Conservation Genetics

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 disappearingeg. Birds are at rate of 100X faster (Pimm et al. 2006 PNAS 103:10941-10946) 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. Yellow Penguin story: mtDNA sequencesBoessenkool 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. Yellow Penguin story: mtDNA sequencesBoessenkool 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 • 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 (http://www.iucn.org/) Species of the Day: Plants Animals Insects

10. Categories from IUCN

11. Biodiversity • IUCN—3 fundamental levels • 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 GeneticsFrankham et al. 2002. 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. 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 11 major genetic issues in conservation biology(Frankham et al.)

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 • 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 Population structure & fragmentation Forensics Outbreeding Small populations Inbreeding Loss of genetic diversity Mutational accumulation Reproductive fitness Extinction Genetic management Identify mgmt units Adaptation to captivity Wild Captive Reintroduction Conservation Genetics

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 cheetahsand 19 polymorphic microsatelliteloci, show low variation • Yet they are surviving wellfor 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)twhere 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

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 87:257-265 * 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 10:419-430 • 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 http://www.fs.fed.us/wildflowers/regions/pacificnorthwest/IronMountain/index.shtml http://www.scientificamerican.com/article.cfm?id=earth-talks-florida-panthe

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