Statistics & Data Analysis Quiz

Mendelian Genetics

• Analysis of the inheritance of physical characteristics from parent to offspring
• Also known as Transmission Genetics
• Gregor Mendel was a monk, mathematician, and gardener
• His work involved controlled breeding experiments

What do we already know about Mendelian Inheritance?

• Model Organism: Pisum sativum (garden pea)
• Effective Model Organism:
  • Short generation time
  • Multiple offspring produced per mating
  • Easy to distinguish characteristics
  • Easily controlled mating
  • Cross & self-breeding possible

Seven Characteristics Studied

• Plant height (tall vs. short)
• Flower color (purple vs. white)
• Flower position (axial vs. terminal)
• Seed (pea) color (yellow vs. green)
• Seed (pea) shape (round vs. wrinkled)
• Pod color (yellow vs. green)
• Pod shape (full vs. constricted)

Inheritance Patterns

• Simple Mendelian Inheritance:
  • Trait influenced by one gene
  • Two variants (alleles) for the gene in the population
• Monohybrid Crosses:
  • Yield a 3:1 phenotypic ratio and 1:2:1 genotypic ratio
  • Prove Law of Dominance & Law of Segregation
• Dihybrid Crosses:
  • Yield a 9:3:3:1 phenotypic ratio and 1:2:1:2:4:2:1:2:1 genotypic ratio
  • Prove Law of Independent Assortment

Review - Experiment 1A

• Parental Generation (P1): Tall (pure breeding) x Dwarf (pure breeding)
• First Filial Generation (F1): Tall
• Conclusion: The tall genetic factor is dominant to the dwarf factor. This is the Principle of Dominance.

Review - Experiment 1B

• Experiment #1B (First Filial Generation): Tall (F1) x Tall (F1)
• Second Filial Generation (F2): 75% Tall and 25% dwarf
• Conclusion: Organisms possess a pair of genetic factors for each trait, with only one member of each pair entering a gamete. During new generation formation, the paired nature is restored in offspring. This conclusion is the Principle of Segregation.
• Meiotic event causing segregation: Anaphase I – no centromere breakage, allowing haploid cells/gametes.

Review - Experiment 2

• Parental Generation (P1): Tall, Red x Dwarf, White (pure breeding)
• First Filial Generation (F1): Tall, Red
• Second Filial Generation (F2): 9-Tall, Red; 3-Tall, White; 3-Dwarf, Red; 1-Dwarf, White
• Conclusion: Each pair of genetic factors assorts independently into gametes, enhancing variation in gametes and offspring. This is the Principle of Independent Assortment.
• Meiotic event causing Independent Assortment: Random Alignment on metaphase spindle

Meiosis creates Segregation and Independent Assortment

• Anaphase I: Separation of homologous chromosome pairs without centromere breakage leads to haploid gametes, which is the source of Segregation
• Metaphase I: Random alignment of homologous pairs leads to very diverse gametes – source of Independent Assortment

Random Alignment (diagram)

• Shows two equally probable arrangements at Metaphase I leading to different chromosome combinations.

Basic Terminology

• Monohybrid Cross: A mating experiment to trace inheritance of a single trait.
• Dihybrid Cross: A mating experiment to trace inheritance of two traits simultaneously.
• Self-Cross: A genetic cross of two genetically identical organisms (for the trait under study).
• Genotype: The pair of genetic factors a organism possesses for a trait (e.g., TT, Tt, tt)
• Phenotype: The observable physical traits of a characteristic (e.g., tall or dwarf)
• Allele: A variant form of a trait (e.g., Tall (T) or dwarf(t)).
• Dominant: The allele that is observed in a hybrid organism (e.g., Tall in Tt).
• Recessive: The allele that is not observed in a hybrid organism (e.g., dwarf in Tt)
• Homozygous: The genotype in which alleles are identical (e.g., TT or tt).
• Heterozygous: The genotype in which alleles are different (e.g., Tt).
• Test-Cross: A genetic cross to determine the genotype of an organism of unknown genotype.

Solution Exercises "word problems"

• Punnett Squares: Charts illustrating genetic cross results
• Meiosis is needed for sexual reproduction
• Indicate gametes using given genotypes (example Zz yy).

Solution Exercises - Practice (example)

• Two white mice (36 white and 12 black)
• Parental genotypes for color

Extensions of Mendelian Principles

• Additional Inheritance Patterns for Single Genes
  • Incomplete Dominance and Co-dominance
  • Multiple Alleles
  • Pleiotropy
  • Incomplete Penetrance and Variable Expressivity
  • Sex Linked (X-linked & holandric)
  • Sex Limited and Sex Influenced
  • Modified Ratios and Pedigrees
  • Multiple Gene Interactions
• Epistasis
• Complementation

Incomplete Dominance

• Neither allele is truly dominant
• Heterozygotes exhibit an intermediate phenotype

Codominance

• Both alleles exhibit dominance
• Heterozygotes exhibit both alleles simultaneously

More Extensions of Mendel's Concepts

• Multiple Alleles (more than 2 variants/alleles)
• Polygenic Inheritance (characteristics controlled by combined influence of several genes)

Sickle Cell Disease

• Hemoglobin is a protein in RBC that transports O2
• HbS and HbS` alleles are codominant
• HbS HbS: typical hemoglobin & O2 transport.
• HbS HbS`: 50% typical hemoglobin; 50% reduced O2 transport.
• HbS HbS: reduced O2 transport
• HbS HbS (homozygous): Sickle Cell Disease
• HbS HbS`: Sickle Cell Trait (carriers)

Which allele is dominant?

• Depends on the phenotypic characteristic considered.
• If anemia is considered abnormal, HbA is dominant
• If phenotype blood-cell shape is considered as abnormal, incomplete dominance exists.
• If hemoglobin molecular composition is considered then codominance exists

Codominance in gene expression

• HbA and HbS alleles code for different hemoglobin forms.
• Single nucleotide difference.
• Missense mutation
• Heterozygotes produce both hemoglobin forms

Take home thoughts

• Definitions of Codominance, Incomplete Dominance and Complete Dominance.
• Interpretation of dominance based on phenotypic level (organismic, cellular, or molecular)

Blood Types

• Antigens & Antibodies
• Gene "H" makes antigen for RBC.
• Genotype produces blood types (A, B, AB, O)
• Gene "I" modifies antigen for specificity

Gene Interactions and Phenotypic Development

• Some genes are subject to environmental influences
• Developmental Genes: affect characteristic development (e.g., palate, fingers).
• Incomplete Penetrance: Less than 100% of individuals with the genotype show the phenotype.
• Variable Expressivity: The range in expression of a trait in different individuals.

Sex Limited & Sex Influenced

• If a gene is autosomal, both males and females carry genotypes
• Sex (Male vs. Female): Can inhibit some autosomal gene expression.
• Sex-limited traits: Expression restricted one sex (e.g., mammary gland development)
• Sex-influenced traits: Expression influenced by sex hormones (e.g., pattern baldness).

Epistasis

• Interaction between two non-allelic genes.
• Result of one genotype "masking/blocking" the expression of a phenotype.
• Examples of epistatic ratios are presented

Recessive Epistasis (Example)

• Shows an example of a recessive epistatic interaction with corresponding phenotypic ratios

Complementation

• Wild type vs. Mutant phenotypes: Multiple genetic sources can cause the same mutant phenotype, as occurs in the case where two different loci code for a given phenotype.
• Example of Complementation Testing with a crossing table

Extra-nuclear Inheritance

• DNA in mitochondria and chloroplasts
• Some genes (not in the nuclear genome) are expressed
• Mitochondrial inheritance (neuropathies & myopathies)
• Mitochondrial genes are involved in ATP generation

Imprinting & Epigenetics

• Imprinting: Marking a gene for cellular recognition (e.g., cytosine methylation)
• Epigenetics: Gene inactivation during gamete formation or early embryonic development, which lasts throughout the lifetime of the organism. This gene is not mutated but is not transcribed/translated; it remains though and may be functional in future generations

Sex as an Inherited Phenotype

• Sexual reproduction: Common in plants and animals, due to diversity.
• Distinguishing Male & Female members in many organisms.
• Development of organisms as either exclusively male or female mandates sexual reproduction occurence in that species.

What is Sex?

• Males have Y and Females have XX chromosomes.
• Genetic sex (XY or XX) determines the development of gonads, leading to either ovaries or testes production.

Various Mechanisms of Sex Determination

• Environmental factors such as surface where the embryo lands can determine sex (e.g., slipper limpet)

Sex Determination by External Environment

• Temperature can determine the sex of some organisms (e.g., Geckos)

Sex Determination by Ploidy and Multiple Alleles

• In honeybees, haploid organisms are males, while females are heterozygous.

Chromosomal Systems of Sex Determination

• Heteromorphic chromosomes have different compositions
• Autosomes are not involved in sex determination
• Homogametic: sex has homologous pair of sex determining chromosomes (e.g., XX females)
• Heterogametic: sex with heteromorphic (unmatched) pair of sex determining chromosomes (e.g., XY males)

Sex Determination in Drosophila melanogaster

• Ratio of X to autosomes determines sex.
• Homodimers and Heterodimers regulate genes.
• Sex-determination involves complex interactions.

Sex Determination in Mammals

• Which is more important for determining sex in humans?
• Many genes are involved, with SRY being critical for male development. Most involved genes are autosomal
• Role of X chromosome, how many genes are present, their essentiality and relationship with "femaleness".

Dosage Compensation in Mammals

• Males and females have different numbers of X chromosomes. A system balances this difference by inactivating an X chromosome in the female

Dosage Compensation in Mammals (detailed explanation)

• X inactivation specific transcript (Xist) RNA attaches to an X chromosome
• Then, the X chromosome condenses to form a Barr body

Mosaic Females

• X inactivation is believed to occur randomly in different cells, causing females to be mosaics with various X-linked trait expressions in their tissues.

X-Linked Inheritance

• X-linked recessive traits occur more often in males
• Examples: Hemophilia, Red-Green Color Blindness

Pedigree Analysis

• Study diagrams displaying family relationships and phenotypes related to a trait, for example, patterns of inheritance.

Test your understanding of key concepts in statistics and data analysis. This quiz covers topics such as data normalization, hypothesis testing, Type I errors, and data visualization methods. Perfect for students looking to reinforce their knowledge in statistical methods.