Basic genetics terminology DNA is the genetic material. The instructions for making and “operating” an organism are written in DNA. DNA is divided into sections called genes.

What a gene does Each gene codes for a single protein. The gene specifies the sequence of amino acids that should be joined together to make a protein. Together the genes determine the characteristics of an organism.

Alleles and genes Alleles are different versions of a gene. If a single gene codes for flower color, white and blue flowers would be coded for by 2 different alleles.

Number of copies of genes You possess two copies of each gene in your body*. One copy is inherited from each parent. For a given gene you may have two different alleles or two copies of the same allele. (* excluding genes on sex chromosomes in males).

Homozygous vs heterozygous A homozygous individual has two copies of a particular allele. (AA) A heterozygous individual has two different alleles. (Aa)

Genotype and phenotype An organism’s genes (its genotype) play a large role in determining its physical appearance (its phenotype). But remember an organism’s phenotype is also affected by the environment.

The relationship between genes and evolution We express evolutionary ideas in terms of genes because genes are the only thing that are passed from one generation to the next.

Process of Natural Selection In the process of natural selection, genes that help organisms to survive and reproduce become more common. Genes that help less or are harmful gradually are eliminated from the population.

Process of Natural Selection Individuals that are the best adapted to their environments (the best camouflaged, best at finding food, etc.) will generally be more successful at breeding than less well adapted individuals. As a result, their genes (which make them well adapted) will be commoner in the next generation than the genes of less well adapted individuals.

Chapter 23. The Evolution of Populations Remember individual organisms do not evolve. Individuals are selected, but it is populations that evolve. Because evolution occurs when gene pools change from one generation to the next, understanding evolution require us to understand population genetics.

Some terminology Population: All the members of one species living in single area. Gene pool: the collection of genes in a population. It includes all the alleles of all genes in the population.

Some terminology If all individuals in a population all have the same allele for a particular gene that allele is said to be fixed in the population. If there are 2 or more alleles for a given gene in the population then individuals may be either homozygous or heterozygous (i.e. have two copies of one allele or have two different alleles)

Detecting evolution in nature Evolution is defined as changes in the structure of gene pools from one generation to the next. How can we tell if the gene pool changes from one generation to the next? We can make use of a simple calculation called the Hardy-Weinberg Equilibrium

Hardy-Weinberg Equilibrium Before discussing Hardy-Weinberg need to review some basic facts about Mendelian Inheritance. In Mendelian Inheritance alleles are shuffled each generation into new bodies in a way similar to which cards are shuffled into hands in different rounds of a card game. The process of Mendelian Inheritance preserves genetic diversity from one generation to the next. A recessive allele may not be visible because it is hidden by the presence of a dominant allele, but it is still present.

Hardy-Weinberg Equilibrium The shuffling process occurs because an individual has two copies of any given gene (one inherited from father and one from mother), but can put only one or the other copy into a particular sperm or egg. E.g. for an individual who is heterozygous Aa 50% of sperm will contain A and 50% will contain a.

Hardy-Weinberg Equilibrium Individuals alleles thus go through a process where they are sorted into gametes (sperm or egg) which combine to form a zygote which will one day again sort alleles into gametes. See Chapter 14 to review Mendelian Inheritance

Hardy-Weinberg Equilibrium Consider a population of 100 individuals. This population will contain 200 copies of any given gene because each individual has two copies. Gene we are interested in has two alleles A and a.

Hardy-Weinberg Equilibrium If 80% of the alleles in the gene pool are A and 20% are a, we can predict the genotypes in the next generation. Basic probability: To determine the probability of two independent events both occurring, you should multiply the probabilities of the individual events together.

Hardy-Weinberg Equilibrium Probability of an AA individual is 0.8*0.8 = 0.64 Probability of an aa individual is 0.2*0.2 = 0.04 Probability of an Aa individuals is 0.2*0.8 = 0.16, but there are two ways to produce an Aa individual so 0.16*2= 0.32. Note these probabilities sum to 1.

Hardy-Weinberg Equilibrium General formula for Hardy-Weinberg is p2 + 2pq + q2 = 1, where p is frequency of allele 1 and q is frequency of allele 2. p + q = 1.

Hardy-Weinberg Equilibrium Hardy-Weinberg equilibrium can be used to estimate allele frequencies from information about phenotypes and genotypes.

Hardy-Weinberg Equilibrium E.g. approx 1 in 10,000 babies are born with phenylketonuria (PKU) (causes retardation if diet is not kept free of amino acid phenylalanine). Disease due to individual being homozygous for a recessive allele k. i.e., the babies’ genotype is kk.

Hardy-Weinberg Equilibrium What is frequency of k allele in population? q2 = frequency of PKU in population = 0.0001. q = square root of q2 or 0.01. Frequency of allele k Therefore p the frequency of the K allele = 1 - 0.01 = 0.99 Frequency of carriers (heterozygotes) in population is 2pq = 2*0.99*0.01 = 0.0198 or almost 2% of population. Much greater than frequency of PKU.

Working with the H-W equation You need to be able to work with the Hardy-Weinberg equation. For example, if 9 of 100 individuals in a population suffer from a homozygous recessive disorder can you calculate the frequency of the disease-causing allele? Can you calculate how many heterozygotes are in the population?

Working with the H-W equation p2 + 2pq + q2 = 1. The terms in the equation represent the frequencies of individual genotypes. [A genotype is possessed by an individual organism so there are two alleles present in each case.] P and q are allele frequencies. Allele frequencies are estimates of how common alleles are in the whole population. It is vital that you understand the difference between allele and genotye frequencies.

Working with the H-W equation 9 of 100 (frequency = 0.09) of individuals are homozygous for the recessive allele. What term in the H-W equation is that equal to?

Working with the H-W equation It’s q2. If q2 = 0.09, what’s q? Get square root of q2, which is 0.3, which is the frequency of the allele a. If q=0.3 then p=0.7. Now plug p and q into equation to calculate frequencies of other genotypes.

Working with the H-W equation p2 = (0.7)(0.7) = 0.49 -- frequency of AA 2pq = 2 (0.3)(0.7) = 0.42 – frequency of Aa. To calculate the actual number of heterozygotes simply multiply 0.42 by the population size = (0.42)(100) = 42.

Other examples of working with HW equilibrium: is a population in HW equilibrium? In a population there are 100 birds with the following genotypes: 44 AA 32 Aa 24 aa How would you demonstrate that this population is not in Hardy Weinberg equilibrium

Three steps Step 1: Calculate the allele frequencies. Step 2: Calculate expected numbers of each genotype (i.e. figure out how many homozygotes and heterozygotes you would expect.) Step 3: Compare your expected and observed data.

Step 1 allele frequencies Step 1. How many “A” alleles are there in total? 44 AA individuals = 88 “A” alleles (because each individual has two copies of the “A” allele) 32 Aa individuals = 32 “A” alleles (each individual one A allele) Total “A” alleles is 88+32 =120.

Step 1 allele frequencies Total number of “a” alleles is similarly calculated as 2*24 + 32 = 80 What are allele frequencies? Total number of alleles in population is 120 + 80 = 200 (or you could calculate it by multiplying the number of individuals in the population by two 100*2 =200)

Step 1 allele frequencies Allele frequencies are: A = 120/200= 0.6. Let p = 0.6 a = 80/200 = 0.4. Let q = 0.4

Step 2 Calculate expected number of each genotype Use the Hardy_Weinberg equation p2 + 2pq + q2 = 1 to calculate what expected genotypes we should have given these observed frequencies of “A” and “a” Expected frequency of AA = p2 = 0.6 * 0.6 = 0.36 Expected frequency of aa = q2 = 0.4*0 .4 =0.16 Expected frequency of Aa = 2pq = 2*.6*.4 = 0.48

Step 2 Calculate expected number of each genotype Convert genotype frequencies to actual numbers by multiplying by population size of 100 AA = 0.36*100 = 36 aa = 0.16*100 = 16 Aa = 0.48*100 = 48

Step 3 Compare Observed and Expected values Observed population is: 44 AA 32 Aa 24 aa Expected population is: 36AA 48Aa 16aa These numbers are not the same so the population is not in Hardy-Weinberg equilibrium. An assumption of the Hardy Weinberg equilibrium is being violated. What are those assumptions?

Hardy-Weinberg Equilibrium Remember that the Hardy-Weinberg equation tells us what we would expect to find if alleles are simply randomly assorted into gametes and gametes come together randomly to produce new genotypes. If a population is found to depart significantly from H-W equilibrium this is strong evidence that evolution is taking place, i.e., the gene pool of the population is changing.

Hardy-Weinberg Equilibrium Five Conditions under which Hardy-Weinberg equilibrium holds: No gene flow – no migration. Random mating – no inbreeding. No mutations. Large population size – reduces effects of chance events No natural selection.

Gene flow Movement of individuals between populations can alter gene frequencies in both populations. Frequent migration may cause populations’ gene pools to become more similar to each other.

Non-random mating Mating preferentially with others that are phenotypically similar to you [in extreme cases inbreeding (mating with relatives)] can prevent random mixing of genes Homozygotes are common in inbred populations.

Inbreeding in California Sea Otters Because inbreeding produces an excess of homozygotes in a population, deviations from Hardy-Weinberg expectations can be used to detect such inbreeding in wild populations.

Inbreeding in California Sea Otters Sea otters, once abundant along the west coast of the U.S., were almost wiped out by fur hunters in the 18th and 19th centuries. photo: www.turtletrack.org

Inbreeding in California Sea Otters California population reached a low of 50 individuals (now over 1,500). As a result of this bottleneck, the population has less genetic diversity than it once had.

Inbreeding in California Sea Otters Population is still at a low density and Lidicker and McCollum (1997) investigated whether this resulted in inbreeding. They determined genotypes of 33 otters for PAP locus, which has two alleles S (slow) and F (fast)

Inbreeding in California Sea Otters The genotypes of the 33 otters were: SS 16 SF 7 FF 10 This gives approximate allele frequencies of S= 0.6 and F = 0.4

Inbreeding in California Sea Otters If otter population in H-W equilibrium, genotype frequencies should be SS = 0.6* 0.6 = 0.36 SF =2*0.6*0.4 = 0.48 FF = 0.4*0.4 = 0.16 However actual frequencies were: SS= 0.485, SF= 0.212, FF =0.303

Inbreeding in California Sea Otters There are more homozygotes and fewer heterozygotes than expected for a random mating population. Having considered alternative explanations for deficit of heterozygotes, Lidicker and McCollum (1997) concluded that sea otter populations show evidence of inbreedng.

Mutation Mutation adds new genes, but generally so slowly that H-W equilibrium not affected. However, mutation and sexual recombination ultimately responsible for the variation that natural selection depends on.

Mutations Mutations are randomly occurring changes in the DNA. Only mutations that occur in cell lines that produce gametes [i.e. the sex cells – sperm and egg] can be passed on. Simplest mutation is a point mutation in which one base is changed or a base is inserted or deleted.

Mutations Changing a base may have no effect if the base change does not change the amino acid coded for or if the change occurs in a non-coding section of the gene. However, some changes alter the amino acid coded for and hence the protein produced (e.g. as occurs in sickle cell anemia), which can have severe effects.

Insertion/deletion mutations In insertion/deletion mutations a base is added or deleted, which because bases are read in groups of three shifts the “reading frame” so that all sequences after the mutation are misread, being off by one base. This almost always produces a non-functional protein

Mutations that alter gene number or sequence Gene duplication is an important source of variation. In gene duplication a section of DNA may be copied and inserted elsewhere in the genome. Often these cause major problems, but sometimes they do not and the overall number of genes is increased. And the new genes can take on novel functions through mutation and selection

Mutations that alter gene number or sequence Humans have about 1,000 olfactory receptor genes and mice about 1,300. These appear all to have been derived from a single ancestral gene. In humans about 60% of these are turned off, but in mice only about 20% are turned off.

Sexual Recombination In the process of meiosis alleles are reshuffled as parental chromosomes exchange portions. This process produces new combinations of alleles in the sex cells produced in meiosis. In addition, the combining of sperm and egg also produces new combinations of alleles.

How populations’ gene pools are altered Natural Selection: as discussed previously selection for or against allele can cause its frequency to change quickly from one generation to the next. However, natural selection is not the only way allele frequencies can change. Chance often plays a role.

Genetic drift Fluctuations in allele frequencies that result from chance are referred to as genetic drift. Chance effects are strongest when populations are small. In a small population it is easy for alleles to be lost or become fixed as a result of chance events.

Large population size If populations are small, chance events can have a large effect on allele frequencies. These chance events can cause the genetic structure to randomly change from one generation to the next. This random change is called Genetic Drift.

Genetic Drift: events that reduce population size Genetic drift is most likely to affect populations after events that greatly reduce population size. Two of the most common are Bottleneck Events and Founder Events

Bottleneck Effect A bottleneck effect occurs when some disaster causes a dramatic reduction in population size. As a result, by chance certain alleles may be overrepresented in the survivors, while others are underrepresented or eliminated. Genetic drift while the population is small may lead to further loss or fixation of alleles.

Bottleneck Effect Humans have been responsible for many bottlenecks by driving species close to extinction. For example, the Northern Elephant seal population was reduced to about 20 individuals in the 1890’s. Population now >30,000, but an examination of 24 genes found no variation, i.e. in each case there was only one allele. Southern Elephant Seals in contrast show lots of genetic variation.

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Founder Effect When populations are founded by only a few individuals (as island communities often are) the gene pool is unlikely to be as diverse as the source pool from which it was derived.

Founder Effect Founder effect coupled with inbreeding explains the high incidence of certain recessive diseases among humans in many isolated communities. For example, polydactylism (having extra fingers) is quite common among the Amish and retinitis pigmentosa a progressive form of blindness is common among the residents of Tristan da Cunha.

Natural Selection Natural selection is generally the main reason populations will deviate from H-W equilibrium. With natural selection certain alleles are selected against or for and so are are rarer or more common than would otherwise be expected in the next generation.

Natural Selection the primary mechanism of adaptive evolution Terms such as “survival of the fittest” and “struggle for existence” do not necessarily mean there is actual fighting for resources. Competition is generally more subtle and success in producing offspring and thus contributing genes to the next generation (i.e. fitness) may depend on differences in ability to gather food, hide from predators, or tolerate extreme temperatures, which all may enhance survival and ultimately reproduction

Natural Selection the primary mechanism of adaptive evolution Three major forms of natural selection: Directional Disruptive Stabilizing

Directional Selection Favors one extreme in the population Average value in population moves in that direction E.g. Selection for darker fur color in an area where the background rocks are dark

Disruptive selection Intermediate forms are selected against. Extremes are favored E.g. Pipilo dardanus butterflies. Different forms of the species mimic the coloration of different distasteful butterflies. Crosses between forms are poor mimics and so are selected against by being eaten by birds.

Stabilizing Selection Commonest form Extreme forms are selected against Birth weights in human babies. Highest survival is at intermediate birth weights. Babies that are too large cannot fit through the birth canal, babies that are born too small are not well developed enough to survive

Natural selection acts on individuals, but its effects accumulate in populations Individuals live or die during a the selection event. But change occurs in the characteristics of the population, not in individuals.

Natural selection acts on individuals, its effects accumulate in populations During a drought on the Galapagos individual ground finch’s beaks did not change, but the populations’ average beak dimensions changed because more small-beaked birds died than large-beaked birds.

Natural selection does not plan ahead. Each generation is result of selection by environmental conditions of the previous generation. Evolution always one generation behind environmental changes.

New traits evolve even though selection acts on existing traits. This occurs because: 1. mutation produces new alleles. 2. In sexually reproducing organisms meiosis and fertilization recombine existing alleles to produce new genotypes.

New traits evolve even though selection acts on existing traits. Artificial selection for oil content in corn. After 60 generations oil levels were well above starting values.

Fig 3.12

Important points about evolution and natural selection The fundamental unit of natural selection is the gene. Only genes are passed on from one generation to the next.

Important points about evolution and natural selection Nothing in nature happens for “the good of the species.” Alleles that sacrifice themselves would disappear from the gene pool.

Important points about evolution and natural selection Organs must be useful at all stages of their evolutionary history Structures cannot pass through intermediate stages where they make an organism less well adapted.

Important points about evolution and natural selection Natural selection cannot fashion perfect organisms for several reasons 1. Evolution is limited by historical constraints. Birds cannot run around on four legs because their forelimbs have evolved into wings.

Important points about evolution and natural selection Natural selection cannot fashion perfect organisms for several reasons 2. Adaptations are often compromises. Auks (a group of seabirds that includes puffins) can fly and use their wings to swim underwater, but the shape and size of the wing is a compromise between the demands of flight and swimming.

polar.alaskapacific.edu/aharding/images/Littl... Little Auk polar.alaskapacific.edu/aharding/images/Littl... Razorbill http://media-2.web.britannica.com/eb-media/16/26016-004-13D8FA4C.jpg

Important points about evolution and natural selection Natural selection cannot fashion perfect organisms for several reasons 3. Selection can only make use of the material that is available. New alleles do not arise on demand.