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Biology Essentials Outcomes

Biology 1001: Essential Outcomes

Principles underlying evolution by natural selection

  • Mutations arise in a population randomly
    • Recombination in sexual reproduction during meiosis (crossing over)
  • If a mutation is favorable, the organism will survive and reproduce to pass on the allele
  • Over time, the frequency of this allele will rise in the population = evolution

Evidence supporting descent with modification from a common ancestor

  • Historical Biogeography
    • Studies of the world distribution of plants and animals
  • Comparative Morphology
    • Comparing anatomical structures of organisms (vestigial structures) and embryonic development similarities
  • Geology
    • Looking at fossils representing organisms

Characteristics of a scientific theory and the importance of falsifiability

  • Theories are testable hypotheses about the natural world
  • Must be falsifiable to be considered scientific
  • Must be objective, not mythical, cannot be a definition, can't be faith-based, and must be reasonably possible to test

Changes in amount of DNA throughout the cell cycle

  • G1: One copy of DNA
  • S: DNA is copied
  • G2: Two copies of DNA
  • M: prophase-metaphase (n=2, c=4) anaphase-telophase (n=2, c=2)

Main features of each stage of mitosis with respect to the cytoskeleton and the chromatin

  • Prophase
    • Chromatin condenses, nucleolus disappears, spindle (microtubules) begin forming and moving to poles, nuclear membrane breaks down
  • Pro-metaphase
    • Microtubules grow from centrosomes towards cell center, spindles attach to chromosome kinetochores
  • Metaphase
    • Spindle microtubules move chromosomes into alignment, chromosomes complete condensation
  • Anaphase
    • Sister chromatids separate and move along spindles using kinetochore motor, some spindles push each other and some pull chromosomes
  • Telophase
    • Spindle disassembles, nucleolus and nuclear envelope reappear

Cytokinesis

  • Cleavage furrow
    • Layer of microtubules stretches across spindle midpoint
    • A band of microfilaments (actin) forms in plasma membrane and tightens to squeeze off cell into two
  • Cell Plate
    • Layer of microtubules in the middle is covered in vesicles across the entire cell
    • Vesicles fuse together to make a new cell wall splitting the cell in half

Structure of a replication bubble

  • Origin of replication is in the middle
  • Replication fork unzips from this point in opposite directions
  • Leading strand (one RNA primer extended) and lagging strand (multiple RNA primers added in Okazaki fragments) for each side of the bubble
  • Linear chromosomes have many simultaneous bubbles, circular chromosomes have only one at a time

Relationship between DNA replication and metaphase chromosome structure

  • DNA has been replicated in Interphase and stays together as two sister chromatids up until Metaphase
  • Each chromosome in Metaphase contains two double helixes (extremely condensed and attached at a centromere)

Difference between DNA damage and mutation

  • Damage is a single-stranded change in the DNA
  • Mutations are any double-stranded change in the DNA sequence
  • Mutations may arise from initial damage and can be good or bad, but are necessary for evolution

Origin of various types of genomic variation

  • SNP's (Single Nucleotide Polymorphisms)
    • Caused by replication errors and tautomeric shifts
  • CNV's (Copy Number Variations)
    • Caused by uneven crossing over
  • In/Del
    • Caused by "slippage" when many of the same nitrogen base are next to each other in a sequence
  • Duplication, Inversion, Translocation, and Large Deletions
    • May occur due to ionizing radiation that creates reactive O2 that steal electrons and break chromosomes
    • Non-homologous end joining pastes the end back together and is highly mutagenic
  • Mobile elements
    • Insertion sequences, transposons, retrotransposons, and retroviruses exist and move throughout the genome
    • Cut and paste or copy and paste mechanisms without the enzyme transposase
    • Increase genetic variability

Main differences between meiosis and mitosis

  • Mitosis
    • Somatic cells
    • One cell division
    • Creates two identical diploid daughter cells
    • No crossing over/recombination
  • Meiosis
    • Gametes
    • Two cell divisions
    • Creates four genetically different daughter cells
    • Crossing over occurs in prophase I
    • Homologous pairs are separated in the first anaphase and chromatids are separated in the second anaphase

Products of meiosis in animals vs. plants, fungi, and algae

  • Animals
    • Meiosis makes haploid gametes, which fuse together at fertilization and grow into diploid organisms through mitosis
  • Plants
    • Diploid sporophytes make haploid spores using meiosis
    • Spores divide by mitosis to create gametophytes, which make gametes by mitosis
    • Gametes fuse together at fertilization to make a diploid zygote, which undergoes mitosis to return to the sporophyte stage
  • Fungi and algae
    • Diploid zygotes create haploid spores by meiosis
    • Spores divide by mitosis to make a gametophyte, which makes gametes by mitosis
    • Gametes fuse together at fertilization to return to a diploid zygote

Characteristics of homologous chromosomes

  • Carry the same genes
  • Centromeres are in the same place
  • Carry the same genes in the same place
  • Different distribution of SNP's and different types of alleles
  • Inherited from different parents

Mechanism by which recombination creates new combinations of alleles

  • Recombination occurs when homologous pairs line up one on top of the other and switch out pieces of their chromosomes at a chiasmata
  • Cutting all four backbones and pasting them to the other chromosome

Various mechanisms by which meiosis generates variation

Page 4:

  • Recombination:
    • Crossing over of the tetrads at the chiasmata creates new combinations of alleles during Prophase I.
  • Random Segregation:
    • Homologous pairs separate at Anaphase I, creating random combinations of maternal and paternal alleles.
    • Sister chromatids also separate randomly during Anaphase II.
  • Random joining of male and female gametes.
  • Segregation of various alleles during meiosis in monohybrid, dihybrid, and sex-linked situations.
  • Random Segregation:
    • Alleles segregate randomly into different haploid gametes.
  • Independent Assortment:
    • Applies to dihybrid crosses.
    • Different traits combine with each other randomly to produce combinations.
  • Sex-linked traits:
    • Linked to the X or Y chromosome.
    • Distributed differently based on offspring sex.
    • Males who inherit one X with the trait are called homozygous and express the trait.
    • Females must inherit two recessive or one dominant allele on an X to express the trait.
  • Other non-Mendelian inheritance patterns:
    • Incomplete dominance, Codominance, Epistasis, Polygenic inheritance, Pleiotropy, inactivation of one X chromosome, etc.

Page 4:

  • Conditions under which allele frequencies in a population will not change.
  • If a population is in Hardy-Weinberg equilibrium:
    • Allele frequencies in a population will not change.
  • Heterozygous advantage:
    • Allele frequencies have already leveled out.
  • Assortative mating:
    • Allele frequencies have already leveled out.
  • Hardy-Weinberg equilibrium assumptions:
    • No mutations occurring.
    • Population is closed to migration.
    • Infinite population size.
    • All genotypes are equally fit.
    • Random mating for the trait being considered.

Page 5:

  • How the dominance status of alleles affects their response to selection.
  • Selection against dominance:
    • Dominant allele disappears entirely.
  • Selection against recessive:
    • Recessive allele decreases in frequency but never completely disappears.
    • It stays hidden in the heterozygotes.
  • Heterozygote advantage:
    • Allele frequencies stabilize at 0.5, maintaining both alleles in the population.
    • Rare alleles will increase in frequency until they are no longer rare.
  • Homozygote advantage:
    • Rare alleles completely disappear.
    • Common allele goes to fixation.
    • Rare alleles are found mostly in heterozygotes, whereas common alleles are found mostly in homozygotes.

Page 5:

  • Relationship between selection and evolution.
  • Selection without evolution:
    • Occurs in heterozygote advantage after allele frequencies level out.
  • Evolution without selection:
    • Attributed to genetic drift and random mutations.
  • Calculate relative fitness from absolute fitness:
    • Absolute fitness is the average number of surviving offspring.
    • Relative fitness is calculated by dividing the absolute fitness of the genotype in question by the absolute fitness of the most successful genotype.
    • Relative fitness should be between 0 and 1.

Page 6:

  • How different types of selection and other evolutionary processes affect levels of heritable variation in a population.
  • Increases variation:
    • Gene flow, mutations.
  • Decreases variation:
    • Heterozygote disadvantage, genetic drift, selection against dominant and recessive alleles, assortative mating.
  • Maintains variation:
    • Heterozygote advantage, disassortative mating.
  • Whether or not a population is at genetic equilibrium (Hardy-Weinberg equilibrium), given observed genotype frequencies.
  • Calculate allele frequencies:
    • (# of homozygotes x 2 + # of heterozygotes) / number of organisms x 2.
    • The other allele frequency is 1 minus the calculated allele frequencies.
    • Plug the calculated allele frequencies into p^2, 2pq, and q^2.
    • If they create the same ratio of offspring, the population is in equilibrium.

Page 6:

  • Which assumptions of Hardy-Weinberg equilibrium have likely been violated, given an observed set of genotype or phenotype frequencies.
  • If lots of homozygotes, there was likely assortative mating.
  • Costs and benefits of reproducing sexually as opposed to asexually.
  • Cost of sexually reproducing:
    • Need to find a mate (could be dangerous).
    • Intrasexual selection causes males to decrease their survival fitness.
    • Males waste energy on sexual dimorphic traits.
    • Only pass on 0.5 of your alleles.
  • Cost of asexually reproducing:
    • More at risk for extinction.
    • Don't get the short-term benefits of sexual reproduction (genetic variability).
    • Fall behind in evolutionary arms race.

Page 6:

  • Why males usually compete for access to females (rather than vice versa), and why in some species this pattern is reversed.
  • Who is choosy and who competes depends on parental investment and potential fitness.
  • In most species, females have higher parental investment and lower potential fitness than males.
  • Females increase their potential fitness through quality offspring, while males increase their fitness through quantity of offspring.
  • Kin selection theory explains the persistence of helpful behavior.
  • Kin selection theory:
    • We help others that are related to us.
    • Our alleles continue to be passed on and our inclusive fitness increases.
  • Situations in which kin selection does or does not favor helping non-descendant relatives.
  • According to Hamilton's rule, kin selection favors helping non-descendant relatives when their relatedness to you multiplied by the benefit to them is greater than the cost to you (rb > c).
  • How asymmetries in relatedness can generate conflict between relatives.
  • Differences in opinion arise on when you should offer help based on the relatedness of other family members to the person in need.
  • Conditions that favor or disfavor cooperation between non-relatives.
  • Repeat interactions and the ability to recognize individuals who cooperate or cheated in the past favor cooperation.
  • One-time interactions or knowing the number of interactions favor selfishness.
  • Most recent common ancestor (MRCA) for a given group(s), given a phylogenetic tree.
  • The closest branching point shared between two groups is the MRCA.
  • Why some traditional groupings of organisms do not reflect evolutionary relationships.
  • Traditional groupings were made using morphological similarities without considering evolutionary history.
  • Relatively close and relatively distant relatives, given a phylogenetic tree.
  • Relatedness on a phylogenetic tree is determined by looking at the most recent common ancestor.

Page 7:

  • Monophyletic and non-monophyletic groupings in phylogenetic trees
    • Monophyletic groups (clades) include the MRCA and all descendants
    • Non-monophyletic groups include species from different lineages (polyphyletic) or include the ancestor but not all descendants (paraphyletic)
  • Parsimony in phylogenetic trees
    • The most parsimonious phylogeny has the least number of evolutionary changes
    • Considered correct until falsified
  • Distinction between homology and homoplasy
    • Homology: similarities due to common ancestry
    • Homoplasy: misleading similarity or dissimilarity due to convergent or divergent evolution
  • Determining the most likely phylogenetic tree
    • Look for synapomorphies (derived and shared traits)
    • Order species based on similarities to the out-group and to each other
  • Criteria used by different species concepts to define species
    • Morphological: based on physical appearance
    • Biological: based on ability to interbreed and produce fertile offspring
    • Phylogenetic: based on shared derived characteristics and evolutionary trees
  • Weaknesses/limitations of different species concepts
    • Morphological: not reliable alone, variation within species and convergent evolution
    • Biological: not applicable to asexual or extinct organisms, geographic separation
    • Phylogenetic: limited by unknown evolutionary history, may rely on morphological features

Page 8:

  • Species concept used in 'real world' examples
    • Morphological species concept used in field guides and for fossilized species
  • Why improving equipment for survival does not always lead to winning an evolutionary arms race
    • As one species evolves, the other species evolves in response
    • Improvement is necessary for survival, but not necessarily for surpassing the other species
  • Costs and benefits of being highly virulent for parasites
    • Cost: host dies sooner, unfavorable for transmission in low population density or direct contact
    • Benefit: quicker reproduction using host machinery, enhanced transmission in dense populations or indirect contact
  • How trade-offs, rapid environmental change, and arms races affect human susceptibility to disease
    • Arms race with parasites: parasites evolve quickly due to large population size and short generation times
    • Rapid environmental change: diseases of civilization, decrease in infectious diseases but increase in autoimmune disorders
    • Antagonistic pleiotropy: trade-offs between different aspects of fitness, harmful alleles kept through heterozygous advantage

Page 9:

  • Examples of proximate and ultimate explanations
    • Proximate explanation: physical and biochemical mechanisms underlying a trait
    • Ultimate explanation: role of natural selection, arms races, history, and chance in creating or continuing a trait
  • Costs and possible advantages of large brains
    • Cost: 2% of mass, 20% of energy
    • Possible advantages: utility hypothesis (survival-related skills) favored by natural selection, mating mind hypothesis (mating-related skills) favored by sexual selection

Skill Development Outcomes:

  1. Deep Learning
  • Making connections, understanding, and applying knowledge
  • Excludes memorization
  1. Serial Dilutions
  • Calculation of CFU/mL using dilution factor and volume of culture plate
  • Dilution factor calculated by dividing final volume by sample volume and multiplying by the denominator of serial dilution fractions
  1. Role of cyclin in the cell cycle
  • Cyclin regulates the rate of cell division and is important in cell cycle checkpoints
  1. Microscope calibration
  • Formula for measuring objects using stage divisions and ocular divisions
  • Calculation of magnification using ocular lens and objective lens
  1. Chi squared statistical analysis

Page 10:

  • Null Hypothesis and Alternate Hypothesis
    • Null Hypothesis states no effect/correlation/will be no change
    • Alternate Hypothesis states there is an effect/correlation/will be a change
  • Chi squared analysis
    • Determines if data is significant enough to support the alternate hypothesis
    • Compares observed values (collected in the study) with expected values (calculated based on null hypothesis)
    • Calculation: x^2 = sum of ((O-E)^2/E)
  • Degrees of freedom and critical value
    • Critical value is compared to chi-square value for statistical significance
    • Can be found on a chart or provided
  • Primary vs secondary scientific articles
    • Primary articles: original data and ideas from scientific investigations reported by scientists
    • Published in journals and contain sections like Abstract, Introduction, Methods, Results, Discussion, References
    • Secondary articles: review and analyze primary sources in more depth

Page 10 (continued):

  • FST Population Genetics
    • FST = 1 - (average heterozygosity expected within populations / heterozygosity expected across total population)
    • HS = (2p1q1 + 2p2q2)/2
    • HT = 2pTqT
    • Use Hardy-Weinberg to calculate p and q values for individual populations, then add population numbers together and recalculate for the total
    • Interpretation of FST values:
      • FST = 0: no disturbance
      • FST > 0.25: significant disturbance
      • FST = 1: complete separation of populations

Page 10 (continued):

  • Allozyme Electrophoresis for genetic variability calculation
    • Takes advantage of the fact that organisms produce allelic variants of enzymes called allozymes
    • Each allozyme has a slightly different amino acid sequence and is the product of a unique allele
    • Genotype at a gene locus coding for an enzyme can be inferred from the number and position of spots observed on gels
    • Genetic variation in a population is the average frequency of heterozygous individuals per locus
    • Calculated by determining the frequency of heterozygotes at each locus and averaging these frequencies over all loci

Page 11:

  • Creating phylogenetic trees using DNA sequencing
    • Phylogenies can be estimated by looking at differences in DNA sequence
    • Species with the most differences is the out-group
    • If no differences, it is the same species and should be drawn on the same vertical line
    • Length of horizontal lines may indicate the

Biology Essentials Outcomes

Biology 1001: Essential Outcomes

Principles underlying evolution by natural selection

  • Mutations arise in a population randomly
    • Recombination in sexual reproduction during meiosis (crossing over)
  • If a mutation is favorable, the organism will survive and reproduce to pass on the allele
  • Over time, the frequency of this allele will rise in the population = evolution

Evidence supporting descent with modification from a common ancestor

  • Historical Biogeography
    • Studies of the world distribution of plants and animals
  • Comparative Morphology
    • Comparing anatomical structures of organisms (vestigial structures) and embryonic development similarities
  • Geology
    • Looking at fossils representing organisms

Characteristics of a scientific theory and the importance of falsifiability

  • Theories are testable hypotheses about the natural world
  • Must be falsifiable to be considered scientific
  • Must be objective, not mythical, cannot be a definition, can't be faith-based, and must be reasonably possible to test

Changes in amount of DNA throughout the cell cycle

  • G1: One copy of DNA
  • S: DNA is copied
  • G2: Two copies of DNA
  • M: prophase-metaphase (n=2, c=4) anaphase-telophase (n=2, c=2)

Main features of each stage of mitosis with respect to the cytoskeleton and the chromatin

  • Prophase
    • Chromatin condenses, nucleolus disappears, spindle (microtubules) begin forming and moving to poles, nuclear membrane breaks down
  • Pro-metaphase
    • Microtubules grow from centrosomes towards cell center, spindles attach to chromosome kinetochores
  • Metaphase
    • Spindle microtubules move chromosomes into alignment, chromosomes complete condensation
  • Anaphase
    • Sister chromatids separate and move along spindles using kinetochore motor, some spindles push each other and some pull chromosomes
  • Telophase
    • Spindle disassembles, nucleolus and nuclear envelope reappear

Cytokinesis

  • Cleavage furrow
    • Layer of microtubules stretches across spindle midpoint
    • A band of microfilaments (actin) forms in plasma membrane and tightens to squeeze off cell into two
  • Cell Plate
    • Layer of microtubules in the middle is covered in vesicles across the entire cell
    • Vesicles fuse together to make a new cell wall splitting the cell in half

Structure of a replication bubble

  • Origin of replication is in the middle
  • Replication fork unzips from this point in opposite directions
  • Leading strand (one RNA primer extended) and lagging strand (multiple RNA primers added in Okazaki fragments) for each side of the bubble
  • Linear chromosomes have many simultaneous bubbles, circular chromosomes have only one at a time

Relationship between DNA replication and metaphase chromosome structure

  • DNA has been replicated in Interphase and stays together as two sister chromatids up until Metaphase
  • Each chromosome in Metaphase contains two double helixes (extremely condensed and attached at a centromere)

Difference between DNA damage and mutation

  • Damage is a single-stranded change in the DNA
  • Mutations are any double-stranded change in the DNA sequence
  • Mutations may arise from initial damage and can be good or bad, but are necessary for evolution

Origin of various types of genomic variation

  • SNP's (Single Nucleotide Polymorphisms)
    • Caused by replication errors and tautomeric shifts
  • CNV's (Copy Number Variations)
    • Caused by uneven crossing over
  • In/Del
    • Caused by "slippage" when many of the same nitrogen base are next to each other in a sequence
  • Duplication, Inversion, Translocation, and Large Deletions
    • May occur due to ionizing radiation that creates reactive O2 that steal electrons and break chromosomes
    • Non-homologous end joining pastes the end back together and is highly mutagenic
  • Mobile elements
    • Insertion sequences, transposons, retrotransposons, and retroviruses exist and move throughout the genome
    • Cut and paste or copy and paste mechanisms without the enzyme transposase
    • Increase genetic variability

Main differences between meiosis and mitosis

  • Mitosis
    • Somatic cells
    • One cell division
    • Creates two identical diploid daughter cells
    • No crossing over/recombination
  • Meiosis
    • Gametes
    • Two cell divisions
    • Creates four genetically different daughter cells
    • Crossing over occurs in prophase I
    • Homologous pairs are separated in the first anaphase and chromatids are separated in the second anaphase

Products of meiosis in animals vs. plants, fungi, and algae

  • Animals
    • Meiosis makes haploid gametes, which fuse together at fertilization and grow into diploid organisms through mitosis
  • Plants
    • Diploid sporophytes make haploid spores using meiosis
    • Spores divide by mitosis to create gametophytes, which make gametes by mitosis
    • Gametes fuse together at fertilization to make a diploid zygote, which undergoes mitosis to return to the sporophyte stage
  • Fungi and algae
    • Diploid zygotes create haploid spores by meiosis
    • Spores divide by mitosis to make a gametophyte, which makes gametes by mitosis
    • Gametes fuse together at fertilization to return to a diploid zygote

Characteristics of homologous chromosomes

  • Carry the same genes
  • Centromeres are in the same place
  • Carry the same genes in the same place
  • Different distribution of SNP's and different types of alleles
  • Inherited from different parents

Mechanism by which recombination creates new combinations of alleles

  • Recombination occurs when homologous pairs line up one on top of the other and switch out pieces of their chromosomes at a chiasmata
  • Cutting all four backbones and pasting them to the other chromosome

Various mechanisms by which meiosis generates variation

Page 4:

  • Recombination:
    • Crossing over of the tetrads at the chiasmata creates new combinations of alleles during Prophase I.
  • Random Segregation:
    • Homologous pairs separate at Anaphase I, creating random combinations of maternal and paternal alleles.
    • Sister chromatids also separate randomly during Anaphase II.
  • Random joining of male and female gametes.
  • Segregation of various alleles during meiosis in monohybrid, dihybrid, and sex-linked situations.
  • Random Segregation:
    • Alleles segregate randomly into different haploid gametes.
  • Independent Assortment:
    • Applies to dihybrid crosses.
    • Different traits combine with each other randomly to produce combinations.
  • Sex-linked traits:
    • Linked to the X or Y chromosome.
    • Distributed differently based on offspring sex.
    • Males who inherit one X with the trait are called homozygous and express the trait.
    • Females must inherit two recessive or one dominant allele on an X to express the trait.
  • Other non-Mendelian inheritance patterns:
    • Incomplete dominance, Codominance, Epistasis, Polygenic inheritance, Pleiotropy, inactivation of one X chromosome, etc.

Page 4:

  • Conditions under which allele frequencies in a population will not change.
  • If a population is in Hardy-Weinberg equilibrium:
    • Allele frequencies in a population will not change.
  • Heterozygous advantage:
    • Allele frequencies have already leveled out.
  • Assortative mating:
    • Allele frequencies have already leveled out.
  • Hardy-Weinberg equilibrium assumptions:
    • No mutations occurring.
    • Population is closed to migration.
    • Infinite population size.
    • All genotypes are equally fit.
    • Random mating for the trait being considered.

Page 5:

  • How the dominance status of alleles affects their response to selection.
  • Selection against dominance:
    • Dominant allele disappears entirely.
  • Selection against recessive:
    • Recessive allele decreases in frequency but never completely disappears.
    • It stays hidden in the heterozygotes.
  • Heterozygote advantage:
    • Allele frequencies stabilize at 0.5, maintaining both alleles in the population.
    • Rare alleles will increase in frequency until they are no longer rare.
  • Homozygote advantage:
    • Rare alleles completely disappear.
    • Common allele goes to fixation.
    • Rare alleles are found mostly in heterozygotes, whereas common alleles are found mostly in homozygotes.

Page 5:

  • Relationship between selection and evolution.
  • Selection without evolution:
    • Occurs in heterozygote advantage after allele frequencies level out.
  • Evolution without selection:
    • Attributed to genetic drift and random mutations.
  • Calculate relative fitness from absolute fitness:
    • Absolute fitness is the average number of surviving offspring.
    • Relative fitness is calculated by dividing the absolute fitness of the genotype in question by the absolute fitness of the most successful genotype.
    • Relative fitness should be between 0 and 1.

Page 6:

  • How different types of selection and other evolutionary processes affect levels of heritable variation in a population.
  • Increases variation:
    • Gene flow, mutations.
  • Decreases variation:
    • Heterozygote disadvantage, genetic drift, selection against dominant and recessive alleles, assortative mating.
  • Maintains variation:
    • Heterozygote advantage, disassortative mating.
  • Whether or not a population is at genetic equilibrium (Hardy-Weinberg equilibrium), given observed genotype frequencies.
  • Calculate allele frequencies:
    • (# of homozygotes x 2 + # of heterozygotes) / number of organisms x 2.
    • The other allele frequency is 1 minus the calculated allele frequencies.
    • Plug the calculated allele frequencies into p^2, 2pq, and q^2.
    • If they create the same ratio of offspring, the population is in equilibrium.

Page 6:

  • Which assumptions of Hardy-Weinberg equilibrium have likely been violated, given an observed set of genotype or phenotype frequencies.
  • If lots of homozygotes, there was likely assortative mating.
  • Costs and benefits of reproducing sexually as opposed to asexually.
  • Cost of sexually reproducing:
    • Need to find a mate (could be dangerous).
    • Intrasexual selection causes males to decrease their survival fitness.
    • Males waste energy on sexual dimorphic traits.
    • Only pass on 0.5 of your alleles.
  • Cost of asexually reproducing:
    • More at risk for extinction.
    • Don't get the short-term benefits of sexual reproduction (genetic variability).
    • Fall behind in evolutionary arms race.

Page 6:

  • Why males usually compete for access to females (rather than vice versa), and why in some species this pattern is reversed.
  • Who is choosy and who competes depends on parental investment and potential fitness.
  • In most species, females have higher parental investment and lower potential fitness than males.
  • Females increase their potential fitness through quality offspring, while males increase their fitness through quantity of offspring.
  • Kin selection theory explains the persistence of helpful behavior.
  • Kin selection theory:
    • We help others that are related to us.
    • Our alleles continue to be passed on and our inclusive fitness increases.
  • Situations in which kin selection does or does not favor helping non-descendant relatives.
  • According to Hamilton's rule, kin selection favors helping non-descendant relatives when their relatedness to you multiplied by the benefit to them is greater than the cost to you (rb > c).
  • How asymmetries in relatedness can generate conflict between relatives.
  • Differences in opinion arise on when you should offer help based on the relatedness of other family members to the person in need.
  • Conditions that favor or disfavor cooperation between non-relatives.
  • Repeat interactions and the ability to recognize individuals who cooperate or cheated in the past favor cooperation.
  • One-time interactions or knowing the number of interactions favor selfishness.
  • Most recent common ancestor (MRCA) for a given group(s), given a phylogenetic tree.
  • The closest branching point shared between two groups is the MRCA.
  • Why some traditional groupings of organisms do not reflect evolutionary relationships.
  • Traditional groupings were made using morphological similarities without considering evolutionary history.
  • Relatively close and relatively distant relatives, given a phylogenetic tree.
  • Relatedness on a phylogenetic tree is determined by looking at the most recent common ancestor.

Page 7:

  • Monophyletic and non-monophyletic groupings in phylogenetic trees
    • Monophyletic groups (clades) include the MRCA and all descendants
    • Non-monophyletic groups include species from different lineages (polyphyletic) or include the ancestor but not all descendants (paraphyletic)
  • Parsimony in phylogenetic trees
    • The most parsimonious phylogeny has the least number of evolutionary changes
    • Considered correct until falsified
  • Distinction between homology and homoplasy
    • Homology: similarities due to common ancestry
    • Homoplasy: misleading similarity or dissimilarity due to convergent or divergent evolution
  • Determining the most likely phylogenetic tree
    • Look for synapomorphies (derived and shared traits)
    • Order species based on similarities to the out-group and to each other
  • Criteria used by different species concepts to define species
    • Morphological: based on physical appearance
    • Biological: based on ability to interbreed and produce fertile offspring
    • Phylogenetic: based on shared derived characteristics and evolutionary trees
  • Weaknesses/limitations of different species concepts
    • Morphological: not reliable alone, variation within species and convergent evolution
    • Biological: not applicable to asexual or extinct organisms, geographic separation
    • Phylogenetic: limited by unknown evolutionary history, may rely on morphological features

Page 8:

  • Species concept used in 'real world' examples
    • Morphological species concept used in field guides and for fossilized species
  • Why improving equipment for survival does not always lead to winning an evolutionary arms race
    • As one species evolves, the other species evolves in response
    • Improvement is necessary for survival, but not necessarily for surpassing the other species
  • Costs and benefits of being highly virulent for parasites
    • Cost: host dies sooner, unfavorable for transmission in low population density or direct contact
    • Benefit: quicker reproduction using host machinery, enhanced transmission in dense populations or indirect contact
  • How trade-offs, rapid environmental change, and arms races affect human susceptibility to disease
    • Arms race with parasites: parasites evolve quickly due to large population size and short generation times
    • Rapid environmental change: diseases of civilization, decrease in infectious diseases but increase in autoimmune disorders
    • Antagonistic pleiotropy: trade-offs between different aspects of fitness, harmful alleles kept through heterozygous advantage

Page 9:

  • Examples of proximate and ultimate explanations
    • Proximate explanation: physical and biochemical mechanisms underlying a trait
    • Ultimate explanation: role of natural selection, arms races, history, and chance in creating or continuing a trait
  • Costs and possible advantages of large brains
    • Cost: 2% of mass, 20% of energy
    • Possible advantages: utility hypothesis (survival-related skills) favored by natural selection, mating mind hypothesis (mating-related skills) favored by sexual selection

Skill Development Outcomes:

  1. Deep Learning
  • Making connections, understanding, and applying knowledge
  • Excludes memorization
  1. Serial Dilutions
  • Calculation of CFU/mL using dilution factor and volume of culture plate
  • Dilution factor calculated by dividing final volume by sample volume and multiplying by the denominator of serial dilution fractions
  1. Role of cyclin in the cell cycle
  • Cyclin regulates the rate of cell division and is important in cell cycle checkpoints
  1. Microscope calibration
  • Formula for measuring objects using stage divisions and ocular divisions
  • Calculation of magnification using ocular lens and objective lens
  1. Chi squared statistical analysis

Page 10:

  • Null Hypothesis and Alternate Hypothesis
    • Null Hypothesis states no effect/correlation/will be no change
    • Alternate Hypothesis states there is an effect/correlation/will be a change
  • Chi squared analysis
    • Determines if data is significant enough to support the alternate hypothesis
    • Compares observed values (collected in the study) with expected values (calculated based on null hypothesis)
    • Calculation: x^2 = sum of ((O-E)^2/E)
  • Degrees of freedom and critical value
    • Critical value is compared to chi-square value for statistical significance
    • Can be found on a chart or provided
  • Primary vs secondary scientific articles
    • Primary articles: original data and ideas from scientific investigations reported by scientists
    • Published in journals and contain sections like Abstract, Introduction, Methods, Results, Discussion, References
    • Secondary articles: review and analyze primary sources in more depth

Page 10 (continued):

  • FST Population Genetics
    • FST = 1 - (average heterozygosity expected within populations / heterozygosity expected across total population)
    • HS = (2p1q1 + 2p2q2)/2
    • HT = 2pTqT
    • Use Hardy-Weinberg to calculate p and q values for individual populations, then add population numbers together and recalculate for the total
    • Interpretation of FST values:
      • FST = 0: no disturbance
      • FST > 0.25: significant disturbance
      • FST = 1: complete separation of populations

Page 10 (continued):

  • Allozyme Electrophoresis for genetic variability calculation
    • Takes advantage of the fact that organisms produce allelic variants of enzymes called allozymes
    • Each allozyme has a slightly different amino acid sequence and is the product of a unique allele
    • Genotype at a gene locus coding for an enzyme can be inferred from the number and position of spots observed on gels
    • Genetic variation in a population is the average frequency of heterozygous individuals per locus
    • Calculated by determining the frequency of heterozygotes at each locus and averaging these frequencies over all loci

Page 11:

  • Creating phylogenetic trees using DNA sequencing
    • Phylogenies can be estimated by looking at differences in DNA sequence
    • Species with the most differences is the out-group
    • If no differences, it is the same species and should be drawn on the same vertical line
    • Length of horizontal lines may indicate the
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