## Gene Trees Versus Allele or Haplotype trees

With mutation in the model, a distinction can now be made between gene trees and haplotype trees. Gene trees are genealogies of genes. They describe how different copies at a homologous DNA region are related by ordering coalescent events. Figure 5.12a shows a simple gene tree for a sample of six copies of an homologous DNA region. This figure is a repeat of the gene tree shown in Figure 5.9, but now we allow some of the DNA replication events to have experienced mutation. Looking back through...

## Info

Mechanisms of uniting gametes (disassortative mating) Mechanisms of zygotic production (Mendel's first law) Zygotic population of next generation Figure 3.8. Model of 100 disassortative mating for phenotype determined by single autosomal locus with two alleles and with all three possible genotypes having distinct phenotypes. The G's refer to genotype frequencies and T's to phenotype frequencies. SUM GAA x GAa + Gaa x Gaa + GAa x Gaa and is needed to standardize the mating probabilities to sum...

## Multiple Patterns in Nested Clade Analysis

No single test statistic discriminates between recurrent gene flow, past fragmentation, and past range expansion in the nested-clade analysis. Rather, it is a pattern formed from several statistics that allows discrimination. Also, as indicated in the above discussion, many different patterns can sometimes lead to the same biological conclusion. Finally, as pointed out with the impala example (Figure 7.6), sometimes the pattern associated with significant clade and nested-clade distances is an...

## Inbreeding

In its most basic sense, inbreeding is mating between biological relatives. Two individuals are related if among the ancestors of the first individual are one or more ancestors of the second individual. Because of shared common ancestors, the two individuals could share genes at a locus that are identical copies of a single ancestral gene (via premise 1 DNA can replicate). Such identical copies due to shared ancestry are said to be identical by descent. In contrast, the same allele can arise...

## Natural Selection on Components of aa Supergene

As explained earlier, the aa supergene consists of two molecular components the presence of R1 inserts in a third of more of the 28S ribosomal genes on the X chromosome and the presence of the X-linked uraa allele that codes for the failure of selective underreplication of inserted rDNA repeats in the fat body polytene tissue. Because of the linkage disequilibrium between the rDNA and the ur locus described earlier, virtually all X chromosomes with the uraa allele also have a third or more of...

## Population Subdivision And System Of Mating

The balance between drift and gene flow is the primary determinant of what fraction of a species' genetic variability is available in local gene pools, but the local system of mating then takes the gene pool variation available at the gametic level and transforms it into genotypic variation at the individual level, as we saw in Chapter 3. Therefore, a full consideration of how genetic variation is distributed between demes, among individuals within a deme, and within individuals (heterozygosity...

## Using Sequence Or Restriction Site Data To Measure Population Subdivision

In our previous models of population subdivision, any pair of homologous genes was classified into one of two mutually exclusive categories The pair was identical by descent or not (for defining Fst) or the pair was heterozygous or not (for defining fst). However, with the advent of restriction site and DNA sequence data, we can refine this categorization by the use of a molecule genetic distance. Suppose, for example, that we have sequence data on a 10-kb locus, and a pair of genes at this...

## Box Neighborjoining Method Of Tree Estimation

Step 1 in neighbor joining is the calculation of the net molecule genetic distance of each haplotype from all other haplotypes in the sample. Letting dik be the molecule genetic distance between haplotype i and haplotype k, the net molecule genetic distance for haplotype i is where n is the number of haplotypes in the sample. The net distances are used to evaluate violations of the molecular clock model. For example, suppose one haplotype lineage experienced a much higher rate of accumulation...

## Units And Targets Of Selection

Most genetic models used in this book have been single-locus models. This emphasis upon single-locus models is typical of much of population genetics. One of the main reasons for the dominance of single-locus models is mathematical tractability. Such a mathematical rationale does not necessarily justify biologically the dominance of single-locus models. The biological adequacy of a single-locus model in describing evolution is a troubling issue because qualitatively new biological features can...

## Gene Flow versus Admixture

The rejection of treeness among populations is usually due to some sort of genetic interchange among the populations, but treeness can be violated either by recurrent gene flow or by rarely occurring, historical episodes of admixture (Cavalli-Sforza et al. 1994). If the lack of treeness is due to rare episodes of admixture, then the tree would still be yielding biologically meaningful information about population history. For example, Cavalli-Sforza et al. (1994) argue that human populations...

## Interactions Of Natural Selection Genetic Drift And Mutation

The balance between genetic drift and mutation was shown in Chapter 5 to influence the rates of mutational substitution (rate of fixation due to drift times the rate of input of new mutations, or 1 2N x 2N ) and the expected level of polymorphism (which is a function of twice the mutation rate divided by the force of drift, or 2 1 (2N) 4N 0). In Chapter 7, the balance of drift and mutation as measured by 0 was shown to influence many properties of the coalescent process under the assumption of...

## Interaction Of Natural Selection With Mutation And System Of Mating

The system of mating can also interact with natural selection to influence evolutionary dynamics and equilibria. However, the interaction of selection with system of mating is more direct than with many other evolutionary forces because system of mating directly influences the average excess (Chapter 8). To illustrate this direct interaction between selection and system of mating, consider the mutation selection balance models of the previous section but now allowing deviations from random...

## Basic Premises Of Population Genetics

Microevolutionary mechanisms work upon genetic variability, so it is not surprising that the fundamental premises that underlie population genetic theory and practice all deal with various properties of deoxyribonucleic acid (DNA), the molecule that encodes genetic information in most organisms. A few organisms use ribonucleic acid (RNA) as their genetic material, and the same properties apply to RNA in those cases. Indeed, the theory of microevolutionary change stems from just three premises...

## Targets Of Selection Below Level Of Individual

In Chapters 11 and 12, fitness phenotypes were always regarded as properties of individual organisms. However, even in those chapters, we saw that the fitness values of specific individuals were important only through their contribution to genotypic values that is, the average fitness phenotype for a group of individuals sharing a common genotype. Consequently, to study natural selection, all we need is a group that shares a common genetic state. We can then assign a genotypic value or average...

## Effective Population Size

As seen above, finite population size has many important evolutionary consequences increasing the average amount of identity by descent, increasing the variance of allele frequencies through time and across populations, and causing the loss or fixation of alleles. As also shown by the above examples and simulations, the rate at which these effects occur is roughly inversely proportional to population size. In an idealized population, we can derive a precise quantitative relationship between...

## Box The Correlation Of Uniting Gametes

In order to show that X is the covariance among uniting gametes, we must first define a random variable to assign to the gametes. In our simple genetic model, the gametes bear only one of two possible alleles, A and a. Let x be a random variable that indicates the allele borne by a male gamete such that x 1 if the male gamete bears an A allele and x 0 if the male gamete bears an a allele. Similarly, let y be a random variable that indicates the allele borne by a female gamete such that y 1 if...

## Founder And Bottleneck Effects

As shown in the previous section, genetic drift causes its most dramatic and rapid changes in small populations. However, even a population that is large most of the time but has an occasional generation of very small size can experience pronounced evolutionary changes due to drift in the generation of small size. If the population size grows rapidly after a generation of small size, the increased population size tends to decrease the force of subsequent drift, thereby freezing in the drift...

## Mcl

Note that the ratio of the expected mean-square treatment to the expected mean-square error is 1 under the null hypothesis that all treatment means are the same (all m j m). Moreover, the ratio of the mean-square treatment to the mean-square error is of the form given by equation A2.31 and therefore has an F distribution with r - 1 and Ej 1 nr - r degrees of freedom. Hence, by partitioning the total variance into two components, MSTR and MSE, we can test the null hypothesis that all treatments...

## Quantitative Genetic Measures Related To Mean

The most straightforward measure related to the mean is the mean phenotype itself, n-. (All the quantitative genetic definitions used in this chapter are summarized in Table 8.2.) The mean f is the average phenotype of all individuals in the population. Alternatively, x can be thought of as the mean phenotype averaged over all genotypes and all environments. Let Pijk be the phenotype of a diploid individual with genotype ij (with ij referring to gamete i and gamete j that came together to form...

## Restriction Endonucleases

The 1960s also marked the discovery of restriction endonucleases commonly called restriction enzymes , enzymes that cleave duplex DNA at particular oligonucleotide sequences, usually of 4,5, or 6 bp in length Linn and Arber 1968 Meselson and Yuan 1968 . For example, the restriction enzyme EcoR1 named from the bacteria, Escherichia coli, from which it was isolated cuts double-stranded DNA where the nonmethylated sequence 5'-GAATTC-3' occurs. Hundreds of other restriction enzymes have been...

## P

A A p w AA - w 1 - p w Aa - w genotype equation 13.6 . The single-locus fitnesses are related to the two-locus fitnesses through a conditional expectation. For example, the single-locus, marginal fitness of the AA genotype is g2AB wAB AB 2gABgAbwAB Ab g bwAb Ab The quantity g B p2 is the conditional frequency of the AB AB genotype given that the individual is AA with probability p2 , and similarly for the other two-locus genotypes that are homozygous for the A allele. Thus, the one-locus...

## Scope And Basic Premises Of Population Genetics

Population genetics is concerned with the origin, amount, and distribution of genetic variation present in populations of organisms and the fate of this variation through space and time. The kinds of populations that will be the primary focus of this book are populations of sexually reproducing diploid organisms, and the fate of genetic variation in such populations will be examined at or below the species level. Variation in genes through space and time constitute the fundamental basis of...

## Importance Of Hardyweinberg

At first, the Hardy-Weinberg law may seem a relatively minor, even trivial, accomplishment. Nevertheless, this simple model played an important role in the development of both genetics and evolution in the early part of the twentieth century. Mendelian genetics had been rediscovered at the start of the twentieth century, but many did not accept it. One of the early proponents of Mendelian genetics was R. C. Punnett of Punnett square fame . Punnett made a presentation at a scientific meeting in...

## N

Frequency of A over all replicate populations is p 1 q 0 p and the variance of the allele frequency is x 2 2 2 Var allele frequency E - pj p 1 - p q 0 - p pq q p pq Hence, equation 4.15 also tells us that eventually drift causes all initial genetic variation to become lost or fixed, the only way to achieve the maximum theoretical variance of pq. Equation 4.15 also provides us with our primary definition of the variance effective size namely, if the actual variance in allele frequency after t...

## Hardyweinberg For Two Loci

The original Hardy-Weinberg model assumed a genetic architecture of one autosomal locus with two alleles. We will now consider a slightly more complicated genetic architecture of two autosomal loci, each with two alleles say A and a at locus 1 and B and b at locus 2 . Otherwise, we will retain all other assumptions of the original Hardy-Weinberg model. However, there is one new assumption. Recall from Chapter 1 that our second premise is that DNA can mutate and recombine. We will retain the...

## Disassortative Mating

Disassortative mating is the preferential mating of individuals with dissimilar phenotypes. This means that there is a negative correlation between the phenotypes of mating individuals. For example, the major histocompatibility complex MHC , mentioned in Chapter 1, is found not only in humans but in mice as well. In mice, genetic variation in MHC induces odor differences. There is disassortative mating at this gene complex in mice that is due to olfactory discrimination of potential mates Potts...