Classification

The main taxonomic groups 

Domain- the largest taxonomic grouping

Kingdom- the classification catergory smaller than domains

Phylum- a group of classes that all share common characteristics

Class- a group of orders that all share common characteristics 

Order- a group of families that all share common characteristics 

Family- a group of genera that all share common characteristics 

Genus- a group of species that all share common characteristics 

Species- a group of closely related organisms that are capable of interbreeding to produce fertile offsping

(Please Cool Off, For Goodness Sake!)

Kingdoms 

1. Prokaryotae

• Example- bacteria
• Prokaryotes, unicellular, no nucleus 

2. Protoctista

• Example-algae, protozoa
• Eukaryotic cells, usually live in water, single-celled

3. Fungi

• Example- moulds, yeasts, mushrooms
• Eukaryotic, chitin cell wall, saprotrophic

Kingdoms

4. Plantae

• Examples- mosses, ferns, flowering plants
• Eukaryotic, multicellular, cell walls made of cellulose, can photosynthesise, contain chlorophyll, autotrophic (produce their own food)

5. Animalia

• Examples- nematodes, molluscs, insects, fish, reptiles, birds, mammals
• Eukaryotic, multicellular, no cell walls, heterotrophic (consume plants and animals)

6. Archaebacteria

• Examples- ancient bacteria (include extremophiles)
• Reproduce asexually

Definitions:

• A group or organisms with similar characteristics that are all potentialy capable of breeding to produce fertile offspring
• A group of organisms in which genes can flow between individuals 

Other definitions of species:

• Ecological species model- based on the ecological niche occupied by an organism. Not very robust as niche definitions vary and many species occupy more than one niche.
• Mate-recognision species model- based on unique fertilisation systems. Difficulty is that many species will mate with or cross-pollinate with other species.
• Genetics species model- based on DNA evidence. Difficult to decide how much genetic difference makes two organisms members of different species.
• Evolutionary species model- based on shared evolutionary relationships between species. There is not always a clear evolutionary pathway for a particular organism.

Limitations of species models

1. Finding the evidence- many living species have never been observed mating. Setting up a breeding programme is time-consuming, expensive and may not prove anything.

2. Plants of different but closely related species frequently interbreed and produce fertile hybrids. 

3. Many organisms do not reproduce sexually.

4. Fossil organisms cannot reproduce and do not, in most cases, have any accessible DNA, but they still need to be classified.

DNA barcodes 

• This involves looking at short genetic sequences from a part of the genome common to particular groups of organisms.
• For example, a region of mitochondrial cytochrome oxidase 1 gene, containing 648 bases, is being used as the standard barcode for most animal species.
• This region cannot be used to identify plants because it evolves too slowly in these organisms to give sufficient differences between species. 

DNA sequencing 

• The base sequences of all or part of the genome of an organism are worked out. 
• DNA sequencing leads to DNA profiling, which looks at the non-coding areas of DNA to identify patterns.
• These patterns are unique to individuals, but the similarity of patterns can be used to identify relationships between individuals and even between species 

• This can be used to separate DNA and RNA fragments, proteins or amino acids according to their size and charge.
• For identifying DNA, the big DNA molecules are cut into fragments by restriction endonucleases. The DNA fragments are aded to a gel containing a dye which binds to the fragments in the gel and will fluoresce when placed under `UV light.
• A dye is also added which moves through the gel slightly faster than DNA so that the current can be turned off before all the samples run off at the end 
• An electric current is passed through the apparatus and the DNA fragments move towards the positive anode, because of their negative charge on the phosphate groups in the DNA.
• The fragments move at different rates depending on their mass and charge.
• Once the electrophoresis is completed, the plate is placed under UV light and the DNA fluoresces and shows up clearly so the pattern of the different bands can be identified.

The theory of evolution

• Living organisms that reproduce sexually show great variety in their appearance 
• Organisms produce an excess of offspring. As a result there is always a struggle for survival, a competition between members of the same species. 
• Organisms that inherit characteristics that give them an advantage in this struggle are most likely to survive and pass on the desired feature to their offspring.
• Organisms that inherit characteristics that put them at a disadvantage will be more likely to die out before they can reproduce. 
• Natural selection is the mechanism by which evolution occurs
• Evolution is a change in the genetic compostition of a population of organisms over several generations, as a result of natural selection acting upon variation, bringing about adaptations and in some cases leading to the development of new species. 

How natural selection works

1. Mutations create alternative versions of a gene (alleles)

2. This creates genetic variation between the individuals of a species (intraspecific variation)

3. A selection pressure (eg. predation, disease, competition) in the environment favours the survival of individuals with advantageous characteristics.

4. These selected individuals survive and reproduce

5. They pass on their characterstics to their offspring (inheritance)

6. Over time the allele frequency will change and over generations this can lead to evolution.

Directional selection- favours a single phenotype, so causes the allele frequency or frequency of a trait to shift in one direction over time 

Adaptation to a niche

A niche is the role of an organism within the habitat in which it lives. Organisms can be adapted to their niche in three ways:

1. Anatomical adaptations- structural features of an organism's body that increase its change of survival. For example, otters have a streamlines shape, making it easier for them to glide through the water. This makes it easier for them to catch pray and escape predators, increasing their chance of survival.

2. Behavioural adaptations- ways an organism acts that increase its chance of survival. For example, possums 'play dead' if they're being threatened by a predator to escape attack. This increases their chance of survival.

3. Physiological adaptations- processes inside an organisms body that increase its chance of survival. For example, brown bears hibernate. They lower their rate of metabolism over winter. This conserves energy, so they dont need to look for food in the months when its scarce. This increases their chance of survival.

Speciation is the formation of a new species. It occurs when populations become reproductively isolated and so there is no gene flow between the populations. 

Isolating mechanisms

• Geographical isolation- a physical barrier such as a river or mountain range separates individuals from an original population.
• Ecological isolation- two populations inhabit the same region, but develop preferences for different parts of the habitat.
• Seasonal isolation- the timing of flowering or sexual receptiveness in some parts of a population drifts away from the norm for the group. This can eventually lead to the two groups reproducing several months apart.
• Behavioural isolation- changes occur in the courtship ritual, display or mating pattern so that some animals do not recognise others as being potential mates.
• Mechanical isolation- a mutation occurs that changes the genitalia of animals, making it physically possible for them to mate successfully with only some members of the group,

Allopatric speciation

• This takes place when populations become geographically isolated.
• This leads to reproductive isolation and so there is no gene flow between the populations.
• When a species evolves in geographical isolation and is found in only one place it is said to be endemic. 

Sympatric speciation

• This takes place when populations are not geographically isolated but instead reproductively isolated.
• This may be because of: mechanical isolation (different shaped genitilia), seasonal isolation (reproductive at different times of the year), behavioural isolation (different courtship behaviour) or hybrid sterility (hybrids of two parents are infertile).
• Gene flow continues to some extent as speciation takes place

There are two main factors which need to be considered when measuring biodiversity at the species level:

1. Species richness- the number of different species in an area

2. Relative abundance- the evenness of distributions of the different species 

Measuring biodiversity

D=N(N-1)/(∑n(n-1))

D=diversity index, 

N=total number of organisms of all species

n=total number of organisms of each individual species

Ex-situ conservation 

• The conservation of components of biological diversity (living organisms) outside their natural habitat.
• It is not always possible to conserve animal species in the world because the conditions that put them under threat of extinction continue.
• Zoos and wildlife parks play an important role in animal conservation (eg. captive breeding programmes)
• There are several problems with captive breeding and reintroduction:

1. There's not enough space/sufficient resources in zoos and parks for all endangered species.

2. It is often difficult to provide the right conditions for breeding.

3. Reintroduction to the wild will be unsuccessful unless the original reason for the species being pushed to the edge of extinction is removed.

4. Animals bred in captivity may have great problems in adjusting to life in the wild.

5. When the population is small, the gene pool is reduced and this can cause problems.

In-situ conservation

• The conservation of ecosystems and natural habitats, and the maintenance and recovery of viable populations of species in their natural surroundings.
• National parks have been set up around the world to protect and conserve native species. Unfortunately poachers can be a problem in some countries.
• Strategies used are: habitat restoration and recovery, sustainable use and management of biological resources and manage recovery programmes for threatened or endangered species, which might involve ex-situ breeding programmes.

Ethical reasons for maintaining biodiversity

• If we destory the biodiversity of an ecosystem, we are denying future generations the opportunity to use these renewable natural resources.
• The natural world and biodiversity are a great source of pleasure for many people.
• If biodiversity is lost when a species becomes extinct, unique combinations of DNA are lost.