Conservation Genetics

The basis for an evolutionary conservation

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• Genetic consequences of small population size and extinction.

• Defining conservation and management units based on population genetics.

Conserving Gene Diversity in Declining Populations

• Loss of genetic diversity primary issue in assessing genetic extinction risks

• Decreases ability of populations to respond adaptively to future environmental change

• Declining populations face two threats related to loss of genetic variation:– Long-term: loss of heterozygosity

– Short-term: Inbreeding depression (ID).

ID is reduced fitness in a given population as a result of breeding of related individuals. Inbreeding, results in more recessive deleterious traits manifesting themselves.

Hardy-Weinberg Equilibrium

The gene pool of a non-evolving population remains constant over multiple generations; i.e., the allele frequency does not change over generations of time.

The Hardy-Weinberg Equation:

1.0 = p2 + 2pq + q2

where p2 = frequency of AA genotype; 2pq = frequency of Aaplus aA genotype; q2 = frequency of aa genotype

A population not in Hardy-Weinberg equilibrium indicates that one or more of the five evolutionary agents are operating in a population

Five agents of evolutionary change

Genetic Drift and Effective Population Size

1. Genetic drift is the reason why we worry about African cheetahs and other species that exist in small populations.

1. Drift is more pronounced in smaller populations.

1. Lower genetic diversity therefore lower ability to adapt to changing conditions.

EFECTIVE POPULATION SIZE (Ne)

The average number of individuals in a population that actually contribute genes to succeeding generations by breeding. Ne << N

Ne can be reduced by the following factors:

a. a higher proportion of one sex may mate;

b. some individuals will pass on more genes by having more offspring in a lifetime than others

c. any severe past reduction in population size may result in the random loss of particular genotypes.

The relationship between Ne and a fixation index. Small populations become inbred more rapidly than large populations, often leading to inbreeding depression.

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Genetic Drift• Genetic drift: Random fluctuation in allele frequencies

over time by chance

• important in small populations

– founder effect - few individuals found new population (small allelic pool)

– bottleneck effect - drastic reduction in population, and gene pool size

Long-term Threat: Loss of HeterozygosityAmos & Balmford. 2001. Heredity 87:257-265.

• Loss of variability (He) is related to:– Lowest Ne reached by declining population

– Time (generations) population remains at lowest Ne

• Loss of He: Ht = Ho (1-[1/2Ne])t, where Ho is initial heterozygosity, Ht is heterozygosity after t generations after a decline to size Ne

• e.g. After 5 generations, large population reduced to Ne of 20 will retain 88% of heterozygosity at neutral loci

Relationship between allelic diversity remaining after a single-generation bottleneck and the original number of alleles for different population sizes.

A Genetic Bottleneck is a Form of Genetic Drift

Once again, small bottlenecked populations = big effect.

In a genetic bottleneck, allele frequency is altered due to a population crash.

Genetic Bottleneck

Other animals known to be affected by genetic bottlenecks include the cheetah and both ancient and modern human populations.

A genetic bottleneck creates random genetic changes without regard to adaptation.

A severe genetic bottleneck occurred in northern elephant seals.

Endangered Species Are in the Narrow Portion of a Genetic Bottleneck and Have Reduced Genetic Variation

Example of Genetic Effects of An Extreme Bottleneck: Mauritius Kestrel

Groombridge et al. 2000. Nature 403:616.

• Severe population decline due to habitat destruction and effects of DDT on hatching success of eggs

• 1974: population = 4 birds; single pair source of all birds in subsequent population

• Under intensive management population increased to 400-500 birds by 1997 but experienced six generations at < 50 birds

Mauritius Kestrel Exhibits Genetic Scars of Near Extinction

• Mauritius kestrel has 72% lower allelic diversity (A) and 85% lower heterozygosity (He) than mean of non-endangered Kestrels

• Analysis of museum skins indicates much higher levels of variation before decline

Causes of Low Variation in Small Populations

• Low variation is likely a consequence of being small rather than a cause.

• Lack of variation is due to the ecological process that made a population small rather than the reason it is small.

• Greater importance of ecology vs genetics in short-term conservation decisions (Lande1988. Science 241:1455-1460)

Inbreeding Depression in Declining Populations

• Loss of fitness due to increased production of homozygous offspring due to matingsbetween relatives in bottlenecked populations.

• Mechanism: increased exposure of deleterious recessives in homozygote which were previously masked in heterozygous individuals

Issues Related to Inbreeding Depression

• Effects of inbreeding maybe transitory

• After being exposed to selection in homozygous individual deleterious mutations are purged from population gene pool

• Example: increase in hatching success in butterfly populations founded form single pairs over time

• Effect of purging not universal -may only affect some traits in some populations

Recovering From Inbreeding Depression

• Solution: outcross inbred population to another outbred population by introducing individuals from outbred population.

• When no outbred population exists some fitness recovery still possible when individuals from other inbred populations used because each small population will be fixed (by chance) for different alleles.

• Examples: Swedish adders (Madsen et al. 1999. Nature 402:34-35) and Illinois Prairie Chickens (Westemeier et al. 1998. Science 282:1695-98).

Recovery of Fitness by Introduction of Immigrants Into Inbred Populations of

Adders and Prairie Chickens

Estimating Levels of Adaptive Variation Using Neutral Markers

• Neutral markers (e.g. microsatellites) frequently used to measure levels of variation in small populations endangered species

• Assumption: level of variation in neutral markers is correlated with adaptive variation

Correlation Between Molecular and Quantitative Measures of Genetic

Variation(Reed & Frankham 2001. Evolution 55:1095-1103)

• Meta-analysis of studies which measured molecular variation and quantitative variation in same organisms.

• Quantitative variation: life history traits, morphology, direct measures of heritable variation in above traits.

• Assumption: quantitative variation more closely related to fitness-related variation in organisms

Magnitude of correlation is low

Correlation between molecular and quantitative variation varies widely among studies

• Molecular measures of genetic variation have only a very limited ability to predict quantitative genetic variability

• When information on a populations short-term evolutionary potential is required quantitative variation should be measured directly

Conclusions (Reed and Frankham 2001)

Comparison of Estimates of Qst

and Fst

• Increase in studies examining relationship between differentiation in neutral molecular (Fst) and quantitative (Qst) variation

• Reviews: – Merila &Crnokrak. 2001. J. Evol. Biol. 14:892-903.– McKay & Latta. 2002. TREE 17:285-291.

• Lack of correlation often found but exceptions occur

• Reason: Fst reflects history and Qst reflects selection

Koskinen et al. 2002. Contemporary fisherian life history evolution in small

salmonid populations. Nature 419:826-830.

• Grayling (Thymallusthymallus) populations founded in small Norwegian lakes with different thermal regimes ~ 100 ybp

• Contrasted differentiation in 17 microsatellites (Fst) with differentiation in life history characteristics (e.g. growth rate) (Qst)

Qst values > Fst

values in all populations

Fst reflects history ofsmall populations created from colonization events

Qst reflects adaptive response by fish to different thermal environments

SpeciationSpeciation

Two species of tree frogs morphologically and reproductively isolated

Gene trees are contained in species trees

Concordance: Gene tree = species tree

Use of Genetic Markers to Identify

“Units of Conservation” in

Natural Populations

• e.g. Daugherty et al.1990. Neglected taxonomy and continuing extinctions of tuatara (Sphenodon). Nature 347:177-179.

• Ancient reptilian lineage - restricted to 12 island groups off of New Zealand

• For conservation purposes all populations classified as belonging to one species (S. punctatus) despite earlier work suggesting multiple species

• Analysis of phylogenetic relationships among individuals using allozyme loci

3 phylogeneticallydistinct lineages identified

1 previouslyunrecognized species restricted to single island -no special status

“Bad TaxonomyCan Kill”

Distribution maps of Galápagos tortoises throughout the archipelago and on Santa Cruz

Russello M A et al. Biol. Lett. 2005;1:287-290

Bayesian phylogenetic tree of extant and extinct Galápagos tortoise taxa

Russello M A et al. Biol. Lett. 2005;1:287-290

Identifying Conservation Management Units: ESUs and MUs

• Evolutionary Significant Units (ESUs): Population(s) within a species with high conservation value because they contain a significant portion of evolutionary history and/or potential

• Management Units (MUs) (Moritz 1994): Genetic distinct hence demographically distinct populations that should be managed as separate “stocks”

Management Units

• MUs (Moritz 1994): Populations that show significant differences in allele frequencies regardless of phylogenetic relationships of alleles

• Populations exchange so few migrants so as to be demographically distinct = separate stocks

• Contrast with ESUs which are operationally defined as being reciprocally monophyletic for mtDNA alleles (Moritz 1994)

MUs are nested within ESUs

Criticism of Moritz’s (1994) Definition of ESUs - Crandall et al. (2000)

• Adaptive variation is what we seek to conserve

• Phylogenetically-defined ESUs focus solely on historical relationships and ignore adaptive differences between populations

• Problem scenarios: – Populations with adaptive differences maintained by

selection but with high gene flow not identified as ESU

– Populations with low gene flow but no adaptive differences will be inappropriately designated as ESUs

Defining ESUs on the Basis of Ecological and Genetic

Exchangeability (Crandall et al. 2000)• Populations classified on the basis of whether they

show recent or historical ecological or genetic exchangeability

• Genetic exchangeability:– Rejected (+) when gene flow is low or accepted (-) when

gene flow is high or populations are genetically similar

• Ecological exchangeability:– Rejected (+) when evidence for population differentiation in

traits that reflect adaptive divergence (e.g. life history traits, morphology)

– Accepted (-) when no divergence in putative adaptive variation

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Black Rhinos in S. Africa-high gene flow-similar habitat use-no separate ESUs

Puritain Tiger Beetles inConnecticut and Chesapeake Bay-low gene flow/fixed mtDNAvariants between pops -use different habitats-separate ESUs

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Value of Exchangeability Criteria

• Logical scheme for identifying ESUsthat excludes populations that show no evidence for adaptive differentiation

• What constitutes evidence for adaptive differentiation?

• Focus of future debate within conservation biology/genetics

A wildlife CSI?

Wildlife Forensics

Wildlife Forensics• Molecular genetic techniques can identify products of

illegal harvest of protected species

• Examples:Detection of Illegal hunting and sale of meat from protected whales

by Japan and Norway (Baker and Palumbi 1996)

IWC instituted a global moratorium on commercial whaling in 1985.

Japan and Norway continued to hunt few species (minke) for “scientific purposes” - meat sold commercially.

• Issue: Were protected species also being illegally harvested andmeat sold as from species that could be hunted?

Genetic Analysis of Whale Meat

• “Undercover” purchase of supposedly-legally hunted fresh whale meat (i.e. minke) in Japanese markets

• Illegal to transport tissues from protected species

• PCR-amplification of whale mtDNA control region sequence in hotel room in Tokyo

• Sequenced in US labs

Analysis of 16 Whale Meat Samples

Samples 19b, 41, 311, WS4 fromProtected species

19b - Humpback41, 3, 11, WS4 -Fin whales

16, 13, 28 -Porpoise and dolphin

Conclusions

• Results of analysis: stricter controls over sale of “scientifically harvested” whale meat

• Meat harvested prior to harvest bans genotyped to monitor distribution

• Other applications: species identity of caviar and seal penises, population origin of poached chimps

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