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 H Aves (birds) Mammalia Teleosts (fishes) Reptilia Plants Insecta Invertebrata 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?

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 Can. J. Fish. Aquat. Sci. 59:

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 Eliminated from mainland Australia ~ 600 yrs ago Protected in Tasmania in 1941

Devil facial tumor disease (DFTD) transmissible tumor, spread by biting tumors spread by allografts, genetically identical (clonal) DFTD is recent (~10 yrs) – but not recognized as non-self by MHC Siddle et al Transmission of a fatal clonal tumor by biting occurs due to depleted MHC diversity in a threatened carnivorous marsupial. PNAS 104:

‘Markers’ of low individual heterozygosity developmental instability fluctuating asymmetry

‘Markers’ of low individual heterozygosity cutthroat trout in hatchery vs. wild ( Leary et al ) 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. Overall specialists generalists Genetic variation present in specialists vs. generalists Heterozygosity as a predictor of adaptability example: zebra musselscounter-example: Asian clam

What are the consequences of absence of variation? yellow perch elephant seal David Smith, UCMP

What are the sources of variation? mutation – rare!! approx mutations per gamete per generation > 100 to 1,000 generations to restore variability via mutation

What are the sources of variation? mutation – rare!! approx 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 withinbetween AA, AA, AA AA, AA, AA AA, AA, AA nonenone AA, AA, AA BB, BB, BB DD, DD, DD noneall AA, AB, CD AA, AB, CD AA, AB, CD all none AA, AB, AD AB, BC, CC DD, BB, AC presentpresent

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 N TIME RECOVERY CRASH bottleneck

Factors that reduce variation within populations Short-term small population size –genetic bottlenecks –founder effect TIME POPULATION SIZE

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 s 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 increase taxonomic biases age at maturity fecundity

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 << << <

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 event N 0.7, 0.1, 0.1, , 0.02, 0.02,

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