Hardy-Weinberg Equilibrium

• Population includes interbreeding organisms and their offspring, or individuals in the same area including asexual species.
• Gene pool refers to all genes within a population.
• The Hardy-Weinberg principle provides a comparison baseline to assess if allele and genotype frequencies change over time.

Hardy-Weinberg Equilibrium (HWE)

• A population in HWE at a specific locus implies no evolutionary forces affect allele frequencies at that locus.
• HWE rests on 5 assumptions: no natural selection, no mutation, no gene flow, no genetic drift, and nonrandom mating.
• The Hardy-Weinberg equation is (p+q)^2 = p^2 + 2pq + q^2.
• If HWE assumptions hold true, allele frequencies will stay constant across generations.
• Genotype frequencies will remain as p^2 + 2pq + q^2.

Selection on Recessive and Dominant Alleles Experiment

• Flour beetles with alleles + and L (+ is normal, L/L is lethal) starting with heterozygotes (50% each) to observe population evolution.
• Over time, the frequency of + allele increased while L decreased, but L never disappeared completely.
• The lethal allele is hidden from natural selection in heterozygotes, which do not harm the individual.

Experiment Showing Heterozygote Superiority

• Drosophila melanogaster fruit flies with V (viable) and L (lethal) alleles started with heterozygous individuals to observe population evolution.
• Over time, the V allele frequency increased while the L allele decreased, but evolution slowed at around .21 frequency of L.
• Natural selection does not eliminate L allele because heterozygotes have an advantage.
• The fitness of the heterozygote is greater than both homozygotes showing heterozygote superiority.
• High percentage of homozygote VV alleles initially, wanted to see if the V allele decreased over time.
• The V allele frequency decreased to around 0.79 (0.21 lethal allele), the lethal allele remained high due to heterozygote advantage.

Selection Intensity and Allele Frequencies

• Strong selection removes deleterious alleles faster (more deaths).
• Weak selection removes deleterious alleles slowly; lethal homozygous recessive genotypes survive more.

Polymorphic Loci

• Alleles are functionally equivalent (neutral theory).
• Mutation-selection balance occurs.
• Heterozygote superiority is present.
• Selection varies for alleles across times, places, ecologies, and sexes.
• Frequency-dependent selection is observed.
• Frequency-dependent selection means genotype or phenotype fitness depends on its frequency in the population.
• Example: elderflower orchids have yellow flowers with higher fitness when less common, lower when more common.
• Bees visit both purple and yellow flowers equally, thus less common flowers have higher reproductive success due to more bee visits.
• Mutation alone causes little evolutionary change without other forces.
• For example, "A" mutates to "a" at 1 per 10,000 copies, then allele "A" frequency decreases slowly over time.
• Mutation-selection balance equates the rate of deleterious allele deletion by selection with the rate of new copy creation by mutation.

Mutation-Selection Balance Experiment

• Drosophila melanogaster were observed, starting with little genetic variation.
• Original flies exposed to 5% NaCl died.
• Six experimental populations of inbred flies were used.
• Two groups under benign conditions, four with salt-spiked food.
• Original population died without mutation or selection.
• A few individuals in benign conditions survived through mutations without selection.
• A good amount in salt conditions survived through mutation and selection.

ΔF508 Frequency

• Heterozygote superiority maintains the ΔF508 allele at a relatively high frequency due to resistance to typhoid fever. -Mouse cells (wild-type, wild-type/ΔF508, and ΔF508/ΔF508) exposed to typhoid fever showed the ΔF508/ΔF508 genotype survived better, indicating resistance.
• Cystic fibrosis alleles are maintained because heterozygotes have superior fitness during typhoid fever epidemics.
• Gene flow involves allele transfer from one population's gene pool to another (dispersal).

Lake Erie Snake Study

• Snakes are either banded or unbanded.
• Most island snakes are unbanded, mainland snakes are banded.
• Unbanded skin helps island snakes blend with limestone.
• Migration from the mainland occurs.
• Natural selection and migration work against each other.
• Gene flow homogenizes allele frequencies across populations, preventing evolutionary divergence unless balanced by an opposing mechanism.
• Populations close together are more genetically similar due to higher dispersal/reproduction rates.
• Genetically different populations are far apart due to reduced movement and mixing of genes.
• Genetic drift involves random allele frequency changes in a population (chance events, not selection).
• Founder effect occurs when a few individuals colonize a new area, leading to allele frequencies differing from the original population due to chance.

Silvereyes Colonization of Islands

• Population size decreases and isolation increases (mainland Australia to Tasmania, New Zealand, etc.) promoting genetic drift causing random allele changes decreasing genetic variation.
• Fewer alleles exist as populations move from island to island, with only a portion of original alleles represented in newly founded populations.

Polynesian Cricket Study

• Crickets moved from Australia, to other Pacific Islands, and then Hawaii.
• Allelic diversity decreased with distance from mainland.
• Hawaii, being the most remote location, had only a few alleles present in the cricket population.

Genetic Drift

• Genetic drift has a larger effect in smaller populations.
• Random chance plays a bigger role when there are fewer individuals.
• Losing or survival of a few individuals can dramatically change allele frequencies.
• In contrast, genetic drift is weaker in large populations due to random fluctuations buffering and more stable allele frequencies.
• Genetic drift causes allele frequency to "drift" to 1.0 or 0 in the absence of other evolutionary forces.

Fixation/Extinction Experiment

• 107 populations of flies, all founders heterozygous for brown eye color (bw^75/bw).
• After 19 generations, bw^75 was lost in 30 populations and fixed in 28 populations.
• Heterozygosity decreased over time faster than expected and resembled starting with a population of 9 instead of 16 (Ne=9).
• The equation for predicting heterozygosity decline in finite populations is Hg+1= Hg (1-1/2N).
• Hg+1 is heterozygosity in the next generation.
• Hg is heterozygosity in the current generation.
• N is the number of individuals in the population.
• Effective population size (Ne) indicates the actual number of reproducing adults.
• It's the size of an "ideal" population losing heterozygosity at the same rate as the actual population, virtually always less than the actual population size.

Factors Making Ne Less Than N

• Number of years to reproductive age.
• Average age in the population.
• Sex ratio of reproducing individuals.
• Non-random mating.
• Any factor reducing genetic contribution of some individuals to future generations.
• Inbreeding is mating between genetic relatives and is a common type of nonrandom mating.
• The coefficient of inbreeding (F) indicates the probability of two alleles at a locus in an individual being identical by descent.
• The heterozygosity relationship of an inbred (HF) population with a random mating (HO) population is HF = HO(1 - F).
• Inbreeding depression presents negative reproductive consequences for a population with a high frequency of homozygous individuals with harmful recessive alleles.
• Inbreeding mainly leads to decreased heterozygosity in populations which causes more homozygotes.

Consequences of Inbreeding

• Lower fertility and fecundity.
• Lower survival rates.
• Asymmetrical development.
• Overall lower lifetime reproductive success (LRS).
• Inbreeding depression becomes more apparent as individuals grow older and are subjected to selection.
• Study on inbreeding depression found a strong relationship between inbreeding and number of eggs failing to hatch in great tits.
• Children of first cousins have higher mortality rates than children of unrelated parents.

Florida Panthers

• Hunting and habitat destruction decreased population size (n) and isolated them from other species.
• Isolation prevented gene flow, leading to no new alleles being introduced.
• Small panther population led to genetic drift.
• Fixed alleles became prevalent, decreasing heterozygosity.
• Lack of other panthers forced inbreeding.
• Inbreeding depression increased homozygosity, causing more deleterious recessive alleles.
• Health and size were reduced.
• Scientists captured panthers from another area, allowed breeding with Florida panthers, allowing gene flow, and reintroduced new alleles.
• Natural selection was allowed to "choose" new beneficial alleles and weed out deleterious ones
• Linked genes are on the same chromosome.
• Linkage equilibrium occurs when allele frequencies at one locus are independent of frequencies at another locus (on same chromosome) and follow Mendel's law of independent assortment.
• Linkage disequilibrium occurs when a pair of alleles from two loci are inherited together in the same gamete more or less often than random chance predicts.

Importance of Linkage Disequilibrium (LD)

• A deleterious allele might be maintained in a population if it's in linkage disequilibrium with an advantageous allele.
• LD can preserve adaptive allele combinations.
• Selection may appear to act on one allele when it's actually due to selection on a linked allele which can mislead studies on evolution.
• If locus A and B are in linkage equilibrium, selection for A will not impact the frequency of B.
• In linkage equilibrium, alleles at one locus are inherited independently of the alleles at another locus.
• Allele frequency at locus B is not influenced by selection acting on an allele at locus A.
• Alleles in linkage disequilibrium reach linkage equilibrium through recombination during sexual reproduction during meiosis, genetic material shuffles, breaking up linked alleles.
• Over many generations, recombination gradually randomizes allele combinations, reducing LD.

Costs of Sexual Reproduction

• Cost of producing males/meiosis.
• Searching for partners is costly in terms of time, energy, and risk.
• Exposure to diseases and parasites.

Alternatives to Sexual Reproduction

• Cell division (many single-celled organisms).
• Parthenogenesis - offspring develop from unfertilized eggs.
• Self-fertilization (in plants and hermaphroditic animals).
• Many organisms reproduce both sexually and asexually.
• John Maynard Smith's null model states a female's reproductive mode (sexual or asexual) does not affect the number of offspring she produces, and the probability that her offspring will survive.

Asexual Reproduction Advantages

• Asexual reproduction has a population growth advantage because every individual can reproduce (no need for mates) and no males are required, so all offspring-producing individuals contribute.
• Sexual reproduction persists despite asexual reproduction's population growth advantage likely because it violates Smith's second assumption and sexual offspring have survival advantages over asexual ones.
• Sexual reproduction is common because recombination reduces linkage disequilibrium, and results in more genetically variable offspring (especially for deleterious alleles).
• Also the potential advantage of creating combinations of beneficial alleles at multiple linked loci.

Disadvantages of Sexual and Asexual Reproduction

• A potential disadvantage of sex is the disassembly, by recombination, of adaptive combinations of beneficial alleles at multiple linked loci.
• A potential disadvantage of asexual reproduction is the accumulation of deleterious mutations.

C. Elegans Experiment

• Worms kept in an environment where they had to cross rugged terrain to find food.
• This imposed selection against deleterious mutations.
• Measured the fitness of three population strains at the end of the experiment.
• Relative to the ancestor, the three strains included only selfing hermaphrodites, hermaphrodites and males, and outcrossing females/males (hermaphrodites unable to make sperm).
• The fitness of only the hermaphrodites decreased.
• The fitness of both the hermaphrodites/males and hermaphrodites unable to make sperm plus males increased.
• Obligately selfing population decreased in fitness.
• The wild-type and obligately outcrossing population increased in fitness with the obligately outcrossing population getting the greatest increase.
• Dosing worms with a chemical mutagen increased mutation rate (lethal to males, prohibited sperm production).
• Only the outcrossing population maintained original fitness.
• The takeaway is that outcrossing maintains fitness against deleterious alleles.

Muller's Ratchet

• Muller's Ratchet describes how asexual populations accumulate deleterious mutations over time.
• Individuals with fewer mutations may be lost due to genetic drift in small populations.
• Population "ratchets" to a state with more deleterious mutations, reducing fitness, since no recombination removes harmful mutations.
• This gradually declines genetic health.
• Genetic load is the burden imposed by the accumulation of deleterious mutations.
• Pathogenic bacteria affected the percentage of outcrossing in a C. elegans experiment.
• Three populations forced to cross a lawn of pathogenic bacteria.
• Three groups of worms were a control group exposed to heat-killed bacteria.
• They had an evolution group exposed to pathogenic bacteria from a stock population.
• A coevolution group was exposed to pathogenic bacteria selected for their ability to infect C. elegans.

Pathogens

• The control maintained a frequency of males at about 20 percent.
• The evolution group made the outcrossing rate evolve to about 80 percent.
• The coevolution group caused the outcrossing rate to increase to 90 percent and it was maintained for the duration of the experiment.
• Pathogens can drive evolutionary changes in host populations.
• Drive these changes particularly in terms of reproductive strategies aimed at enhancing genetic diversity in response to selective pressures.
• Coevolutionary pressure from pathogens specifically adapted to infect the host seems to lead to the most extreme and sustained changes in outcrossing behavior.
• Selective forces favoring sexual reproduction include changing environments and host parasite-pathogen interactions.
• The Red Queen Hypothesis implies that sex is adaptive during perpetual arms races between biological antagonists.
• Promotes genetic diversity, thereby allowing hosts to evolve rapidly and better resist evolving pathogens.
• In Curt Lively snail study: trematodes consumed the gonads of snail species with obligately sexual or parthenogenic females.
• Males may be more susceptible to trematode infections than females.
• Explaining the correlation between higher parasite load and more males in the population.
• Lab experiments showed a consistent hypothesis: As total infection increased, male frequency increased.
• Showing that parasites select in favor of sex.