Definitions:

• Genotype: genetic make up of an organism
• Phenotype : physical traits of an organism (determined by the genotype). The phenotype is determined by the interaction of the genotype and the environment. Fig. 21.19
• Allele: particular form of a gene
• Population: a group of individuals of the same species (organisms) that live in a particular environment
• Gene pool: sum of all alleles in a population Fig. 21.3
• Genetic structure: the distribution of alleles in the individuals of a population (heterozygous, homozygous)
• Natural selection ( Darwin's main conclusions) :
  • The observation that some organisms to reproduce more successfully than others is called natural selection
  • natural selection is the result of the interaction between a population of individual organisms and the environment in which they live
  • The end product of natural selection is the successful adaptation of a population to its environment.

• Norm of reaction: range of possible phenotypes from a single genotype. The environment is the decisive factor that influences the range of phenotypes. Sometimes the norm of reaction has no breadth i.e. a given genotype demands a particular phenotype (ABO blood groups). Environments contribute to the norm of reaction. For example, the acidity of soil determines the color of hydrangea (varies from blue to pink)
  Temperature is the most predominant factor and has a strong influence on a variety of physiological processes. Body size of drosophila is controlled by temperature so is development time, stress resistance. Drosophila in regions with a cold climate have a larger body compared to species in the tropics. Simultaneously, body size exhibits phenotypic flexibility within the same population ( same genotype achieves a larger body size when completing their larval development at lower temperatures).

• Artificial selection: selection of specific traits (phenotypes) in domestic animals. ( dogs: grate dane , chiuawa)
  

  Fig. 21.4 Many different vegetables are derived from the "wild mustard " This is an example of how may different variation rose from a single gene pool

  Fig. 21.5 Genetic variation demonstrated in an Artificial Selection laboratory experiment

Number of individual alleles ( #A and #a) present in a population:
    #A = 2N_AA + N_Aa
    #a = 2N_aa + N_Aa

Total number of alleles present in a population:
# of alleles = 2N_AA + 2N_Aa + 2N_aa = 2N

Allele Frequencies:
    p = frequency of allele A     p = (2N_AA + N_Aa) / 2N
    q = frequency of allele a     q = (2N_aa + N_Aa) / 2N

The gene pool is the sum of all alleles in a population. The genetic structure of a population is determined by the arrangement of alleles into genotypes. That means, the genetic structure of two populations with the same gene pool may be different ( e.g. the frequency of homozygous could be very different between two populations).

Fig. 21.6 Example of an allele frequency calculation

Conclusions:

• p + q = 1 .     If there is one locus for two different alleles, and the frequency of one allele has been calculated, the frequency of the other allele can be obtained by subtraction (q = 1 - p).

  Populations with the same gene pool have the same allele frequencies, even though the distribution of the alleles in each population may be different ( the genotype frequencies are different).

The Hardy Weinberg equations explain why dominant alleles in a population do not replace the recessive alleles. Using the equations it is possible to determine if a population is genetically changing .
Assumptions

• population is very large
• population is isolated to avoid exchange with other populations
• individuals are mating randomly
• allele frequencies in gametes are the same as in the population
• no selective forces act on the population.

Fig. 21.7 Calculation of the Hardy Weinberg genotype frequencies

If the allele frequency from one generation to another changes, then one or more of the Hardy Weinberg assumptions must have been violated. Exposure to selective pressure (last of the Hardy Weinberg assumptions) is most common reason for a natural population to deviate from the Hardy Weinberg equilibrium. Natural habitats always exert selective pressure (competition for food, space, predation) resulting in natural selection
This leads to a definition of evolution: a change through time on an average set of characteristics of a population. This be a change in the genetic structure of a population or a change in the gene pool. The changes produce a different range of phenotypes.

Origin of Biological Variations.

• Point mutations: many altered genes will produce functional proteins
• Frame shift mutations: often produce large changes and result mostly in nonfunctioning proteins
• Macrolesions : loss of part of a chromosome ( does not produce viable orhanisms)

Mutation rate: frequency of mutation per reproductive cycle. Mutations are generally low in natural populations (Metazoans, metaphytes : 10^-5 mutations / reproductive cycle, bacteria: 10^-8 mutations / division )

Fate of mutation : most mutations are harmful and are not carried on the next generation. As a result of many million years of survival, organisms are very complex and have highly integrated systems, thus random changes are usually for the worst. Some mutations are neutral, a few may be beneficial.
: Only the organism which mutated has the mutation. Must be in the DNA of the gametes. If heterocygous, only a 50% chance of passing it on. Model calculations show that most mutations have a 37% chance to be lost. Natural selection discards harmfull mutations.

• Sexually reproducing organisms introduce genetic variation in each new generation (crossing over of chromosomes). This recombination increases phenotypic variations in a population ( more so than mutations) it does not change the frequency of alleles, however, it generates new combinations of alleles. Sexual reproduction results in better adaptation ( natural selection) to a changing environment. ( Rotifers response to variation in food supply)

  Recombination example: Consider two genes that have an influence on size.   Alleles s and l make the an individual smaller, alleles S and L make an individual larger. The following two individuals mate with each other

  female that is SlsL (maternal chromosome)  sLSl (paternal chromosome) mates with
  male that is sLSl (maternal chromosome)   SlsL (paternal chromosome)
  Possible genotype of the offspring after crossing over of the red marked alleles
  

      SLSL (maternal chromosome)   S LSL (paternal chromosome)
  Thus two average sized individuals can produce an offspring of extreme size

  sexual vs asexual reproduction: asexual reproduction is faster (more offspring in shorter time), no energy expanded in finding mate, well adapted to an environment (less genetic variation which could upset adaptation). Sexual reproduction is more successful during environmental changes, stress. Extinction rate of pathenogens is higher , however, some bacteria adapt very fast.

• immigration/emigration : Movement of new individuals into an existing population or movement of a population into a different geographical (climatic) zone.

  Genetic Drift
  In contrast to natural selection, genetic drift refers to a statistically significant change in population allele frequencies resulting from random events (and not from selection, emigration or immigration). Genetic drift can also result in the loss of alleles from a population or to the introduction of a new allele irregardless of the survival or reproductive value of the gene pairs (alleles) involved. As a random statistical effect, genetic drift can occur only in small, isolated populations in which the gene pool is small enough that chance events have a substantial effect.

  Fig. 21.8 Example of genetic drift : Bottleneck Effect (e.g. survivors of a disease)

  As a result of the Bottleneck Effect, the reduced gene pool could be significantly different from the original gene pool. For example the northern elephant seal population in California was reduced to less than 20 animals in the 1890s. The gene pool of the present population (approx. 30000 animals ) is very homogeneous. Similar African leopards are descendants of a few animals.

• The Founder Effect

  Founder Effect     When new populations are started by a small number individuals its genetic ratio than the original could be very different from the original population. For example a plant population derived from a single seed. Killer bee population in the Americas.
  Fig. 21.1 In the late 70ies probably less than 100 fruit flies (drosophila suboscura) invaded the western hemisphere.

• Biological Fitness (describes the likelihood of an individual to pass genes on to a future generation).
  This is an important mechanism to influence genetic variation. For example in colder climates certain phenotypes may be better off and reproduce more frequently. Thus reproductive success and survival, propagate phenotypes that are different , resulting in certain phenotypes (and genotypes) to become more abundant in a population. This in turn will change the allele frequency in a population. In this context linkage is also very critical. (sometimes a change in one allele affects other alleles). I case of overgrassing atilopes with a longer neck Gerenuk are biologically more fit since they can reach more green leaves
  Biological fitness does not neccessarily depend on physical fitness or winning a battle, sometimes avoiding combat is more effective means of survival.
  
  On a molecular level a mutation in a structural gene or a regulatory gene can be a critical mechanism that drives biological fitness such as the acquired resistance of a plant to a herbicide. Biological components also relate to biological fitness. Even though long tail feathers have no apparent advantage or increase survival chances, they are prevalent in male peacocks because of the female's choice of a mate.

• Components of fitness
  
  • Individual fitness ( passed on to the organisms own offspring)
    Inclusive fitness ( sum of individual fitness an components reflecting influence of individual's relatives, kin selection (in social organisms), etc.
  • the number of offspring per individual is also important (two strategies: many, non-fit oder a few very fit)

• Fitness and natural selection
  Natural selection determines the extend to with an individual contributes to offsprings of future populations. The largest contribution is done by those whose phenotype is best adapted to the environment, because the survive and can reproduce successfully. Selection occurs at phenotypic level, since the phenotype interacts with the environment . A good example of natural selection is a phenomenon that affected over 70 species of moths in England during the industrial revolution. Prior to 1800 the typical pecies of moths had light patterns. Because of the presence of environmental pollutants (soot) they changed their color to dark.

• Forms of Selection : Fig. 21.12
  • Stabilizing selection: Reduction in variance , mean state of population is preserved. Applies to most population
    Fig. 21.13 Stabilizing Selection ( add. example )

  • Directional selection: results in shift of mean state
    Evolutionary history of the horse The early ancestor of the horse was the small Hyracotherium of the early Eocene. The evolutionary changes involved changes in teeth, leg length, and toe structure

  • Disruptive selection: Bimodal distribution resulting in two different phenotypic populations.
    Fig. 21.14 Both extremes are favored at the expense of the mean variety. This is is relatively uncommon, but it can provide a modle for speciation without the need for geographic isolation.

• Selection limits the range of variation
  Selection increases the overall adaptation to an environment, but it is random with respect to future pre-adaptation (i.e. no pre-adaptation). The alleles present in a population are determined by the history of the population and its evolutionary development. Selection can occur on various levels including populations and species. (e.g. social insects). Selection affects strongly features that are directly linked to growth and reproduction. Selection is a directed force, it is non random (unlike mutations) and produces non random changes in a population over time (evolution)

Classification of organisms
Organisms can be divided into three major domains : Eubacteria, Archaea, Eukarya. The domains are futher divided into so called kingdoms    Fig. 1.10 .
The kingdoms include the following:

• Bacteria( the most ancient kingdom): bacteria are composed of prokaryotic organisms. They are single cell organisms, have a cell wall, and lack membrane-bound organelles.
• Archea: Archaebacteria are prokaryotic organisms but differ from bacteria in metabolism, lipid structure and habitat. Archaebacteria include methanogens, halophiles, thermophiles, acidophiles. (In earlier schemes, bacteria and archea were considered as ome kingdom : Monera)
• Protista (most ancient eukaryotic kingdom): protists include a variety of eukaryotic body (single or multi-celled ), heterotrophic or autotrophic organisms. Protists are mostly aquatic organisms: Dinoflagellates, diatoms, algea, giardia, giant kelp
• Fungi: Fungi are a eukaryotic, heterotrophic, single celled or multicellular organisms. They obtain their energy by decomposing dead and dying organisms and absorbing their nutrients from those organisms. Fungi in clude mushrooms, yeast, allomyces
• Plantae Plants are immobile, multicellular, photosynthetic eukaryotes. Cells have a cellulose containing cell wall.
• Animalia: Animals are mobile, multicellular, heterotrophic eukaryotes. Cells are lacking cell walls ( most having a cell coat).

Hierarchical Order (Linnaean System): Fig. 23.11

The Linnaean system ( Carolus Linnaeus ,1677-1705 ) of classification divides all organisms into large groups.
Within a kingom organisms are further ranked into sub-groups or taxa (Taxonomy deals with the identification and naming of organisms) and ranked in a hierarchical order. Organism are named using a species name followed by a genus name. Based on the biological description a species are individuals identical in most of their important features. They consist of an interbreeding population which is isolated from other groups.

Taxonomic classifications such as the hierarchical ranking in Fig. 23.11 is based on observable characteristics:

• External structure: skin, scales
• Internal structure: circulation system, respiration.
• The structure of the immature stages (embryo).
• Nutrition, e.g. autotrophic, heterotrophic.
• behavior

Example of how man is classified
• Kingdom : Animalia
• Phylum : Vertebrata
• Class : Mammalia
• Order : Primates
• Family : Hominidae
• Genus : Homo
• Species : sapiens

Taxonomic classifications based on observable characteristics are not very accurate A less biased taxonomic system uses similarities on the molecular level such as comparision of DNA or RNA sequences and/or amino acid sequences of proteins. The most common method to classify bacteria is based on 16SrRNA homologies. The data from such analyses can be used in phylogenic studies, e.g. establishing evolutionary relationships within a group of organisms which are descendends from a common ancestor. The data is usually represented in form of a dendrogram

Origin of Species
Evolution has a variety of meanings. The above definition " Evolution is the result of natural selection which produces non random changes in a population over time" requires that all organisms are linked via descent to a common ancestor. Evolution does not mean a better organism, populations simply adapt to their current surroundings. A phenotype that is successful at one time may be unsuccessful at another. The mechanisms which change genetic variation (mutation, natural selection, genetic drift, recombination etc.) are also the mechanism of evolution.

As mentioned earlier, species may be defined as : individuals identical in most of their important features, occupying a uniform area, and distinguishable from related groups. How do species arise ? The fossil record documents two types of speciation:

• anagenesis (standart model of evolution): is the evolution within a lineage. Gradual change of a population over long periods of time, until the descendants are so different that they are transformed into a new pecies.
• Cladogenesis: formation of two separate species from a common ancestor, by splitting the ancestral lineage. The two groups are independent of each other and do not interbreed.

Reproductive isolation is one of the causes for speciation.

• Prezygotic barrier: impedes mating
  • geographic isolation
  • temporal isolation
  • behavioral isolation
  • mechanical isolation
  • gamete isolation
• Postzygotic isolation: a zygote is formed but it is prevented from developing into an adult
  • hybrid zygote abnormality (non viable)
  • hybrid infertility or reduded viability ( e.g. mule = sterile)
• Other factors
  • Mobility: highly mobile species have higher gene flow in sub populations ) migrational birds vs snails)
  • generalists : exploid different sources of making a living . There is no strong selection pressure in different environments ( e.g. roaches)
  • Specialists: experience selection pressure when habitat changes ( Kuala bear food source: eucalyptus leaves )

Sympatric Speciation : Speciation without physical separation of the separating populations. Restrictions in gene flow may be caused by behavioral differences or genetic differences that appear within a population. Certain insects and parasites arise by host-race speciation.

• Ploidy changes : new species arise if a mutation causes the formation of a tetraploid zygote : PIC 2413 Tetraploid hybrids of Tragopogon in Washington State Fig. 23.6
• behavioral changes : new food source for Rhagoletis fruit flies

Allopatric Speciation: Speciation through physical separation of populations

• Geographic isolation : Mountain ranges, bodies of water, deserts. Geographic barriers can be created or eliminated by climatic changes. Islands are populated by founder populations which then will undergo speciation.

  Examples:

  • Palaeognathae
  • Evolution canyon

  • drosophila in Hawaii Fig. 22.4
    

  • Galapagos: Map   geology   Darwin's voyage   Origin of Species   Finches
      Galapagos finches Fig. 22.5-1   Fig. 22.5-2

  • Textbook model of allopatric separation Fig. 22.3

  • allopatric separation at the margins
    Marginal population inhabit the peripheral regions. Conditions may be different from the mean range of the population. Therefore selective pressure on a marginal population can lead to speciation.