Variation and Selection in Populations

In our primate relatives and in other mammals, lactase is expressed only in ________ so that they can obtain nutrition from their mother's breast milk by breaking down the sugar ________. Transcription of the _______-encoding gene shuts down after weaning in these species

Early humans inherited _______ genes, from their primate ancestors, that behave the same way. Modern humans in eastern Asia, parts of Africa, and of indigenous heritage in North and South America and Australia, still have _______ genes that are turned off in later childhood. These people are thus _______ ________ as adults, and their diets include little or no milk or other dairy products

So why can many people in other ethnic groups drink milk as adults?

In populations that raised domesticated cattle, the ability for adults to derive nutrition from ______ likely provided a survival and/or reproductive advantage to individuals with these mutations. This advantage led to a rapid ________ in the frequencies of variants that continue lactase expression in adulthood, so the frequency of these alleles is now over ____% in European and central sub-Saharan African populations

Population genetics

Populations
Gene pool
Sample

Allele
Monomorphic
Polymorphic

Genotype frequencies (define and explain how to determine)

How does genotype frequency work for recessive traits such as blue eyes? (3-story)

Consider a sample of 20 humans of which 16 individuals have dark eyes, meaning that they are either _______ for the A, or dominant dark eye allele, or they are _________ for A and the recessive "blue eye" allele a. The other four people have blue eyes and thus are ___ ________. The sample has two phenotypes (name them) in relative proportions (_______ frequencies) of 16/20 = 80% and 4/20 = 20%, respectively

Suppose that DNA analyses show that of these 20 individuals,12 are of genotype AA, 4 are Aa, and 4 are aa. In this sample, the AA genotype frequncy is ___/___ = ___; the Aa genotype frequency is ___/___ = ___; and the aa genotype frequency is also ___

The _____ ______ is the proportion of gene copies in a population that are of a given allele type. Why is the total number of gene copies two times the number of individuals and what does this mean for our hypothetical population of 20 ppl?

Of course, both homozygotes and heterozygotes contribute to the frequency of an allele. But homozygotes contribute to the frequency of a particular allele ______, while heterozygotes contribute _______

To find the frequencies of A and a, you first use the number of people with each genotype to compute the number of A and a alleles.
What is the result for A and a alleles (12 AA, 4 Aa 4 aa)

Next, you add the 28 A alleles to the 12 a alleles to find the total number of ______ ______ sampled (40); as expected, this is ______ the number of people in the sample. Finally, you divide the number of each ______ by the total number of ______ ______ to find the proportion, or frequency, for each allele. 
For the A allele, the allele frequency is ___/___ = ___
For the a allele, the allele frquency is ___/___ = ___

An equivalent way to calculate the frequncy of any allele is to use the following formulas based on genotype frequencies:

Substituting the genotype frequencies at the top of the fig. into these formulas will yield the same _____ ______ shown at the bottom of the figure that were determined from counting individual gene copies

The simplifying assumptions that allowed Hardy and Weinberg to formulate this principle involve both the nature of the population and the nature of the genetic variation under investigation: (5)

If a population is a reasonably ______ fit to the preceding assumptions for the locus of interest, then ______ _______ will not change over time, and only _______ _______ may change briefly to reach proportions predicted by the frequencies of alleles that make up each genotype. The population is then in _____ ______ ______ (explain)

Of course, no actual population is a ______ fit to these assumptions for an ideal population. All populations are _____; alternative genotypes can make a difference in ______; ______ occur constantly; migration into and out of a population is _______; and many _______ of interest, such as those that cause diseases, affect the ability to survive or reproduce

Nevertheless, even when many of the assumptions do not apply, the Hardy-Weinberg equilibrium is still remarkably robust at providing estimates of ______ and ______ frequencies in real populations over a limited number of breeding generations. The discovery of frequencies that are ______ with the HWE can sometimes provide scientists with insight into special biological properties of particular genes and population

In diploid sexual populations, ______ frequencies are transformed by the mating system into _______ frequencies. The law of segregation and also random mating in such a population have two important consequences, name them 

If A-carrying sperm fertilize A-carrying eggs, ___ zygotes will be formed. Because the genotype of a sperm is independent of the genotype of the eggs it _______, we can apply the ______ rule so as to multiply the frequency of A sperm (p) by the frequency of A eggs (also p) to find the frequency of AA zygotes: ___ * ___ = ___. Similarly, the frequency of aa zygotes among the progeny, which must result from fertilization of ___-carrying eggs (whose frequency is q) by ___-carrying sperm (whose frequency is also q), is the product of ___*___ = ___.

Finally, ___ zygotes result either from the fertilization of A eggs by a sperm, with a frequency of ___*___ = ___, or from the fertilization of a eggs by A sperm, also occurring at a frequency of ___*___ = ___. The total frequency of Aa zygotes is thus ___+___=___

The resemblance of the Hardy-Weinberg square shown in the fig. to the Punnett squares that we first encountered in the visual representation of formal genetics in CH2 is not a coincidence. Where does the similarity result from?

In the original Punnett square for crosses between heterozygotes, the top and left sides were divided into two equal sectors representing the equal frequencies of each genetically distinct class of ______ or _____ produced by two individual ________.

If we replace the gametes from the two single parents with the male and female gametes produced by the population as a whole, then the fig is a metaphorical representation of the sperm produced by all breeding males along the left side, and of eggs produced by all breeding females along the top. (explain 2-story)

The key finding from the analysis shown is that the ______ _______ of zygotes arising in a large, ______ mating population of sexually reproducing diploid organisms that satisfies all the Hardy-Weinberg assumptions are p² for ____, 2pq for ____ and q² for ____. These genotype frequencies are known as the ______ _______ proportions

Why must the genotype frequencies sum up to 1? How can the Hardy-Weinberg proportions be expressed as a binomial equation?

You should note that p² + 2pq + q² = (__ + __)²; this makes sense because (p + q) represents all the _____ and also all of the _____ produced by all the adults, and this is precisely what the HW square is illustrating. Thinking about the pools of sperm and eggs in a population in this way allows us to extend the HW prediction in (Eq 20.2) to genes that have more than ____ alleles

Recall that the ABO blood groups are determined by three alleles of a single gene: IA, IB, and i. If we call the frequencies of these three alleles in the population p, q and r, respectively, what would be the predicted HWE genotype frequencies?

Populations with genotype frequencies in HW proportions will be in equilibrium, meaning that the _____ and _____ frequencies will remain _______ over the generations, as long as the assumptions remain valid. You can use the rules for computing allele frequencies from genotype frequencies (card 16) to compute algebraically the ______ frequencies of the next generation and show that they do not ______

From the Hardy-Weinberg equation for a gene with two alleles, you know that p² of the individuals are ____, all of whose alleles are A, and 2pq of the individuas are ____, half of whose alleles are ____. Thus, remembering that p+q = 1 (and therefore q = 1 - p), the frequency of allele A in the progeny off the original generation will be:

Similarl, p = 1 - q, and the frequency of the a allele in the next-generation population is: (state the equation)
As you can see, the allele frequencies among the progeny are the _____ as those among the parents; they remain p and q

The potential for equilibrium provides the the answer to the question of the extinction of recessive traits like hair color in blondes and redheads. In the absence of a fitness difference or other major deviations from HW assumptions, neither of these phenotypes will go ______ simply because their phenotypes are caused by _______ alleles. Instead, the frequencies of the alleles and genotypes that produce these hair colors will stay ______ over time

Even if a population is not currently at HWE, one generation of random mating can be sufficient to establish ______. State an extreme example (3-story)

Why can you consider the pools of both sperm and eggs as reflecting the allele frequencies? What does the gamete pool predict the next generation of insects on this island will be distributed in HW proportions?
What is the lesson?

have the allele frequencies also changed as the population goes from the first to the second generations? (explain)

These frequencies are the same as those in the _______ generation. Thus, even though the genotype frequencies have changed dramatically from the first generation to the next, the ______ frequencies have not. Note that htis is true of both dominant and recessive alleles. The conservation of allele proportions principle holds from each generation to the next, as long as the population is sufficiently _______ and mates at _______, alleles are not lost by ________ or ________, and alleles are not gained by ________ or _________

Under what circumstances do sex-linked genes, such as those on the X chromosome of humans, take several additional generations to reach HWE?

The requirement for these extra generations is a consequence of the fact that males have only one _____ _______ while females two. Why is allele frequency in males in the next generation equal to the allele frequency in females of the present generation?

The allele frequency in females of the in females of the next generation will be equal to the ______ frequency in males and females of the present generation (why?)

The most useful DNA markers for forensic analysis are ________ ________ loci that are highly variable in human populations. To enable comparisons of DNA samples, law enforcement agencies in the US and many other countries focus on ___ unlinked _____ ______ ______ loci (SSRs) found throughout he human genome. The results obtained are deposited in a database called the Combine DNA Indexing System (CODIS)

From a practical perspective, criminal investigators and juries need to be able to conclude that a perfect match at all 13 ______ loci between the suspect and the sample under the victim's fingernails is not simply a _______ match

Why were the SSRs chosen for CODIS selected?

The critical data from these surveys consist of the _______ frequencies for the 13 loci. From these allele frequencies, investigators can use the HW equation to calculate the likelihood of a match of the ________ genotype for any _____ locus. Because the CODIS loci are _______ and alleles at each locus are statistically _________ of alleles at the other loci, forensic scientists can simply ________ together the expected genotype frequencies for each separate locus to obtain the expected ________ of any observed 13-locus genotype

Suppose that the DNA profile common to both the crime scene sample and the suspect was heterozygous for alleles of one CODIS locus, with allele frequencies of 0.05 and 0.03, respectively, and homozygous for an allele of a second locus, whose freqency is 0.04. Even though more than 20 alleles for each CODIS SSR can be distinguished, the genotype frequency for any particular heterozygous genotype is still:

Thus, the match probability for a random person in the population having the particular two-locus genotype seen in the crime scene sample would be:

The match probability becomes very small for any given 13-locus CODIS genotype (why?)

Suppose the 13-locus match probability for the DNA sample under the fingernails of the crime victim is 7.7 * 10^-15, which is in the range of those typically found in forensic investigations We could compare the likelihood of obtaining a perfect match if the DNA is from the ______, which is 100% or 1, against the likelihood of obtaining a match if the DNA were from a _______, ______ person, which is 7.7 * 10^-15. Thus, it is 1/7.7 * 10^-15 = 1.3 * 10¹⁴ times more likely than the DNA is from the ______ than that is from a ______, _______ person.

If all populations were always in HWE for every locus, the HW equation would lead us to conclude that all allele frequencies would be forever _______ and thus the ______ between different populations. And yet, different populations of the human species have dramatically different proportions of individuals with _____ eye color, reflecting variations in the _____ frequencies of a SNP upstream of the OCA2 gene that is responsible for this _______ phenotype

Many other loci in the human genome, such as the one responsible for ______ tolerance/intolerance, also display geographical differences in allele frequency

Monte Carlo simulation (4-story)

In the example shown in the fig. the computer ran six Monte Carlo simulations initialized with populations of just 10 individuals who are all set to be heterozygotes (3-story)

Although the average of populations is not too far from the 0.5 predicted by the HW equation, the values for each separate experiment guide each individual simulated population down a different path of ______ ______, defined as a change in allele frequencies as a consequence of the randomness of inheritance due to sampling error from one generation to the next

Why does genetic drift occur?

In four of the six simulated runs shown in the fig, genetic drift culminated in the loss, or _______, of one or the other of the two original alleles by generation 18. In each of these instances, the ________ effects of changes in _______ frequency from one generation to the next caused extinction of one allele, and ______ of the remaining allele. When do geneticists consider a population to be fixed at a locus?

Population size has a _______ effect on allele frequency dynamics, as seen by comparing the experiments in (pt a) with another experiment with six simulations of populations that are initially all ________ but that have 500 members rather than 10 (part b). If we follow the lines representing each of the latter populations, we can see that single generation changes in _______ frequency are always relatively small

Because these changes in allele frequency are ______, the traditional HW equation provides good estimates of ______ and ______ frequencies in large population over the course of a few generations. But a series of _____ changes can still add up to ______ consequences over the long run, so each of these populations will eventually become _______ for one allele or the other many generations later than those shown in part b

When does founder's effect occur and when does bottleneck effect occur?

Mutation– variant DNA sequence in individual genome that was not present in either parent (explain the three possibilities)
Explain the molecular clock

Although fitness (define) is an attribute associated with each _______, it cannot be measured within a single individual  (why?)

However, by considering all the individuals of a particular _______ together as a group, it becomes possible to measure the relative _______ for that genotype. Thus, for population geneticists, fitness is a _______ measurement only. Nevertheless, differences in fitness can have a profound effect on the _______ frequencies within a population

Fitness has two basic components: _______ and _______ ______. The fitness of individuals possessing variations that help them ______ and ______ in a changing environment is relatively high; the fitness of individuals without those adaptive variations is relatively _____. In nature, the process that progressively eliminates individuals whose fitness is ______ and chooses individuals of ______ fitness to survive and become the parents of the next generations is known as ______ _______