Population Genetics The “Modern Synthesis” of evolution is Darwinism

1. Population Genetics The “Modern Synthesis” of evolution is Darwinism enlightened by the understanding of molecular genetics which has been gained since Darwin. The key to understanding how evolution occurs is a move from viewing genetics in terms of individuals and their alleles to -- the frequencies of those alleles among the genes of all individuals comprising a population.

2. We know about genes and particulate inheritance. Darwin did not. He was neither the first not the last to accept blended inheritance. He wrote before Mendel had described recessive traits. To explain evolution, he fell back into a second error: the inheritance of acquired traits. Most phenotypes, resulting from the influence of many genes, do seem to be inherited as if blended. Without a mechanism for particulate inheritance, it was hard to establish the concept.

3. Mendel’s genetics disappeared into the literature until the beginning of the 20th century. The rediscovery of Mendelian genetics led to a number of leading biologists claiming that evolution resulted from inheritance of mutations. Evolution, in this view, moved rapidly and by jumps, rather than gradually, as Darwin had believed. Failures to accept “the modern synthesis” of Mendelian genetics and Darwinian evolution persisted into and after WWII - e.g. Lysenko.

4. To understand the modern synthesis, we need to consider the genetics of populations, rather than individuals. Consider a Punnett square for a single trait cross:  (male) ½A ½a ½A AA Aa  (female) ½a Aa aa in describing this cross, we have shown the effects of meiosis: 1/2 the sperm carry A, 1/2 a, and similarly for the eggs.

5. Now recognize that the fractions of these two alleles in the population may not be equal, and there may be more than two alleles. The sum of all alleles for a trait in the population is the gene pool for that trait. We measure fraction p of the genes in this gene pool are of type A, and fraction q are type a (assuming males and females are genetically similar). Now the Punnett square looks like this: male pA qa pA p2AA pqAa female qa pqAa q2aa

6. A mating like this does not change gene frequencies. Evolution is a change in the composition of the gene pool. Gradual change is called microevolution. In a population that had those allele frequencies, they would remain unchanged indefinitely if the conditions for Hardy-Weinberg equilibrium held.

7. What are the conditions? 1. Large population size 2. No migration (gene flow occurring through immigration or emigration) 3. No mutation 4. Random mating (no assortative mating) 5. No natural selection Do the conditions often apply (or apply for long)?

8. The Hardy-Weinberg Law is a null hypothesis. It holds (as what is called the Hardy-Weinberg equilibrium) when things don’t change, i.e. 1. In large populations there is no genetic drift. In small populations random events (mortality of a single individual) may materially affect gene frequency. This happens in small island popula- tions or populations of endo (internal) parasites. 2. There is no movement between populations, that would be gene flow. The genes moved would change the frequencies in both source and recipient populations.

9. 3. There is no mutation. If one A mutated to a per 100 alleles, then what was 50% A in the starting population would become 49%A after mutation. Actual mutation rates are about 1/106 per gene, but that translates to about 1 mutation per gamete for us. We are, thus, each unique. 4. Mating (fertilization) occurs randomly. If blondes would only marry blondes (real ones) (blond hair being recessive), there would be a much higher frequency of the blond phenotype. Let’s look at an example of this:

10. We can figure out gene frequencies in a population if we know the frequency of the recessive phenotype. For these individuals, knowing the phenotype frequency we also know the genotype and gene frequencies. The frequency of the recessive phenotype is q2. That is also the frequency of the homozygous recessive genotype. Then the frequency of the recessive gene is the square root of q2  q. Now for the example:

11. We start with 100 people (50% male). 1 out of 10 is a natural blond. That means q2 = .1, and q=.316. p = 1 – q = .684. Those would be the values indefinitely if mating were random, but… If blondes only mate with blondes, then the 5 blond males mate with the 5 blond females, and produce 10 blond children in the next generation. As to the other 90 (or 180 genes): p2 = (.684)2 (·100)  46 are homozygous for dark hair (or 92 dark-haired genes), and 2pq = 2(.684)(.316) (100)  44 are heterozygous (another 44 genes for dark hair)

12. The overall frequency for the dark hair gene among the mating population of dark-haired individuals is: 136/180 = .755… Assuming that the dark haired individuals mate randomly: male gametes .75B .25b .75B .5625 BB .1875 Bb female gametes .25b .1875 Bb .0625 bb BB and Bb have the dark hair phenotype. Take these fractions and use them to correct to total 90 individuals to keep the population constant in size  51BB + 34Bb are dark haired, 5bb are blonds

13. Add these to the 10 blonds from assortative mating, and now there are 15 blonds instead of 10 out of 100, and 85 instead of 90 with dark hair. The phenotypic and genotypic frequencies have changed; microevolution has occurred. But, how often does assortative mating of the sort presented in this example occur in nature?

14. 5. No natural selection occurs. When natural selection occurs the survival and reproduction of different phenotypes differs. Some have higher survival and/or reproduction; they leave behind a larger fraction of the offspring that form the next generation (differential reproductive success). Their genes represent a greater fraction of the gene pool in the next generation. A numerical example: selection against the sickle cell gene. We will conveniently forget the advantageous effects of being heterozygous.

15. An example of selection: Sickle cell anemia Begin with 50% of the genes S and 50% s. The initial, randomly mated cross is: .5S .5s .5S .25 SS .25 Ss .5s .25 Ss .25 ss We will assume the .25ss die without reproducing. Now calculate new gene frequencies. The 75% of the population of offspring surviving to reproduce are the ‘whole’ population. Now 66% of the genes are S and .33 are s

16. The cross in the 2nd generation is: .66S .33s .66S .44SS .22Ss .33s .22Ss .11ss Natural selection against the homozygous recessives has reduced the fraction from 25% to 11% in one generation. It would further reduce the fraction each generation, but since there are fewer of them, fewer would be selected against, as well. N.B. natural selection - acts on phenotypes - selects only among variants present

17. Natural selection acts on phenotypic variation. Where does the variation come from? Ultimately, all genetic variation in living organisms originates as mutations. The variation we observe in a population is also determined by: 1) recombination (sexual reproduction) 2) the spread of variants in a population due to drift, and 3) the effects of environmental variation on the relative success of different phenotypes.

18. One view of the amount of genetic variation in a species is the fraction of its genes that are hetero- zygous. That fraction in part indicates the amount of outcrossing (breeding with unrelated members of the species) and in part reflects the history of the species. Cheetahs went through a severe bottleneck within the last 10,000 years; only 0.07% of their genes are heterozygous. Humans have not gone through a bottleneck like that; 7% of our genes are heterozygous.

19. Why are so many genes not heterozygous? - because altered alleles are not as ‘good’ as the ones that persist. Others have been removed by selection.

20. While examples indicate how gene frequencies can change, the most common cause of genetic change (microevolution) in natural populations is natural selection… Natural selection can occur in different ways. We categorize the basic types of natural selection into three forms: stabilizing selection, directional selection, and diversifying (or disruptive) selection.

21. Modes of Natural Selection

22. 1) Stabilizing selection - - acts against extreme forms, favors intermediates - one example: human birth weights

23. 2) diversifying (or disruptive) selection - acts against intermediates, favors extremes - example - selection of different coloration patterns in Papilio to resemble noxious but unrelated butterflies

24. 3) directional selection - favors one extreme, selects against the opposite extreme - shifts the phenotype distribution curve in one direction. Numerous examples: industrial melanism pesticide or drug resistance

25. There is another form of selection: 4) sexual selection - leads to evolution of secondary sexual characters - results in sexual dimorphism - usually males evolve showy characters, e.g.: a) tails of peacocks; peahens are drably colored b) antlers of deer or caribou - females lack antlers c) colors of male mallards at breeding time,... - Why? usually females choose mates, showiest or most dominant male gets a large harem, others remain generally unmated

26. So, to take a human view, imagine John Travolta in Saturday Night Fever, or... (Sorry, I couldn’t find a good copy of the classic pose in a white polyester suit, strutting his stuff)

27. These are Wodaabe men from Niger in a pose off, where the women select the most beautiful men. They are wearing lipstick and other makeup, where the males of many animal species are naturally decorated (e.g. cardinals, peacocks, birds of paradise).

28. Questions about selection: 1) Are most genes subject to the intense natural of (most) of these examples? No! These extreme examples make evolution more apparent, and occurring more rapidly. 2) Are some genes strongly conserved through the varieties of living things? Yes! For example, there have been only a handful of changes in the base sequence of cytochrome C from bacteria to man. 3) Is all genetic variation adaptive? No! Much of the variation is neutral. None of the variants confers a selective advantage.

29. Does natural selection “perfect” organisms? No! Why? 1. Organisms are locked into historical constraints. 2. Adaptations are compromises. 3. Not all evolution is adaptive. Chance frequently plays a large role. 4. Selection can only act on (and edit) variations (phenotypes) that exist.