STF1053 BIODIVERSITY

LU4

GENETIC DIVERSITY

PART I

The Evolution of Populations and BiodiversitySTF1053 BIODIVERSITY

Population GeneticsCombines Darwinian selection and Mendelian inheritancePopulation genetics is the study of genetic variation within a population - Importance of quantitative characters.In the 1940s, a comprehensive theory of evolution, called modern synthesis, was formed. Until then, many did not accept that Darwins theory of natural selection could drive evolution

Modern synthesis combined discoveries from different fields including paleontology, taxonomy, biogeography, and population genetics.It emphasizes the importance of populations as units of evolution, with natural selection as the most important mechanism of evolution, and backs up the idea of gradualism.Allele frequencies define gene pools 55Say that we have 500 flowering plants 480 with red flowers, 20 with white flowers and that the alleles express themselves by pure Mendelian inheritance.

We know: Of the red, some will be RR and some Rr; Suppose 320 red are homozygous (RR) and 160 are heterozygous (Rr). The white will be only rr.

We know there are 1000 copies of the genes for color (we know this because the plants are diploid). Thus, the allele frequencies are (in both males and females):Allele frequencies define gene pools 55 (cont.)320 x 2 (RR) + 160 x 1 (Rr) = 800 R;800/1000 = 0.8 (80%) R

160 x 1 (Rr) + 20 x 2 (rr) = 200 r; 200/1000 =0.2 (20%) rRememberA population is a localized group of individuals of the same species. A species is a group of populations whose individuals have the ability to breed and produce fertile offspring

Individuals near a population center are, on average, more closely related to one another than to members of other populations.

A populations gene pool is the total of all genes in the population at any one time

If all members of a population are homozygous for a particular allele, then the allele is fixed in the gene poolThe Hardy-Weinberg TheoremThe Hardy-Weinberg Theorem is used to describe a non-evolving population*Shuffling of alleles by meiosis and random fertilization have no effect on the overall gene pool.

* Natural populations are not expected to actually be in Hardy-Weinberg equilibrium. Deviation from H-W equilibrium usually results in evolution. Understanding a non-evolving population, helps us to understand how evolution occurs.The Hardy-Weinberg Theorem (cont.)Assumptions of the H-W Theorem:

Large population size: small populations can have chance fluctuations in allele frequencies (e.g. fire, storm)

No migration: immigrants can change the frequency of an allele by bringing in new alleles to a population

No net mutations: if alleles change from one to another, this will change the frequency of those alleles

Random mating: if certain traits are more desirable, then individuals with those traits will be selected and this will not allow for random mixing of alleles

No natural selection: If some individuals survive and reproduce at a higher rate than others, then their offspring will carry those genes and the frequency will change for the next generationHardy-Weinberg EquilibriumThe gene pool of a non-evolving population remains constant over multiple generations; i.e., the allele frequency does not change over generations of timeHardy-Weinberg Equation

where p2 = frequency of RR genotype; 2pq = frequencyof Rr plus rR genotype; q2 = frequency of rr genotypeHardy-Weinberg Equation (cont.)

Hardy-Weinberg Equation (cont.)

Hardy-Weinberg Equation (cont.)But we know that evolution does occur within populations. What causes it?

Microevolution refers to changes in allele frequencies in a gene pool from generation to generation. Represents a gradual change in a population.Causes of microevolutionGenetic driftGenetic drift is the alteration of the gene pool of a small population due to chance.

Causes of microevolution (cont.)Two factors may cause genetic drift:Bottleneck effect may lead to reduced genetic variability following some large disturbance that removes a large portion of the population. The surviving population often does not represent the allele frequency in the original population.

Causes of microevolution (cont.)Founder effect may lead to reduced variability when a few individuals from a large population colonize an isolated habitat (example, retinitis pigmentosa).

http://www.wnycvi.org/html/retinitis_pigmentosa.htmlCauses of microevolution (cont.)Gene flow is genetic exchange due to the migration of fertile individuals or gametes between populations.

Causes of microevolution (cont.)Mutation is a change in an organisms DNA and is represented by changing alleles.

Mutations can be transmitted in gametes to offspring, and immediately affect the composition of the gene pool.Natural SelectionGenetic (heritable) variation exists within and between populations. Exists both as what we can see (e.g. eye color) and what we cannot see (e.g. blood type).

Remember, not everything that we see is due to the genotype, the environment can alter an individuals phenotypeNatural Selection (cont.)

Map butterflies (color changes are due to seasonal difference in hormones)

Variation within populationsMost variations occur as quantitative characters (e.g. height) that vary along a continuum usually indicating polygenic inheritance. Few variations are discrete (e.g. red versus white flower color)

Polymorphism is the existence of two or more forms of a character, in high frequencies, within a population. This applies only to discrete characters. An example would be the red versus white flower color.Variation between populationsGeographic variations are differences between gene pools due to environmental factors. Natural selection may contribute to geographic variation. It often occurs when populations are located in different areas, but may also occur in populations with isolated individualsHow is genetic variation preserved?Diploidy often hides genetic variation from selection in the form of recessive alleles (i.e. the dominant allele is expressed and the recessive allele can be maintained as a silent gene.)

Dominant alleles hide recessive alleles in heterozygotes.How is genetic variation preserved? (cont.)Balanced polymorphism is the ability of natural selection to maintain stable frequencies of at least two phenotypes. Includes:

Heterozygote advantage is one example of a balanced polymorphism, where the heterozygote has greater survival and reproductive success than either homozygote (Example: Sickle cell anemia where heterozygotes are resistant to malaria)How is genetic variation preserved? (cont.)Neutral variation is genetic variation that results in no competitive advantage to any individualExample: human fingerprints

How is genetic variation preserved? (cont.)A Closer Look at Natural Selection as the Mechanism of Adaptive EvolutionNatural Selection increases the frequencies of certain alleles over a period of time that includes many generations. The way that natural selection works is two folds:

Evolutionary (Darwinian) fitness Contribution of an individual to the gene pool, relative to the contributions of other individuals: the number of offspring may be greater or less than the number of offspring produced by others..

Relative fitnessContribution of a genotype to the next generation, compared to the contributions of alternative genotypes for the same locusSurvival doesnt necessarily increase relative fitness; relative fitness is zero (0) for a sterile plant or animalNatural selection maintains sexual reproductionSex generates genetic variation during meiosis and fertilization. This is the advantage of using sexual reproduction as opposed to asexual reproduction

Generation-to-generation variation may be of greatest importance to the continuation of sexual reproduction

However, there are disadvantages to using sexual reproduction. Asexual reproduction produces many more offspring.

The variation produced during meiosis greatly outweighs this disadvantage, so sexual reproduction is here to stay.Natural selection maintains sexual reproduction (cont.)

Demonstrates what happens when all individuals are female, versus half female/half male. Because males dont reproduce, the overall output is lower for sexual reproduction.

Sexual selection leads to differences between sexesSexual dimorphism is the difference in appearance between males and females of a speciesIntrasexual selection is the direct competition between members of the same sex for mates of the opposite sex. This gives rise to males most often having secondary sexual equipment such as antlers that are used in competing for females

In intersexual selection (mate choice) one sex is choosy when selecting a mate of the opposite sex. This gives rise to often amazingly sophisticated secondary sexual characteristics, e.g. peacock feathers.Sexual selection leads to differences between sexes (cont.)

LU4

GENETIC DIVERSITY

PART II

MENDEL AND THE GENE IDEASTF1053 BIODIVERSITY

Mendel and the gene idea

A. Gregor Mendels DiscoveriesMendel brought an scientific and mathematical approach to studying heredity this is the field of Genetics.

He studied peas. Why?Peas have a variety of characters that were easily studied. Characters are heritable features (eg. Flower color). Each variant of a character is called a trait (eg. Purple or white flower).

Some selected traits used by Mendel were: flower color, seed color, seed shape, and stem length.Gregor Mendels Discoveries (cont.)

Gregor Mendels Discoveries (cont.)Mendel was extremely lucky in choosing the pea plant with which to work. This is because, the pea plant traits that he studied are all discontinuous traits.

This means that they are either one way or the other, there is no in between. For example, pea plants have either purple or white flowers; smooth or wrinkled seeds. These traits have no gradations.

This is important, because it allowed Mendel to discern how traits are passed from one generation to the next. There are many traits that have gradations.

One example is the carnation flowers colors

Gregor Mendels Discoveries (cont.)There were other reasons that Mendel used pea plants:

Stamens (male reproductive organs) could be removed to control mating. (There would be no self-fertilization.) Thus, he could mate male and female gametes as he chose and could control his experiments.

This was be done by taking pollen (sperm) from one plant, and adding it to the carpel (female organ) of another plant that had its stamen removed

By fertilizing plants by hand, the parents of each pea seed would be knownGregor Mendels Discoveries (cont.)

Gregor Mendels Discoveries (cont.)In addition, Mendel used only true-breeding plants. With these plants, the traits remain constant after self fertilization. (This means that the plants contain two identical genes both genes encode the same trait.)

For example, because a pea plant has only genes for white flowers, if it self-fertilizes, all the offspring will only have genes for white flowers. Thus, the trait is constant in each generation.Gregor Mendels Discoveries (cont.)For his breeding experiments, Mendel did the following in which he tracked heritable characteristics for three generations (Figure 14.3):

Produced offspring by hybridization. Hybridization is the mating of two (2) true-breeding individuals.True-breeding parents are called the P generation.Hybrid offspring are called the F1 generation.He then allowed the F1 generation to self-pollinate, the offspring of this group are called the F2 generation.

Note the ratio of three purple to one white flower!!Gregor Mendels Discoveries (cont.)

#Note the ratio of three purple to one white flower!!Gregor Mendels Discoveries (cont.)By observing those three generations, Mendel laid the foundation for two important principles:

Law of SegregationLaw of Independent Assortment

There are multiple versions of the same gene (each version is a different allele

Each organism inherits two (2) alleles for each character; one allele from each parent.

If the two alleles are different, then the dominant allele is fully expressed; the recessive allele has no noticeable effect on the organisms appearance

The two alleles for each character separate during gamete production (Occurs during meiosis) - SegregationLaw of SegregationLaw of Segregation (cont.)A Punnett Square is a device for predicting the results of a genetic cross between two individuals of known genotypes. It is used to illustrate the 3:1 ratio that Mendel observed in the F2 generation.

Homozygous: contains identical alleles for a characterHeterozygous: contains two different alleles for a characterPhenotype: an organisms traitsGenotype: an organisms genetic makeupPunnett Square

Punnett Square (cont.)

Ratio 1:2:1Ratio 3:1

Punnett Square (cont.)One of the things we can do with a Punnett Square is to devise a way to reveal the genotype of an unknown organism. This is done by doing a Testcross

By breeding an organism of unknown genotype with an organism with a homozygous recessive individual, we can determine the genotype of the unknown individual. The ratio of phenotypes in the offspring is used to determine unknown genotypeTestcross

Law of Independent AssortmentMendel did his experiments by following only a single character at a time. Instead, one can follow two characters at a time, to demonstrate the Law of Independent Assortment

Each allele pair segregates independently from other allele pairs during gamete formation

These experiments use whats called a dihybrid cross

Dihybrid Cross

#Note that the combination of two traits gives a 9:3:3:1 ratio!

Extending Mendelian GeneticsThere are many factors that make genetics not as straight forward as Mendel saw. These include:Incomplete dominanceDominance vs. co-dominanceMultiple allelesPleiotropyEpistasisPolygenic inheritanceEnvironmental impact on gene expression

Incomplete DominanceF1 hybrids have a phenotype somewhere in between the phenotypes of the two parents.

Incomplete dominance in snapdragon color

Dominance vs. co-dominanceBoth alleles are equally expressed. Example: Tay-Sachs disease

Homozygous recessive do not produce an enzyme to metabolize lipids that accumulate in brain cells, which causes the cells to die.

Heterozygotes produce the enzyme but only at half the amount produced in homozygous dominants. You dont see the symptom of the disease, because half the normal amount of enzyme is sufficientMultiple AllelesMost genes have more than two (2) alleles. Example: Blood type = A; B; AB; O

PleiotropyMost genes affect an organism in many ways; they dont affect just one phenotypic character. Example The many effects of sickle cell anemia

EpistasisOne gene affects the expression of another gene

An example of epistasis. In this case, the gene for color is B where BB = black, and bb = brown. But a second gene, C, determines whether pigment can be produced. C allows for pigment to be produced, c does not allow pigment to be produced (albino).

Polygenic InheritanceTwo or more genes affect one phenotypic character; the opposite of pleiotropy. These are called quantitative characters. Example, skin color, where three genes impart color.

A simplified model for polygenic inheritance of skin colorEnvironmental impact on gene expressionEnvironmental factors/conditions may alter gene expression.

Effect of environment on phenotype.LU4

GENETIC DIVERSITY

PART III

PHYLOGENETIC RELATIONSHIP

STF1053 BIODIVERSITY

Genetic diversityGenetic diversity is a level of biodiversity that refers to the total number of genetic characteristics in the genetic makeup of a species.

Importance of genetic diversityAccording to the lead researcher in the study, Dr. Richard Lankauof, "If any one type is removed from the system, the cycle can break down, and the community becomes dominated by a single species."

Survival and AdaptationGenetic diversity plays a huge role in the survival and adaptability of a species. When a species environment changes, slight gene variations are necessary for it to adapt and survive.

A species that has a large degree of genetic diversity among its individuals will have more variations from which to choose the most fitting allele. Species that have very little genetic variation are at a great risk.

With very little gene variation within the species, healthy reproduction becomes increasingly difficult, and offspring often deal with similar problems to those of inbreedingAgricultural RelevanceWhen humans initially started farming, they used selective breeding to pass on desirable traits of the crops while omitting the undesirable ones.

Selective breeding leads to monocultures: entire farms of nearly genetically identical plants. Little to no genetic diversity makes crops extremely susceptible to widespread disease.

Bacteria morph and c change constantly. When a disease causing bacteria changes to attack a specific genetic variation, it can easily wipe out vast quantities of the species.

If the genetic variation that the bacterium is best at attacking happens to be that which humans have selectively bred to use for harvest, the entire crop will be wiped out.Agricultural Relevance (cont.)A very similar occurrence is the cause of the infamous Potato Famine in Ireland.

Since new potato plants do not come as a result of reproduction but rather from pieces of the parent plant, no genetic diversity is developed, and the entire crop is essentially a clone of one potato, it is especially susceptible to an epidemic.

In the 1840s, much of Irelands population depended on potatoes for food. They planted namely the lumper variety of potato, which was susceptible to a rot-causing mold called Phytophthora infestans.

This mold destroyed the vast majority of the potato crop, and left thousands of people to starve to death.Coping with Poor Genetic DiversityCheetahs are a threatened species. Extremely low genetic diversity and resulting poor sperm quality has made breeding and survivorship difficult for Cheetahs only about 5% of cheetahs make it to adulthood

About 10,000 years ago, all but the jubatus species of cheetahs died out. The species encountered a population bottleneck and close family relatives were forced to mate with each other, resulting in inbreeding

However, it has been recently discovered that female cheetahs can mate with more than one male per litter of cubs. They undergo induced ovulation, which means that a new egg is produced every time a female mates. By mating with multiple males, the mother increases the genetic diversity within a single litter of cubs.A population bottleneckA population bottleneck (or genetic bottleneck) is an evolutionary event in which a significant percentage of a population or species is killed or otherwise prevented from reproducing, and the population is reduced by 50% or more, often by several orders of magnitude

Population bottlenecks increase genetic drift, as the rate of drift is inversely proportional to the population size. They also increase inbreeding due to the reduced pool of possible mates

A population bottleneck (cont.)A population is the collection of interbreeding organisms of a particular species.

A population shares a particular characteristic of interest most often that of living in a given geographic area

In taxonomy population is a low-level taxonomic rank.

As commonly used , individual refers to a person or to any specific object in a collection.

A population bottleneck (cont.)Allele frequency is a measure of the relative frequency of an allele at a genetic place (locus) in a population. Usually it is expressed as a proportion or a percentage.

In population genetics, allele frequencies are used to depict the amount of genetic diversity at the individual, population, or species level.AlleleAn allele ( from the Greek allelos, meaning each other) is one member of a pair or series of different forms of a gene

Usually alleles are coding sequences.

An individual's genotype for that gene is the set of alleles it happens to possessGeneA gene is a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions.

The physical development and phenotype of organisms can be thought of as a product of genes interacting with each other and with the environmentChromosomesChromosomes are organized structures of DNA and proteins that are found in cells.

A chromosome is a singular piece of DNA, which contains many genes, regulatory elements and other nucleotide sequences.

Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.

The word chromosome comes from the Greek (chroma, color) and (soma, body) due to their property of being stained very strongly by some dyes.

Chromosomes vary extensively between different organismsDNA SequenceA DNA sequence or genetic sequence is a succession of letters representing the primary structure of a real or hypothetical DNA molecule or strand, with the capacity to carry information.

The possible letters are A, C, G, and T, representing the four nucleotide subunits of a DNA strand adenine, cytosine, guanine, thymine bases covalently linked to phospho-backbone.

In the typical case, the sequences are printed abutting one another without gaps, as in the sequence AAAGTCTGAC, going from 5' to 3' from left to right.DNA Sequence (cont.)A succession of any number of nucleotides greater than four is liable to be called a sequence. With regard to its biological function, which may depend on context, a sequence may be sense or anti-sense, and either coding or noncoding

DNA sequences can also contain junk DNA.

Sequences can be derived from the biological raw material through a process called DNA sequencing.

DNA Sequence (cont.)In some special cases, letters besides A, T, C, and G are present in a sequence.

These letters represent ambiguity. Of all the molecules sampled, there is more than one kind of nucleotide at that position. The rules of the International Union of Pure and Applied Chemistry are as follows:A = adenineC = cytosineG = guanineT = thymine