Genetic Drift

Genetic drift is the process of change in genetic information in a population. It is caused by random chance or events. These random events result in changes in allele frequencies within the population.  Genetic drift is not natural selection (http://www.biology-online.org/dictionary/Genetic_drift).   Genetic drift does not allow for adaptation.  Natural selection is the force behind adaptation.  Genetic drift along with natural selection, mutation, and migration can lead to evolutionary change (http://evolution.berkeley.edu/evosite/evo101/IIIDGeneticdrift.shtml).  Genetic drift is seen more in smaller population sizes than in larger population sizes.  There are two types of genetic drift.  There is the founder effect and the bottleneck effect.  The founder effect is when a few individuals move to a new area.  This may cause there to be less genetic variation within the population being founded.  The bottleneck effect is when the population is decreases by a certain event.  For example, the events may include anything from natural occurrences, such as hurricanes, tornadoes, floods, ect., to human inflected causes, such as hunting or land/habitat destruction(http://evolution.berkeley.edu/evosite/evo101/IIID3Bottlenecks.shtml).  This website also gives a couple of examples of each type of genetic drift.  Genetic drift also may cause alleles to become fixed.  It is where only one allele is present in the population due to lack of genetic flow.  There are a few ways to keep the population from getting to the point of allele fixation or to reverse allele fixation.  People can work on rebuilding the habitat that the populations once had.  This will allow them to be better suited for their environment and allow for the population to grow in size.   After the habitat is established, new members of the species can be brought in from other areas to supply genetic variation.  If there is a barrier between two populations, a channel or pathway can be formed to allow the two populations to migrate to the other areas to allow gene flow to occur.

Phenotypic Plasticity

The environment, the phenotype, and the genotype of an organism are closely related. They play off each other, ultimately affecting the organism. Phenotypes are usually defined as the appearance of a genetically controlled trait; however, this is not always the case. The environment can influence the phenotype of an organism as well. The word describing the environment’s impact on phenotype is phenotypic plasticity. Phenotypes that are plastic have individuals with the same genotype but have different phenotypes due to the variation in their environments. Phenotypic plasticity is able to evolve and is adaptive. Environments frequently change. The changes in environment can disrupt an organism’s ability to cope with the environment and thus lower fitness. Phenotypic plasticity allows the balance between an organism’s phenotype and the environment to be restored. Grasshoppers and their mandibles provide a good example of phenotypic plasticity. Most grasshoppers prefer leafy, lush food such as leaves.  They have special mouthparts called mandibles that move horizontally to crush the leaves between the two mandibles. Phenotypic plasticity can be seen in grasshopper mandible size when their diet changes. Drought or climate change is usually the reason for this. When the food becomes more fibrous the mandibles become larger and more muscle attachments appear. The change in environmental climate caused a shift in vegetation, which caused the grasshopper mandible to change. Other examples of phenotypic plasticity can be seen in the change in polar bear diet due to the increase in global temperatures or in aphid colonies where females produce offspring best suited for the environment the colony is facing. Phenotypic plasticity is not the same as adaptations. Phenotypic plasticity is a direct and intentional shift. Phenotypic plasticity allows organisms of the same genotype to vary in their phenotypes.

http://www.eeb.cornell.edu/agrawal/pdfs/whitman-and-agrawal-2009-Ch_1-Phenotypic-Plasticity-of-Insects.pdf

http://evolution.berkeley.edu/evolibrary/news/090501_climatechange

Mimicry

In chapter 10 the textbook talks about one instance of mimicry. Mimicry is when one species has developed similar characteristic to a model, that is not closely related to it. The example in the textbook discusses the tephritid fly that mimics the jumping spider in order to keep from becoming prey to the jumping spiders. This form of mimicry is odd because it is unusual for the prey animal to mimic its predator. It was described as "a sheep in wolves clothing." There are many different forms of mimicry. The adaptation of mimicry increases the animal's fitness by reducing its chances of being preyed on or by increasing its ability to capture prey. The evolution process is slow, but sometimes it does not take a great deal of variation to increase one's fitness over another of the same species. One site I found talks about the Eastern tiger swallowtail caterpillar and says that " any mutation that occurred which made one caterpillar look 2% more turd-like than the others would give that caterpillar a greater chance of survival," (Montgomery). That sums up the evolution process for this form of mimicry in my opinion; the caterpillar would have an increased fitness just because it had a slight similarity to something that repels its normal predators. Then since it is a heritable trait it would be passed on and become more common. The predator would eventually become aware of the ones that are a little similar to scat, and we would see an arms race to become more similar to and to be able to identify the actual caterpillar.
 

More Information at:
http://www.eoearth.org/article/Biological_mimicry
http://www.christs.cam.ac.uk/darwin200/pages/index.php?page_id=g6

Trade offs relating to adaptive evolution

I remember reading about tradeoffs last semester in my ecology course and it interested me. In chapter 10 of our textbook, it goes into more detail about trade offs and adaptive evolution. A tradeoff is an inescapable compromise between one trait and another. There are many factors that limit adaptive evolution, some being tradeoffs, functional constraints, and lack of genetic variation. Many examples of tradeoffs are mentioned throughout this chapter. For examples, in fruit bats and flying fox bats, large testes help bats win at sperm competition but oppose metabolic costs that lead to the evolution of smaller brains. Another examples of a tradeoff used in this chapter can be seen in the tropical plant Begonia involucrata. Upon researching mimicry between female and male plants, Schemske and Agren discovered a tradeoff: the larger the female flowers on an inflorescence, the fewer flowers there are. Tradeoffs can be found everywhere. A few examples that I found using the almighty Google are some organisms tend to be move slower so that they can have a larger body size. Another example I found can be seen in the male peacock. His brightly colored tail may be great for attracting a females for mating, but his bright tail will also easily attract a predator.

Visit these links for more detailed examples of biological tradeoff:

http://www.pnas.org/content/104/suppl.1/8649.full

http://www.ncbi.nlm.nih.gov/pubmed/15266369

Hardy-Weinberg Principles

Under the hardy-Weinberg principle, there is no selection, no mutations, no migration, no chance of events and individuals choices to show that evolution does not occur.  You can use the hardy-Weinberg equation to see if a population is evolving along with seeing if the population is inbreeding.  If the population is not evolving, the numbers that are calculated from the equation should come out to be around the same numbers.  When a huge change in the numbers occurs, this indicates that evolution is occurring.  Under the hardy-Weinberg principle, we need to consider if all populations mate at random.  Most people would just think that all populations mate randomly.  However, there are some populations that breed asexually.  When you have populations that self-fertilize, you have what is called inbreeding or breeding among relatives.  In interbreeding, you will see a large amount of Homozygotes within the population.  By using the hardy-Weinberg equation, you could detect if inbreeding is occurring in nature. We know that selection occurs when individuals of a certain phenotypes survive and reproduces at higher rates than individuals of other phenotypes.   Mutations occur when there is a change in the codon of amino acids in the DNA.  In many cases, the mutation is silent or slightly harmful.  Silent mutations have no effect on the DNA sequence or phenotype.  This occurs because if the change is with the third codon there is no change with the amino acid and genetic code.  Mutations alone are not enough to cause evolution, but along with a selective force over time can cause evolutionary change.  This is seen in the research that is being done with the HIV virus. Studying the HIV virus has help see evolution occurring and mutation rate within the population. http://vir.sgmjournals.org/content/79/6/1337.full.pdf  Show the HIV mutation rate and its role in genetic variation.

http://www.ucl.ac.uk/~ucbhdjm/courses/b242/InbrDrift/InbrDrift.html Talks about inbreeding and the effects on evolution and genetics. 

http://scienceray.com/biology/botany/self-pollination-vs-cross-pollination/ shows self-fertilization. 

The role of genetic drift in evolution

Genetic drift is one of the major mechanisms that drive evolution. Genetic drift is the gradual change in the genome of populations over time, even in the absence of natural selection. Natural selection works on mutations which impact survival, favoring those which enhance the chances of survival. It is therefore the mechanism behind adaptation, the process of gradually “fitting” an organism to a particular niche in a given environment. Genetic drift, on the other hand, works on all mutations, including those which offer no survival advantage. Over time, it can produce changes in the genome which can lead to speciation even without environmental pressure. It can even resist and counter the effects of adaptation to weaker natural selection forces, which is why many harmful mutations continue to exist.
Genetic drift is a stochastic process, or it operates on random chance, and is affected by factors such as breeding population size, the geographical spread and consequent isolation of breeding groups, ecological disasters such as famine, epidemics, volcanoes and earthquakes, and yes, even asteroid strikes. Here's how it works:
The DNA of organisms is made up of genes. Each gene encodes for one protein. Many organisms are diploid, having paired homologous chromosomes. Each chromosome in a pair has a separate copy of the gene, so in a diploid organism, there are two copies of each gene, called alleles. If they are identical, then the organism is homozygous for the trait expressed by that gene. If the two alleles of the gene are not identical, then the organism is heterozygous for that trait. While in a given diploid organism, only two copies or alleles of a gene can exist, in the population there might be many more. For example, for a given gene, there might be 9 variants or 9 alleles in the population living in one country. Any individual in that population has 2 out of those 9 possible alleles. The distribution of the 9 alleles in that population is static at any given time, but over the course of time it may change. It may be that right now alleles 2 and 7 are more prevalent, accounting for 50% of the entire population. But perhaps a few thousand years ago, alleles 5 and 9 were the most prevalent. This change in the frequency of different alleles over time is in fact evolution, and genetic drift is one important cause for it.
 There are many ways in which genetic drift works. The most simple is a random disaster. Suppose there is a breeding population of 10,000 living in a given area. A volcano erupts nearby, and all the organisms living in proximity die. This has nothing to do with natural selection, because no member of the population is evolutionarily better suited to surviving hot molten lava, or to breathing searing hot poisonous gases.  In other words, this kind of disaster does not selectively kill the weaker or the ones with bad genes, it simply kills whatever happened to be close by. As a result of this disaster, half the population dies. The remaining half will probably not have exactly the same allele distribution as the whole population did. For example, for a certain gene A, which has 9 alleles, it may be that prior to the disaster , the population as a whole had an allele frequency distribution such that allele 1 occurred in 32% of the population. But because of random chance, more organisms with allele 1 lived near the volcano, therefore they died in disproportionately high numbers, and after the disaster the frequency of allele 1 falls to 18%. The same principle applies to all alleles of all genes.

Visit these websites for more information about genetic drift:

 http://www.talkorigins.org/faqs/genetic-drift.html

http://anthro.palomar.edu/synthetic/synth_5.htm

Mutation Types

Mutations are the source of new alleles in a species. Mutations can be beneficial, harmful, or have no effect. There are many types of mutations. The first type of mutation is a point mutation. A point mutation changes only a singe base pair. So if your DNA read ACTGTA a point mutation DNA would read ACTTTA, the highlighted T is where your point mutation occurred. Point mutations occur because random errors in DNA synthesis or random errors in the repair of damaged sites. Replacement substitutions are a form of point mutation that results in an amino acid change. On the other hand, point mutations that do not change the amino acid are called silent substitutions. Amino acids are coded from the three base pair codon, but some codons code for the same amino acid. For example if the codon TAC codes for the amino acid leucine and TAT also codes for leucine. The C to T point mutation would be a silent mutation since it codes for the same amino acid. The Wobble Hypothesis states that the third base pair in an anticodon can align in several ways to allow it to recognize more than one base in the codons of mRNA. A second form of mutation is Transversion. A transversion mutation occurs when a purine is substituted for a pyrimidine or vise versa. A purine in DNA is either adenine or guanine. A pyrimidine is cytosine, thymine, and in the case of RNA uracil. So if your DNA sequence read ATCGAT the mutated strand would read AACGTA. The highlighted letters are where a transversion mutation occurred. The pyrimidine thymine was replaced with a purine adenine. Another type of mutation is a transition mutation. This is very similar to a transversion mutation. In a transition mutation a purine is replaced with another purine or a pyrimidine is replaced with another pyrimidine. If your sequence read TAGCTATACG the mutated strand could read TAGTTATGCG. In your mutated strand the pyrimidine cytosine was replaced with another pyrimidine thymine. The purine adenine was replaced with another purine guanine. Insertions occur when extra base pairs are added into the DNA. So for example your DNA reads TAGTCG an insertion would be the highlighted area TAGGATTCG. A Deletion occurs when a section of the DNA is deleted. So in the same strand, TAGTCG, a deletion would result in the shortened strand of TAGG, where TC was deleted. Since DNA is read in codons an insertion or deletion can change the whole meaning of DNA’s message. So if your original strand read MAX WAS MAD the deletion of the first M would make the sentence not understandable: AXW ASM AD. There are other possible mutations but, all mutations have the ability to produce new phenotypes if they change the gene product. A mutation can have the three effects on an individual. In most cases it does not have an effect. Mutations create new alleles which is necessary for natural selection to occur.

http://evolution.berkeley.edu/evolibrary/article/mutations_03

http://www.youtube.com/watch?v=eDbK0cxKKsk

http://ghr.nlm.nih.gov/handbook/mutationsanddisorders/possiblemutations

Homology

Homology is the study of likeness, the similarity between species that results from inheritance of traits from a common ancestor. The study of similarities is broken up into three main categories: structural, developmental, and molecular homology.

Structural homology is looking at a particular part of the body and comparing structures. So for example, forelimbs in vertebrates. The vertebrate forelimbs are used for different functions but have the same arrangement of bones. Looking at structural homologies can prove that a group on species evolved from a common ancestor. When comparing the structural components of a human, a horse, and a dolphin we can see that they have the same sequence. These three vertebrates all have an ulna and a radius, followed by carpals, metacarpals, and then phalanges. The structural similarities of these vertebrates suggest they evolved from a common ancestor. The theory of evolution helps to express this. The previous theory, theory of special creation, has a very hard time explaining these similarities. The second kind of homology is developmental homology. Developmental homology looks and compares embryos of various species. Using the vertebrate example again we can look at the embryos of snake, cat, bat, and human. These four vertebrates look very similar to each other during early development. Two key characteristics to look at is the pharyngeal pouches and the tail. Humans who don’t have gills or a tail develop these two characteristics while still in the womb. The gills interestingly enough contribute to the development of the lower jaw. These developmental traits connect these vertebrates. As development continues the vertebrates look extremely different. The third type of homology is molecular homology. One version of this is shared flaws in the genome. Shared flaws in the genome suggest that they developed from a common ancestor. It is an important concept because it can test the relationships between modern taxa. Molecular homology looks at the similarity of species on the molecular level. They look at the species DNA and compare it to another’s DNA. These three forms of homology help scientists to make connections between different species and to help prove the Theory of Evolution.

http://www.bio.miami.edu/dana/160/160S11_3.html

http://www.csun.edu/~dgray/Evol322/Chapter2.pdf

http://evolution.berkeley.edu/evolibrary/article/lines_08

The age of the Earth

A topic in these chapters that has always interested me was the age of the Earth discussed in chapter 2 section 3. Studies of strata, the layering of rocks and earth, gave naturalists an appreciation that Earth may have been through many changes during its existence. These layers often contained fossilized remains of unknown creatures, leading some to interpret a progression of organisms from layer to layer. Nicolas Steno was one of the first Western naturalists to appreciate the connection between fossil remains and strata. His observations led him to formulate important stratigraphic concepts such as the law of superposition and the principle of original horizontality. In the 1790s, the British naturalist William Smith hypothesized that if two layers of rock at widely differing locations contained similar fossils, then it was very plausible that the layers were the same age. Smith's student, John Phillips, later calculated by such means that Earth was about 96 million years old. Other naturalists used these hypotheses to construct a history of Earth, though their timelines were inexact as they did not know how long it took to lay down stratigraphic layers. In 1830, the geologist Charles Lyell, developing ideas found in Scottish natural philosopher James Hutton, popularized the concept that the features of Earth were in perpetual change, eroding and reforming continuously, and the rate of this change was roughly constant. This was a challenge to the traditional view, which saw the history of Earth as static, with changes brought about by intermittent catastrophes. Many naturalists were influenced by Lyell to become "uniformitarians" who believed that changes were constant and uniform. One method of aging the Earth is through a process called radiometric dating. Rock minerals naturally contain certain elements and not others. By the process of radioactive decay of radioactive isotopes occurring in a rock, exotic elements can be studied over time. By measuring the concentration of the stable end product of the decay, coupled with knowledge of the half life and initial concentration of the decaying element, the age of the rock can be calculated. Typical radioactive end products are argon from potassium-40 and lead from uranium and thorium decay. If the rock becomes molten, as happens in Earth's mantle, such nonradioactive end products typically escape or are redistributed. Thus the age of the oldest terrestrial rock gives a minimum for the age of Earth assuming that a rock cannot have been in existence for longer than Earth itself. The age of the Earth is 4.54 ± 0.05 billion years. This age is based on evidence from radiometric age dating of meteorite material and is consistent with the ages of the oldest-known terrestrial and lunar samples. Following the scientific revolution and the development of radiometric age dating, measurements of lead in uranium-rich minerals showed that some were in excess of a billion years old. The oldest such minerals analyzed to date are small crystals of zircon from the Jack Hills of Western Australia and are at least 4.404 billion years old. Comparing the mass and luminosity of the sun to the magnitudes of other stars, it appears that the solar system cannot be much older than those rocks. Ca-Al-rich inclusions (inclusions rich in calcium and aluminum) – the oldest known solid constituents within meteorites that are formed within the solar system – are 4.567 billion years old, giving an age for the solar system and an upper limit for the age of Earth. It is hypothesized that the accretion of Earth began soon after the formation of the Ca-Al-rich inclusions and the meteorites. Because the exact amount of time this accretion process took is not yet known, and the predictions from different accretion models range from a few millions up to about 100 million years, the exact age of Earth is difficult to determine. It is also difficult to determine the exact age of the oldest rocks on Earth, exposed at the surface, as they are aggregates of minerals of possibly different ages.


For more information about the age of the Earth, check these websites out:

http://douthat.blogs.nytimes.com/2012/11/19/marco-rubio-and-the-age-of-the-earth/

http://www.talkorigins.org/faqs/faq-age-of-earth.html

http://creation.com/age-of-the-earth