basic premise: genetic variation is valuable for fitness
TRANSCRIPT
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
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
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 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
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RECOVERY
CRASH
bottleneck
Factors that reduce variation within populations
• Short-term small population size– genetic bottlenecks– founder effect
TIME
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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?
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