct eg. dinosaurs
Concerns today is the rate which species are disappearing eg. Birds are at rate of 100X faster (Pimm et al PNAS 103: ) than in the past
CO2 entering into the oceans affecting coral reefs (Zeebe et al 2008 Science 321:51-52)

4. Extinction

5. Extinction

6. Megadyptes waitaha sp.nov. Mt DNA aid with species confirmation
Yellow Penguin story: mtDNA sequences Boessenkool et al 2009 (Pro R Soc B)
M. waitaha
Used morphological (Ancient bones) characters to identify ancient species
Megadyptes waitaha sp.nov.
Mt DNA aid with species confirmation
M. antipodes

7. Sample collections and breeding range = blue region
Yellow Penguin story: mtDNA sequences Boessenkool et al 2009 (Mol Ecol)
Sample collections and breeding range = blue region
Haplotype network using control region (mt DNA)
Boessenkool et al 2009

8. IUCN Categories Vulnerable Endangered Critically endangered
10% prob of extinction over 100 years
Endangered
20% prob of extinction over 20 years or 5 generations
Critically endangered
50% prob of extinction over 10 years or 3 generations
IUCN Scale:
Not Evaluated (NE)
Data Deficient (DD)
Least Concern (LC)
Near Threatened (NT) eg. yellow lady’s slipper
Vulnerable (VU)
Endangered (EN) eg. great basin pocket mouse
Critically Endangered (CR)
Extinct in the wild (EW) eg. greater sage-grouse
Extinct (EX)

9. International Union for Conservation of Nature(
Species of the Day:
Plants
Animals
Insects

10. Categories from IUCN

11. Biodiversity IUCN—3 fundamental levels Why conserve it? Ecosystem
Species
Genetic
Why conserve it?
Values
“To keep every cog and wheel is the first precaution of intelligent tinkering”—A. Leopold

12. Ecosystem Services
Essential biological services provided naturally by healthy ecosystems
Oxygen production by plants
Clean water and air
Flood control
Carbon sequestration
Nutrient cycling
Pest control
Pollination of crops
$33 trillion value (global GNP = $18 trillion)

13. Genetic Diversity
Genetic markers are very useful and very popular for assessing genetic diversity of species
Heterozgosity on average is 35% lower in endangered species than non-threatened species
Be careful on the assumption that molecular makers such as allozyme, microsatellites and even AFLP are neutral (usually)
Quantify adaptive variation wherever possible

14. Conservation Genetics Frankham et al. 2002
Conservation Genetics Frankham et al Introduction to Conservation Genetics. Cambridge Univ. Press
Conservation genetics is the application of genetics to preserve species as dynamic entities capable of coping with environmental change
Genetic management of small populations
Resolution of taxonomic uncertainties
Identifying and defining units of conservation within and between species
Use of genetic information for wildlife forensics
Address genetic factors that affect extinction risk and genetic management to minimize or mitigate those risks

15. 11 major genetic issues in conservation biology (Frankham et al.)
Inbreeding and inbreeding depression
Loss of genetic diversity and adaptive potential
Population fragmentation and loss of gene flow
Genetic drift becomes more important than natural selection as main evolutionary force
Accumulation of deleterious mutations (lethal equivalents)
Adaptation to captivity and consequences for captive breeding and reintroductions
Taxonomic uncertainties masking true biodiversity or creating false biodiversity
Defining ESUs and management units within species
Forensic analyses
Understand species biology
Outbreeding depression

16. 5 Broad categories of conservation genetics publications (Allendorf and Luikart)
Management and reintroduction of captive populations, and the restoration of biological communities
Description and identification of individuals, genetic population structure, kin relationships, and taxonomic relationships
Detection and prediction of the effects of habitat loss, fragmentation and isolation
Detection and prediction of the effects of hybridization and introgression
Understanding the relationships between adaptation or fitness and the genetic characters of individuals or populations

17. Other topics Phylogeography Landscape genetics Island populations
Distribution of gene lineages in space and time
Landscape genetics
Combination of landscape ecology and population genetics
Dispersion of alleles across a landscape
Island populations
More later

18. Evolutionary genetics Taxonomic uncertainties
Understanding species biology
Introgression
Conservation Genetics
Population structure & fragmentation
Forensics
Small populations
Outbreeding
Inbreeding
Mutational accumulation
Loss of genetic diversity
Reproductive fitness
Extinction
Next lecture!
Genetic management
Identify mgmt units
Adaptation to captivity
Wild
Captive
Reintroduction

19. Genetic affects of small population size
Effective size (Ne) usually much smaller than census size, compounding genetic effects
Genetic drift—loss of alleles
Fixation in extreme case
Loss of adaptive potential?
Inbreeding
Decreases heterozygosity
Expression of deleterious recessive mutations
Chance of extinction of locally adapted forms
Reintroduction of other forms may not be successful

20. Locally adapted forms Phenotype – product of genotype and environment
VP = VG + VE
Types of phenotypic variation:
Morphology
Peppered moths in UK
Gazelles in Saudi Arabia
Bighorn sheep in Alberta
Behavior
Migration in birds and salmon
Feeding behavior of garter snakes
Adaptation to local conditions
Yarrow in Sierra Nevada
Countergradient variation
Genetic effects counteract environmental effects; thus, genetic differences are opposite to observed phenotypic differences

21. Lacking genetic diversity
Cheetahs have not fair well (multiple bottlenecks)
Genetic diversity greatly reduced
Isozyme (Stephen O’Brien et al. 1983) 47 enzymes and all = monomorphic ( 2 pop – n=55)
14 reciprocal skin grafts from unrelated individuals were not rejected (O’Brien 1985)
In 2008, using n=89 cheetahs and 19 polymorphic microsatellite loci, show low variation
Yet they are surviving well for now

22. Small population - specific problems
Island population are much more vulnerable to extinction
Claustrophobic events eg. hurricanes, human disturbances, poaching and selling of “prized organisms”
Lucas Keller and Peter Arcese have been studying island populations of song sparrows and have found large reductions in population size
Small immigration (1-2) recover diversity in 1-2 generations (Keller et al 1994, Keller, 1998)

23. Inbreeding
Extreme example in humans

24. Inbreeding Loss of heterozygosity and accumulate deleterious alleles
Fitness reduction in the offspring = inbreeding depression
Most severe in large populations since rare alleles can persist as “het” individuals
Damaging to the offspring but not so much for a population

25. Inbreeding
In small populations, major deleterious effects are removed (purging) and hence individuals might still have reduce fitness but not be greatly affected by inbreeding depression and yet “fixation” of mildly deleterious alleles
Deleterious recessives seems to be the major cause of inbreeding depression

26. Inbreeding avoidance
Effective with large populations however inbreeding is unavoidable when populations are reduced in size eg. captive programs
Examples in dogs (pure breeds ie types), due to human selection and highly inbreed practices, these dogs now have lower genetic diversity than most mammals even compared with Pandas

27. Inbreeding coefficients
Inbreeding coefficient (F) range from 0 to 1 where 0=fully outbred and 1=completely inbred
F=0 eg. if two fully outbred heterozygous parents
F=0.25 eg. if siblings mated
F=0.5 eg. selfing heterozygote
Inbreeding can be estimated over time by:
Ft= 1-(1-1/2Ne)t where t = # of generation and Ne is the harmonic mean of Ne in each generation
By estimating the changes in heterozygosity using neutral markers, you can estimate the amount of inbreeding in a population
Note FIS, stats can also give you an estimate of inbreeding within a single generation
Fis 0=no inbreeding and 1 = full inbreeding Fst 0=(no population structure) and 1 =full separate populations >0.2 strong structuring (Fst = fixation index measures the degree of inbreeding of subpopulations relative to the total population
Fit=

28. Inbreeding depression and cost
Cost of inbreeding depression (genetic load) can be in the form of phenotypic disadvantage, mistiming of critical events eg. flowering time or time of metamorphosis leading to possible death of a population especially when immigration has stopped
Purging of deleterious alleles might be possible without the lost of fertility or viability, this theory is better for animals (if they survive) than for plants
Once loci are fixed, only mutations can restore genetic diversity in the absence of immigration
Lab populations used for inbreeding studies fair better than wild populations due to less selective pressures
Amos and Balmford (2001) Heredity 87: * have a different take on inbreeding depression
Inbreeding could be a positive affect on populations

29. Outbreeding depression
Decrease in fitness resulting from outcrosses of individuals from differentiated populations
Possibly due to additive effects of alleles conferring advantages under different environments or breaking up of co-adaptive gene complexes
Particularly important when we are doing genetic “rescue”
Genetic and environmental backgrounds needs to match if at all possible

30. Island population – specific issues
Wilson et al (2009) Conservation Genetics 10:
Island populations = lower genetic variation (lower allelic richness) vs mainland populations
However a lot depend on the size and remoteness of the island
Private alleles resulting from drift or mutation or perhaps natural selection could provide genetic richness on islands verses mainland populations
History of the island (possible refugia events) could also help with preservation of genetic richness of a species
Pattern of neutral genetic variation may not reflect the variation at adaptive loci
Study of island populations verses mainland populations are a necessity when considering conservation issues

31. Genetic restoration
Documentation and discovery of genetic decline of a population(s) are the first steps
Why the reduction of genetic diversity eg. predation, habitat destruction, human hunting and possible inbreeding as a second step
Restoration of genetics diversity is a possible next step
Introduction from captive stock or other wild population
Local adaptation might be lost and possible out breeding depression

32. Possible genetic consequences of immigrants: genetic rescue

33. Genetic restoration Genetic resource banks
For plants there are 1,300 genebanks throughout the world eg. Svalbard Global Seed Vault, Millennium Seed Bank project – Kews Garden (UK)
For animals there are many DNA banks (for sperm/eggs/embryos) eg. Centre for Reproduction of Endangered Species – San Diego Zoo, Calif.
Issues to think about:
May not work eg. technical failures, in viable specimens
Preservation problems
Specimens are “frozen in time” may not adapt to new environment

34. Extreme genetic restoration
Propagation for plants
Cloning in animals
Ethically are these the right things to do?

35. Use of genetics in conservation biology
Systematics
Clarification of species eg. defining the species in the field
Identification of lineages in need of conserving
Priorities for conservation
Hybridization effect and conservation of rare species

36. Genetics in conservation biology
Genetics data does not always = conservation of species
Pocket gophers (Geomys colonus)
List as endangered in Georgia (<100 = n)
Allozymes and RFLP of mtDNA no differences with much commoner pocket gopher (G. pinetis)
Hence the population in Georgia was no longer red listed

37. Genetics in conservation biology
Species at their edge of the ecological range could certainly have problems
Morphologically they could look different due to diet, environment etc.
Genetically they could be very similar
Think domestic dogs eg. mountain beaver

38. Genetic diversity as ESU
DNA sequencing has been more and more affordable and abundant
Moritz had invoked “evolutionarily significant units (ESU) for conservation
Molecular ecologist would use haplotypes as possible distinctive units to identify management units
Construction of phylogeny and comparative phylogeography are used for the identification or sinking subspecies or populations

39. Molecular markers in Conservation genetics
PCR based markers to reduce tissue need
Big caution with contamination and mis-amplifying of heterozygotes (excessive homozygotes)
Allozymes, microsatellites, mitochondrial sequencing and MHC sequencing are all very useful molecular markers
Genome sequences can help with SNP identification and use for creating other molecular markers for conservation studies
Sampling size is a big problem for analysis ie lack statistic confidence