Genetic Threats / Conservation Genetics

Big cats, hungry dogs, and little mice

Don Waller

Botany - UW

Florida pocket mouse

Cheetah

Ivorybilled Woodpecker

• The magnificent Ivory-billed Woodpecker has become a symbol of the bottomland forest wilderness that once extended across the southern United States. The largest woodpecker north of Mexico and the third largest in the world, the Ivory-billed Woodpecker inhabits mature swampy forests, roaming large areas in search of dead and dying trees infested with beetle larvae, its primary food. Ivory-billed Woodpeckers were probably never common, but by the 1930s, their habitat had been destroyed.

• Thought to be extinct for >30 years – rediscovered (?) 2005

• NOT SEEN SINCE . . .

Aka the “Lord God” bird

Why did it disappear?

Ivory-billed Woodpecker

“Almost no forests today can maintain an Ivory-billed Woodpecker population”

All species exist as populations

What are we doing?

• Why is this the 6th extinction?

• Why is it “unnatural”?

• What are the causes?• Why don’t we have an

‘IPCC’ to deal with this issue?

Why these patterns?

Why these patterns?

Why are most threatened species tropical?

Why is human population growth rate correlated with numbers of threatened species?

Species face many threats

Deforestation

Burning

Erosion

So does genetics matter?If habitat destruction, over-exploitation, pollution, and introduced species are driving most species extinct, should we be concerned about genetics?

Why books & journals about Conservation Genetics?.

What uses does it have?

Conservation genetics is a growing field

• Rapid increase in interest and publications

• Uses multiple approaches . . – Theory, experiments, & case studies

• New journal:• Benefiting from population

genetics theory, and perhaps contributing to it

Outline

• Why is diversity threatened?– Which species are going extinct?

• Conservation genetics case studies– Florida Panther, African lions, & cheetahs– Florida pocket mouse & Isle Royle Wolves– Illinois Prairie Chickens – genetic rescue?– Indiana Royal Catchfly & other plants– Did we purge the genetic load in Speke’s gazelle?

• Lessons regarding genetic hazards?– Short term: Inbreeding– Long Term Threats:

• Drift and the fixation of mutations• The loss of quantitative genetic variation

Outline

• Other uses of Conservation Genetics?– Evolutionarily unique species – ‘living fossils’

• Do bigger branches deserve more protection?

– Forensics, etc.

• Rules for captive breeding & reintroductions

Florida Panther• Puma concolor coryi

– Sub-species of cougar– Restricted in its range– Carnivore: small pop size

• Symptoms:– Cryptochordism– Kinked tail & cowlick– Worst semen quality of any felid (cat)

• What would you do?

Florida Panther

• Built highway underpasses• Brought in some comely female Texas cougars

– Why from Texas? Why females?

• Effects:– 8 females introduced, 5 had kittens– Appears to be working - no kinked tails, 1 cowlick• Prescription: 20%, then 2.5% / gen. to reduce deleterious alleles

Lions in Ngorongoro Crater(Packer et al. 1991)

• 1962 epizootic: – Down to 9 Females, 1 Male– 7 more males in 1964-65– But only 15 founders

• 1975 on: N ~ 75-125• Symptoms:

– Low genetic diversity– Sperm abnormalities– Low reproduction

• In need of genetic rescue?

Cheetahs

• Fastest land mammal• One of the most

threatened – why?

• Subject to many of the same genetic problems as the Florida panther: – Mis-shapen sperm– Undescended testicles– Low infant survival

Cheetahs

• Fastest land mammal• One of the most

threatened – why?

Missingvariation

Going to the dogs . . Wolves

• Once argued that wolves are adapted to close inbreeding by virtue of their pack structure

• Tested in captive wolves in Scandanavia• Inbreeding produced declines in:

– Juvenile weight– Reproductive success– Longevity– Sight - congenital blindness emerged– Laikre & Ryman (Cons Biol 1991)

Gray wolves on Isle RoyaleWayne et al. 1991

• Migrated to island in 1949 – Only 1 mtDNA haplotype => 1 pair?– Feed on moose mostly

• Population increased to 50 (1980)• Declined to 14 by 1990

– Susceptible to canine parvovirus

• Genetics– 50% loss in Het (vs. 40-65% loss predicted from Ne est)– Restriction fragment results: Island Mainland

Average % difference 28% 68%% Fixed 42% 15%

Royal catchfly – Silene regia

• Large populations produce abundant viable seeds

• Small populations (<50-100) produce seeds but these are inviable

• Why?

Fitness declines in small populations

• Fewer seeds and sharp pop. declines in small pops of Gentiana germanica (Fischer & Matthies 1998)

• Seed & seedling size and survival decline in smaller pop’s of Gentiana pneumonanthe (Oostermeijer et al.1994)

• Seed viability declines in smaller populations in

Silene regia (Menges 1991)

Extinction and Ne in Clarkia pulchella

Newman & Pilson 1997 founded experimental populations of this annual plant with the same N, but different Ne's (due to relatedness of founders)

after 3 gen's, the low Ne pop. had lower germination and survival

only ~ 21% of large Ne pop’s

At end, only 31% of low Ne pop's remained vs. 75% of large Ne pop's

Conclusion:

Ne matters to persistence

Genetic rescue in Scarlet Gilia

• Heschel and Paige (1995) found that adding pollen from a distant population to two small populations significantly increased their seed size and germination percentage, whereas transferring pollen to a large population had no effect. – Cons. Biol. 9: 126-133.

• Termed ‘genetic rescue’

The Beach Mouse

• Peromyscus polionotus• Florida island beach mouse• Lacy et al. (1996; 1998) investigated 3

subspecies• Inbreeding affected many traits:

P.p. s P.p. r P.p.l. Litter F: many char's litter size ** Mom's F: P(litter) & litter size litter size NS "Effects of selection on inbreeding depression varied substantially among populations, perhaps due to different histories of inbreeding and selection"

The Beach Mouse

The genetic load was unequally partitioned among founder pairs – different founders contributed to different parts of the load (affecting different fitness components)Thus, inbreeding depression for individual fitness components reflects a few highly deleterious alleles. Such genetic loads tend to diverge among natural populations

due to both drift and selection (purging).

Inbreeding depression is universaldifferent alleles contribute to inbreeding depression of different fitness components in different environments.

Speke’s Gazelle

• Smallest gazelle, a migratory ungulate, native to Somalia and Ethiopia

• Threatened by the loss of grazing land to livestock + hunting + drought + habitat fragmentation + . . .

Height: at shoulder 1.6-2 ft.Length: 3.1-3.5 ft.Weight: 33-55 lbs.

The Speke’s Gazelle story

• In the late 1960s, the St. Louis Zoological Park became concerned about the fate of Speke's gazelle (Gazella spekei). Because of warfare in Somalia, they decided to start a captive-breeding program using all the animals in captivity he could locate: 1 male and 3 females.

• The descendents of this bottlenecked population appeared to show less inbreeding depression.

• Were deleterious recessive mutations purged by selection from this population?

Templeton, A. R., and B. Read. 1983. The elimination of inbreeding depression in a captive herd of Speke's gazelle. pp 241–261 in C. M. Schonewald-Cox et al., Ed. Genetics and conservation: a reference for managing wild animal and plant populations. Addison–Wesley, Reading, Massachusetts.

The Speke’s Gazelle story

• Templeton & Read claimed that this inbreeding purged much of the genetic load, but . . .

• Willis & Wiese ‘97 and Kalinowski et al. 2000 questioned this result and their analysis of the data..

– impact of inbreeding was mostly in the 1st generation, but selection could not have acted so quickly

– "Evidence for genetic improvement of the SG herd is too weak for this breeding program to be used as a paradigm for the breeding of other endangered species"

Sumatran Rhino

Most unique of 5 rhino species but RARE smallest; also known as Hairy Rhino ~400 on Malay peninsula, Borneo, & SumatraRemnant Borneo population of ~70 DNA evidence - unique; Isolated for 1000's of yrsWill not breed in captivity (21/39 died)

To inter-breed or not?

What to do?

• Dilemma: genetic rescue or genetic swamping?– Given an isolated population potentially suffering from

inbreeding, should germplasm from other populations be introduced?

– Case: Sumatran Rhino– Case: Florida Panther

• Females from Texas introduced genetic rescue

– Case: Prairie chickens in Illinois – also rescued

• Danger? – Locally adapted genotypes can cause “outbreeding

depression”

So what traits do “extinction-prone” species share?

• Rare! Like top carnivores

• Large – Most large mammals are threatened – and may have

stopped evolving

• Specialized– Adapted to particular resources– Or a particular place = Endemic, e.g. to islands– The Tropics have by far the most diversity, but most of

these species are rare

• Social & / or Migratory– Passenger Pigeon, bison, Great Auk, etc.

Why?

Small Ne

Anything that reduces Ne increases genetic threats

• Ne = (4Nm x Nf)/ (Nm + Nf)

• As sex ratio skews, Ne

• In sharp-tailed grouse, the operational sex ratio is 1:10

• So when N=280, Ne = just 50 – This implies a 1% reduction in

Heterozygosity per generation

• Management goal: reduce skewing of sex ratios in small populations

Genetic process in large vs. small populations

Large, outcrossing Small inbred Favorable

Mutations

Neutral Mutations

Deleteriousmutations

Occasional sweeps

Drift to fixation - low variation

Drift allows mut’s of moderateeffect to fix => drift loadDeterministic selection

low load - short-lived

Drift sustains variation

regular simultaneous sweeps Time

What happens under inbreeding?

• Homozygosity & gene identity (idd) INCREASE Note: There is no change in allele frequency This causes deleterious recessive mutations to co-occur causing . .

• Inbreeding Depression= decline in fitness upon inbreedingReflects deleterious recessive alleles

• Variance among families & lines INCREASES but DECREASES within lines

• Possible loss of lines & families (this can decrease overall genetic diversity)

Inbreeding affects the Frequencies of genotypes

Increased homozygosityWithin population (consanguineous) inbreeding changes the frequency of genotypes (but not alleles) by increasing the frequency of homozygotes while decreasing heterozygotes:

Genotype: AA Aa aa

H-W equilibrium p2 2pq q2

Inbred population p2 + F pq 2pq (1-F) q2 + F pq

Note: symmetric increase in homozygotes

deficiency of heterozygotes => gives formula to est F

Deficiency of heterozygotes

What causes inbreeding depression?

• The accumulation of deleterious mutations with (at least partial) directional dominance:

homozygosity

Inbreeding decline in Drosophila Data from Ehiobu, Goddard, & Taylor, 1989, TAG 77: 123.

N=20 for 8 gen’s

N=4 for 3 gen’s

1 gen. full-sib mating

= .66

Fitness = viability x fecundity

Inbreeding depression

e(-A)

Inbreeding depression

Wf = W0 - F pq s (1-2h)

Thus, inbreeding depression will be most pronounced when:– There is a lot of inbreeding (F high)– Mutations are highly deleterious (s>0) (or many)– Mutations are recessive (h~0)– mutations are moderately frequent in the population– (q appreciable, so pq is high)

The load of deleterious recessive mutations can accumulate

Inbreeding

Small Ne Drift & Fixation

declines in Inbreeding

performance depressionLoss of S alleles

Inability to mate These are self-incompatibility genes in plants

What kinds of inbreeding exist?

• Within individual– Fi = P(2 alleles at a locus are idd)

• Between individuals– Fj,k = P(allele at a locus in j is idd to allele there in k)

• Within populations– FIS = deficiency of heterozygotes relative to random mating

• Among populations – due to subdivision

– FST = deficiency of het’s in a subdivided population relative

to the whole population

Types of Genetic Hazard

1. Inbreeding depression (consanguinity)2. Fixation via drift (drift load)3. Mutational meltdown4. Declines in quantitative genetic variation

ALL genetic hazards can be overcome by crossing among populations

(although outbreeding depression may be a problem)

Genetics & ecology interact

Slower

Faster

How do deleterious alleles accumulate?

• Added by mutation; purged by selection• Can become fixed in small populations

• Theoretically a function of Ne

• How great a threat is it?• How effective is purging by inbreeding or founder

effects in small populations?– alleles with s < 1 / 2 Ne are invisible to selection

– Thus mildly deleterious mutations will continue to fix even if strongly deleterious ones are purged

What influences genetic variation?

Mutation

Drift

Gene flow

GENETICVARIATION Selection

EnvironmentPopulation size & structure

+

-

+-

+/-

What kind of variation do we need to sustain?

• Quantitative genetics: Partitioning phenotypic variation into genetic and environmental components: VT = VA + VD + VI + VE

– localizing genes - QTL analysis– determining the effects of different alleles– determining the heritability (h2) of traits

(& thus response to selection)

h2 = VA / VT

• Yet we usually use genetic markers to measure and monitor genetic diversity (easier)

Review: Measures of genetic variation

• Within a population– Number of alleles at a locus - n– Proportion polymorphic loci - P– Allele frequency - p– Heterozygosity - He & Ho– Gene Diversity - D– Linkage Disequilibrium - – Inbreeding - F

• Among populations– Subdivision: F-st (or G-st)– Nei’s Genetic distance

Useful tools

• Molecular genetics: Provide techniques to measure genetic variation and understand the underlying basis for it. Can also use to identify “genetic units” in nature like:– Species– Evolutionary Significant Units– Ecotypes

• Ne = the size of an “ideal population” with the same rate of loss of genetic variation by drift as the population being described (N)

HOW LARGE?

• Obviously the greater Ne the lower the rate of loss of genetic variation

• For long-term maintenance of H, Ne 1000s seems prudent

• Even in the short-term, Ne 500 is much better than 50 (as in 50-500 rule)

‘Mutational meltdown' dynamics

SLOW (~100 gen’s)

Mutation - quantitative genetic equilibrium(Lande 1995)

• Drift - mutation equilibrium approach:Expected rate of loss of Vg and Het due to drift = 1 / 2 Ne per gen

dVg / dt = Vm - Vg / 2Ne

So, at equilibrium, Vg = 2 Ne Vm

If h2 ~ 0.5, Vg ~ Ve

• How fast is genetic variation produced via mutation?– Rate of phenotypic divergence via drift among inbred lines– Rate of response to selection in inbred lines– Vm ~ 0.001 x Ve (Lande 1975; Lynch 1988)

• So Ne ~ 500 should allow variation to be maintained– But only ~10% of Vm is quasi-neutral (potentially adaptive)– So Vm ~ 0.0001 x Ve => Ne of 5000 needed to maintain variation

Topics in Conservation Genetics

• Evolutionary uniqueness – “living fossils”– Why conserve the Tuatara?

• How best to breed in captivity?– Are there rules?

• Where to locate reserves?– Centers of endemism & biodiversity hotspots

• Forensics– Where did that whale meat come from?

• Grizzly Bear – demographic monitoring

• Cheetahs– Why undescended testicles & deformed sperm?

Genetic concerns under captivity?

• Issue: Do small captive populations lose genetic variation over time? How much?

• Happens because of inbreeding, small Ne, and artificial selection

• Geneticists can provide guidelines - take advantage of genetic planning

Rules for Captive Breeding

1. Minimize the loss of genetic variation2. Maximize demographic viability3. Minimize (artificial) selection

Should we intentially inbreed to purge inbreeding depression?

Fin(Mediterranean)Fin (Iceland)

RESULTS

Unknown #10,11, 12

Unknown #13

Blue(North Pacific)

Blue(North Atlantic)

Gray

Unknown #1b

Humpback(North Atlantic)Humpback(North Pacific)

Unknown #9

Minke(North Atlantic)

Minke(Antarctica)Minke(Australia)Unknown #1a,2, 3, 4, 5, 6, 7, 8

GeneticForensics

Where did your sushi

/whale meat come from?

Forensics??

Steve Palumbi

Trimming Twigs on the Tree of Life

http://www.tolweb.org/tree/

Don WallerUniversity of Wisconsin

Madison, Wisconsin USA

Which twigs are being pruned?

In broad terms, we are losing just what one would expect:

– Big, wide-ranging Things – the Big Things that run the world

– Habitat specialists – Rare species– Local endemics– K-selected species

Are we reducing the Tree of Life to bansai form?

Trading TwigsAre some twigs more important than others?Which evolutionary contexts are being lost or altered?

Do bigger /basal branches deserve more protection?

(Recent work suggests that Tuatara have actually changed significantly in form since the Mesozoic)

Tuatara

Why conserve the Tuatara?

Sphenodon – endemic to New Zealand

F. Allendorf

All by itself

‘Living Fossil’

Only species in this Genus, Family, and Order (!)

The extinction “vortex”

• Loss of habitat and fragmentation leads to• Declines in population size and isolation• leads to inbreeding and smaller colony size• leads to reductions in reproductive success• leads to

'vicious cycle' = positive feedback

Threats multiply and interact

Summary

1. Humans are now causing the 6th greatest wave of extinction of all time.

2. Agriculture, development, and resource use are massively reducing and fragmenting habitats.

3. Rare, local (endemic), specialized, and big species are more prone to extinction.

These commonly occur in the tropics.

4. Habitat loss & fragmentation reduce population size and increase genetic isolation

5. Small isolated populations lose molecular and quantitative genetic variation and drift more.

Summary

6. Reduced genetic variation and increased drift limit the ability of small and isolated populations to adapt to changing environments.

7. Drift and inbreeding increase the expression of recessive deleterious mutations, causing inbreeding depression.

8. Inbreeding effects accumulate over generations.

9. Population-level fixation and inbreeding can depress fitness even when crosses within inbred populations reveal no inbreeding effects.

We can expose such effects by crossing a small population with a big one – allowing “genetic rescue”

Summary

10.Small asexual and inbred populations are also subject to mutational meltdown – a long-term threat.

11.Ecological and genetic forces are rarely independent and can interact to create an “extinction vortex.”

12.We also use genetic techniques to monitor exploited populations and species (forensics).

13.We are learning more about genetic threats and how to use genetic markers to diagnose and monitor these threats

But this has not yet become routine . .

10 Key genetic issues

1. Effective population size - Ne

2. Inbreeding (F) and inbreeding depression ()

3. Out-breeding depression

4. Accumulation of deleterious mutations (U)

5. What maintains genetic variation?

6. Genetic deterioration in captivity

7. Genetic diversity and extinction

8. Minimum viable population size

9. Measuring differences among populations

10. Relative importance of these genetic issues