Selection and Evolution#

Variation#

有两种不同的variation：

• continuous variation - human height / mass
• discontinuous variation - ABO blood groups, albinism haemophilia

Source of variation:

• crossing over
• independent assortment
• mutation
• random mating
• random fusion of gametes (random fertilisation)

The examples of environmental factors:

• length of sunlight hours
• supply of nutrients
• availability of water
• temperature range
• oxygen level

How the environment affects the phenotype:

1. phenotype results from the interaction of genotype and environment

2. environment may limit the expression of genes

3. e.g. the mass / height differs

4. different individual experiences different environment factors

5. environment may trigger gene

   • temperature and change in animal colour
   • high temperature and gender in crocodiles
   • UV light and melanin production
   • wavelength of light and, flowering / fruit colour

6. environment effect usually greater on polygenes

7. environment may induce mutation (affecting phenotype)

The additive effect of genes: if a feature is controlled by 2 or more unlinked genes, then these genes have an additive effect:

The height of a plant is controlled by two unlinked genes H / h and T / t, these two genes have an additive effect:

• The recessive alleles h and t contribute x cm to the plants height
• The dominant alleles H and T contribute 2x cm to the plants height

The following genotypes will have the following phenotypes:

• h h t t: $x + x + x + x = 4x$ cm
• H H T T: $2x + 2x + 2x + 2x = 8x$ cm
• H h T t: $2x + x + 2x + x = 6x$ cm
• H H T t: $2x + 2x + 2x + x = 7x$ cm
• H h T T: $2x + x + 2x + 2x = 7x$ cm
• h h T t: $x + x + 2x + x = 5x$ cm
• H h t t: $2x + x + x + x = 5x$ cm

Natural Selection#

1. Overproduction of offspring

   Individuals in population have great reproductive potential, and produce many offspring.

   BUT numbers in population remain roughly constant

   Individuals have a struggle for existence and survival due to selection pressure, environmental factors act as a selection pressure and affect the chance of survival of an organism

   • Biotic environmental factors - predation, intraspecific 种内的 competition of limited resources, disease
   • Abiotic environmental factors - light availability, water supply, soil pH

2. Variation occurs

   • There is genetic variation, which is primarily caused by random mutations resulting in formation of new alleles
   • There is variation in phenotype, including discontinuous variation and continuous variation

3. Survival of the fittest

   The individuals with advantageous alleles and characteristics have selective advantage / higher fitness are more likely to survive, reproduce and pass on advantageous alleles to offspring

   On the other hand, individuals with disadvantageous alleles and characteristics die

   • Advantageous alleles and characteristics are selected for
   • Disadvantageous alleles and characteristics are selected against

4. 很长很长时间之后…

   After many generations, the frequency of advantageous alleles in the population increases, the accumulated variation results in adaptation and speciation

The importance of variation:

• make sure the individuals can survive and adapt in a changing environment

• avoid low genetic diversity

  Low genetic diversity = susceptible to disease / environmental changes

Types of natural selection:

• stabilizing selection 向同一个特征演化
• directional selection 往一个趋势演化
• disruptive selection 向不同趋势演化，并逐渐分裂成不同的物种

Stabilizing selection	Directional selection	Disruptive selection
- Intermediate phenotypes are selected for. - Both extreme phenotypes are selected against.	- One extreme phenotype range is selected for.	- Both extreme phenotypes are selected for. - Intermediate phenotypes are selected against.
- Stabilising selection keeps allele frequencies relatively constant over generations. - Things stay as they are.	- Directional selection produces a gradual change in allele frequencies over time. - This usually happens when there is a change in environment / selection pressures or a new allele has appeared in the population that is advantageous.	- Disruptive selection maintains high frequencies of two different sets of alleles and different phenotypes (polymorphism) in a population.

Examples of stabilising selection:

Examples of directional selection:

Pale and dark moth:

Selection pressure is predation by birds. The darker moths are better camouflaged 伪装 on the dark bark and are more likely to survive.

颜色和环境更加接近的会存活下来

The development of strains of antibiotic resistant bacteria (e.g. MRSA)

1. There is genetic and phenotypic variation in bacteria. A random gene mutation might cause some bacteria to become resistant to an antibiotic.
2. When the population is treated with this antibiotic (selection pressure), the resistant bacteria have a selective advantage / fitter in the environment, so they are more likely to survive and reproduce, passing on antibiotic resistance alleles to next generation
3. Those non-resistant bacteria die.
4. Frequency of antibiotic resistance alleles increases in offspring over time.
5. Over time the whole population of bacteria becomes antibiotic resistant.

Example of disruptive selection: 不同鸟的喙有不同的功能

Genetic Drift and Gene Flow#

There are 3 main mechanisms that alter / change allele frequencies in a population:

1. natural selection
2. genetic drift - founder effect and bottleneck effect
3. gene flow - migration

The Hardy-Weinbery principle#

在一个理想的大群体中，如果没有外界干扰，那么基因频率和基因型频率会一代代“原地不动”，永远保持不变。

The Hardy-Weinbery equations allow for the calculation of allele and genotype frequencies within populations.

• For alleles

  $$p + q = 1$$

  $p$: the frequency of dominant allele A

  $q$: the frequency of dominant allele a

• For grnotypes

  $$p^2 + 2pq + q^2 = 1$$

  $p^2$: homozygous dominant AA

  $2pq$: heterozygous Aa

  $q^2$: homozygous recessive aa

使用Hardy-Weinbery priciple时有五个条件：

这一般与$\chi ^2$ test一起使用，将Hardy-Weinbery principle作为null hypothesis，如果不符合$H_0$，则正在发生进化（directional selection is occurring in the population）

Artificial Selection#

对植物进行人工选择的目的

• disease resistance in food crops 免疫疾病

• increased crop yield 增加产量

  dwarf varieties less susceptible to being knocked over by weather (e.g. wind) and use more energy into seeds than height

• hardiness to weather conditions (e.g. drought tolerance) 忍受极端天气

• better tasting fruits 更好吃

• large or unusual flowers 更具观赏性

对动物进行人工选择的目的

• cows, goats and sheep that produce lots of milk or meat 产奶
• chickens that lay large eggs 更大的鸡蛋
• domestic dogs that have a gentle nature 更温顺的宠物犬
• sheep with good quality wool 更好的羊毛
• horses with fine features and a very fast pace 更优质的马匹

The process of selective breeding / artificial selection:

1. Humans select parents with desired traits to breed them together. 把“优质”的个体配在一起
2. Offspring are tested, and those offspring which have the desired traits are chosen to be bred together. 筛掉不好的个体，继续配
3. This process is repeated for man generations. 一直重复

The disadvantages of artificial selection:

• Result of inbreeding
• Not for survivial
• Not just genes controlling the desired traits are involved in the process of artificial selection, all genes of the selected organisms are involved 无法精确控制哪些优质的基因会被传递下去，所有的基因会参与到遗传中。

Artificial selection会造成inbreeding近亲繁殖，近亲繁殖的后果是：

• Frequency of desired alleles increases, homozygosity increases 好的特征能被保留

• But this leads to loss of alleles and loss of genetic variation and lowered genetic diversity. 但是会降低基因多样性

• The chance of harmful recessive alleles combining to show their effects in phenotype as homozygous increases. 有危害的recessive alleles会更容易表达出来

• This leads to loss of fitness, and loss of hybrid vigour/inbreeding depression.

Artificial selection的方式：

1. Artificial insemination

   To maximize offspring from suitable male, allows…

   • long-distance mating
   • avoid inbreeding depression.

2. Embryo transplantation

   To maximize offspring from suitable female.

The difference of artificial selection and natural selection:

Evolution#

Evolution - a process leading to speciation from pre-existing species over time

Speciation - the formation of new species

When a new species forms, it is reproductively isolated from pre-existing species

The 3 definitions of species:

1. biological species

   • a group of organisms with similar morphology and physiology
   • can breed together to produce fertile offspring
   • reproductively isolated from other species

2. morphological species

   a group of organisms that share many physical features that distinguish them from other species

3. ecological species

   a population of individuals of the same species living in the same area at the same time

Reproductive isolation可以体现在多个方面：

• individuals not recognising one another as potential mates or not responding to mating behaviour 不会把不同的物种视作交配对象
• animals being physically unable to mate 无法交配
• incompatibility of pollen and stigma in plants 同样不匹配
• inability of a male gamete to fuse with a female gamete 配子无法结合
• failure of cell division in the zygote无法细胞分裂
• non-viable offspring (offspring that soon die) 短命的后代
• viable but sterile offspring. 无法生育的后代

The theory of evolution:

1. formation of new species from pre-existing species
2. phenotype is changed
3. over many generations
4. as a result of natural selection
5. change in gene pool

There are 2 types of speciation:

1. Allopatric Speciation - caused by geographical isolation
2. Sympatric Speciation - not caused by geographical isolation

Isolation对于evolution的影响：

• 会造成allopatric speciation和sympatric speciation
• 一个是geographical isolation，一个是behavioural isolation
• 这都会阻止gene flow
• 它们会面临不同的selective pressure
• natural selection会造成change in allele frequencies, 并使gene pool发生改变
• over many generations, they are reproductively isolated

Evolutionary Relationship#

Nucleus和mitochondria中的DNA可以展示进化关系（evolutionary relationship），越相似的DNA序列，说明二者的关系越近。

How to tell evolutionary relationship

1. Obtain base sequences of DNA in two species/organisms and obtain amino acid sequences of some specific proteins in two species/organisms

   提取DNA

2. Compare base sequences of DNA and amino acid sequences of proteins in two species/organisms

   比较DNA序列

3. Based on molecular clock hypothesis which assumes a constant rate of mutation over time, the more similar the sequences are, the more closely related the two species/organisms are and the less time ago they shared a common ancestor

在mitochondria中的DNA（一般写完成$mtDNA$）比在细胞核中的DNA更适合研究evolution，因为：

• mutation在mitochondria中发生得更快
• 更容易提取 - not protected by histone
• large quantity in body
• no enzyme to repair DNA mutations
• no mixing of DNA at fertilisation, it’s only inherited from mother