Interact box 31 Genetic drift
Genetic drift can be simulated with either Populus or PopGene.S2. Try using Populus and following the instructions here. Under the Model menu, select Mendelian Genetics and then Genetic Drift. Make sure the Monte Carlo tab is selected. The simulation dialog has entry fields for Population Size N and Number of Loci or replicates . Number of generations shown in the graphs can be specified as 3N or a fixed number of generations Other with radio buttons the program will automatically set the...
Box 22 Protein locus or allozyme genotyping
Determining the genotypes of individuals at enzymatic protein loci is a rapid technique to estimate genotype frequencies in populations. Protein analysis was the primary molecular genotyping technique for several decades before DNA-based techniques became widely available. Alleles at loci that code for proteins with enzymatic function can be ascertained in a multi-step process. First, fresh tissue samples are ground up under conditions that preserve the function of proteins. Next, these protein...
D7s820
What does the amelogenin locus tell us and how did you assign an expected frequency to the observed genotype Is it likely that two unrelated individuals would share this 10-locus genotype by chance For this genotype, would a match between a crime scene sample and a suspect be convincing evidence that the person was present at the
Problem box 31 Applying the binomial formula
Two independent laboratory populations of the fruit fly Drosophila melanogaster were observed for two generations. The populations each had a size of N 24 individuals with an equal number of males and females. In the first generation, both populations were founded with fA p 0.5. In the second generation, one population showed fA p 0.458 and the other fA p 0.521. What are the chances of observing these allele frequencies after one generation of genetic drift Shifting our perspective, we can use...
Loc729311
CNN2 NDUFS7 MKNK2 ATCAY ZBTB7A L C19orf10 PLAC2 ZNF136 OR10H1 COPE CILP2 MGC4093 LOC653583 DHX34 LIN7B TIP39 DPRX CNOT3 RPS9 NALP8 Figure 2.17 Maps for human chromosomes 18 left and 19 right showing chromosome regions, the physical locations of identified genes and open reading frames labeled orf along the chromosomes, and the names and locations of a subset of genes. Chromosome 18 is about 85 million bp and chromosome 19 is about 67 million bp. Maps from NCBI Map Viewer based on data as of...
Markov chains
The next step in understanding genetic drift is to consider its effects in a large number of replicate populations. Instead of focusing on allele frequency in just a single population like in the last section, let's now explore the case where there is a collection of numerous independent but identical populations an infinite number of replicate populations is sometimes called an ensemble in physics and mathematics . Using the approach of genetic drift in multiple finite populations, this...
Problem box 21 answer
Using the allele frequencies in Table 2.3 we can calculate the expected genotype frequencies for each locus D3S1358 2 0.2118 0.1626 0.0689 D21S11 2 0.1811 0.2321 0.0841 D18S51 0.0918 2 0.0084 vWA 0.2628 2 0.0691 FGA 2 0.1378 0.0689 0.0190 D8S1179 2 0.3393 0.2015 0.1367 D5S818 2 0.3538 0.1462 0.0992 D13S317 2 0.0765 0.3087 0.0472 D7S820 2 0.2020 0.1404 0.0567. As is evident from the allele designations, the amelogenin locus resides on the sex chromosomes and can be used to distinguish...
Thinking like a population geneticist
All scientific fields possess a body of concepts that define their domain as well as a specialized vocabulary used to express these concepts precisely. Population genetics is no different and the entirety of this book is designed to introduce, explain, and demonstrate these concepts and their vocabulary. What may be unique about population genetics among the natural sciences is the way that its practitioners approach questions about the biological world. Population genetics is a dialog between...
10
Frequency of aa Frequency of AA Frequency of aa Frequency of AA Figure 2.6 A De Finetti diagram for one locus with two alleles. The triangular coordinate system results from the requirement that the frequencies of all three genotypes must sum to one. Any point inside or on the edge of the triangle represents all three genotype frequencies of a population. The parabola describes Hardy-Weinberg expected genotype frequencies. The dashed lines represent the frequencies of each of the three...
Interact box 23 Assortative mating and genotype frequencies
The impact of assortative mating on genotype frequencies can be simulated in PopGene.S2. The program models several non-random mating scenarios that can be selected under the Mating Models menu. The results in each case are presented on a De Finetti diagram, where genotype and allele frequencies can be followed over multiple generations. Start with the Positive w o dominance model of mating. In this case only like genotypes are able to mate e.g. AA mates only with AA, Aa mates only with Aa, and...
F3
Figure 2.3 Mendel self-pollinated indicated by curved arrows the F2 progeny produced by the cross shown in Figure 2.2. Of the F2 progeny that had a yellow phenotype three-quarters of the total , one-third produced all progeny with a yellow phenotype and two-thirds produced progeny with a 3 1 ratio of yellow and green progeny or three-quarters yellow progeny . Individuals are represented by diamonds since pea plants are hermaphrodites. Figure 2.3 Mendel self-pollinated indicated by curved arrows...
Box 21 DNA profiling
The loci used for human DNA profiling are a general class of DNA sequence marker known as simple tandem repeat STR , simple sequence repeat SSR , or microsatellite loci. These loci feature tandemly repeated DNA sequences of one to six base pairs bp and often exhibit many alleles per locus and high levels of heterozygosity. Allelic states are simply the number of repeats present at the locus, which can be determined by electrophoresis of PCR amplified DNA fragments. STR loci used in human DNA...
21 Mendels model of particulate genetics
Mendel's breeding experiments. Independent assortment of alleles. Independent segregation of loci. Some common genetic terminology. In the nineteenth century there were several theories of heredity, including inheritance of acquired characteristics and blending inheritance. Jean-Baptiste Lamarck is most commonly associated with the discredited hypothesis of inheritance of acquired characteristics although it is important to recognize his efforts in seeking general causal explanations of...
F2
The F2 progeny appeared in the phenotypic ratio of 9 round yellow 3 round green 3 wrinkled yellow 1 wrinkled green. How did Mendel go from this F2 phenotypic ratio to the second law He ignored the wrinkled smooth phenotype and just considered the yellow green seed color phenotype in self-pollination crosses of F2 plants just like those for the first law. In the F2 progeny, 12 16 or three-quarters had a yellow seed coat and 4 16 or one-quarter had a green seed coat, or a 3 yellow 1 green...
22 HardyWeinberg expected genotype frequencies
Hardy-Weinberg and its assumptions. Each assumption is a population genetic process. Hardy-Weinberg is a null model. Hardy-Weinberg in haplo-diploid systems. Mendel's laws could be called the original expectations in population genetics. With the concept of particulate genetics established, it was possible to make a wide array of predictions about genotype and allele frequencies as well as the frequency of phenotypes with a one-locus basis. Still, progress and insight into particulate genetics...
D351358
Figure 2.8 The original data for the DNA profile given in Table 2.2 and Problem box 2.1 obtained by capillary electrophoresis. The PCR oligonucleotide primers used to amplify each locus are labeled with a molecule that emits blue, green, or yellow light when exposed to laser light. Thus, the DNA fragments for each locus are identified by their label color as well as their size range in base pairs. a A simulation of the DNA profile as it would appear on an electrophoretic gel indicates the anode...
Inbreeding coefficient and autozygosity in a pedigree
The effects of consanguineous mating can also be thought of as increasing the probability that two alleles at one locus in an individual are inherited from the same ancestor. Such a genotype would be homozygous and considered autozygous since the alleles were inherited from a common ancestor. If the two alleles are not inherited from the same ancestor in the recent past, we would call the genotype allozygous alio- means other . You are probably already familiar with autozygosity, although you...
Interact box 21 Genotype frequencies
PopGene.S2 short for Population genetics simulation software is a population genetics simulation program that will be featured in several Interact boxes. Here we will use PopGene.S2 to explore interactive versions of Figs 2.5 and 2.6. Using the program will require that you download it from a website and install it on a computer running Windows. Simulations that can be explored with PopGene.S2 will be featured in Interact boxes throughout this book. Find Interact box 2.1 on the text web page...