CAMPBELL BIOLOGY. Chapter 13

Transcription

1 Lecture 10 Population Genetics CAMPBELL BIOLOGY Chapter 13 Hox Genes Control development Hox genes need to be highly regulated to get expressed at the right time and correct level to orchestrate mammalian development in utero. Mario Capecchi won the Nobel Prize in 2007 for his research on Hox genes & their role in defining the mammalian development plan. Individual Hox genes were mutated in mice and the effects of the mutations observed. In TCD last week at History Society! 1

2 The study of populations is intimately related to the study of evolution. It is the population, not the individual that evolves. Evolution can be defined in terms of what happens to the genetic structure of a population over time. Typically populations undergo changes in: Size Composition Behaviour i.e. number of individuals i.e. the extent of phenotypic variation i.e. mating behaviour Charles Darwin saw evolution in these terms. He agreed with Malthus who proposed that populations could in theory increase in size exponentially. But not in practice because of resource limitations: food and space Natural Selection Darwin proposed that in most situations in nature there will be competition to survive and reproduce and that this was governed by a process he called natural selection That any being, if it vary however slightly, in any manner profitable to itself will have a better chance of surviving This implies a better chance of reproducing leaving offspring If the variation which increased the chances of survival were to be inherited, then the offspring would also have a better chance of survival and reproduction Over time any gene variant that contributed to a selective advantage would increase in frequency in the population 2

3 Populations, Gene Pools and Gene Frequencies A population is defined as: A group of individuals that interbreed freely and randomly In general a population will consist of members of a species between which breeding can occur Such a population shares what is called a Gene Pool = the sum of all alleles at all gene loci in the population As an example imagine a population of wild flowers in which there are two types which differ in colour The single flower colour locus has 2 alleles: A for pink flowers which is completely dominant over the allele a for white flowers Calculating Allele and Genotype frequencies Suppose the imaginary population consists of 500 individual plants 20 of these produce white flowers (homozygous recessive): a a The remaining 480 have pink flowers: 320 are homozygous AA 160 are heterozygous A a We can define the genetic structure of the population i.e. the composition of the gene pool in terms of: or (1) the genotype frequencies i.e. frequency of AA, Aa and aa (2) the allele frequencies i.e. Frequency of A Frequency of a 3

4 Genetic structure of the parent population s gene pool 1. Calculating Genotype frequencies Genotype Frequencies Calculating Allele Frequencies in the population Genotype Frequency x 2 x 2 Number of alleles in gene pool ( ) ( ) Allele frequency p = frequency of A = 0.8 q = frequency of a = 0.2 4

5 What can allele frequencies tell us about a population? (1) Whether the gene pool is stable or undergoing change (2) We can estimate the rate of change (3) If we know the rate of change we can make predictions about likely future trends (4) This has important applications in conservation of wild populations and in captive breeding programmes Is there any rule which defines how gene pools behave from generation to generation? Yes: the Hardy-Weinberg Theorem or Equation The Hardy-Weinberg theorem This is a fundamental concept in Population Genetics It states that: the frequencies of alleles and genotypes in a population s gene pool will remain constant from generation to generation unless it is acted upon by factors other than sexual recombination Put another way: on its own, the shuffling of alleles during meiosis and fertilization has no effect on the overall genetic structure of a population over time The Hardy-Weinberg theorem describes a non-evolving population! 5

6 The Hardy-Weinberg theorem also states the conditions under which gene frequencies are not expected to change: 1. The population is infinitely large or at least large enough so that no sampling errors occur 2. Within the population mating occurs at random 3. There is no selective advantage for any genotype i.e. all gametes are equally viable and fertile 4. There is no mutation no migration These parameters describe a non-evolving population Deriving the Hardy-Weinberg equation We saw earlier how we can use genotype frequencies to calculate allele frequencies in our imaginary wild flower population p = frequency of A = 0.8 q = frequency of a = 0.2 These actually represent the probabilities of finding a given type of gamete (A or a) in the gene pool What happens to genotype frequencies in the next generation? We can use the rule of multiplication of probabilities, to calculate the frequencies of the 3 possible genotypes in the next generation 6

7 Allele and genotype frequencies in the second generation Types of sperm q = 0.2 a A p = 0.8 aa pq=0.16 AA p 2 =0.64 A p = 0.8 Aa pq=0.16 a q = 0.2 Types of egg aa q 2 =0.04 Genotype Frequencies p 2 = 0.64 AA 2pq = 0.32 Aa q 2 = 0.04 aa Allele Freq s p = 0.8 A q = 0.2 a From this we can derive a general formula that describes allele and genotype frequencies in a population Hardy-Weinberg equation = p 2 + 2pq + q 2 = 1 This formula enables us to calculate allele frequencies if we know the frequency of genotypes This can be used to calculate the % of the human population that carries alleles for an inherited disease 7

8 e.g. Cystic Fibrosis a recessive inherited disease in humans Affected individuals are homozygous recessive cf cf and occur with a frequency of 1 in 1600 in the population Therefore q 2 = 1/1600 and q = 1/40 = The allele frequency of the mutant cf allele is The allele frequency of normal / wild type allele CF is p = 1 q = What is the frequency of CF carriers? Heterozygotes 2pq = 2x0.975x0.025= i.e. approximately 1 in 20 people have the genotype CF cf Heterozygotes are termed carriers of the disease allele We have discussed: (1) How populations can be defined in terms of the alleles they contain i.e. the Gene Pool (2) How to calculate genotype and allele frequencies (3) The Hardy-Weinberg theorem which describes how allele and genotype frequencies remain the same from generation to generation unless acted upon by factors other than recombination When allele frequencies do not change from generation to generation the population is said to be in a Hardy-Weinberg equilibrium This describes an essentially non-evolving population 8

9 A non-evolving population is the exception rather than the rule If a population is evolving, then allele frequencies will change over time i.e. the composition of the gene pool will change from one generation to the next Let s look at the kinds of forces that drive changes in allele frequencies i.e. the forces that drive evolution Because changes in a population s gene pool is evolution on a small scale, we refer to it as microevolution Microevolution occurs even if the frequency of alleles are changing for only a single locus If we track allele and genotype frequencies in a population over many generations, some loci will show a Hardy-Weinberg equilibrium but alleles at other loci will be changing There are 5 causes of microevolution. Each one is the opposite of the conditions required for a Hardy-Weinberg equilibrium to be maintained: Factors promoting equilibrium Factors driving microevolution 1. A very large population size 1. Genetic drift 2. Isolation from other gene pools 2. Gene flow 3. No mutation 3. Mutation 4. Random mating 4. Non-random mating 5. No selection for 5. Natural selection advantageous alleles 9

10 1. Genetic drift Every new generation in a population draws its alleles from the previous generation If this occurs at random and the population is very large, then the allele frequencies in the new generation will be the same But if the population undergoes a large reduction in size, then (a) the statistical probabilities can be drastically altered and (b) the allele frequencies in the new generation can differ dramatically from the parental generation Random changes in allele frequencies because of chance fluctuations in population size is called: Genetic Drift We can observe the effects of Genetic Drift on allele frequencies in an imaginary population over three generations 10

11 What might cause Genetic Drift? Any natural disaster that causes a population crash will have a high probability of changing allele frequencies in the next generation e.g. Natural disasters fires, floods, earthquake, severe winters The result is that the gene pool of the small number of survivors may not be representative of the original population - a situation known as The Bottleneck effect Certain alleles will be over-represented in the survivor population and other alleles will be under-represented 11

12 Genetic drift may also occur if a new population is established on an isolated island by a few individuals The most extreme case would be the founding of a new isolated population by one pregnant animal or a single plant seed. Genetic drift caused in this way is said to be due to the Founder Effect. The Founder Effect probably account for the high frequency of certain inherited disorders e.g. Huntington s Chorea (neurodegenerative disorder) in regions of South America, This is thought to be due to the founding of new communities during the 17 th century by individual sailors of European origin who unwittingly carried the disease allele, 2. Gene Flow A precondition of Hardy-Weinberg equilibrium is that the gene pool is a closed system i.e. closed to influences from other gene pools Most populations are not completely isolated! Therefore a population may gain new alleles or lose alleles as a result of a process called Gene Flow biology.unm.edu/ccouncil/biology_203/images/popgen/bugflow.gif Gene Flow is genetic exchange between different gene pools (population due to the migration of fertile individuals or gametes Gene flow between plant communities might take place entirely by exchange of gametes i.e. pollen carried on the wind or by bees Gene flow tends to reduce gene pool differences between populations 12

13 3. Mutation A mutation is any change in the nucleotide sequence of an organism s DNA. A new mutation that is transmitted in the gametes can change the gene pool of a population by substituting one allele for another. For any one gene locus, mutation alone does not have much quantitative effect on a large population in a single generation. This is because the occurrence of a mutation at any given gene locus is a very rare event - typically 1 in 10 5 to 10 6 gametes. If an allele has a frequency of 0.50 in the gene pool and it mutates to become a new allele at a rate of mutations per generation, it would take 2000 generations to reduce the frequency of the original allele from 0.50 to

14 If a new mutant allele increases its frequency by a significant amount in a population: its not because mutation is generating the new allele in abundance its because individuals carrying the mutant allele are producing a disproportionate number of offspring as a result of natural selection or genetic drift Mutation can have an extremely powerful effect on the rate of evolution especially if a mutation confers a major adaptive or selective advantage e.g. a mutant allele which confers resistance to rat poison Mutation is also the original source of the genetic variation that serves as the raw material for natural selection 4. Non-random mating For a population to be in Hardy-Weinberg equilibrium an individual of any genotype must be able to choose mates at random In practice, individuals usually mate more often with close Neighbours than with more distant members of the same population especially in species that do not disperse far This gives rise to neighbourhood effects which in turn can lead to inbreeding The most extreme case of inbreeding is self-fertilization which is particularly common in species that are both male and female i.e. hermaphrodites e.g. many plants can self-fertilize Inbreeding causes the relative frequency of genotypes to deviate from what is expected from Hardy-Weinberg equilibrium 14

15 5. Natural Selection Hardy-Weinberg equilibrium requires that all individuals in a population are equal in their ability to survive and produce viable, fertile offspring. This condition is probably never completely met. Populations consist of varied individuals and on average some variants leave more offspring than others. This differential success in reproduction is due to natural selection. Of all the agents driving microevolution, selection is the most likely to adapt a population to its environment. An interesting example of how powerful a force natural selection can be, is provided by the peppered moth Biston betularia. Before % of moths were light-coloured and wellcamoflaged against their predators. As the Industrial Revolution advanced, pollutants especially soot, darkened the surfaces on which the moths would land. Light-coloured moths on dark surfaces were easy prey for birds. The previously rare dark-coloured moths suddenly gained a huge selective advantage. A single dominant allele C was responsible for dark colour. Over a 50 year period, there was a rapid increase in the frequency of the C allele. 15

16 The wonderful wildlife on the Galapagos Islands, for example, the blue-footed boobies, Sula nebouxii excisa was such an inspiration to Charles Darwin that it prompted him to formulate his theory of evolution (1861). 16