# Classification

Animals are classified into groups, and this classification is known as taxonomy. This classification is done by looking for homologous features between different organisms, looking for a similar underlying design form which the two animals evolved from. A species of creatures will have many homologous features, and have evolved from a common ancestor and are grouped into the same genus. Horses, zebras, donkeys all belong to the gene Equus. Genus is then grouped into families, that are grouped into orders, that are grouped into classes that are grouped into phylum, grouped into kingdoms. Below is the full classification of the bacterium e.coli.
This classification reflects the evolutionary history of this bacteria, all animals of the proteobacteria have a common ancestor and this evolutionary history is known as phylogeny.

## Five Kingdoms

The five kingdoms are;
* Prokaryotae
* Protoctista
* Fungi
* Plantae
* Animalia
Prokaryotes features vs the other four kingdoms are found below.
* Protoctists - simple eukaryotic organisms, many of which are unicellular, and may be autotrophic (an organism that can trap an inorganic carbon source using energy from light or from chemicals) or heterotrophic (an organism needing a supply of organic molecules as its carbon source). Most of them are aquatic or live in moist conditions such as the soil.
* Fungi - simple eukaryotic organisms that feed heterotrophically, they have cell walls but they contain materials such as chitin, no cellulose unlike plants. Some are unicellular.
* Plants - multiceulluar eukaryotic that feed via photosynthesis. They have chloroplast and walls full of cellulose.
* Animals - multiceulluar eukaryotic organisms that feed heterotrophically. No cell walls, no chloroplasts and no large sap-filled vacuoles.

# Genetic variation

Genetic variation is caused by;
* Mutation
* Random mating between organisms
* Random fertilisation
* Crossing over between chromatids of homologous chromosomes during meiosis
The last 3 of these factors reshuffle alleles within a population, giving offspring combinations which differ from their parents and from others - phenotypic variation. However, mutation can create entirely new alleles, perhaps by a mistake during DNA replication creating a new base sequence. This is likely how sickle cell anemia occurred, due to gene mutation. It takes awhile to show up because it is usually recessive (since if it is not, it usually kills the recipient before they can pass it on)
Mutations that occur in reproductive organs can pass to gametes and thus will be passed to the zygote created by two gametes.

# Overproduction

Rabbits are a prime example of how overproduction can lead to problems - they produce perhaps 50 offspring per year and if all these survive - perhaps due to lack of natural predators and a large amount of food available then their numbers will soar. In this case, 1859 Australia, after being introduced, they seriously affected the amount of food available for sheep. Usually, most of their offspring would die before they could reproduce.
Environmental factors come into play to keep their numbers down. Biotic factors are those such as predators, or just in general caused by other living organisms. Abiotic factors are non-living components, such as water supply. If the pressure of these factors is sufficiently large, then the population size will decrease.
Myxomatosis was introduced to control rabbit numbers, and was helped by the overcrowding that occurred due to their large numbers (other disease were also easily transmitted).

# Natural Selection

Not all animals are created equal. Some of the rabbits in the above section will be born with a better chance of survival, due to genetic variation. Coat colour for example, will affect whether a rabbit will survive - for example, a white coat for a rabbit living in a snow-laden area will do well, whereas a black coated one will not do well, and is likely to be quickly eaten. This is said to be a selective advantage for the white-coated rabbit, and this rabbit is much more likely to survive and pass on its genes. This is known as natural selection.

## Evolution

Most of the time, stabilising selection is the status quo - natural selection serves only to keep things the same. The things that can (and do) affect this is a new environmental factor, or a new allele. Thus, survival of the fittest.

### Changing Environments

If the environment changes, slowly or quickly, possibly in the case of global warming, those animals with thin (or no) coats of hair and good haemostasis systems will be able to survive to reproduction age, and thus the alleles that makeup these changes will be more likely to be passed on, and over time nearly all of the specie will have them.

### Allele

Random mutations usually cause the organism to die, or be less adjusted to their surroundings. However, occasionally mutations may cause a specie to have a genetic advantage, such as an allele mutation that leads to a moth having a more camouflaged body, and thus is able to blend in better with its surroundings, survive longer and thus reproduce more. An example of this exact variation occurred in London at the industrial revolution. Before the industrial revolution occurred peppered moths were mainly white with black spots as this was most effective at blending in with the lichen on the trees, however as more and more pollution was related into the air the trees became black. This meant the mainly white moths could easily be seen by the birds and picked off; the peppered moths, with the genetic mutation that meant they were mainly black, now thrived. This allele will then be passed more than the allele for the un-camouflaged wings, and thus evolution occurs. Natural selection gives some alleles a better chance of survival than others.

## Darwin-Wallace Evolution theory

This is a theory about how evolution might occur was put forward by Charles Darwin and Alfred Wallace in 1856.
* Observation 1 - Organisms produce more offspring than are needed to replace parents
* Observation 2 - Natural populations tend to remain stable in size over long periods
* Observation 3 - There is variation among the individuals of a given species
* Deduction 1 - There is a struggle for existence
* Deduction 2 - The best adapted variants will be selected for by the natural conditions at the time - natural selections. The best variants have a selective advantage.

## Examples

Below are a few examples of how selection pressures can cause changes in allele frequencies, leading to evolution.

### Antibiotic resistance

When a person takes an antibiotic to treat a bacterial infection, bacteria sensitive to it will die. But if there is a mutation, providing a resistance to the antibiotic, due to the way bacteria divide, they have a tremendous selective advantage. This bacteria becomes ten thousand million within 24 hours, all resistant to antibiotics, whilst the bacteria without the resistance are killed off. The different antibiotics we use place selection pressures on bacteria.

### Sickle Cell Anemia

Sickle cell anemia is a disease in which a allele that produces part of haemoglobin does not work correctly and causes sickling of red blood cells, and those who are homozygous (have both copies of the allele) suffer from sickle cell anemia, which usually kills them. This puts them at a selective disadvantage - they are much less likely to reproduce because they die before they can. However, in East Africa, 50% of babies are born as carriers, and 14% are homozygous.
The reason for this is that malaria is prevalent in these areas, and usually kills much earlier on than sickle cell anemia. This is relevant, since those that are heterozygous sickle cell anemia (carriers, only 1 copy) are much less likely to suffer from a serious attack of malaria than those who have two healthy alleles. Thus, the allele stays prevalent because heterozygous carriers are much more likely to survive to reproduction age as they are more likely to survive an onset of malaria.
Suggested reading: Malaria

## Artificial Selection

Artificial selection is when humans purposefully apply selection pressures to a population, such as the development of modern cattle. Since cattle have been domesticated for a long time, they have been improved by people selecting features such as docility, fast growth rates and high milk yields. This is known as selective breeding, choosing alleles conferring these features, and over generations these alleles will increase in frequency.

# Speciation

Speciation is how new species occur - something not described so far. To understand how new species are created, we must first define a species. Most biologists accept;
* A group of organisms, with similar morphological, physiological, biochemical and behavioral features, which can interbreed to produce fertile offspring, and are reproductively isolated from other species.
This section describes how two organisms can become reproductively isolated.

## Allopatric

Allopatric speciation is that which geographical isolation, that is, two groups of the same species have been separated, by a stretch of water or a forest animal being separated by areas of the forest being cut down. The group of that species in the new location find that the selection pressures are very different, resulting in different alleles being selected from. Over time, these changes affect the morphological, physiological, biochemical and behavioral features to the point where the original group cannot breed with the group in the new location. Thus, a new species is born. Speciation occurs as a result of different selection pressures that arise in the differing habitats. The result is that over time, different alleles are favoured by natural selection thus resulting in the aforementioned changes. Speciation is known to have occurred when the two new species are reproductively isolated.

## Sympatric

Sympatric speciation is the way in which new species arise without the original species being separated by a geographical barrier. The most common way this occurs is polyploidy.
A polyploid organism is one with more than two complete sets of chromosomes in its cells, and can be caused by meiosis going wrong in that one gamete is formed with two sets of chromosomes, one with none. If two such gametes fuse, the zygote gains 4 complete sets, a tetraploid. However, this tetraploid cannot breed with its diploid parent - it's gametes will be diploid, and thus if they fuse with a normal haploid gamete (such as that of its diploid parent) since there will be 3 sets of chromosomes, and no way to evenly split them. Thus, a new specie in just one generation.
An autopolyploidy, the one described above, contains 4 sets of chromosomes all from the same species. However, an allopolyploidy contains 2 from one species and two from another closely-related species. Meiosis occurs more frequently, since the chromosome sets are not identical, providing a less muddled situation than when an autopolyploidy attempts meiosis. Thus it may be able to produce many gametes and is fertile, and is once again for the same reason a new species.