Lab Practical #1

Three Domains of Life

1. Bacteria

   • Cell Type: Prokaryotic (no nucleus or membrane-bound organelles)

   • Cell Structure: Peptidoglycan cell walls

   • Genetic Material: Circular DNA, no introns in genes

   • Reproduction: Binary fission (asexual)

   • Examples: Escherichia coli, Streptococcus

   • Environment: Ubiquitous, found in soil, water, and inside organisms

2. Archaea

   • Cell Type: Prokaryotic

   • Cell Structure: Unique lipid membranes, no peptidoglycan in cell walls

   • Genetic Material: Some genes have introns, more similar to eukaryotes

   • Reproduction: Binary fission

   • Examples: Halophiles (salt-lovers), Thermophiles (heat-lovers)

   • Environment: Extreme environments (hot springs, deep-sea vents), but also normal environments

3. Eukarya

   • Cell Type: Eukaryotic (nucleus and membrane-bound organelles)

   • Cell Structure: Cellulose (plants), chitin (fungi), or none (animals, protists)

   • Genetic Material: Linear chromosomes, introns present

   • Reproduction: Asexual or sexual

   • Examples: Animals, plants, fungi, protists

   • Environment: Found in diverse habitats

Kingdoms of Eukarya

1. Protista (Protists)

   • Mostly unicellular, some multicellular (algae)

   • Can be autotrophic (photosynthetic) or heterotrophic

   • Examples: Amoeba, Paramecium, Kelp

2. Fungi

   • Mostly multicellular (except yeasts)

   • Cell walls made of chitin

   • Heterotrophic decomposers (absorb nutrients)

   • Examples: Mushrooms, Mold, Yeast

3. Plantae (Plants)

   • Multicellular and autotrophic (photosynthetic)

   • Cell walls made of cellulose

   • Examples: Mosses, Ferns, Flowering plants

4. Animalia (Animals)

   • Multicellular and heterotrophic (ingest food)

   • No cell walls, most have nervous systems

   • Examples: Insects, Mammals, Fish

Identifying the Five Kingdoms Under a Microscope

1. Kingdom Monera (Bacteria & Archaea)

   • Nucleus: ❌ No (prokaryotic)

   • Cell Wall: ✅ Yes (peptidoglycan in bacteria, different in archaea)

   • Chloroplasts: ❌ No

   • Movement: ✅ Some (flagella)

   • Examples: E. coli, Streptococcus

2. Kingdom Protista (Protists)

   • Nucleus: ✅ Yes (eukaryotic)

   • Cell Wall: ❌/✅ Some have cell walls (cellulose in algae)

   • Chloroplasts: ✅ Some (Euglena, algae)

   • Movement: ✅ Some (cilia, flagella, pseudopodia)

   • Examples: Amoeba, Paramecium, Euglena

3. Kingdom Fungi

   • Nucleus: ✅ Yes (eukaryotic)

   • Cell Wall: ✅ Yes (chitin)

   • Chloroplasts: ❌ No

   • Movement: ❌ No

   • Examples: Yeast, Bread mold

4. Kingdom Plantae (Plants)

   • Nucleus: ✅ Yes (eukaryotic)

   • Cell Wall: ✅ Yes (cellulose)

   • Chloroplasts: ✅ Yes (photosynthetic)

   • Movement: ❌ No

   • Examples: Elodea leaf cells, Onion skin cells

5. Kingdom Animalia (Animals)

   • Nucleus: ✅ Yes (eukaryotic)

   • Cell Wall: ❌ No

   • Chloroplasts: ❌ No

   • Movement: ✅ Some (muscle cells, ciliated cells)

   • Examples: Cheek cells, Muscle cells

Definitions for each term related to phylogenetics and evolutionary biology:

1. Apomorphy – A derived character state that is unique to a particular taxon or group, distinguishing it from its ancestors. Example: Feathers in birds.

2. Synapomorphy – A shared derived character found in two or more taxa that was inherited from their most recent common ancestor. It is useful in defining monophyletic groups. Example: Mammary glands in mammals.

3. Plesiomorphy – An ancestral character state that was present in a common ancestor and retained in some or all of its descendants. Example: Vertebrae in all vertebrates.

4. Symplesiomorphy – A shared ancestral character found in multiple taxa, but it does not necessarily indicate a close evolutionary relationship because it was inherited from a distant common ancestor. Example: Having four limbs in reptiles, birds, and mammals.

5. Homoplasy – A character that appears similar in different taxa but evolved independently, not due to common ancestry. This can be due to convergent evolution or parallel evolution. Example: Wings in bats and birds.

6. Ancestral Character State – The original trait present in the common ancestor of a group before any evolutionary changes occurred. Example: The presence of a tail in early vertebrates.

7. Derived Character State – A new trait that has evolved from the ancestral state, distinguishing a specific lineage. Example: The loss of a tail in great apes (humans, gorillas, chimpanzees).

8. Monophyletic Group (Clade) – A group consisting of an ancestor and all of its descendants. This is the preferred grouping in cladistics. Example: Mammals (all organisms descending from the most recent common mammalian ancestor).

9. Paraphyletic Group – A group that includes an ancestor and some, but not all, of its descendants. This often happens when a subset of descendants is excluded from classification. Example: Reptiles (excluding birds, even though birds share a common ancestor with reptiles).

10. Polyphyletic Group – A group that includes organisms from different ancestors and does not include their most recent common ancestor. These groups are based on convergent traits rather than shared ancestry. Example: Warm-blooded animals (including birds and mammals, but not their common ancestor).

    Calculating the mean and variance of a dataset

    1. Mean (Average)

    The mean is the sum of all the values divided by the number of values

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    2. Variance

    Steps to Calculate Variance:

    1. Subtract the mean from each data point.

    2. Square each result.

    3. Sum the squared differences.

    4. Divide by n for population variance or n−1 for sample variance.

Meaning of a 95% Confidence Interval (CI)

A 95% confidence interval is a statistical range that estimates where the true population parameter (e.g., mean) is likely to fall 95% of the time if we were to take multiple samples. It provides a measure of uncertainty around an estimate.

How to Interpret a 95% Confidence Interval

• Example: Suppose we calculate a 95% confidence interval for the average height of students as (165 cm, 175 cm).

  • This means we are 95% confident that the true population mean height lies between 165 cm and 175 cm.

  • If we repeatedly took samples and calculated confidence intervals, 95 out of 100 times, the true mean would be within the interval.

  • It does not mean that there is a 95% probability that the true mean is within this specific interval. The true mean is fixed, and the interval either captures it or doesn’t.

How to Interpret the ANOVA Output

Step 1: Check the p-value

• If p < 0.05 → Reject the null hypothesis → At least one group is significantly different.

• If p > 0.05 → Fail to reject the null hypothesis → No significant difference among groups.

Step 2: Check the F-statistic

• A larger F-value suggests greater differences between group means.

• The F-ratio is the variance between groups divided by the variance within groups.

Step 3: If Significant, Perform Post Hoc Tests

• ANOVA tells if there’s a difference but not where the difference is.

• Use Tukey’s HSD, Bonferroni, or Dunnett’s test to compare specific group pairs.

Stages of Meiosis and Allele Movement in Gamete Formation

Meiosis is a two-stage cell division process that produces haploid gametes (sperm & eggs) from a diploid parent cell. It ensures genetic diversity by reshuffling alleles through crossing over and independent assortment.

Meiosis I: Separation of Homologous Chromosomes

🔹 Purpose: Reduces chromosome number from diploid (2n) to haploid (n) and shuffles alleles.

1. Prophase I

• Chromosomes condense.

• Homologous chromosomes pair (synapsis) and form tetrads.

• Crossing over (recombination) occurs at chiasmata, exchanging alleles between homologous chromosomes.

• Result: New combinations of alleles (genetic variation).

2. Metaphase I

• Tetrads align randomly along the metaphase plate (independent assortment).

• Result: Different combinations of maternal and paternal chromosomes can go to each daughter cell.

3. Anaphase I

• Homologous chromosomes separate, moving to opposite poles.

• Result: Each new cell gets a mix of maternal and paternal chromosomes (allele shuffling).

4. Telophase I & Cytokinesis

• Two haploid cells form, but chromosomes are still duplicated (sister chromatids remain attached).

Meiosis II: Separation of Sister Chromatids

🔹 Purpose: Further divides cells to create haploid gametes (n).

5. Prophase II

• Chromosomes re-condense (no crossing over).

6. Metaphase II

• Chromosomes align individually at the metaphase plate.

7. Anaphase II

• Sister chromatids separate and move to opposite poles.

• Result: Each chromatid becomes an independent chromosome, ensuring only one copy of each allele per gamete.

8. Telophase II & Cytokinesis

• Four haploid gametes (sperm or eggs) form.

• Each gamete has one allele per gene and is genetically unique due to crossing over & independent assortment.

How Meiosis Relates to Allele Movement

1. Crossing Over (Prophase I) – Swaps alleles between homologous chromosomes, creating new allele combinations.

2. Independent Assortment (Metaphase I) – Random alignment of homologous pairs leads to different allele combinations in gametes.

3. Segregation of Alleles (Anaphase I & II) – Each gamete gets only one copy of each allele from each parent.

Result: Gametes are genetically unique, leading to variation in offspring when fertilization occurs

Life Cycle of Sac Fungi (Ascomycota) & Spore Types in Asci

Sac fungi (phylum Ascomycota) have a haploid-dominant life cycle with both sexual and asexual reproduction. Their defining feature is the production of ascospores inside sac-like structures called asci during sexual reproduction.

1. Asexual Reproduction (Imperfect Stage)

🔹 Occurs when conditions are favorable

• Haploid mycelium produces conidia (asexual spores) via mitosis.

• Conidia are dispersed by wind/water and germinate into new mycelia.

• No genetic recombination, only clonal propagation.

2. Sexual Reproduction (Perfect Stage)

🔹 Occurs when conditions are stressful, leading to genetic recombination

Step 1: Plasmogamy (Fusion of Cytoplasm)

• Two haploid hyphae of different mating types (+ and -) fuse, forming a dikaryotic (n + n) mycelium.

• The dikaryotic stage dominates until the fungus forms reproductive structures.

Step 2: Karyogamy (Fusion of Nuclei)

• In specialized structures (e.g., ascocarps), dikaryotic cells undergo nuclear fusion to form a diploid (2n) zygote inside an ascus (plural: asci).

Step 3: Meiosis & Spore Formation

• The diploid nucleus undergoes meiosis, producing four haploid nuclei.

• Each haploid nucleus undergoes mitosis, resulting in eight haploid ascospores inside each ascus.

Step 4: Spore Dispersal & Germination

• Ascospores are released and germinate into new haploid mycelia, completing the cycle.

How the Life Cycle Influences Spore Types in Asci

1. Asexual spores (Conidia)

   • Form outside specialized structures.

   • Produced by mitosis.

   • Genetically identical to the parent.

2. Sexual spores (Ascospores)

   • Form inside asci (unique to Ascomycota).

   • Produced by meiosis + mitosis, resulting in eight genetically diverse spores.

   • Promote genetic variation and survival under harsh conditions.

Key Takeaways

✅ Sac fungi alternate between haploid and dikaryotic stages, with a brief diploid phase.
✅ Ascospores form inside asci through sexual reproduction, ensuring genetic diversity.
✅ Conidia allow rapid asexual reproduction under favorable conditions.

Testing Cross Over Frequencies with Expected Cross Over Frequencies

1. Define the Expected Frequencies

Based on genetic mapping or Mendelian inheritance, you can predict the expected crossover frequency. For example:

• In a two-point cross, the expected crossover frequency between two genes can be derived from their genetic map distance (in cM, centimorgans). A 1 cM distance corresponds to a 1% crossover frequency.

• For genes that are unlinked, you might expect 50% crossover frequency if the genes assort independently.

2. Calculate the Expected Frequencies

• For a two-point cross, suppose you are working with two genes, A and B.

• The genetic distance between them is given (say 15 cM), which implies a 15% crossover frequency.

For a sample of 100 offspring, the expected frequencies for each genotype (if crossover occurs at 15% frequency) would be:

• Parental (no crossover): 70% of 100 = 70 offspring

• Recombinant (crossover): 30% of 100 = 30 offspring

3. Perform the Chi-Squared Test

• (Observed - Expected)²/Expected

• (O no cross over - E no cross over)²/E no cross over + (O cross over - E cross over)²/E cross over

The three main forms of natural selection are:

1. Directional Selection

• Definition: This type of selection favors one extreme phenotype over others, leading to a shift in the overall population toward that phenotype.

• Example:

  • Peppered Moths: During the industrial revolution, darker moths were favored because they were better camouflaged against soot-covered trees, whereas lighter-colored moths were more visible to predators.

• Effect: The frequency of the favored phenotype increases over time, and the population shifts in one direction.

2. Stabilizing Selection

• Definition: This type of selection favors the intermediate phenotype and eliminates the extreme phenotypes. It reduces variation in the population and maintains the status quo.

• Example:

  • Human Birth Weight: Babies with very low or very high birth weights have higher mortality rates. The optimal birth weight range for survival is intermediate, so over time, most babies are born within this optimal range.

• Effect: The population becomes more uniform, with less variation in the trait.

3. Disruptive Selection

• Definition: This type of selection favors both extreme phenotypes and selects against the intermediate phenotype. It can lead to the development of two distinct populations or phenotypes.

• Example:

  • Darwin’s Finches: On the Galápagos Islands, finches with either very large or very small beaks were better able to exploit different food sources (large seeds for large beaks, small seeds for small beaks), while those with intermediate-sized beaks were less efficient at either.

• Effect: The population can split into two distinct groups, potentially leading to speciation.

Summary:

• Directional Selection: Favors one extreme phenotype.

• Stabilizing Selection: Favors the intermediate phenotype.

• Disruptive Selection: Favors both extreme phenotypes and selects against the intermediate.

The Hardy-Weinberg Equilibrium Equation

The equation is written as:

p2+2pq+q2=1

Where:

• ppp = frequency of the dominant allele (A)

• qqq = frequency of the recessive allele (a)

• p2p^2p2 = frequency of the homozygous dominant genotype (AA)

• 2pq2pq2pq = frequency of the heterozygous genotype (Aa)

• q2q^2q2 = frequency of the homozygous recessive genotype (aa)

1. Calculating Allele Frequencies from Genotype Frequencies

If you know the genotype frequencies (AA, Aa, aa), you can calculate the allele frequencies using the following steps:

Step 1: Identify the Genotype Frequencies

Suppose you know the following genotype frequencies in a population:

• AAAAAA = 0.36

• AaAaAa = 0.48

• aaaaaa = 0.16

Step 2: Use Genotype Frequencies to Calculate Allele Frequencies

You can calculate the allele frequencies ppp (dominant) and qqq (recessive) using the following relationships:

• p2p^2p2 is the frequency of the homozygous dominant genotype (AAAAAA).

• 2pq2pq2pq is the frequency of the heterozygous genotype (AaAaAa).

• q2q^2q2 is the frequency of the homozygous recessive genotype (aaaaaa).

Since you know q2=0.16q^2 = 0.16q2=0.16 (frequency of aa), you can calculate qqq (the frequency of allele aaa):

q=0.16=0.4q = \sqrt{0.16} = 0.4q=0.16​=0.4

Now that you know qqq, you can calculate ppp using the equation:

p+q=1p + q = 1p+q=1p=1−0.4=0.6p = 1 - 0.4 = 0.6p=1−0.4=0.6

So, the allele frequencies are:

• p=0.6p = 0.6p=0.6 (frequency of allele A)

• q=0.4q = 0.4q=0.4 (frequency of allele a)

Step 3: Check the Genotype Frequencies

Now that you know ppp and qqq, you can calculate the expected genotype frequencies:

• p2=(0.6)20.36 (frequency of AA)

• 2pq=2(0.6)(0.4)=0.48 (frequency of Aa)

• q2=(0.4)2=0.16 (frequency of aa)

The expected genotype frequencies match the observed ones in this example, confirming Hardy-Weinberg equilibrium.

2. Calculating Genotype Frequencies from Allele Frequencies

If you know the allele frequencies (ppp and qqq), you can calculate the genotype frequencies using the Hardy-Weinberg equation.

Step 1: Know the Allele Frequencies

Let's say you know the following allele frequencies:

• p=0.7p = 0.7p=0.7 (dominant allele A)

• q=0.3q = 0.3q=0.3 (recessive allele a)

Step 2: Calculate the Genotype Frequencies

Using the Hardy-Weinberg equation, calculate the expected genotype frequencies:

• Homozygous dominant (AA): p2=(0.7)2=0.49

• Heterozygous (Aa): 2pq=2(0.7)(0.3)=0.42

• Homozygous recessive (aa): q2=(0.3)2=0.09

So, the expected genotype frequencies would be:

• AA = 0.49

• Aa = 0.42

• aa = 0.09

The effects of different forms of selection on genotype frequencies and allele frequencies

1. Directional Selection

• Genotype Frequencies:

  • Favors one extreme phenotype, increasing the frequency of AA or aa.

• Allele Frequencies:

  • Increases the frequency of the favored allele and decreases the frequency of the other allele.

2. Stabilizing Selection

• Genotype Frequencies:

  • Favors the intermediate phenotype, increasing the frequency of Aa.

  • Decreases the frequencies of AA and aa genotypes.

• Allele Frequencies:

  • Allele frequencies tend to stay stable, but extreme alleles (A or a) decrease in frequency.

3. Disruptive Selection

• Genotype Frequencies:

  • Favors both extreme phenotypes, increasing the frequencies of AA and aa.

  • Decreases the frequency of Aa (heterozygous intermediate phenotype).

• Allele Frequencies:

  • Increases the frequency of both extreme alleles (A and a), while decreasing the frequency of the intermediate allele (Aa).

Skull Measurements

1. Cranial Length (CL):

   • Measurement from the glabella (the smooth part of the forehead above the nose) to the occipital protuberance (the prominent bone at the back of the skull).

2. Cranial Breadth (CB):

   • The maximum distance across the skull from one side to the other, usually measured between the parietal bones (sides of the skull).

3. Facial Breadth (FB):

   • The maximum distance across the face, typically between the zygomatic bones (cheekbones).

4. Skull Length (SL):

   • The measurement from the glabella to the most posterior point of the skull, including the occipital region.

5. Foramen Magnum Distance to Back (FM):

   • The distance from the foramen magnum (the hole at the base of the skull) to the back of the skull (occipital bone).

6. Facial Projection Length (FPL):

   • The distance from the nasal aperture (opening of the nose) to the most anterior point of the face, usually measured at the maxilla.

Indices:

• cranial index = (Cranial breadth/cranial length)*100

• Skull Proportion Index = (skull length/cranial breadth)×100

• Foramen Magnum index = (FMD to back/skull length)*100

• facial projection index = (facial projection length/skull length)*100