Module 4- Chapter 6:7 - Professor Brenda Anderson PDF

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Professor Brenda Anderson...

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Basics of Evolution: To understand the basics of nervous system evolution, you need to understand the basics of evolutionary theory. As you read through this document and answer the questions in the accompanying homework assignment, please pay careful attention to whether the terms are referring to a mechanism or an outcome of a mechanism. Biological evolution refers to the observed pattern of change in organisms that inhabit the Earth over time. Natural selection (aka, survival of the fittest) is the process that underlies the pattern of changes in species over time as well as the development of new species. (here we see evolution is a phenomenon or pattern, while natural selection is a mechanism drives the pattern.) A species is a group of individuals that can or does interbreed. Therefore, the species is the largest gene pool for lineages in natural conditions. Therefore, evolution is the pattern of change within and across species, and natural selection the mechanism that explains the pattern. 

Most often think of natural selection as driving changes in species, but it can also drive stability within a species. In other words, it can refine what already works well.

Nature selects characteristics within species. These characteristics are called phenotypes. Phenotypes are influence by two factors, environment and genes.Therefore a phenotype is the result of an interaction between the genotypes and the environment. (https://www.nature.com/scitable/definition/phenotype-phenotypes-35) [for the sole use of students at Stony Brook University as per the TEACH act] a) Example: Height is a phenotype that may be influenced by as many as 700 genes. Even so, only 80% of height may be determined by genes. The other 20% may be under the influence of the environment. For example, the availability of food and its nutritional quality likely influences height. Therefore height is an interaction between many genes and the environment (https://ghr.nlm.nih.gov/primer/traits/height). There have been statistically

significant differences in height over time, presumably because of increasing food availability (see graph below).

https://www.nature.com/articles/pr2012189

[for the sole use of students at Stony Brook University as per the TEACH act] The four propositions underlying the theory of evolution through natural selection are:    

(1) Individuals within a species show variation. (2) Offspring tend to inherit their parents’ characteristics (aka phenotypes). (3) Each species produces more offspring than can survive. (4) Offspring struggle and compete for survival. 

Environmental pressures prefer some characteristics over others.

The three necessary and sufficient conditions for natural selection to occur are: (1) variation (2) inheritance (3) a struggle for existence Which of the following is a correct statement? a) Variation causes evolution. b) The change in species over time is referred to as natural selection, which occurs through the mechanism of evolution. c) Conditions in nature can preferentially select phenotypes, causing species to change over time. d) All of the above

[For additional help, see https://evolution.berkeley.edu/evolibrary/article/evo_01 ] [for the sole use of students at Stony Brook University as per the TEACH act] Descent with modification. Since offspring compete to survive and nature selects those that survive, phenotypes will survive in different proportions in subsequent generations. The different proportion of phenotypes in subsequent generations is referred to as descent with modification. (consider whether descent with modification is a result, or a cause). To describe the probability of survival and reproduction related to a characteristic (phenotype), we use the term “Fitness.”

https://evolution.berkeley.edu/evolibrary/article/evo_27 Ninety five percent of camel colored beetles survive while only 33 of green beetles survive. Which beetles have greater fitness? 

Example: If there are two phenotypes, A and B, the proportion of offspring that survive represents the “fitness” for each phenotype. 



In other words, phenotype A would have greater fitness than B if if within the second generation we find 80% of individuals with phenotype A survive and only 40% of the individuals with characteristic B survive. Natural selection drives fitness. In other words, some phenotypes will provide advantages that increase the likelihood of survival and reproduction within the existing environment, while others may reduce the potential for survival and reproduction. Yet others will have little value either way. (step back and ask yourself if fitness is an outcome or a mechanism/driver? Is natural selection an outcome/observation or a mechanism/driver?)

The fitness of a phenotype is determined by a) Selective pressures in the environment b) The proportion of offspring with the phenotype c) Evolution d) Descent with modification The fitness of a phenotype is reflected by a) Selective pressures in the environment b) The proportion of offspring that survive c) Evolution

d) Descent with modification Descent with modification is reflected by a) Natural selection b) Fitness c) The differential representation of phenotypes across generations [for the sole use of students at Stony Brook University as per the TEACH act] Natural selection can produce three patterns of inheritance (see Figure 2)   

Stabilizing Directional Diversifying

Darwin’s illustration of finch beak variations. We usually think natural selection produces variation, but we need to make a distinction between directional selective and diversification. How the finches played a role in the theory of evolution: https://youtu.be/l25MBq8T77w Darwin noted that in the Galapagos, finches segregated by islands had faced different environmental pressures. Despite all the birds belonging to a single original population, the strong selective features on any single island exaggerated the beak shapes of the finches that inhabited that island. For example, Islands with worms better supported the survival of finches with long narrow beaks. Islands with relatively more seeds selected for birds with shorter, stronger beaks. Over time the species diversified by island as shown in c below. In contrast, if all the islands selected for narrow beaks, we might say there was directional selection. [for the sole use of students at Stony Brook University as per the TEACH act] Selection can also lead to stabilization (see a) below), which refers to the refining or reduced variation in a phenotype.

If you are confused, see this site http://www.sparknotes.com/biology/evolution/naturalselection/section1/

Diversification may be most likely when a) The species has little variation b) The species begins to inhabit segregated locations with different selective pressures c) The phenotype is unrelated to fitness d) All of the above [for the sole use of students at Stony Brook University as per the TEACH act]Take note that one critical feature for the survival of species is variation. Only through variation can species survive changes in selective pressures as the environment changes. Example: When our ancestral hominids (earliest humans) moved from wet forests full of edible vegetation to dry grassland, they began to consume meat. The reduced availability of vegetation and greater reliance on meat for nutrition selected for phenotypes that supported meat consumption and digestion. Tooth morphologies that supported tearing tissue rather than grinding were selected.

These environments also selected against other phenotypes such as chambers in the stomach that support fermentation of fibrous plants, which were no longer available for food. [ADD REFERENCE] One specific feature of the environment that provides selective pressure is mates. Mates often have preferences for phenotypes. When mates prefer phenotypes, we have sexual selection. Example: A male peacock attracts a potential mate’s attention by displaying his feathers. The female has not developed long tail feathers, because the males have no such preference.

The male peacocks feathers attract the attention of a female, increasing the probability he will mate. Sexual selection can increase the likelihood of mating and reproduction, but the same phenotypes that increase the potential for reproduction may also be disadvantages for the individual. The feathers of the male peacock may also make him more vulnerable to predators, but in this case the advantage for attracting mates clearly outweighs any disadvantages. Which of the following is an example of natural selection

a) Changes in the proportional representation of phenotypes when the species moves to a new location b) Changes in the proportional representation of phenotype when the environment changes over time c) Changes in a phenotype despite having no relationship to fitness d) All of the above e) A&B f) B&C Reproduction: Asexual or sexual? Earlier we saw that the critical factors that support evolution are variation, inheritance and a struggle for existence. We also saw that selective pressures (natural or sexual selection) are related to survival and reproduction. Let’s consider further the sources of variance. Some organisms reproduce by asexual reproduction. Through this process offspring would be a single genetically identical copy of a single parent, with the exception, perhaps, of some copy errors, which will be discussed below. Overall, there would be little variation in species that reproduce asexually. [for the sole use of students at Stony Brook University as per the TEACH act] Sexual reproduction requires two parents, each contributing genetic information to the offspring so that each offspring is a hybrid, so to speak, of the two parents (https://learn.genetics.utah.edu/content/basics/inheritance) (https://learn.genetics.utah.edu/content/basics/diagnose/). Each child ends up with a different set of genes (with the exception of identical twins). Thus, each offspring (or monozygotic twin set) is unique. The uniqueness of each offspring have led to the suggestion that sexual reproduction can increase variation. Mathematical models suggest it isn’t so simple. We would expect that most individuals will end up with a mixture of genes. Different versions of genes are called alleles. We’ve learned when studying Mendelian patterns of inheritance that we could have three possible alleles BB, Bb or bb. If BB or bb have more fitness than Bb, then sexual reproduction could reduce survival.

Figure 5: Mendelian pattern of inheritance Therefore, we can’t assume sexual reproduction is always beneficial for a species. Nevertheless, it has been reported that 99.9% of eukaryotes can reproduce sexually, although not all use sexual reproduction as their only strategy for reproduction. Of course a subset of eukaryotes (e.g., mammals) use sexual reproduction only. [for the sole use of students at Stony Brook University as per the TEACH act] If sexual reproduction can have disadvantages, why is it so prevalent? We might look for answers in species that can switch from one to the other form of reproduction. If we assume that sexual reproduction offers advantages in the conditions in which it occurs most often in species that use both types of reproduction, then what are the conditions that foster sexual reproduction in those species? Sexual reproduction occurs more often when a) the environment changes rapidly, b) selection varies over space, c) organisms aren’t well suited for the environment, and d) the population size is limited rather than infinite (https://www.nature.com/scitable/topicpage/sexual-reproduction-and-theevolution-of-sex-824). When would asexual reproduction be ideal? 1. 2. 3. 4.

When the environment is changing is rapidly When the species is expanding into new environments When the organism thrives in a stable environment None of the above

Jumps in variation Sudden changes in phenotypes can occur through mutations. Mutations are spontaneous changes in sequences of DNA that code for a molecule that has function

(aka genes). These spontaneous changes can produce a rapid form of evolution. [for the sole use of students at Stony Brook University as per the TEACH act] Earlier we noted that phenotypes are characteristics, and phenotypes are determined by genotypes. Genes are made of DNA, which codes for RNA. RNA codes for proteins. Proteins produce structure and the functional parts of our bodies, which make up the phenotypes. This relationship between DNA, RNA and proteins is considered the “central dogma” of molecular biology (https://learn.genetics.utah.edu/content/basics/centraldogma/).

Each time a cell divides, DNA must be copied. DNA is two strands of nucleotides wound around each other in the form of a double helix. In the picture to the left, you can see a short section of DNA showing that it is a double helix. Below you can see a simpler depiction of the structure.

Careful study of the structure of DNA reveals two backbones that are connected to nucleotides in the middle. The nucleotides have weak bonds that hold the two strands together.

(http://www.mammothmemory.net/biology/dna-genetics-and-inheritance/dna-basepairing/dna-double-helix.html) [for the sole use of students at Stony Brook University as per the TEACH act] There are four nucleotides, adenine (A), thymine (T), cytosine (C) and guanine (G). The nucleotides are bound to a sugar backbone (see green above). The two strands are held together by the hydrogen bonds between the nucleotide pairs. Cytosine binds to guanine and adenine binds to thymine. In the image below, you see the common base pair arrangements.

Adenine (A) should bind with thymine (T), and Cytosine (C) should bind with guanine (G) Bases in the DNA sometimes bind incorrectly. For example, when copied, a pair, A-T becomes the pair G-T with G mistakenly replacing A.

[for the sole use of students at Stony Brook University as per the TEACH act] One potentially common copy error comes from “wobble,” which refers to a shift in the location of the bond, which in turn leads to the wrong base pairs bonding. (Pray, Leslie, A., 2008, DNA Replication and Causes of Mutation. Nature Education 1(1):214. Posted at https://www.nature.com/scitable/topicpage/dna-replication-and-causes-of-mutation-409)

A sequence of base pairs is referred to as a “gene,” which provides instruction for RNA and, in turn, proteins. We know that genes are copied from cell to cell, and from generation to generation. We might ask how accurate the copying process is? Copy errors are not uncommon. Fortunately, many errors are corrected by polymerase enzymes. Although these enzymes are good at correcting errors, they are not perfect. A second process, mismatch repair, steps in and reduces the copy errors even further. With these two corrective mechanisms, we are left with ~1 error per 100,000 nucleotides. This rate varies. Some parts of the genome are more error prone than others. Some organisms have lower error rates than others. If there is ~1 error per 100,000 nucleotides, then each time a cell divides in humans, there should be ~120,000 mistakes. The “proofreading” process, carried out by DNA polymerase, corrects about 99% of the copy errors. Mismatch repair reduces the mistakes even further. (https://www.nature.com/scitable/topicpage/dna-replication-and-causesof-mutation-409) -In asexual reproduction, variability would arrive solely from these copy errors

-In sexual reproduction, a set of the mother’s genes is combined with the fathers to produce an individual with a unique set of genes. But individuals also have copy errors. Each human likely starts out with about 60 copy errors. Once these errors become permanent, they are referred to as mutations. Mutations are simply alternative forms of a gene, or alleles. [An extra bit of detail if you are interested: You might think that these copy errors are mutations. It is a little more complicated, if you want to be precise. The errors don’t “officially” produce a mutation until the complementary strand is formed. That complementary strand will have incorrect nucleotides. At this point, the mechanisms for error detection are incapable of detecting the error, and it becomes permanent. Each time the complementary strand is copied, the error is copied. All copies from this line thereafter will be incorrect (i.e., have the mutation).] [for the sole use of students at Stony Brook University as per the TEACH act] Mutations are alternative forms of a gene (i.e., alleles). Mutations can make us different from our parents, but what do they do? -Most mutations are silent. By silent, we mean, they have no effect on a phenotype. -Other mutations are expressed, but benign. For example, eye color is expressed, but has no effect on fitness. -Some mutations reduce fitness: Rare mutations affect cell function, behavior, or lead to disease. When they reduce survival or the potential for reproduction, they reduce fitness. -Rare mutations increase the probability of survival and reproduction ( see the example below). [for the sole use of students at Stony Brook University as per the TEACH act] Mutations could occur in cells unrelated to reproduction, which would effects subsequent cells, but not offspring. Only when the mutation occurs in the gamete, will the mutation be passed on to offspring. A gamete is a male or female germ cell with a single set of unpaired chromosomes. Gametes are able to unite with a germ cell from the other sex to form a zygote (i.e, fertilized ovum). The figure below focuses on the pattern of mutations and their fitness over generations.

What in the figure above represents phenotype? Where do you see examples of mutations? Is heritability reflected in this image? How is descent with modification reflected in the image above? Evolution is complicated. We can think of it as being like the economy and job market. Conditions change over space and time. Over time, skills that were once valued, sometimes lose their value (e.g., the skills of a blacksmith are no longer highly valued). Similarly, the fitness associated with phenotypes can change over time. For example, a mutation, the C282Y allele, that was once likely very beneficial in Northern Europe, can now cause health problems. The C282Y allelle causes excessive iron absorption, otherwise known as hemochromatosis. Heath et al., (2016) write, “The mutation arose in continental Europe no earlier than 6,000 years ago, coinciding with the arrival of the Neolithic agricultural revolution. Here we hypothesize that this new Neolithic diet, which originated in the sunny warm and dry climates of the Middle East, was carried by migrating farmers into the chilly and damp environments of Europe where iron is a critical micronutrient for effective thermoregulation…Humans are tropical animals and climate is a major selective force on geographic variation in allele frequencies (Hancock et al., 2008; Laland and O'Brien, 2010; Veeramah and Novembre, 2014). Here we have shown that the geographic distribution of the C282Y allele for iron retention in contemporary Europe is associated with increasingly chilly and damp environments of human occupation during the Neolithic. “ (Heath KM et al., 2016 Am J. Physical Anthropology 160(1), 86-101). Similarly, just as skills may be valued in one location and not another, some mutations may have value in some locations and not others. We can presume that C282Y would have had little effect on fitness for individuals who stayed in the Middle East, but increased fitness for individuals who migrated to cold wet climates in Europe.

Individuals with two copies of either the C282Y or H63D alleles can develop high iron levels, absorb too much iron in tissues (e.g. liver), and eventually develop associated health problems (e.g., cirrhosis of the liver) (https://www.mayoclinic.org/diseases-conditions/hemochromatosis/symptomscauses/syc-20351443). High blood iron levels, however, do not usual...