Basic premise:

genetic variation is valuable for fitness

What is variation?described at the individual level as homozygous, heterozygous

AA Aa

described at the population level as monomorphic, polymorphic

Measurement of variation

# alleles per locus

proportion of loci that are polymorphic in a population (P)= # polymorphic loci

number loci examined

proportion of loci that are heterozygous among all genes (H)

= % of genes at which average individual is heterozygous

Measurement of variation

P HAves (birds) 0.10 0.043 Mammalia 0.15 0.036Teleosts (fishes) 0.15 0.051Reptilia 0.22 0.047Plants 0.26 0.071Insecta 0.33 0.081Invertebrata 0.40 0.100

from Nevo 1978

What is fitness?

= relative ability of a genotype, or individual, to survive

and reproduce

Basic premises

• more offspring are produced than will survive or reproduce

• individuals differ in their ability to survive and reproduce

• some of these differences are genetically based

• at reproductive age, genotypes that promote survival, or production of more offspring, will be more abundant in the population and will passed on disproportionately

• It is very difficult to distinguish differences in fitness among genotypes from ‘accident’ or other factors

Evidence that variability is important?

• centuries of breeding studies – hybrid vigor

• heterosis – enhancement of fitness due to increased heterozygosity

• Evidence:– growth rate of Coot clam decreased after genetic

bottleneck (loss of variation) (Koehn et al. 1988; Meffe and Carroll p.168)

– efficiency of oxygen intake in American oyster decreased (Koehn and Shumway 1982)

– Florida panther: sperm defects, cowlicks, kinked tails, cryptorchidism – reduced after increasing diversity through outbreeding (Pimm et al. 2006)

Evidence that variability is important?

Evidence that variability is important?

Chinook salmon:• 82% of outbred salmon resistant to whirling

disease - 56% of inbred salmon resistant

• absence of 3 alleles resulted in complete susceptibility to whirling disease

Arkush, D. K., et al. 2002. Can. J. Fish. Aquat. Sci. 59:159-167.

MHC (major histocompatibility complex)

- immune system protects by recognition of ‘non-self’ proteins (e.g., graft rejection)

- most highly variable portion of genome

Tasmanian devil (Sarcophilus harrisii)currently ~ 10,000-100,000Eliminated from mainland Australia ~ 600 yrs agoProtected in Tasmania in 1941

Devil facial tumor disease (DFTD)transmissible tumor, spread by bitingtumors spread by allografts, genetically identical (clonal)

DFTD is recent (~10 yrs) – but not recognized as non-self by MHC

Siddle et al. 2007. Transmission of a fatal clonal tumor by biting occurs due to depleted MHC diversity in a threatened carnivorous marsupial. PNAS 104:16221-16226

‘Markers’ of low individual heterozygosity

• developmental instability

• fluctuating asymmetry

‘Markers’ of low individual heterozygosity

cutthroat trout in hatchery vs. wild (Leary et al. 1985) 57% reduction in # polymorphic loci

29% reduction in average # alleles per locus 21% reduction in average heterozygosity per locus

of 51 fish:– 10 fish missing one pectoral fin– 3 fish missing 2 fins– many had deformed vertebral columns

Plants Inverts. Verts. Overallspecialists 0.04 0.06 0.04 0.05generalists 0.08 0.15 0.07 0.11

Genetic variation present in specialists vs. generalists

Heterozygosity as a predictor of adaptability

example: zebra mussels counter-example: Asian clam

What are the consequences of absence of variation?

• yellow perch

• elephant sealDavid Smith, UCMP

What are the sources of variation?

mutation – rare!!approx. 10-6 mutations per gamete per generation

> 100 to 1,000 generations to restore variability via mutation

What are the sources of variation?

mutation – rare!!approx. 10-6 mutations per gamete per generation

sexual reproduction – blending of genes, and rearrangement of genes

Distribution of variation:

Variation is present• within individuals

• among individuals within populations

• among populations

Source of variation Populations within between

AA, AA, AA AA, AA, AA AA, AA, AA none none

AA, AA, AA BB, BB, BB DD, DD, DD none all

AA, AB, CD AA, AB, CD AA, AB, CD all none

AA, AB, AD AB, BC, CC DD, BB, AC present present

Factors that reduce variation within populations

• Short-term small population size

– genetic bottleneck – a dramatic collapse in numbers

– founder effect – a very small number of colonists that originate a new population

Factors that reduce variation within populations

• Short-term small population size– genetic bottlenecks– founder effect

0

200

400

600

800

1000

1200

1400

N

TIME

RECOVERY

CRASH

bottleneck

Factors that reduce variation within populations

• Short-term small population size– genetic bottlenecks– founder effect

TIME

PO

PU

LA

TIO

N S

IZE

Factors that reduce variation within populations

• Short-term small population size– genetic bottlenecks

– founder effect

Elephant seals:

N = unknown (thousands) 20 30,000 late 1800s 1890 1960s

24 loci examined all monomorphic

David Smith, UCMP

Factors that reduce variation within populations

• Short-term small population size– genetic bottlenecks

– founder effect

Huntington’s chorea

- neural function decay, leading to death

- frequent in South Africa, and near Lake Maracaibo, Venezuela

- single gene, dominant allele

- founder effect

- weak selection

Factors that reduce variation within populations

• Short-term small population size– genetic bottlenecks– founder effect

THE BAD NEWS:

Effects of small population size are cumulative – a population is, in effect, going through a serious bottleneck every generation – perennial low numbers erode genetic variation

THE GOOD NEWS: A single bottleneck generation will not eliminate most of the genetic variation in a population Crucial issue is whether the population remains small or grows

to a relatively large size

How to avoid the consequences of bottlenecks:

increase population size rapidly

Issues with intrinsic rate of increasetaxonomic biasesage at maturityfecundity

Factors that reduce variation within populations

• Short-term small population size– genetic bottlenecks

– founder effect

Retention of genetic variation in a small population of constant size:

# generations N 1 5 10 1002 75 24 6 <<16 91.7 65 42 <<110 95 77 60 <120 97.5 88 78 850 99 95 90 36

100 99.5 97.5 95 60

Factors that reduce variation within populations

• Short-term small population size– founder effect– genetic bottlenecks

• Long-term small population size– genetic drift– inbreeding

Factors that reduce variation within populations

• genetic drift: random loss of variation due to stochastic events

Factors that reduce variation within populations

genetic drift

• Qualitatively genetic variance (or heterozygosity) will be lost

Factors that reduce variation within populations

genetic drift

• Quantitatively specific alleles will either be lost or retained :

Average number out of 4 alleles retained:

original allele frequency before founder eventN 0.7, 0.1, 0.1, 0.1 0.94, 0.02, 0.02, 0.0250 3.99 3.610 3.63 2.02 2.02 1.231 1.48 1.12

Factors that reduce variation within populations

genetic drift

Loss of alleles is more critical than loss of variation (heterozygosity)

WHY?

http://darwin.eeb.uconn.edu/simulations/drift.html

Small populations of constant size always lose heterozygosity through time

• More alleles are lost in populations founded by small numbers of individuals

– The smaller the population is, the more rapidly heterozygosity is lost

• Alleles which have low frequencies in the original population tend to be lost much more easily in the founder population than alleles with high frequencies