3.7.3 Evolution may lead to speciation

Individuals within a population of a species often show a wide range of variation in their phenotypes - this is due to both genetic and environmental factors. Variation often results from a mutation and further variation results from meiosis and the random fertilisation of gametes during sexual reproduction. We need to know about a few ways in which we can get variation; genetic factors, and environmental factors.

Genetic factors:
It is important to recognise that within a population all members have the same genes. Genetic differences occur as members have different alleles of these genes. Genetic variation arises from:

• Mutations: sudden changes to genes and chromosomes. These may be passed on to the next generation.
• Meiosis: Produces new combinations of alleles before they are passed onto gametes
• Random fertilisation of gametes: Produces new combinations alleles. The offspring are therefore different to the parents. Which gamete fuses with which at fertilisation is also random adding to the variety of offspring two parents can produce.

Environmental factors:

A lot of variation is due largely to environmental influences. Environmental influences include 

 climatic conditions, pH, and food availability. These influences affect the way the organisms genes are expressed. E.g a flower might have a gene to be tall but if it grows in low light then it will not be tall, it will be short. It is important to realise that some characteristics blend into one another forming a continuum (for example, mass and height). Characteristics that display this type of variation are not controlled by a single gene but by many (polygenes). Environmental factors play a major role in determining where on the continuum an organism lies. E.g. individuals genetically predetermined to be the same height may grow to be different heights due to variations in environmental factors (such as diet). This type of variation is the product of polygenes and the environment. If we measure the heights of a large population of people and plot the number of individuals against heights on a graph we will probably obtain a bell-shaped curve known as a normal distribution curve. 

Natural selection

The environmental factors that limit the population of a species are called selection pressures. These include predation, disease, and competition. Selection pressures determine the frequency of all alleles within the gene pool (a gene pool is the total number of all the alleles of all the genes of all the individuals within a particular population at a given time). The process of evolution by mean of natural selection depends upon a number of factors:

• Organisms produce more offspring than can be supported by the available supply of food/light/space...etc
• There is genetic variety within the populations of all species
• A variety of phenotypes that selection operates against

Populations rarely increase in size at such a rate, meaning that death rates must be high. High reproductive rates have evolved in many species to ensure a sufficient large population survives to breed and produce the next generation. This compensates for a high death rate from e.g. predation, competition (for food and water), extremes of temperature, natural disasters such as earthquakes/fires, and disease. Some species have evolved lower reproductive rates and a higher degree of parental care - lower death rates that result help to maintain their population size. 

Ultimately, there are too many offspring for the available resources meaning there is intraspecific competition amongst individuals for the limited resources available. The greater the numbers of offspring the greater this competition is and the more die int he struggle to survive. These deaths are not random. It follows that in a population individuals best suited to the prevailing conditions (e.g better able to escape from predators/catch prey/obtain light/resist disease/find a mate) are more likely to survive than those less well adapted. These individuals are more likely to breed and pass off their more favourable allele combinations to the next generation which will therefore have a different allele frequency than the previous generation. The population will have evolved a combination of alleles that are better adapted to the prevailing conditions. This selection process does depend on individuals of a population being genetically different from one another.

Variation provides the potential for a population to evolve and adapt to new circumstances. Conditions change over time. Having a wide range of genetically different individuals in the population means that some will have the combination of genes needed to survive in almost any new set of circumstances. Populations sowing little individual genetic variation are often more vulnerable to new diseases and climate changes. It is also imperative that a species is capable of adapting to changes resulting from the evolution of other species (e.g if their predators become faster, they must be better adapted to hiding). All in all, the larger a population is and the more genetically varied the individuals within it the greater the chance that one/more individuals will have the combination of alleles that lead to a phenotype which is advantageous in the struggle for survival. These individuals are more likely to breed to produce offspring and pass on their more favourable allele combinations. 

So there are three types of selection that we need to know about:

• Directional selection changes the phenotypes of a population by favouring phenotypes that vary in one direction from the mean of the population. Basically, selection for one extreme phenotype.
• Within a population there is a range of genetically different individuals in respect of any one phenotype. This continuous variation forms a normal distribution curve (a bell shaped curve). This curve has a mean that represents the optimum value for the phenotypic characteristic under the existing conditions.
• If the environmental conditions change the optimum value for survival will change. Some individuals (either left or right of the mean) will pass on a combination of alleles with the new optimum for the phenotypic character. This results in the mean moving to either the left or right of its original position.
• Directional selection results in one extreme of a range of variation being selected against in favour of the other extreme/the average.
• Stabilising selection preserves the average phenotype of a population by favouring average individuals. Basically, selection against the extreme phenotypes.
• Stabilising selection tends to eliminate the extremes of the phenotype range within a population and with it the capacity for evolutionary change.
• Tends to occur where the environmental conditions are constant over a long period of time
• An example is fur length in mammalian species. Individuals with shorter fur will be advantageous hotter years because they can lose body hear more rapidly whilst individuals with longer fur will be advantageous in colder years. If the temperature is a constant 10 degrees neither extreme will be at an advantage and they will be select against those with average fur length.
• The mean is constant but there will be fewer individuals at each extreme
• Disruptive selection favours individuals with extreme phenotypes rather than hose with phenotypes around the mean of the population.
• This is the opposite of stabilising selection
• It favours extreme phenotypes at the expense of the intermediate phenotypes
• This is the most important in bringing about evolutionary change (although it is the least common form of selection).
• It might arise if temperatures alternate between extreme highs and lows in summer and winter, respectively. This might ultimately lead to two separate species of the mammal (one with long fur which is active in winter, and one with short fur which is active in summer).

Allelic frequency

We know that the gene pool is all the alleles of all the genes of all the individuals in a population at a given time. The number of times an allele occurs within a gene pool is referred to as the allelic frequency. The allelic frequency is affected by selection and selection is due to environmental factors. This in turn means that environmental changes therefore affect the probability of an allele being passed on in a population and hence the number of times it occurs within the gene pool. 

NOTE: environmental factors fo not affect the probability of a particular mutant allele arising. All they do is affect the frequency of a mutant allele that is already present in the gene pool.

Speciation

Speciation si the evolution of new species from existing ones. A species is a group of individuals that have a common ancestry and so share the same genes but different alleles and are capable of breeding to produce fertile offspring. Basically, members of a specie are reproductively separated from other species. The most important way i which new species are formed is through reproductive separation followed by genetic change due to natural selection. 

Suppose that a population becomes separated and undergoes different mutations. This will result in it becoming genetically different from the other populations. Each population of the original species will experience different selection pressures as the environment will be slightly different. Natural selection will then lead to changes in the allelic frequencies of each population. The different phenotypes each combination of alleles produces will be subject to selection pressures that will lead to each population becoming adapted to its local environment. This is called adaptive radiation and results in changes to the allele frequencies of each population. As a result of these changes to allele frequencies it is possible that  the populations would no longer be able to breed to produce fertile offspring and each population would not be a different species with its own gene pool.

Genetic drift can take place in smaller populations because the genetic diversity is less. The relatively few members possess a smaller variety of alleles than the members of a large population. As these few individuals breed the genetic diversity of the population is restricted to those few alleles in the original population. As there are only a small number of different alleles in the original population there is not an equal chance of each being passed on. Those passed on will quickly affect the whole population as their frequency is high. Any mutation to one of these alleles that is selectively favoured will also more quickly affect the whole population as its frequency will also be high. The effects of genetic drift will be greater and the population will change relatively rapidly making it more likely to develop into a separate species. In larger populations the effect of a mutant allele will be less because its frequency is less in the larger gene pool. The effects of genetic drift will be less and development into a new species is likely to be slower. 

There are two forms of speciation:

• Allopatric speciation
• Describes the form of speciation where two populations become geographically separated. This may be the result of a physical barrier between two populations which prevents them interbreeding.
• Barriers include oceans/rivers/mountain ranges/deserts
• If environmental conditions either side of the barrier vary, natural selection will influence the two populations differently and each will evolve leading to adaptations to their local conditions.
• These changes may take hundreds/thousands of generations but ultimately may lead to reproductive separation and therefore the formation of a separate species
• Sympatric speciation
• This describes the form of speciation that results within a population in the same area, leading them to become reproductively separated

Lastly, there are a few key terms we need to commit to memory regarding isolating mechanisms:

• Geographical - populations are isolated by physical barriers such as oceans/mountain ranges/rivers
• Ecological - populations inhabit different habitats within the same area and so individuals rarely meet
• Temporal - the breeding seasons of each population do not coincide so they do not interbreed
• Behavioural - mating is often preceded by courtship which is stimulated by the colour/markings of the opposite sex/the call/particular actions of a mate. Any mutation which causes variations in these patterns may prevent mating
• Mechanical - Anatomical differences may prevent mating occurring (e.g it may be physically impossible for the penis to enter the vagina)
• Gametic - the gametes may be prevented from meeting due to genetic/biochemical incompatibility
• Hybrid sterility - Hybrids formed from the fusion of gametes from different species are often sterile because they cannot produce viable gametes.

3.7.2 Populations

As we know from 3.7.4, a population is a group of organisms of the same species in a particular area at a particular time that can potentially interbreed. All the alleles of all the genes of all the individuals in a population at a given time are known as the gene pool. The number of times an allele occurs within the gene pool is referred to as the allelic frequency.

The Hardy–Weinberg principle provides a mathematical model, which predicts that allele frequencies will not change from generation to generation. The principle makes an assumption that the proportion of dominant and recessive alleles of any gene in a population is constant from one generation to the next. This can be the case if the following conditions are met:

No mutations arise

The population is isolated (there is no flow of alleles into or out of the population)

There is no selection pressure (all alleles are equally likely to be passed onto the next generation)

The population is large

Mating with the population is random

A good way of understanding the principle is to look at a gene that has two alleles, a dominant one (A) and a recessive one (b)

Let the probability of allele A = p

Let the probability of the allele a = q

We can write two equations from this. The first is: 

p + q = 1.0

This is because the probability of one plus the other must be 100% (1.0)

There are only four arrangements of the two alleles, AA + Aa + aA + aa. The probability of all four added together must equal 100% (1.0). It follows that…

p² + 2pq + q² = 1

where p is the frequency of the dominant allele and q is the frequency of the  recessive allele of the gene.

3.7.4 Populations in ecosystems

Ecology is the study of the inter-relationships between organisms and their environment. The environment includes the abotic/non-living factors (e.g rainfall and temperature, light, pH, humidity) and the biotic/living factors, (e.g. competition and predation).

Ecosystems are dynamics made up of a community and all the non-living factors of its environment. A good example is a pond as it has its own community of plants to harbor sunlight energy to supply organisms in it and nutrients (e.g nitrate/phosphate ions) are recycled within the pond. There are two main processes to consider within ecosystems:

• the flow of energy through the system
• the cycling of elements within the system

Each species within an ecosystem is made up of a group of individuals that make up a population. A population is a group of individuals of one species that  occupy the same habitat at the same time and are potentially able to interbreed. An ecosystem can only support a certain size of population - this is known as the carrying capacity and it can vary as a result of:

• the effect of abiotic factors
• interactions between organisms (e.g intraspecific and interspecific competition/predation)
• Intraspecific competition - occurs when individuals of the same species compete with one another for resources such as food/water/breeding ground. the greater the availability the larger the population can grow.
• Interspecific competition - occurs when individuals of different species compete for resources. One species will usually have a competitive advantage over the other and the population size of this species will gradually increase as the other diminishes, leading to the complete removal of the weaker species (competitive exclusion principle). The principle states that when two species are competing for limited resources the one that uses these resources most effectively will eliminate the other. 

A community is all the populations of different species living and interacting in a particular place at a particular time.

A habitat is the place where an organism normally lives and is characterized by physical conditions and other types of organism present. There can be many habitats in a single ecosystem. Within each habitat there are smaller units with their own microclimate known as microhabitats. 

An ecological niche describes how an organism fits into the environment. it refers to where an organism lives and what it does there and includes all the biotic and abiotic conditions to which an organism is adapted to survive/reproduce/maintain a viable population. No two species occupy the exact same niche. This is known as the competitive exclusion principle.

Population size

The population size is the number of individuals in a population.

It is tricky to plot the growth of microorganisms on a graph of population against time as the populations may grow rapidly. In cases such as these we can use a logarithmic scale to represent the number of bacteria.

However, population growth rate can change if limiting factors are present. For example (I am using bacterium as an example):

• As the population grows mineral ions are consumed
• The population becomes so large that bacteria at the surface prevent light reaching those at lower levels
• Other species in the pond may use bacteria as food/compete for light/minerals
• Environmental factors ,at bring limiting factors such as: Winter might bring cooler temperatures and lower light intensity/less light availability.

Over winter the population size is often fairly constant as conditions do not really change. The carrying capacity of a population that can be sustained depends on the limiting factors. Each population has optimum abiotic factors which influence it's carrying capacity for that particular ecosystem.

Predation

This occurs when an organism is consumed by another. The effect of the predator-prey relationship on population size:

• predators eat prey reducing population size of prey
• fewer prey available so predators are in greater competition for leftover prey
• predator population reduces
• with fewer predators, prey population increases
• with more prey, the predator population increases.

Investigation population

The abundance of a population is the number if individuals of a species in a given space. To measure population size we take a representative sample and use the following sampling techniques:

Non-motile organisms

• random sampling using frame quadrats or point quadrats
• A frame quadrat is a square divided by wire/string into equally sized subdividions
• A point quadrat is a horizontal bar supported by one, or two, legs. there are 10 holes at set intervals along the bar through which a long pole can be dropped and the number of species that touch each pin is recorded
• How we do this randomly is lay out two tape measures at right angles along the study area/obtain a series of coordinates from a random number generator/place a quadrat at the intersection of each pair of coordinates and record the species within it
• systematic sampling along a belt transect
• It may be more useful sometimes to measure species abundance and distribution in a systematic rather than random way e.g when there is gradual change).
• A belt transect can be made by laying tape across the ground in a straight line. A frame quadrat is laid down alongside the line and the species within it are recorded giving a record of species in a continuous belt.

Random sampling with quadrats and transects measures abundance. It can be measured in a number of ways including:

• frequency (the likelihood of the species appearing in the quadrat). It is useful for abundant species such as grass but des not give information about the quantity or detailed distribution of the species
• percentage cover (an estimate of the area within a quadrat that a species covers). It is useful when a species is hard to count. This means that data can be collected rapidly and individual plants need not be counted but is a pain when organisms overlap.

Motile organisms

• Mark-release-recapture
• A known number of animals are caught, marked, and released back into the community and some time later a number of individuals are collected again and the number of marked individuals is recorded.
• The population size can be calculated as it = ((total no. of individuals in first sample + total no. of individuals in second sample)/number of marked individuals recaptured).
• There are various assumptions that this technique relies on that we must learn:
• The proportion of marked to unmarked individuals in the second sample is the same as the proportion of marked to unmarked individuals in the population as a whole
• The marked individuals distribute themselves evenly when reintroduced
• The population has a definite boundary so there is no immigration/emigration
• There are few (if any) births/deaths in the population
• The method of marking is not toxic/will not rub off/does not make the individual more liable to predation etc

Succession

ecosystems are dynamic - they change very often (day to day) as population sizes fluctuate. The term we use to describe these changes is succession, it takes place in a series of stages. At each stage a new species colonises the area which changes the environment making it less suitable for the existing species (so the last one is outcompeted) and more suitable for more adapted species. Eventually these changes result in a less hostile environment which is easier for species to survive in.

1. The first stage is colonisation by pioneer species. These have special adaptations to live in the harsh conditions:
• asexual reproduction to allow rapid multiplication from a single organism
• vast production of wind dispersed seeds/spores to reach isolated lands
• rapid germination (no period of dormancy)
• ability to photosynthesise as other food is usually not available.
• ability to fix nitrogen from the atmosphere (as, if there is soil, it will not have much nutrients)
• tolerance to extreme conditions
2. As the pioneer species die and decompose they release sufficient nutrients to support a community of small plants, for example. As these die and new species come the environment keeps changing until the climax community contains species such as deciduous oak woodlands. This state is stable and usually lasts a long period of time.

The standard pattern for succession is as follows:

1. non-living (abiotic) environment becomes less hostile
2. a greater number and variety of habitats and niches
3. increased biodiversity
4. more complex foo webs
5. increased biomass

Secondary succession

This occurs when land that has been cleared returns to it's climax community - it usually occurs more rapidly than the above as soil already exists etc. Because the land has been altered, e.g b a forest fire, the climax community will be different.

Conservation

This is the management of the Earth's natural resources by humans. It involves managing succession in a way that prevents a change to the next stage, conserving the current stage of succession. E.g in moorland at higher land in the UK the grazing by sheep has prevented the land from reaching it's climax community. If the factor that is preventing further succession is removed then the ecosystem develops naturally into its climax community (secondary succession).

3.7.1 Inheritance

So it might be an idea to start off this topic with learning some key words...

• Genotype is the genetic constitution (make-up) of an organism
• Phenotype is the observable characteristics that results from the expression of the genotype and the environment
• A gene is a length of DNA that codes for a polypeptide chain
• An allele is one of the different forms of a gene
• The locus is the position of a gene on a chromosome. 

NOTE:
Genes can exist in two or more forms - these are the different alleles of a gene. Some genes have more than two allelic forms. If this is the case the organism is said to have multiple alleles for the character but since there are only two chromosomes in a homologous pair it follows that a maximum of two of the alleles in existence can be present in the organism (it can be one allele if it is homozygous, see below). Examples of this include the human ABO blood system. Instead of using lower and uppercase letters to represent recessive and dominant alleles of these genes, each allele is linked to a letter that represents the gene. For example, in the human blood system there are three alleles associated with the gene I. These are represented as I^A, I^B, and I^O.

There can only be one allele of a gene at each locus of any chromosome. In homologous chromosomes (these occur in diploid organisms) there are two loci each carrying one allele of a gene (one from mummy and one from daddy). If the alleles are the same (e.g blue eyes) then the organism is homozygous blue eyed. If each allele is different (e.g one for blue eyes one for brown eyes) then the organism is heterozygous for the characteristic that is expressed. Which characteristic is expressed depends on which is dominant - in this case, brown eyes are dominant over blue so the individual would be heterozygous brown eyed. If both alleles are dominant they can both be expressed in the phenotype. This is known as codominance. For example, white and red splodgy petals for a plant with an allele for red pigment and an allele for white pigment - both alleles contribute to the phenotype.

NOTE: If the allele is not dominant, it is recessive.

Genetic diagrams

Genetic crosses
These represent all the possible allele combination of the offspring - they can therefore also be used to determine the percentage chance of obtaining each outcome. However, it is very rare that the actual results of genetic crosses are the same as predicted results. These discrepancies are due to statistical error. It is pure chance that determines which gamete fuses with which gamete.

Monohybrid crosses represent only one genotype and therefore feature - e.g the alleles for eye colour. This shows how a single characteristic is passed on from parent to child. In practice many characteristics are actually inherited together. Dihybrid inheritance refers to the inheritance of two characteristics by two different genes located on different chromosomes. E.g a dihybrid cross might represent the alleles for both eye and hair colour. Since they are different genes they would have different codes - e.g the letter 'B/b' for eye colour alleles and 'E/e' for hair colour alleles. The offspring from the first generation will produce up to four types of gamete because the genes for hair colour and eye colour are situated on different chromosomes so, as the chromosomes arrange themselves at random along the equator during meiosis, any two alleles can combine with any other two alleles.


NOTE: It is important to realise in breeding, the first generation is known as the first filial (F1) whilst the second generation is known as the second filial (F2)


Sex-linkage

Females have two X sex chromosomes at pair 23, males have one X and one Y sex chromosome. Females produce the same gametes (in that they all contain an X chromosome), males produce different gametes (as in half have an X chromosome and half have a Y chromosome).

All genes carried on either X or Y chromosomes are said to be sex-linked. it is important to realise that the Y chromosome is much shorter than the X chromosome, and the X chromosome has no equivalent portion of the Y chromosome (past of it basically just isn't there). Characteristics controlled by recessive alleles on the non-homologous part of the 23rd pair chromosomes will ore frequently appear in men because there is no part on the Y chromosome that might have a dominant allele - so it must be expressed. 

Specifically, an X-linked disorder is a disorder cased by a defective gene on the X chromosome. An example is haemophilia. It is can be caused by a recessive allele with an altered DNA base sequence that codes for a faulty protein. This protein does not function but is required in the clotting process - therefore the individual cannot clot blood.

Autosomal linkage

Any two genes that occur on the same chromosome are linked - all the genes on a singe chromosome form a linkage group. The 22 chromosomes that are not sex chromosomes are known as autosomes. When there are two or more genes carried on the same autosome, it is known as an autosomal linkage.

If two genes are on different alleles, there are four possible combinations of the alleles in the gametes. If the two genes are linked there are only two possible combinations of the alleles in the gametes (provided there is no crossing over).

Epistasis

Epistasis arises when the allele of one gene affects or masks the expression of another in the phenotype. For example, say that gene 'B/b' cannot be expressed without allele A. Therefore if the organism is homozygous for ‘aa’, 'B/b' cannot be expressed.

The chi-squared test

This is used to test the null hypothesis - the null hypothesis is based on the assumption that there will be no statistically significant difference between sets of observations and any difference is due to chance alone. The chi-squared test is a means of determining whether any deviation between the observed and expected numbers in an investigation are significant or not. There are criteria:

• sample size must be relatively large (over 20)
• data must fall into discrete categories - e.g heads and tails
• only raw counts can be used - no percentages/rates etc
• is it used to compare experimental results with theoretical ones.

The formula is as follows...

In English this means chi-squared = sum of ((observed numbers - expected numbers)^2/expected numbers)

Next we read the obtained value off the chi-squared distribution table to determine whether or not any deviation (from the expected values) is significant. we need to know the number of degrees of freedom to do this. This is the number of classes minus 1.

In the chi-squared test the critical value is p=0.05 (5%). Read off from the degree of freedom to the critical value. If your figure is equal to or greater than p=0.05 then the deviation is not significant and the null hypothesis is accepted and we can assume that the results are due to chance. If the deviation is less than p=0.05 the null hypothesis is rejected as there is another factor other than chance that is affecting the results basically. 

The chi-squared test can be used in genetics to determine whether the difference in expected and obtained values for ratios of gametes of offspring were due to chance or another factor. The null hypothesis will state that there is no difference between the observed and expected results.