Conservation

Genetics and extinction

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Conservation Genetics

• 5 major extinction events

• Rate of extinction today is of concern

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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. 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)

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Extinction

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Extinction

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Yellow Penguin story: mtDNA sequences

Boessenkool et al 2009 (Pro R Soc B)

• Used morphological (Ancient bones) characters to identify ancient species

• Megadyptes waitaha sp.nov.

• Mt DNA aid with species confirmation

M. waitaha

M. antipodes

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Haplotype network using control region (mt DNA)

Sample collections and breeding range =

blue region

Boessenkool et al 2009

Yellow Penguin story: mtDNA

sequencesBoessenkool et al

2009 (Mol Ecol)

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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 slipperVulnerable (VU)Endangered (EN) eg. great basin pocket mouseCritically Endangered (CR)Extinct in the wild (EW) eg. greater sage-grouseExtinct (EX)

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International Union for Conservation of Nature(http://www.iucn.org/)

Species of the Day:PlantsAnimalsInsects

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Categories from IUCN

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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

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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)

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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

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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

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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

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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

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Genetic effects 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

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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

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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 19

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)

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Inbreeding

• Extreme example in humans

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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

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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

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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

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Possible genetic consequences of immigrants: genetic rescue

http://www.scientificamerican.com/article.cfm?id=earth-talks-florida-panthe

http://www.fs.fed.us/wildflowers/regions/pacificnorthwest/IronMountain/index.shtml

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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

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Extreme genetic restoration

• Propagation for plants

• Cloning in animals

• Ethically are these the right things to do?

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