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When does genetic randomization happen?

When does genetic randomization happen?


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When two parents (regardless of species) reproduce in sexual reproduction each offspring is generally a random combination of genetic traits from each parent. Their developed traits then depend on the expression of each of their genes per established genetic combinatory science. All well and good.

Now my question - when does the actual randomization of genes for a given offspring happen? Does it happen when the individual sperm and egg cells are formed, or does it happen when they combine?

So does every one of a female's eggs have the same genetics, and every one of a male's sperm have the same genetics, and when the two combine it is randomized to form the zygote?

Or is each egg unique and each sperm unique, and already "pre-randomized", and the combination to form the zygote is then a straight-forward addition?

Or is it some variation or combination of those two options? Maybe the answer actually even differs across species, or across plants vs animals, or fish vs mammals, or something?


Randomisation happens in the forming of the the egg and the sperm. In a first approximation, the egg and the sperm receive a random single chromosome of each of the chromosome pairs during meiosis.

More randomisation happens due to the possibility of crossing over when homologous chromosomes exchange chromosome parts.

EDIT: In terms of the question, bothe the egg and the sperm are pre-randomised.


Your view of the randomization of the parent traits seem a bit wrong and it makes the question a little unclear. But still, I think we can answer it…

The randomization happens at the moment of the creation of sperms and ovules. The two "randomizing processes" are segregation and recombination.


How do random mating, genetic drift, and natural selection influence allele frequency?

Genetic drift is a chance phenomenon: it takes place when a small sub-population is established from a larger population. It alters allele frequency randomly in very short time. Generally genetic drift is associated with loss of genetic variations .

Natural selection is a slow and directional process. Due to natural forces of selection organisms with particular characters are chosen in each generation while others perish at faster rate. Thus there is a slow but steady increse in frequency of those alleles which are responsible for development of favourable characters, but these changes in allele frequency may take thousands of years to happen.

Random mating prevents change in allele frequency (as described in Hardy Weinberg law) in a population when other evolutionary forces are not acting though that does not happen in nature.


Assumptions and pitfalls of Mendelian randomization

Causal inferences drawn from MR studies are only valid if the rather strict assumptions of the method are met [4]. First, the genetic instrument Z must be associated with the exposure X. This must be a reliably established association, not merely based on the study sample at hand. Second, the genetic instrument Z must not be associated with the confounding factors U. Third, the genetic instrument Z should only be related to the outcome Y through its association with the exposure X. Figure 1a shows a directed acyclic graph of the situation when these assumptions hold.

The first assumption is the least problematic. Indeed, large-scale genome-wide association studies (GWASs) have produced large numbers of rather reliable gene–trait associations [1, 2]. Assuming that a genetic instrument (either a single allele or a linear combination of several alleles) for X is available, the remaining assumptions become crucial. As has been pointed out, it is never possible to prove definitively that these assumptions hold. Instead, their validity must be weighed based on biological knowledge [4, 5].

If the genetic instrument is directly (or via some intervening variable other than X) associated with the outcome of interest, MR will produce incorrect or at least biased results because an observed association between Z and Y would not only tell about the association between X and Y. This would happen if the genetic variant had pleiotropic effects, influencing not only X but also Y, as in Fig. 1b. Notably, recent genome-wide analyses point towards significant pleiotropic effects for different health outcomes [1, 2]. The situation is more challenging when polygenic scores (PSs) combining several alleles are used as instruments. Crucially, in this situation, the assumptions of MR should hold for all variants included in the allele score [9]. Thus, for unbiased MR results, none of the included alleles should have a pleiotropic effect on the outcome Y. This can be problematic for studies using PSs as instruments—which is increasingly common as the GWAS approach points towards highly polygenic effects for complex traits—if pleiotropy turns out to be more widespread than has been previously thought. Recently, multivariable MR has been developed to address pleiotropy [5].

Besides pleiotropic effects, LD between the genetic instrument Z and some other allele(s) that influence Y would violate the assumptions of MR (Fig. 1c). While the LD structure is generally known, using a PS as an instrument complicates the situation here also. Finally, the assumptions would be violated also by a pleiotropic effect on (or LD with a pleiotropic variant on) the confounding factors U (Fig. 1d). For example, socioeconomic status is an important confounder for many health outcomes. A recent GWAS identified 74 loci associated with educational attainment, many of them in regions regulating gene expression in the brain [10]. Thus, if researchers were to include some of these loci in a PS genetic instrument for some X for which educational level is a confounder, bias might be introduced through the association of the genetic instrument and educational attainment.

Furthermore, even if the assumptions of MR hold, there are additional limitations. One potential concern is that genetic variants (including PSs) are often only weakly associated with exposures of interest, making them weak instruments [4]. This is reflected in imprecise estimates, necessitating large samples for adequately powered studies. However, in addition to this statistical limitation, there is a potential biological concern: do we expect the (typically) small change in X, induced by Z, to have a biologically meaningful effect on Y?

Despite the underlying assumptions and potential limitations, MR is a promising tool for causal inference in (epi)genetic epidemiology, as is illustrated by the study of Dekkers and colleagues [3]. These authors interrogated the causal relationship between blood lipids and genome-wide DNA methylation, and show that differential methylation is the consequence, rather than the cause, of inter-individual variation of blood lipids. To do this, they used a clever strategy that involved performing MR in a stepwise manner.


Genetic drift

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Genetic drift, also called genetic sampling error or Sewall Wright effect, a change in the gene pool of a small population that takes place strictly by chance. Genetic drift can result in genetic traits being lost from a population or becoming widespread in a population without respect to the survival or reproductive value of the alleles involved. A random statistical effect, genetic drift can occur only in small, isolated populations in which the gene pool is small enough that chance events can change its makeup substantially. In larger populations, any specific allele is carried by so many individuals that it is almost certain to be transmitted by some of them unless it is biologically unfavourable.

Genetic drift is based on the fact that a subsample (i.e., small, isolated population) that is derived from a large sample set (i.e., large population) is not necessarily representative of the larger set. As might be expected, the smaller the population, the greater the chance of sampling error (or misrepresentation of the larger population) and hence of significant levels of drift in any one generation. In extreme cases, drift over the generations can result in the complete loss of one allele in an allele pair the remaining allele is then said to be fixed.

The Editors of Encyclopaedia Britannica This article was most recently revised and updated by Kara Rogers, Senior Editor.


Types of mutations

Broadly, mutations fall into two categories &mdash somatic mutations and germline mutations &mdash according to the authors of &ldquoAn Introduction to Genetic Analysis, 7th Ed&rdquo (W.H Freeman, 2000). Somatic mutations occur in their namesake somatic cells, which refers to the various cells of one&rsquos body that are not involved in reproduction skin cells for example. If the replication of a cell with a somatic mutation is not stopped, then the population of aberrant cells will expand. However, somatic mutations cannot be passed on to an organism&rsquos offspring.

On the other hand, germline mutations occur in the germ cells or the reproductive cells of multicellular organisms sperm or egg cells for example. Such mutations can be passed on to an organism&rsquos offspring. Moreover, according to the Genetics Home Reference Handbook, such mutations will carry over to pretty much every cell of an offspring&rsquos body.

However, based on how a DNA sequence is changed (rather than where), many different types of mutations can occur. For instance, sometimes an error in DNA replication can switch out a single nucleotide and replace it with another, thereby changing the nucleotide sequence of only one codon. According to SciTable published by the journal Nature Education, this type of error, also known as a base substitution can lead to the following mutations:

Missense mutation: In this type of mutation the altered codon now corresponds to a different amino acid. As a result an incorrect amino acid is inserted into the protein being synthesized.

Nonsense mutation: In this type of mutation, instead of tagging an amino acid, the altered codon signals for transcription to stop. Thus a shorter mRNA strand is produced and the resulting protein is truncated or nonfunctional.

Silent mutation: Since a few different codons can correspond to the same amino acid, sometimes a base substitution does not affect which amino acid is picked. For example, ATT, ATC and ATA all correspond to isoleucine. If a base substitution were to occur in the codon ATT changing the last nucleotide (T) to a C or an A, everything would remain the same in the resulting protein. The mutation would go undetected, or remain silent.

Sometimes a nucleotide is inserted or deleted from a DNA sequence during replication. Or, a small stretch of DNA is duplicated. Such an error results in a frameshift mutation. Since a continuous group of three nucleotides forms a codon, an insertion, deletion or duplication changes which three nucleotides are grouped together and read as a codon. In essence it shifts the reading frame. Frameshift mutations can result in a cascade of incorrect amino acids and the resulting protein will not function properly.

The mutations mentioned thus far are rather stable. That is, even if a population of aberrant cells with any of these mutations were to replicate and expand, the nature of the mutation would remain the same in each resulting cell. However, there exists a class of mutations called dynamic mutations. In this case, a short nucleotide sequence repeats itself in the initial mutation. However, when the aberrant cell divides, the number of nucleotide repeats can increase. This phenomenon is known as repeat expansion.


RESULTS

Out of 356 student responses analyzed, few defined or attempted to apply the concept of genetic drift without using misconceptions. Even though questions from both data sets specifically asked students to define genetic drift, 31.5% (n = 112) of responses failed to address drift at all (Table 2). Among responses that addressed drift (n = 244), only 11.5% (n = 28) indicated some knowledge of the definition of genetic drift. Overall, 83.2% (n = 203) of the responses that addressed drift contained at least one misconception (Table 2). Some responses (n = 25) hinted at knowledge of genetic drift (e.g., included the term random or chance), but were too vague to be fully evaluated. Note that, because some responses indicated knowledge of genetic drift but also contained misconceptions, the percentages provided here sum to greater than 100%.

Table 2. Frequency of different types of responses observed in full data set (n = 356), in only those responses that addressed drift (n = 244), and before (n = 85) and after (n = 122) introductory instruction

a p Values indicate significance of Fisher's exact tests comparing counts of responses before and after instruction.

b Values in a column may sum to greater than 100%, because a response could indicate knowledge of drift and contain a misconception.

c The first cell in this column is calculated from all responses collected before instruction (n = 159). The rest of the cells in this column are calculated from the responses that addressed drift (n = 85).

d The first cell in this column is calculated from all responses collected before instruction (n = 160). The rest of the cells in this column are calculated from the responses that addressed drift (n = 122).

Categories of Student Misconceptions Regarding Genetic Drift

In responses that addressed drift (n = 244), we identified five overarching categories of misconceptions: Novice Genetics, Novice Evolution, Associating Genetic Drift with Other Evolutionary Mechanisms, Associating Genetic Drift with Population Boundaries, and Developing Genetic Drift Comprehension. These overarching categories are further divided into 16 distinct misconceptions that we describe below and summarize in Table 3. We also describe the frequency of each misconception (Table 3). We further divide the frequency of each misconception into those collected before and after introductory genetic drift instruction (case study data set) and those collected from students enrolled in upper-division biology courses (concept inventory data set) (Table 3).

Table 3. Categories of misconceptions, student quotes, and the frequency with which students employed these misconceptions a

a Frequencies are based on the subset of responses that addressed drift (n = 244), not the total number of responses (n = 356).

b Responses from the case study project.

c Responses from the concept inventory project.

Our detailed description of the misconceptions begins with the most novice overarching categories (Novice Genetics and Novice Evolution) and concludes with the most advanced category (Developing Genetic Drift Comprehension). The two categories presented in the middle (Associating Genetic Drift with Other Evolutionary Mechanisms, Associating Genetic Drift with Population Boundaries) do not represent a progression rather, some responses in each category range from novice to developing comprehension. Within the overarching categories of misconceptions, we have listed misconceptions in decreasing order from highest to lowest percentage of responses that addressed drift (Table 3). It is important to recognize that although some misconceptions we describe indicated more advanced knowledge than others, responses in the most advanced category still differ in key ways from an expert's conception of genetic drift.

We use quotes from students to illustrate the misconceptions encompassed by each overarching category. In the interest of brevity, we include the most salient sections of a response, rather than complete responses. In some cases, we may have used additional information included in a response to analyze a student's conceptions in order to classify his or her misconceptions. We have lightly edited some quotes for clarity, but have left grammatical and syntax errors when they do not hinder the interpretation of a quote.

Category 1: Novice Genetics.

Although a number of definitions for genetic drift exist (Masel, 2012), biologists generally define genetic drift as a change in the allele frequencies within a population resulting from random sampling error from generation to generation (Futuyma, 2005 Barton et al., 2007). Some responses in our sample recognized genetic drift was associated with genetics, but did not recognize it as an evolutionary mechanism. These definitions of genetic drift tended to be vague and brief, indicating only superficial knowledge of genetics.

The most common misconception in Novice Genetics was the idea that genetic drift is, or results in, shared traits or shared genes. In some cases, responses stated or implied that genetic drift causes some differences among individuals, but natural selection causes many differences among individuals:

“Genetic drift is more likely [than natural selection] because they share many of the same habitats and seem to be similar.”

“Genetic drift equals family members…I would have to assume these two butterflies are similar in DNA because of similar shape and habits but not full related because of color and preferred areas to be like meadows and forests.”

Some responses in Novice Genetics vaguely described genetic drift as gradual genetic change in a population without describing a mechanism of change:

“Genetic drift = gradual change in genes.”

“[This is genetic drift because] their similar characteristics indicate that over time the genetics of the species slowly changed.”

A few responses in Novice Genetics defined genetic drift as occurring when genes or traits are passed from one individual to another. Responses were not always specific about the units between which traits or genes were passed. Some described genes passing from parent to offspring through reproduction, but others described the transmission of traits between individuals:

“Genetic drift is when certain desirable characteristics that may occur through mutation are passed on to offspring.”

“Genetic drift is the flow of genes from one individual to another.”

Category 2: Novice Evolution.

Responses in the Novice Evolution category defined genetic drift as an evolutionary mechanism but conflated the definition of genetic drift with novice conceptions of evolution. The answers indicated little or no knowledge of random occurrences. The most common misconception in Novice Evolution has also been identified and described in studies of students’ misconceptions regarding natural selection (e.g., Bishop and Anderson, 1990 Nehm and Reilly, 2007). These responses defined genetic drift as the process, or result, of the environment causing change over time, attributing this change to “adaptation,” by which they seemed to mean acclimation to environmental characteristics. Some responses containing this misconception explicitly stated that change resulted from a need to survive:

“Genetic drift is the most reasonable answer because the sun brings out brightness like the bright butterfly and the shade is dark like the darker butterfly.”

“Genetic drift is genes change over time to fit world changes.”

“Genetic drift [occurred] because the butterflies[’] color changed depending on where they spent the most time.”

“Genetic drift is when a species changes due to a specific need to survive or thrive.”

Another misconception in Novice Evolution defined genetic drift as an evolutionary mechanism in which change results from mating between individuals from different species:

“The butterflies were the same color and liked the same environments but began breeding with butterflies of different kinds, possibly because of food scarcity or wind currents.”

“Genetic drift is change due to breeding.”

Lastly, a few responses in Novice Evolution contained the misconception that genetic drift is a mechanism of evolutionary change that occurs when natural selection cannot or is not occurring. The descriptions in these responses were so superficial that despite the use of key terms like natural selection, the responses failed to indicate any understanding of evolutionary processes. This misconception was not common, but was very clearly articulated in two responses collected from students in different courses in response to different questions:

“[Genetic drift is] the genetic changes that occur when a population is not under selection.”

Category 3: Associating Genetic Drift with Other Evolutionary Mechanisms.

Biologists recognize natural and sexual selection, mutation, gene flow, and genetic drift as distinct evolutionary mechanisms. Responses in Associating Genetic Drift with Other Evolutionary Mechanisms confused genetic drift with other evolutionary mechanisms or with evolution in general. The definitions in these responses indicated developing comprehension of evolution, but did not indicate knowledge of genetic drift.

The most common misconception in Associating Genetic Drift with Other Evolutionary Mechanisms defined genetic drift as random mutation. About half of these responses explained that genetic drift results from mutations, while the other half defined genetic drift as the process of mutation or the accumulation of mutations over time. In some cases, students specified a precise mechanism of mutation:

“Genetic drift = change in a population due to mutation.”

“Genetic drift is the drifting of genes during mutations. A base pair is usually cutoff, that alters the gene sequence leading to changed genes.”

Another misconception in this category defined genetic drift as gene flow. Specifically, these responses described genetic drift as the process of alleles entering or leaving populations or as the process of alleles from different populations “mixing.” Some responses described the movement of genes, rather than the movement of alleles. Notably, Nehm and Reilly (2007) identified this misconception in undergraduates’ responses to an open-response item designed to measure knowledge of natural selection:

“Genetic drift involves the movement of alleles out of populations/gene pools to new environments.”

“Gene exchange between different populations of animals. Results in an increase or decrease of a specific type of gene.”

The third misconception in Associating Genetic Drift with Other Evolutionary Mechanisms defined genetic drift as natural selection. In some cases, these definitions of natural selection were nuanced and accurate in other cases, responses were less detailed, but implied or described an interaction between traits and the environment resulting in differential reproductive success, survival, or fitness. One response defined genetic drift as sexual selection:

“Genetic drift occurs because survival of the fittest so if some alleles that are passed down to offspring provide a benefit, those alleles are more likely to get passed on to their offspring.”

“Genetic drift is the gradual change in the frequency of specific alleles in a population to be more or less common [and]…occurs when there is a change in the environment that makes specific traits more or less favorable for fitness.”

Finally, a few responses in this category defined genetic drift as any change in allele frequencies:

“Genetic drift is when there is a change in the allele frequency of a population.” “Drift is the alteration of genes by anything, including chance.”

Category 4: Associating Genetic Drift with Boundaries between Populations.

Biologists recognize the founder effect to be one scenario in which genetic drift can occur. Essentially, when a small random sample of individuals from a larger population become the founders of a new population, they are likely to carry only a fraction of the genetic variation of the original population (Futuyma, 2005). Additionally, founding populations are often small and are therefore likely to be further impacted by genetic drift for many generations following the founding event. Moreover, genetic drift and natural selection can lead to reproductive isolation in a peripheral population, such as a founding population. This process is called peripatric speciation (Futuyma, 2005). No responses in Associating genetic drift with boundaries between populations came close to indicating knowledge of the nuanced concepts just described. However, these responses defined genetic drift as movement, separation, and/or speciation, which hinted at knowledge of, or at least exposure to, founder effect as an example of genetic drift.

The most common misconception in Associating Genetic Drift with Population Boundaries defined genetic drift as migration, by which responses typically seemed to mean emigration. In the interest of preserving student ideas, we have also used the term migration to describe emigration or immigration. In some cases, responses described migration followed by adaptation to the environment. The descriptions of adaptation in these responses were similar to those in Novice Evolution in that they described adaptation as acclimation to environmental characteristics, but these responses were distinct in that they also discussed the movement of individuals. The units discussed in these responses included individuals, species, and populations. Some responses discussed individuals or groups moving to locations better suited to their traits.

The terms migration and gene flow are often used interchangeably by experts, who recognize that migration is an evolutionary process only when it leads to a change in allele frequencies. There was no indication that students understood this subtlety. The responses in this category differed from those that defined genetic drift as gene flow, because they did not mention the movement of alleles or genes:

“Genetic drift is when a certain species migrates to another location.”

“Genetic drift would be where members of a population with different traits move to an environment that fits those traits.”

“Genetic drift would take place if the butterflies would have migrated to another climate and adapted to their surroundings by the means of migrations.”

A similar misconception defined genetic drift as the separation or isolation of populations. In some cases, responses discussed separation followed by adaptation, by which they seemed to mean acclimation, to a new environment:

“Genetic drift generally happens when part of a species population is separated and become[s] distinguished and change[s].”

“Genetic drift is when members of the same species get separated by environmental forces and over time develop differently.”

The third misconception in this category defined genetic drift as speciation. While it is possible for genetic drift to contribute to speciation, these responses did not provide an explanation for how speciation would occur. About half of these responses defined genetic drift as speciation following the separation of populations:

“These species of butterflies were once the same then slowly over time began shifting into one species that prefer sunny meadows and another that prefers dense woodlands.”

“Genetic drift occurs when an offshoot of a population starts to develop traits that separate it from the original population, usually by a chance act.”

“Genetic drift happens when two species become isolated from each other or no longer reproduce, creating a cross breeds.”

Category 5: Developing Genetic Drift Comprehension.

Biologists recognize many nuances of the process of genetic drift. For example, genetic drift can result from random sampling of gametes during sexual reproduction, as well as random sampling of individuals, and their gametes, resulting from a population bottleneck (Futuyma, 2005). Experts recognize drift occurs in all finite populations, but is likely to have a more pronounced impact given a small effective population size (Barton et al., 2007). Experts also know genetic drift can, but does not always, lead to the fixation of alleles, and that genetic drift tends to decrease genetic variation within a population and increase variation among populations (Frankham et al., 2002).

Responses in Developing Genetic Drift Comprehension indicated some knowledge of genetic drift. However, the definitions in this category placed inaccurate limitations on the circumstances under which genetic drift can occur.

The most common misconception in Developing Genetic Drift Comprehension defined genetic drift as, or as resulting from, an isolated event, often a catastrophe. These responses did not recognize genetic drift as a process occurring each generation:

“Genetic drift is where there is some event that decreases the variation in a population.”

Another misconception in Developing Genetic Drift Comprehension limited genetic drift to small populations:

“Genetic drift is a change in allele frequency due to a random genetic occurrence in a small population.”

The least common response in Developing Genetic Drift Comprehension described genetic drift as allele fixation, rather than describing fixation as a potential result of genetic drift:

“[Genetic drift is] when an allele gets fixed on a population.”

“[Genetic drift is] allele fixation due to limited gene pool.”

“[Genetic drift is when] a random event knocks out one genotype.”

Vague Responses That Hinted at Knowledge of Genetic Drift

Responses that hinted at knowledge of genetic drift used terms such as random or chance but otherwise did not indicate knowledge of genetic drift. In some cases, the term random or chance was embedded in misconceptions, but in most cases these responses were simply too vague to evaluate:

“Genetic drift is all about chances to the outcome of the offspring.”

Responses Indicating Some Knowledge of Genetic Drift

Responses indicating some knowledge of drift ranged considerably in quality. Some responses provided precise and nuanced definitions of genetic drift, others gave brief but accurate descriptions of drift, and some responses included misconceptions.

The following quote was one of the most articulate responses in our sample. In particular, the subtle and precise language differentiates this response from responses containing misconceptions. Though the response discusses an event or catastrophe leading to genetic drift—like responses in Developing Genetic Drift Comprehension—the use of the introductory clause “for instance” suggests that the student recognizes this is one example of drift, rather than the only circumstance under which drift takes place:

“Genetic drift is evolution that occurs purely by chance. For instance, an F1 generation could have 10 red flowers, 10 pink flowers, and 10 white flowers. If all the white flowers are accidentally killed or something happens, their genes will not be passed on to future generations.”

In contrast, the next quote demonstrates how a response can indicate some knowledge of genetic drift and contain a misconception. The first sentence of the response confuses genetic drift with selection, while the second sentence indicates knowledge of genetic drift:

“[Genetic drift occurs when] through sexual or natural selection, certain alleles are favored. Additionally, it may just so happen that an allele becomes more or less prevalent though it neither helps nor harms individuals within a population.”

Results of Statistical Analyses

We used statistical analyses to address three predictions about student learning. We tested these predictions using data from the case study project (n = 319), because this project collected data before and after introductory-level genetic drift instruction. We predicted that 1) the number of students who did not address drift, 2) the number of responses that indicated some knowledge of the definition of genetic drift, and 3) the number of responses containing at least one misconception would all be different before and after instruction.

All three of the predictions about student learning were supported by our data (Table 2). In all cases, students exhibited more knowledge of genetic drift after instruction. The number of responses that did not address drift was significantly different before and after instruction (Fisher's test, p < 0.0001 Table 2), suggesting that students in these courses did not address drift before instruction because they had little or no knowledge of the concept. To test our second and third predictions, we examined only the responses from the case study data set in which students addressed drift (n = 207). The number of responses indicating some knowledge of genetic drift was different before and after instruction (p = 0.005 Table 2). Additionally, the number of responses containing at least one misconception was different before and after instruction (p < 0.0001 Table 2).

When we examined the frequency of student responses containing each of the 16 distinct misconceptions at different stages of instruction, we noticed that while some misconceptions were less common among students who had received genetic drift instruction, other misconceptions were more common following instruction (Table 3). Specifically, the misconceptions in Novice Genetics and Novice Evolution were less common after introductory instruction and among upper-division students, whereas misconceptions in Developing Genetic Drift Comprehension were absent before instruction, but increasingly common with more instruction (Table 3). The frequency of misconceptions in Associating Genetic Drift with Other Evolutionary Mechanisms and Associating Genetic Drift with Population Boundaries remained about the same before and after introductory instruction, but among upper-division students these two categories diverged (Table 3). Misconceptions in Associating Genetic Drift with Other Evolutionary Mechanisms were substantially more common among upper-division students than among introductory students, whereas misconceptions in Associating Genetic Drift with Population Boundaries were less common among upper-division students than among introductory students (Table 3).


11.2 Mechanisms of Evolution

The Hardy-Weinberg equilibrium principle says that allele frequencies in a population will remain constant in the absence of the four factors that could change them. Those factors are natural selection, mutation, genetic drift, and migration (gene flow). In fact, we know they are probably always affecting populations.

Natural Selection

Natural selection has already been discussed. Alleles are expressed in a phenotype. Depending on the environmental conditions, the phenotype confers an advantage or disadvantage to the individual with the phenotype relative to the other phenotypes in the population. If it is an advantage, then that individual will likely have more offspring than individuals with the other phenotypes, and this will mean that the allele behind the phenotype will have greater representation in the next generation. If conditions remain the same, those offspring, which are carrying the same allele, will also benefit. Over time, the allele will increase in frequency in the population.

Mutation

Mutation is a source of new alleles in a population. Mutation is a change in the DNA sequence of the gene. A mutation can change one allele into another, but the net effect is a change in frequency. The change in frequency resulting from mutation is small, so its effect on evolution is small unless it interacts with one of the other factors, such as selection. A mutation may produce an allele that is selected against, selected for, or selectively neutral. Harmful mutations are removed from the population by selection and will generally only be found in very low frequencies equal to the mutation rate. Beneficial mutations will spread through the population through selection, although that initial spread is slow. Whether or not a mutation is beneficial or harmful is determined by whether it helps an organism survive to sexual maturity and reproduce. It should be noted that mutation is the ultimate source of genetic variation in all populations—new alleles, and, therefore, new genetic variations arise through mutation.

Genetic Drift

Another way a population’s allele frequencies can change is genetic drift (Figure 11.7), which is simply the effect of chance. Genetic drift is most important in small populations. Drift would be completely absent in a population with infinite individuals, but, of course, no population is this large. Genetic drift occurs because the alleles in an offspring generation are a random sample of the alleles in the parent generation. Alleles may or may not make it into the next generation due to chance events including mortality of an individual, events affecting finding a mate, and even the events affecting which gametes end up in fertilizations. If one individual in a population of ten individuals happens to die before it leaves any offspring to the next generation, all of its genes—a tenth of the population’s gene pool—will be suddenly lost. In a population of 100, that 1 individual represents only 1 percent of the overall gene pool therefore, it has much less impact on the population’s genetic structure and is unlikely to remove all copies of even a relatively rare allele.

Imagine a population of ten individuals, half with allele A and half with allele a (the individuals are haploid). In a stable population, the next generation will also have ten individuals. Choose that generation randomly by flipping a coin ten times and let heads be A and tails be a. It is unlikely that the next generation will have exactly half of each allele. There might be six of one and four of the other, or some different set of frequencies. Thus, the allele frequencies have changed and evolution has occurred. A coin will no longer work to choose the next generation (because the odds are no longer one half for each allele). The frequency in each generation will drift up and down on what is known as a random walk until at one point either all A or all a are chosen and that allele is fixed from that point on. This could take a very long time for a large population. This simplification is not very biological, but it can be shown that real populations behave this way. The effect of drift on frequencies is greater the smaller a population is. Its effect is also greater on an allele with a frequency far from one half. Drift will influence every allele, even those that are being naturally selected.

Visual Connection

Do you think genetic drift would happen more quickly on an island or on the mainland?

Genetic drift can also be magnified by natural or human-caused events, such as a disaster that randomly kills a large portion of the population, which is known as the bottleneck effect that results in a large portion of the genome suddenly being wiped out (Figure 11.8). In one fell swoop, the genetic structure of the survivors becomes the genetic structure of the entire population, which may be very different from the pre-disaster population. The disaster must be one that kills for reasons unrelated to the organism’s traits, such as a hurricane or lava flow. A mass killing caused by unusually cold temperatures at night, is likely to affect individuals differently depending on the alleles they possess that confer cold hardiness.

Another scenario in which populations might experience a strong influence of genetic drift is if some portion of the population leaves to start a new population in a new location, or if a population gets divided by a physical barrier of some kind. In this situation, those individuals are unlikely to be representative of the entire population which results in the founder effect . The founder effect occurs when the genetic structure matches that of the new population’s founding fathers and mothers. The founder effect is believed to have been a key factor in the genetic history of the Afrikaner population of Dutch settlers in South Africa, as evidenced by mutations that are common in Afrikaners but rare in most other populations. This is likely due to a higher-than-normal proportion of the founding colonists, which were a small sample of the original population, carried these mutations. As a result, the population expresses unusually high incidences of Huntington’s disease (HD) and Fanconi anemia (FA), a genetic disorder known to cause bone marrow and congenital abnormalities, and even cancer. 4

Concepts in Action

Visit this site to learn more about genetic drift and to run simulations of allele changes caused by drift.

Gene Flow

Another important evolutionary force is gene flow , or the flow of alleles in and out of a population resulting from the migration of individuals or gametes (Figure 11.9). While some populations are fairly stable, others experience more flux. Many plants, for example, send their seeds far and wide, by wind or in the guts of animals these seeds may introduce alleles common in the source population to a new population in which they are rare.


Novel genetic patterns may make us rethink biology and individuality

Professor of Genetics Scott Williams, PhD, of the Institute for Quantitative Biomedical Sciences (iQBS) at Dartmouth's Geisel School of Medicine, has made two novel discoveries: first, a person can have several DNA mutations in parts of their body, with their original DNA in the rest -- resulting in several different genotypes in one individual -- and second, some of the same genetic mutations occur in unrelated people. We think of each person's DNA as unique, so if an individual can have more than one genotype, this may alter our very concept of what it means to be a human, and impact how we think about using forensic or criminal DNA analysis, paternity testing, prenatal testing, or genetic screening for breast cancer risk, for example. Williams' surprising results indicate that genetic mutations do not always happen purely at random, as scientists have previously thought.

His work, done in collaboration with Professor of Genetics Jason Moore, PhD, and colleagues at Vanderbilt University, was published in PLOS Genetics journal on November 7, 2013.

Genetic mutations can occur in the cells that are passed on from parent to child and may cause birth defects. Other genetic mutations occur after an egg is fertilized, throughout childhood or adult life, after people are exposed to sunlight, radiation, carcinogenic chemicals, viruses, or other items that can damage DNA. These later or "somatic" mutations do not affect sperm or egg cells, so they are not inherited from parents or passed down to children. Somatic mutations can cause cancer or other diseases, but do not always do so. However, if the mutated cell continues to divide, the person can develop tissue, or a part thereof, with a different DNA sequence from the rest of his or her body.

"We are in reality diverse beings in that a single person is genetically not a single entity -- to be philosophical in ways I do not yet understand -- what does it mean to be a person if we are variable within?" says Williams, the study's senior author, and founding Director of the Center for Integrative Biomedical Sciences in iQBS. "What makes you a person? Is it your memory? Your genes?" He continues, "We have always thought, 'your genome is your genome.' The data suggest that it is not completely true."

In the past, it was always thought that each person contains only one DNA sequence (genetic constitution). Only recently, with the computational power of advanced genetic analysis tools that examine all the genes in one individual, have scientists been able to systematically look for this somatic variation. "This study is an example of the type of biomedical research project that is made possible by bringing together interdisciplinary teams of scientists with expertise in the biological, computational and statistical sciences." says Jason Moore, Director of the iQBS, who is also Associate Director for Bioinformatics at the Cancer Center, Third Century Professor, and Professor of Community and Family Medicine at Geisel.

Having multiple genotypes from mutations within one's own body is somewhat analogous to chimerism, a condition in which one person has cells inside his or her body that originated from another person (i.e., following an organ or blood donation or sometimes a mother and child -- or twins -- exchange DNA during pregnancy. Also, occasionally a person finds out that, prior to birth, he or she had a twin who did not survive, whose genetic material is still contained within their own body). Chimerism has resulted in some famous DNA cases: one in which a mother had genetic testing that "proved" that she was unrelated to two of her three biological sons.

Williams says that, although this was a small study, "there is a lot more going on than we thought, and the results are, in some ways, astoundingly weird."

Because somatic changes are thought to happen at random, scientists do not expect unrelated people to exhibit the same mutations. Williams and colleagues analyzed the same 10 tissue samples in two unrelated people. They found several identical mutations, and detected these repeated mutations only in kidney, liver and skeletal body tissues. Their research examined "mitochondrial DNA" (mtDNA) -- a part of DNA that is only inherited from the mother. Technically all women would share mtDNA from one common female ancestor, but mutations have resulted in differences. The importance of Williams' finding is that these tissue-specific, recurrent, common mutations in mtDNA among unrelated study subjects -- only detected in three body tissues -- are "not likely being developed and maintained through purely random processes," according to Williams. They indicate "a completely different model &hellip. a decidedly non-random process that results in particular mutations, but only in specific tissues."

If our human DNA changes, or mutates, in patterns, rather than randomly if such mutations "match" among unrelated people or if genetic changes happen only in part of the body of one individual, what does this mean for our understanding of what it means to be human? How may it impact our medical care, cancer screening, or treatment of disease? We don't yet know, but ongoing research may help reveal the answers.

Christopher Amos, PhD, Director of the Center for Genomic Medicine and Associate Director for Population Sciences at the Cancer Center, says, "This paper identifies mutations that develop in multiple tissues, and provides novel insights that are relevant to aging. Mutations are noticed in several tissues in common across individuals, and the aging process is the most likely contributor. The theory would be that selected mutations confer a selective advantage to mitochondria, and these accumulate as we age." Amos, who is also a Professor of Community and Family Medicine at Geisel, says, "To confirm whether aging is to blame, we would need to study tissues from multiple individuals at different ages." Williams concurs, saying, "Clearly these do accumulate with age, but how and why is unknown -- and needs to be determined."

As more and better data become available from high-throughput genetic analyses and high-powered computers, researchers are identifying an increasing number of medical conditions that result from somatic mutations, including neurological, hematological, and immune-related disorders. Williams and colleagues are conducting further research to examine how diseases, other than cancer or even benign conditions, may result from somatic changes. Williams, Moore and Amos will employ iQBS's Discovery supercomputer for next-generation sequencing to process subjects' DNA data. Future analyses will include large, whole-genome sequencing of the data for the two individuals studied in the current report.

Williams explains, "We know that cancer is caused by mutations that cause a tumor. But in this work, we chose to study mutations in people without any cancer. Knowing how we accumulate mutations may make it easier to separate genetic signals that may cause cancer from those that accumulate normally without affecting disease. It may also allow us to see that many changes that we thought caused cancer do not in many situations, if we find the same mutations in normal tissues."

Just as our bodies' immune systems have evolved to fight disease, interestingly, they can also stave off the effects of some genetic mutations. Williams states that, "Most genetic changes don't cause disease, and if they did, we'd be in big trouble. Fortunately, it appears our systems filter a lot of that out."

Mark Israel, MD, Director of Norris Cotton Cancer Center and Professor of Pediatrics and Genetics at Geisel, says, "The fact that somatic mutation occurs in mitochondrial DNA apparently non-randomly provides a new working hypothesis for the rest of the genome. If this non-randomness is general, it may affect cancer risks in ways we could not have previously predicted. This can have real impact in understanding and changing disease susceptibility."


Genetics: The Study of Heredity

Genetics is the study of how heritable traits are transmitted from parents to offspring. Humans have long observed that traits tend to be similar in families. It wasn’t until the mid-nineteenth century that larger implications of genetic inheritance began to be studied scientifically.

Natural selection

In 1858, Charles Darwin and Alfred Russell Wallace jointly announced their theory of natural selection. According to Darwin’s observations, in nearly all populations individuals tend to produce far more offspring than are needed to replace the parents. If every individual born were to live and reproduce still more offspring, the population would collapse. Overpopulation leads to competition for resources.

Darwin observed that it is very rare for any two individuals to be exactly alike. He reasoned that these natural variations among individuals lead to natural selection. Individuals born with variations that confer an advantage in obtaining resources or mates have greater chances of reproducing offspring who would inherit the favorable variations. Individuals with different variations might be less likely to reproduce.

Darwin was convinced that natural selection explained how natural variations could lead to new traits in a population, or even new species. While he had observed the variations existent in every population, he was unable to explain how those variations came about. Darwin was unaware of the work being done by a quiet monk named Gregor Mendel.

Inheritance of traits

In 1866, Gregor Mendel published the results of years of experimentation in breeding pea plants. He showed that both parents must pass discrete physical factors which transmit information about their traits to their offspring at conception. An individual inherits one such unit for a trait from each parent. Mendel's principle of dominance explained that most traits are not a blend of the father’s traits and those of the mother as was commonly thought. Instead, when an offspring inherits a factor for opposing forms of the same trait, the dominant form of that trait will be apparent in that individual. The factor for the recessive trait, while not apparent, is still part of the individual’s genetic makeup and may be passed to offspring.

Mendel’s experiments demonstrated that when sex cells are formed, the factors for each trait that an individual inherits from its parents are separated into different sex cells. When the sex cells unite at conception the resulting offspring will have at least two factors (alleles) for each trait. One inherited factor from the mother and one from the father. Mendel used the laws of probability to demonstrate that when the sex cells are formed, it is a matter of chance as to which factor for a given trait is incorporated into a particular sperm or egg.

We now know that simple dominance does not explain all traits. In cases of co-dominance, both forms of the trait are equally expressed. Incomplete dominance results in a blending of traits. In cases of multiple alleles, there are more than just two possible ways a given gene can be expressed. We also now know that most expressed traits, such as the many variations in human skin color, are influenced by many genes all acting on the same apparent trait. In addition, each gene that acts on the trait may have multiple alleles. Environmental factors can also interact with genetic information to supply even more variation. Thus sexual reproduction is the biggest contributor to genetic variation among individuals of a species.

Twentieth-century scientists came to understand that combining the ideas of genetics and natural selection could lead to enormous strides in understanding the variety of organisms that inhabit our earth.

Scientists realized that the molecular makeup of genes must include a way for genetic information to be copied efficiently. Each cell of a living organism requires instructions on how and when to build the proteins that are the basic building blocks of body structures and the &ldquoworkhorses&rdquo responsible for every chemical reaction necessary for life. In 1958, when James Watson and Francis Crick described the structure of the DNA molecule, this chemical structure explained how cells use the information from the DNA stored in the cell’s nucleus to build proteins. Each time cells divide to form new cells, this vast chemical library must be copied so that the daughter cells have the information required to function. Inevitably, each time the DNA is copied, there are minute changes. Most such changes are caught and repaired immediately. However, if the alteration is not repaired the change may result in an altered protein. Altered proteins may not function normally. Genetic disorders are conditions that result when malfunctioning proteins adversely affect the organism. [Gallery: Images of DNA Structures]

In very rare cases the altered protein may function better than the original or result in a trait that confers a survival advantage. Such beneficial mutations are one source of genetic variation.

Another source of genetic variation is gene flow, the introduction of new alleles to a population. Commonly, this is due to simple migration. New individuals of the same species enter a population. Environmental conditions in their previous home may have favored different forms of traits, for example, lighter colored fur. Alleles for these traits would be different from the alleles present in the host population. When the newcomers interbreed with the host population, they introduce new forms of the genes responsible for traits. Favorable alleles may spread through the population. [Countdown: Genetics by the Numbers &mdash 10 Tantalizing Tales]

Genetic drift

Genetic drift is a change in allele frequency that is random rather than being driven by selection pressures. Remember from Mendel that alleles are sorted randomly into sex cells. It could just happen that both parents contribute the same allele for a given trait to all of their offspring. When the offspring reproduce they can only transmit the one form of the trait that they inherited from their parents. Genetic drift can cause large changes in a population in only a few generations especially if the population is very small. Genetic drift tends to reduce genetic variation in a population. In a population without genetic diversity there is a greater chance that environmental change may decimate the population or drive it to extinction.



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