Evolution

Two major mechanisms drive evolution. The first is natural selection, a process causing heritable traits that are helpful for survival and reproduction to become more common in a population, and harmful traits to become more rare. This occurs because individuals with advantageous traits are more likely to reproduce, so that more individuals in the next generation inherit these traits. Over many generations, adaptations occur through a combination of successive, small, random changes in traits, and natural selection of those variants best-suited for their environment. The second major mechanism is genetic drift, an independent process that produces random changes in the frequency of traits in a population. Genetic drift results from the role probability plays in whether a given trait will be passed on as individuals survive and reproduce. Though the changes produced in any one generation by drift and selection are small, differences accumulate with each subsequent generation and can, over time, cause substantial changes in the organisms.

This process can culminate in the emergence of new species. Indeed, the similarities between organisms suggest that all known species are descended from a common ancestor (or ancestral gene pool) through this process of gradual divergence.  Evolution in organisms occurs through changes in heritable traits)  particular characteristics of an organism. In humans, for example, eye color is an inherited characteristic, which individuals can inherit from one of their parents. Inherited traits are controlled by genes and the complete set of genes within an organism’s genome is called its genotype. The complete set of observable traits that make up the structure and behavior of an organism is called its phenotype. These traits come from the interaction of its genotype with the environment. As a result, not every aspect of an organism’s phenotype is inherited. Suntanned skin results from the interaction between a person’s genotype and sunlight; thus, suntans are not passed on to people’s children.

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However, people have different responses to sunlight, arising from differences in their genotype; a striking example is individuals with the inherited trait of albinism, who do not tan and are highly sensitive to sunburn.  Heritable traits are propagated between generations via DNA, a molecule which is capable of encoding genetic information. DNA is a polymer composed of four types of bases. The sequence of bases along a particular DNA molecule specify the genetic information, in a manner akin to a sequence of letters specifying a text or a sequence of bits specifying a computer program. Portions of a DNA molecule that specify a single functional unit are called genes; different genes have different sequences of bases. Within cells), the long strands of DNA associate with proteins to form condensed structures called chromosomes. A specific location within a chromosome is known as a locus). If the DNA sequence at a locus varies between individuals, the different forms of this sequence are called alleles.

DNA sequences can change through mutations, producing new alleles. If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism. However, while this simple correspondence between an allele and a trait works in some cases, most traits are more complex and are controlled by multiple interacting genes.  An individual organism’s phenotype results from both its genotype and the influence from the environment it has lived in. A substantial part of the variation in phenotypes in a population is caused by the differences between their genotypes. The modern evolutionary synthesis defines evolution as the change over time in this genetic variation. The frequency of one particular allele will fluctuate, becoming more or less prevalent relative to other forms of that gene. Evolutionary forces act by driving these changes in allele frequency in one direction or another. Variation disappears when an allele reaches the point of fixation)  when it either disappears from the population or replaces the ancestral allele entirely.

Variation comes from mutations in genetic material, migration between populations (gene flow), and the reshuffling of genes through sexual reproduction. Variation also comes from exchanges of genes between different species; for example, through horizontal gene transfer in bacteria, and hybridization) in plants. Despite the constant introduction of variation through these processes, most of the genome of a species is identical in all individuals of that species. However, even relatively small changes in genotype can lead to dramatic changes in phenotype: chimpanzees and humans differ in only about 5% of their genomes.  Genetic variation comes from random mutations that occur in the genomes of organisms. Mutations are changes in the DNA sequence of a cell’s genome and are caused by radiation, viruses, transposons and mutagenic chemicals, as well as errors that occur during meiosis or DNA replication. These mutagens produce several different types of change in DNA sequences; these can either have no effect, alter the product of a gene, or prevent the gene from functioning.

Studies in the fly _Drosophila _melanogaster suggest that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70 percent of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial. Due to the damaging effects that mutations can have on cells, organisms have evolved mechanisms such as DNA repair to remove mutations. Therefore, the optimal mutation rate for a species is a trade-off between costs of a high mutation rate, such as deleterious mutations, and the metabolic costs of maintaining systems to reduce the mutation rate, such as DNA repair enzymes.[Some species such as retroviruses have such high mutation rates that most of their offspring will possess a mutated gene.

Such rapid mutation may have been selected so that these viruses can constantly and rapidly evolve, and thus evade the responses of the human immune system. Mutations can involve large sections of DNA becoming duplicated, which is a major source of raw material for evolving new genes, with tens to hundreds of genes duplicated in animal genomes every million years. Most genes belong to larger families of genes of shared ancestry).

Novel genes are produced by several methods, commonly through the duplication and mutation of an ancestral gene, or by recombining parts of different genes to form new combinations with new functions. For example, the human eye uses four genes to make structures that sense light: three for color vision and one for night vision; all four arose from a single ancestral gene. An advantage of duplicating a gene (or even an entire genome) is that overlapping or redundant functions) in multiple genes allows alleles to be retained that would otherwise be harmful, thus increasing genetic diversity.  Sequences of DNA that can move about the genome, such as transposons, make up a major fraction of the genetic material of plants and animals, and may have been important in the evolution of genomes. For example, more than a million copies of the Alu sequence are present in the human genome, and these sequences have now been recruited to perform functions such as regulating gene expression.

Another effect of these mobile DNA sequences is that when they move within a genome, they can mutate or delete existing genes and thereby produce genetic diversity.  Natural Selection is the process by which genetic mutations that enhance reproduction become, and remain, more common in successive generations of a population. It has often been called a “self-evident” mechanism because it necessarily follows from three simple facts: Heritable variation exists within populations of organisms. Organisms produce more offspring than can survive. These offspring vary in their ability to survive and reproduce. These conditions produce competition between organisms for survival and reproduction. Consequently, organisms with traits that give them an advantage over their competitors pass these advantageous traits on, while traits that do not confer an advantage are not passed on to the next generation.

The central concept of natural selection is the evolutionary fitness) of an organism. This measures the organism’s genetic contribution to the next generation. However, this is not the same as the total number of offspring: instead fitness measures the proportion of subsequent generations that carry an organism’s genes. Consequently, if an allele increases fitness more than the other alleles of that gene, then with each generation this allele will become more common within the population. These traits are said to be “selected for”. Examples of traits that can increase fitness are enhanced survival, and increased fecundity. Conversely, the lower fitness caused by having a less beneficial or deleterious allele results in this allele becoming rarer they are “selected against”. Importantly, the fitness of an allele is not a fixed characteristic, if the environment changes, previously neutral or harmful traits may become beneficial and previously beneficial traits become harmful.

Natural selection within a population for a trait that can vary across a range of values, such as height, can be categorized into three different types. The first is directional selection, which is a shift in the average value of a trait over time  for example organisms slowly getting taller. Secondly, disruptive selection is selection for extreme trait values and often results in two different values becoming most common, with selection against the average value. This would be when either short or tall organisms had an advantage, but not those of medium height. Finally, in stabilizing selection there is selection against extreme trait values on both ends, which causes a decrease in variance around the average value. This would, for example, cause organisms to slowly become all the same height.

A special case of natural selection is sexual selection, which is selection for any trait that increases mating success by increasing the attractiveness of an organism to potential mates.[58] Traits that evolved through sexual selection are particularly prominent in males of some animal species, despite traits such as cumbersome antlers, mating calls or bright colors that attract predators, decreasing the survival of individual males. This survival disadvantage is balanced by higher reproductive success in males that show these hard to fake, sexually selected traits.  An active area of research is the unit of selection, with natural selection being proposed to work at the level of genes, cells, individual organisms, groups of organisms and even species. None of these models are mutually exclusive and selection may act on multiple levels simultaneously. Below the level of the individual, genes called transposons try to copy themselves throughout the genome. Selection at a level above the individual, such as group selection, may allow the evolution of co-operation, as discussed below.

Genetic drift is the change in allele frequency from one generation to the next that occurs because alleles in offspring are a random sample) of those in the parents, as well as from the role that chance plays in determining whether a given individual will survive and reproduce. In mathematical terms, alleles are subject to sampling error. As a result, when selective forces are absent or relatively weak, allele frequencies tend to “drift” upward or downward randomly (in a random walk). This drift halts when an allele eventually becomes fixed), either by disappearing from the population, or replacing the other alleles entirely. Genetic drift may therefore eliminate some alleles from a population due to chance alone. Even in the absence of selective forces, genetic drift can cause two separate populations which began with the same genetic structure to drift apart into two divergent populations with different sets of alleles.

The time for an allele to become fixed by genetic drift depends on population size, with fixation occurring more rapidly in smaller populations. The precise measure of populations that is important here is called the effective population size, which was defined by Sewall Wright as a theoretical number representing the number of breeding individuals that would exhibit the same observed degree of inbreeding.  Although natural selection is responsible for adaptation, the relative importance of the two forces of natural selection and genetic drift in driving evolutionary change in general is an area of current research in evolutionary biology. These investigations were prompted by the neutral theory of molecular evolution, which proposed that most evolutionary changes are the result of the fixation of neutral mutations that do not have any immediate effects on the fitness of an organism. Hence, in this model, most genetic changes in a population are the result of constant mutation pressure and genetic drift.

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