Cycle 1 & 2

Principles underlying evolution by natural selection: variation, heritability, differential reproduction, change in genotype of the population

Variation- mutations – virons with a certain mutation that causes them to be resistance will survive longer than those without

Heritability- Resistance is passed on from parent to offspring

Differential Reproduction- Not all virons ill reproduce. The virons that are resistant to the drug/ treatment are more likely to reproduce.

Change in Genotype of Population- viral population will change overtime. Natural selection will occur due to environmental pressures and genotypes that favour the environment will persist.

evidence from the fossil record, historical biogeography, comparative morphology and molecular biology that support the idea of descent with modification from a common ancestor

Adaption by Natural Selection – the product of natural selection is evolutionary adaption. Eg. wing of a bird.

Fossil Record – this record provides evidence of ongoing change in biological lineages. Evolution of modern birds can be traced from a dinosaur ancestor through fossils.

Historical Biogeography –Geographical distribution relates to evolutionary history relating to Darwin’s theories. E.g. species on oceans are common to the on the nearest mainland. Species from one continent are closely resembled.

Comparative Morphology- Homologous Traits (characteristics that are the same in two species because they are inherited from their common ancestor). All four legged vertebrae come from a common ancestor. The specific structural differences like bones and joints do not interfere with these similarities.

characteristics of a scientific theory and the importance of falsifiability

• Scientific Theory - “coherent set of testable hypotheses that attempt to explain facts about the natural world”

• Attempt to prove a theory false is how a theory is defined as a fact.

• Theories achieve status of facts after there are repeated and rigorous efforts to falsify them and all efforts have failed.

• an assertion that is difficult to prove (unfalsifiable assertion) is not scientific (e.g. Bertrand Russel proposed that there is a small flying tea pot in space orbiting the earth but it’s too small that telescopes can’t detect it.) The burden of proof rests on the people making the assertions to proclaim that their assertion is true.

• Evolution is a TRUE theory – fact

• This is true because there is so much evidence it would be perverse to deny it.

changes in amount of DNA throughout the cell cycle

• ‘n’ represents one copy of all an organisms nuclear chromosomes.

main features of each stage of mitosis with respect to cytoskeleton and chromatin

structure of a replication bubble

Replication Bubble – occurs when unwinding creates two Y’s joined together at their tops. Action on either side of the replication fork mirrors itself.

relationship between replicated DNA and metaphase chromosomes

In S phase, the DNA becomes replicated, so now there’s 2 copies in the cell. The metaphase chromosomes are these 2 copies of DNA that become condensed and joined at the centromeres. Each sister chromatid is identical (formed by DNA replication). This is how the cell maintains the inheritance of sameness.

Mechanism of Proofreading

• depends on the ability of polymerases to back up and remove mispaired nucleotides from DNA stand. Only when the most recently added base is correct will the polymerase continue ahead allowing for stabilized hydrogen bonds

Steps:

1. Polymerization occurs in new chain 5’ to 3’.

2. Rarely DNA polymerase adds a mismatched nucleotide

3. DNA polymerase recognizes the mismatch base pair. The enzyme reverses, using its 3’ to 5’ exonuclease to remove the mismatched nucleotide from the strand

4. DNA polymerase resumes its polymerization extending the new chain 5’ to 3’.

In bacteria the error rate is 1 in a million nucleotides

Mechanism of Mismatch Repair

Recognizes the distortions through the enzyme catalyzing mismatch repair. This occurs after DNA polymerase proofreads.

Steps:

1. Repair enzymes moves along the helix scanning DNA for distortions in the newly synthesized nucleotide chains.

2. If the enzyme encounters distortion, they remove a portion of the new chain including the mismatched nucleotides.

3. The gap left by the removal is filled by DNA polymerase using the template strand

4. DNA ligase seals the nicks left to complete the repair.

This mechanism is also used to repair DNA damage done by chemicals and radiation like the UV in sunlight.

• People with Xeroderma Pigmentosum, (faulty repair mechanism), develop skin cancer easily.

General Trends in Cost of DNA Sequencing

• Cost have been decreasing as technology advances and becomes readily available

Relative Distribution of Various Components of Genome Sequence

• 55%: over half of your genome is dead, viruses, mobile elements, transposons junk

• 10%: introns are valuable but don’t code, they get transcribed but not translated

• 10%: is essential (e.g. telomeres) 2% of the genome codes

• 25%: unknown (likely junk)

proportion of human genome coding for protein

• of the 10% of essential of DNA only 2% codes for proteins

difference between DNA damage and mutation

DNA Damage – physical abnormalities that can be recognized by enzymes

• they can be correctly repaired by certain enzymes

• e.g. pyrimidine dimers

• If its nots a double stranded change its just DNA damage not a mutation

Mutation – change in BASE SEQUENCE of DNA

• This change is replicated with the cell

• May cause change in protein function and regulation if occurs in 2% of coding DNA

• DNA Damage that does not kill the cell by blocking replication can cause replication errors which cause mutations.

different types of genomic variation among humans

• SNP: single nucleotide polymorphisms

  • Mismatch, Excision and Proofreading fail to fix the nucleotide and since it is not repaired, SNP’s are created and replicated to create a new nucleotide sequence.

• Biological Mutagens: can cause diseases (retro transpons, mobile elements)

• Insertion Sequences

• Non- Homologous End Joining (NHEJ) – joins ends of broken chromosomes and slap them together

• CNV (copy number variations) - change in the number of copies of a chunk of DNA

• Inversion: some parts of DNA are flipped or in opposite order

why African populations have more unique SNPs than other populations (ie. Asian or Caucasian).

• African people have far more variation, one to the other, than other people on the earth.

• This interpreted to mean that African populations (genomes) are the oldest, populations had far more time to diverge.

• About 50000 years ago people migrated out of Africa into the middle east populating the earth.

difference between insertion sequences, transposons and retrotransposons

Insertion Sequences:

• cut and paste

• contains genes only for its own mobility

• simplest type of transposable elements.

• Transposase enzymes catalyze some of the recombination reactions for inserting or removing the movable element from the DNA.

• Inverted Repeat: ends of the IS enables the transposase enzyme to identify the ends of TE.

Transposons:

• Not jumping genes since always move by backbone recombination and never in the air.

• Cut and paste

• have an inverted sequence at each end enclosing a central region with one or more genes. These inverted regions however are insertion sequences which provide the transposase for movement of the element.

Retrotransposons:

• move via copy and paste

• mobile DNA transcribed into RNA, then RNA is reverse transcribed into DNA (using reverse transcriptase), new DNA is then inserted into genome.

why mobile elements are considered to be biological mutagens

• Biological Mutagen: physical or chemical agent that changes the genetic material of organism, thus increasing the frequency of mutation

• Mobile elements can damage genome of host cell in different ways which leads to disease.

• Transposable elements (IS, Transposons) are biological mutagens because they increase genetic variation.

• Mobile Elements in DNA for a long time are subject to mutation like the other DNA and can alter it into a non-mobile residual sequence in the DNA.

role of tautomeric shifts in mutagenesis

• A-T, G-C are most stable, bases appear in these forms. Sometimes these bases can switch from their keto to enol tautomer form (Thymine can pair with guanine and cytosine can pair with adenine).

• Spontaneous tautomeric shifts can cause incorrect base paring

• This improper pairing is not a mismatch, it will not be protected by proofreading as it doesn’t distorts the helix.

• Mutation occurs doe to inherit instability in structure of bases giving rise to mutations.

mechanism of substitution mutagenesis during DNA replication

• type of mutation where one base pair is substituted for another base pair.

• Point Mutation (Silent, Missense, Non Sense) where a single base pair is replaced and could affect protein genes code for.

mechanism of in/del mutagenesis during replication

• Insertion/ Deletion

• Caused by slippage during replication

• Regions of repeated sequences are susceptible to in/del mutations

• New strand loops since too long and has insertion

• Template strand loops: deletion

• Mutation is undirected but NOT RANDOM

• There are regions of genomes that are “hot spots”

mechanism of chromosomal rearrangements resulting from double strand breaks

• Cells can fix backbones, but it still can make mistakes

• E.g deletion, duplication, insertion

• Pieces may get inverted when putting them back together

role of UV, ionizing radiation and ROS in mutagenesis

• Reactive Oxygen Species (ROS) is damaging as it breaks DNA backbones

• Strong Radiation (e.g. x-rays)

• Ionizing radiation cause ROS that damage DNA

• UV: Photons have enough energy to destabilize electron cloud and will end up with covalent bonds linking one thymine’s to the next on the same DNA backbone

• 2 DNA backbones, 2 thymine’s end up bonded together

• Thymine Dimers: they must be fixed

• Thymine dimers repaired by excision repair and detecting dimers and cutting them out.

Cycle 4

the basic mechanism of DNA recombination in meiosis

Required:

1. Two DNA molecules that differ from one another

2. A mechanism for bringing the DNA molecule into close proximity

3. Collection of enzymes to cut, exchange and paste DNA back together.

• Enzymes break the covalent bond in each of the four backbones

• The free ends are exchanged and reattached to those of the other DNA molecule.

the stage of meiosis when recombination occurs

• Recombination occurs only in prophase of meiosis 1

evolutionary advantages of gene duplication

• Provides base material for further evolution (more raw material for evolution)

• 2 copies of gene: one can diverge to do a different job or one can be expressed in different conditions.

• Zygote brings mom and dad’s DNA into the same cell

• In fungi recombination occurs in the zygote but in nowhere else (plants or animals).

• During prophase 1 of meiosis chromosome pair up and generate diversity

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

Animals:

1. Meiosis occurs forming gametes (egg or sperm) (1n)

2. For sperm each of the four cells produced are functional but only of the four eggs are.

3. Fertilization occurs to form a zygote (2n)

4. Mitosis then occurs duplicate cells.

Plants:

1. Fertilization produces the sporophytes (diploid 2n)

2. After sporophytes grow they undergo meiosis to produce haploid spore genetically different

3. Spores undergo mitosis and grow into haploid gametophytes

4. Some nuclei of gametophytes develop into eggs or sperm nuclei.

5. These eggs/ sperm from a specific gametophyte are genetically identical since they arise from mitosis

6. Fusion of haploid egg and sperm produce zygote to produce the zygotic sporophyte.

The gametophyte is most seen in plants. Female gametophyte remains in flowering part of plant while pollen when released fertilizes the egg of the same species creating a zygote sporophyte.

Fungi and Algae:

1. Diploid stage is limited to the zygote produced by fertilization of two haploid gametes (negative and positive haploids).

2. Diploid zygote undergoes meiosis to produce haploid phase immediately after.

3. Mitotic divisions occur only in haploid phase to produce spores

4. Spores germinate to produce haploid individuals which grow by mitosis.

5. Eventually positive and negative gametes are formed by differentiation of some of the cells (genetic information is still identical since all is mitosis).

main differences between meiosis and mitosis

Mitosis

• sameness: same number of chromosomes, same DNA sequence

• product contributes to the body that makes them

• sister chromatids of each chromosome are attached to different spindles and move in opposite direction.

• Produces 2 identical cells, same # of chromosomes.

Meiosis

• halved chromosome number (from 2n to n) and recombined DNA sequence.

• Occurs only in specialized tissues that produce gametes or spores

• Sister chromatids of one chromosome are attached to the same spindle and move in same direction in anaphase 1

• Only occurs in reproductive tissue

• DNA replication does not proceed after Meiosis 2 is done

• Resulting daughter cells are not genetically identical

characteristics of homologous chromosomes

• They have the same genes arranged in the same order in the DNA of the chromosome.

• Paternal Chromosome is from male parent

• Maternal Chromosome is from female parent

• Chromosomes have consistent shape & banding pattern

• They carry the same genes but different alleles

• Alleles have similar but distinct DNA sequences which encode varying RNA or proteins.

Timing of meiosis in vertebrate life cycle

• When men sexually mature – being to produce gametes (cells in meiosis)

• Engaging in sexual recombination

• Men are always producing gametes

• Females don’t engage in sexual recombination – meiosis occurs before they are born

• Recombination occurred before birth – finished meiotic combination

• Pregnant women are 3 generations of DNA sitting there that could suffer mutations.

reason why meiosis I is "reductional" and meiosis II is "equational"

Meiosis 1: chromosome # reduced in half- diploid to haploid

Meiosis 2 – # of chromosomes remains unchanged, similar to that of mitosis

changes in C and n during meiosis

how homologues pair in order for all non-sister chromatids to participate in recombination

• Homologous chromosomes have same genes but different genes(alleles)

• DNA sequences are similar enough to form meiotic pairing but different enough to create recombination’s

• They pair on top of each other rather than side to side

• Regions in which non sisters cross are called cross-overs or chiasmata
  

mechanism by which recombination creates new combinations of alleles

• Recombo does not switch alleles of a given gene but rather all the DNA sequence stretching from the site of recombo to the ends of the participating chromatid is exchanged.

mechanism by which recombination creates copy number variation (CNV)

• Unequal recombination when chromosomes are not paired up properly are CNV’s.

• Can be caused by improper alignment or errors in crossing over causing duplications or deletions

• Duplications can be good as one copy can diverge to evolve while other keeps original function. Gene duplication can increase genomic complexity.

mechanism of recombination during prophase

• Occurs when chromosomes pair and crossover by cutting and pasting of backbones

• Recombination requires cutting and pasting 4 DNA backbones

• Mobile elements move by recombination, never floating around

role of cohesin and synaptonemal complex

• As homologous chromosomes pair they are held tightly together by a protein framework called the synaptonemal complex.

• This complex disassembles towards the end of prophase 1

• Cohesion holds and regulates sister chromatids separation mitosis and meiosis

randomness of alignment of homologous pairs at metaphase I

• All maternal chromosomes may line up to be pulled to one pole while the paternal chromosome to the other but it is more likely a mixture of paternal and maternal chromosomes to each pole.

• The number of possibilities depends on the number of chromosome pairs in a species. It is 2^{number of chromosome pairs}

• This randomness is responsible for the independent assortment of alleles of two genes.

• The possibility that two children of the same parents could receive the same combo of maternal and paternal chromosomes is (2³²)²

relationship between distance separating genes and the likelihood of recombination between them

• The more distance between genes along a chromatid the more likely recombination is going to happen. Because a gene is closer together they are more likely to stay together during recombination (crossing over) see simutext section 2 pg. 11)

way in which meiosis can be thought of as a kind of DNA "repair".  That is, how can you inherit mutations on both homologues of chromosome 6 but give a chromosome 6 with no mutations to your offspring?

• Recombination provides variability that increases the chance of advantageous combinations of alleles in certain environments.

• Recombination may be able to fix bad genes

• Chromosomes formed by recombination can have more good genes than their originals

• Although they have mutations the combination of segments from both chromosomes may be advantageous in a specific environment

• Independent assortment could case all the preferred genes to go to one pole and mutations to another causing some gametes with no mutations.

overall, various mechanisms by which meiosis generates variation

1. Recombination of homologous chromosomes

2. Different combo of maternal and paternal chromosomes segregated to poles in anaphase 1

3. Different combo of recombinant sister chromatids segregated to the poles during A11.

4. Set of male and female gametes that unite in fertilization.

mechanisms giving rise to aneuploid products of meiosis

• Aneuploidy: unbalanced

• Non disjunction – failure to disjoin the homologues pairs at meiosis 1

• Problems in M1 cannot be fixed in M2 as the cytoskeleton of M2 cannot compensate for the problems made.

• Mis-division – chromatids fail to separate in meiosis 2

Cycle 5

characteristics of Mendel's work that set him apart as a genetic researcher

• Gregor Mendel experiments with pea plants answered questions on how traits were inherited through offspring in 1860’s.

• He was able to contradict the blending theory of inheritance which suggested traits blend evenly through mixing parents blood.

• He studied characters (inheritable characteristics) and their variations (traits).

• He did not know that the segregation of chromosomes to gametes influenced the inheritance patterns.

• Unique because he studied characteristics in a statistical/ quantitative way.

components of Mendel's explanatory model

• Mendel prevented self-fertilization (since his garden peas contained both sperm (pollen) and eggs in the same plant by cutting of the anthers. He used an anther from one plant and applied it to the stigma (where the eggs are). This is called cross pollinating.

• The plants he used were true- breeding (when self-fertilized, they passed traits without change from one generation to the next.

• Seeds were the result of the experiment which were scored for seed traits like smooth or wrinkled or for adult traits which include flower color.

• Results in the F₁ generation were the same traits as the P(parental) generations (purple flowers). In the F₂ generation there was a 3:1 ratio of purple and white flowers.

• First Theory: the adult plants carry a pair of factors that govern the inheritance of each character.

• Allele – different versions of a gene that produce different traits of a character (two alleles of one gene that govern traits).

• Second Theory: if an individual’s pair of genes consist of different alleles one allele is dominant over the other recessive one.

• Dominant alleles code for functional enzymes and determine the genotype. The recessive allele codes for the non-functional enzyme. Dominant alleles don’t inhibit recessive ones.

• Three results of experiment:

• The genes that govern genetic characters are present in two copies in individuals.

• If different alleles are present in an individual’s pair of genes, one allele is dominant over the other

• The two alleles of a gene segregate and enter gametes singly.

• Theory 3: Principle of segregation- as gametes are formed half of the gametes carry one allele and the other half carry the other allele. Zygote receives one allele from each parent gamete.

distribution of progeny, given parental genotypes in monohybrid, dihybrid and sex-linked crosses

• The progeny from a mono hybrid cross:

  • ¼ homozygous dominant, ½ heterozygous, ¼ homozygous recessive

• For sex- linked traits, the trait is carried on the X chromosome so on both chromosomes of the female but only one for the male.

parental genotypes, given distribution of progeny in monohybrid dihybrid and sex-linked crosses

• A monohybrid cross is a mating between two individuals with different alleles at one genetic locus of interest.

• The characters being studied in a monohybrid cross are governed by two or multiple alleles on homologous chromosomes. Work backwards from above.

location of various alleles on homologues

• Particular site on a chromosome at which a gene is located is called the locus of the gene

• Alleles are located on same locus of gene on each homologues pair

segregation of various alleles during meiosis in monohybrid, dihybrid and sex-linked situations

• Pair of alleles separate as gametes are formed in (M1)

• ½ of the gametes carry one allele and other half carry other allele

• During fertilization the zygote receives one allele from male and one from the female.

• Chromosome Theory of Inheritance: genes and alleles are carried on chromosomes (Walton Sutton)

number of different gametes produced, given parental genotype

• Monohybrid Cross: 3:1 phenotypic ratio (Rr and Rr)

• Dihybrid Cross: 9:3:3:1 phenotypic ratio (RrWw and RrWw)

arrangement of genes and alleles on homologous chromosomes in a dihybrid organism

• Dihybrid: a zygote produced from a cross that involves 2 characters, heterozygous for 2 traits.

• The genes for each character is located at different pairs of homologous pairs (one gene is found on chromosome 6 while another is found on chromosome 8 but still involved in the same cross.

• Can also be located at different loci of the homologous chromosome.

• Separation in meiosis and gamete formation is independent of separation of other pairs, as in the independent assortment of the alleles of different genes.

how independent assortment creates 4 different products of meiosis from a dihybrid parent

• Independent Assortment: The alleles of the genes that govern the two characteristics segregate independently during meiosis.

• Random alignment of homologous chromosomes pairs in meiosis ensures that R alleles for seed shape can be delivered independently to a gamete with either the Y or y allele.

application of the sum and product rule of probability

Product Rule

• Defined as the probability that two or more events whom are independent of each other will occur. Individual probabilities are multiplied.

• E.g., the sex of one child has no effect on the sex of the next child therefore the probability of having four girls in a row is ½x ½ x ½ x ½ = 1/16

• E.g. probability of producing a PP zygote from two Pp parents is (½ x ½ = ¼)

Sum Rule

• Applies when several different events all give the same outcome, there are six ways to get a sum of 7 when rolling two dice. (six ways of getting the same outcome).

• The frequency of getting each combo is 1/6 x 1/6 = 1/36

• The probabilities of rolling a total of 7 is the sum of the independent combos. 1/36 + 1/36 +1/36 +1/36 + 1/36 + 1/36 = 1/6

• Probability of production of Pp offspring: Each of the ways to get Pp is ¼ + ¼ = ½

• Test Cross – cross between an individual with homozygous recessive and heterozygous. This test is used to determine if an individual is dominant homozygous or heterozygous. If homozygous then all phenotypes will be of the dominant allele. If heterozygous it will be half.

pattern of offspring expected, given mechanism of epistasis

• Epistasis: genes interact with one or more alleles of a gene at one locus inhibiting or masking the effects of one or more alleles of a gene at a different locus.

• When one gene can mask the effect of another gene at a different location

• A gene is epistatic to another if it eliminates or inhibits the activity of the gene.

• Dihybrid crosses that involve epistatic interactions produce distributions that differ from 9:3:3:1

• E.g labs with alleles BB or Bb have black fur and bb is brown fur.

  • The dominant allele E however permit pigment deposition

  • ee blocks off almost all pigment disposition therefor making labs yellow

  • thus E is epistatic to the B gene.

distinction between codominance and incomplete dominance

• Incomplete Dominance: occurs when the effects of recessive alleles can be detected to some extent in heterozygous (blend).

  • E.g. Sickle cell disease is homozygous recessive but when heterozygous for this gene, have a condition known as sickle cell trait which is a milder form of the disease since the individual still produces normal polypeptides.

  • E.g. – red and white flower = pink flower

• Codominance: when alleles have approximately equal effect in individuals making the two alleles equally detectable in heterozygous.

• E.g. Blood Type, spotted cots

• If phenotype exists because one allele can’t compensate for other: Incomplete dominance********

way in which inheritance of polygenic traits show that inheritance is not "blended"

• Polygenic Inheritance: several to many different genes contribute to the same character e.g. height, skin color, body weight in humans, length in corn.

• Also known as quantitative traits.

• Graph of distribution of people in each class resembles a bell curve (highest in middle lowest on extremes)

• Some children aren’t intermediate relative to their parents. We are not just a blend of our parents but rather quantitative traits contribute to phenotypes thereby causing variants in a specific trait.

• Expression of a genetic phenotype can be influenced by the environment

  • Poor nutrition during infancy can limit growth

description of pleiotropic genes

• Pleiotropy: single genes affecting more than one character of an organism

• E.g. sickle cell disease (caused by a recessive allele of a single gene) affects hemoglobin structure, blood vessel blockage, which can damage tissues and organs in the body producing a wide-ranging of symptoms.

mechanism by which X inactivation accomplishes doseage compensation for X linked genes

• Since males have one x chromosome and females have two, one of the x chromosomes in females is inactive.

• Females although they have two copies for the genes on X, do not need twice as many products from these genes.

• Barr Body: the inactive condensed x chromosome seen in the nucleus of female mammals. Inactivation is not incomplete

• As a result of this equalizing method the activity of most genes carried on the X chromosome is essentially the same in cells of males and females.

Cycle 6

general pathway of eukaryotic membrane protein production.

• Transcribed in nucleus – translated in cytoplasm – packed by ER, vesicles, golgi complex –packed in membrane bound vesicles – then taken to membrane

general physiology of skin/hair pigmentation.

• Skin and Hair come from melanin

• Made by specialized skin cells called melanocytes

• There are two types of melanin:

  • pheomelanin (yellow to red)

  • Eumelanin (black)

• Melanin is stored in melanosomes and each type has its own melanosome

• Melanocytes transfer mature melanosomes to cells called keratinocytes which give skin and hair tis colour.

• Red melanosomes: red or blonde hair

• Black melanosomes: create black hair or dark skin

• A mixture of black and red melanosomes creates brown hair and skin

characteristics of dominant alleles.

• In heterozygotes, the allele that determines the phenotype is the dominant allele

• Which allele makes the “always on protein”

• Black melanin is dominant since it is always on unless suppressed by hormone

which allele in a heterozygote is dominant, given the biochemical mechanism of action of allele products.

• Check offspring production.

• Will give you biochemical mechanism and determine what allele is dominant

whether or not the dominance status of an allele affects its frequency over time in a population.

• Dominance/ recessives does not influence selection.

• Dominance does not cause selection towards it.

• Being dominant or recessive affects phenotype but if equal chance of survival (no selection), being dominant or recessive has no influence over fait of allele.

  • E.g. blonde hair won’t die out since it does not make you more likely to survive

function of black, brown and red MC1R alleles as described in SimuText.

• Melanocortin 1 receptor (MC1R) lies on membrane of melanocytes and is triggered by hormones

• Depending on signal received or not, the MC1R receptor tells the melanocytes to produce eumelanin or pheomelanin.

Black Allele:

• B allele

• When MC1R is activated or on cyclic AMP levels in the cell are high and melanocyte produces eumelanosomes.

• Even if ASP is present (R allele) eumelanosomes are still produced

• Dominant over brown allele

Red Allele:

• R allele

• ASP released by nearby cells inactivates MC1R and cAMP levels fall

• Even without ASP it is inactive

• When cAMP levels are low enough the cell produces pheomelanosomes.

• R allele is recessive to both W and B since they are at least somewhat activated, increasing cAMP and overriding the always of R version

Brown Allele:

• W allele causes both types of melanin to be produced

• Recessive to the b allele

explanation for spotted coat color in pigs as described in SimuText.

• S is derived from the B allele which is always on

• In most cells the S allele however produces pheomelanin only as it contains a mutation that destroys MC1R’s ability to function at all.

• Back mutations can occur during mitosis that restore MC1R’s ability to function as a B allele during mitosis.

  • As a result, an SS cells can sometimes produce SS and SB daughter cells.

• Since they compose of both, they are mosaics with red fur but black spots.

conditions under which allele frequencies change, or not, in a population over time

Difference between quantitative and qualitative variation

• Quantitative Variation: individuals differ in small incremental ways (height, weight, number of hairs)

• This data is displayed in bar graphs or a curve (width of curve represents variation)

• Qualitative Variation: exist in two or more discrete states, and intermediates forms are often absent. Eg snow geese either have blue or white feathers, no pale blue.

• Polymorphism: existence of discrete variants of a character. These traits are called polymorphic.

• Human A, B, AB, O blood types is a Biochemical Polymorphism.

Sources of phenotypic variation, and which of these is/are heritable

• Genetic Differences between Individuals

• Genotypic and phenotypic variation is not perfectly correlated since different genotypes can have the same phenotype (dominant and homozygous).

• Differences in the Environmental factors

• Acidity of soil influences flower color

• Interaction between Genetics and Environment: one field of wheat could produce more grain due to the availability of nutrients but could be also affected by genetic differences in two different fields.

• Only genetically based variation is subject to evolutionary change.

• Natural selection operates on the entirety of a phenotype not genotype as phenotype is what turns out to be successful or not.

Meaning of directional, stabilizing, disruptive selection

• Directional Selection: when individuals at one end of the spectrum are most fit. The traits mean value is shifted left or right after selection.

• E.g. predatory fish promote directional selection for guppies to larger bodies since smaller bodies are feed on more.

• Very common in artificial selection since aimed at increasing or decreasing specific phenotypic traits.

• Shifts a phenotypic trait away from the existing mean.

• Stabilizing Selection: individuals expressing intermediate phenotypes have the highest fitness.

• Reduces phenotypic variation in population

• Most common mode of selection in familiar traits like newborns weight.

• Disruptive Selection: when extreme phenotypes have increased phenotypes than intermediates.

• The extreme phenotypes promote polymorphism since the extremes become more common.

• Least common mode of selection.

• Increases phenotypic variation.

How each of the above modes of selection affects phenotypic variation in a population

• See above

Meanings of gene pool, genotype frequencies, allele frequencies, genetic equilibrium

• Gene Pool: sum of all alleles at all gene loci in all individuals in a population

• Genotypic Frequencies: percentages of individuals possessing each genotype.

• Allele Frequencies: relative abundance of different alleles.

• Genetic Equilibrium: the point at which neither allele frequencies change in succeeding generations.

How to calculate allele frequencies, given observed genotype frequencies

• p and q represent the allele frequencies

How to calculate genotype frequencies expected under genetic equilibrium

• Genetic Equilibrium: point at which neither allele frequencies nor genotype frequencies change in succeeding generations.

• P² and q² are the expected genotypic frequencies for homozygous genotypes and 2pq is the genotypic frequency of the homozygous genotype.

• These frequencies stay the same from population to population that are under genetic equilibrium.

(p + q) x (p + q) = p² + 2pq + q²

Identify populations that are, or are not, at genetic equilibrium, given observed genotype frequencies

• The Hardy-Weinberg principle is a null that serves as a reference point for evaluating circumstances where evolution may occur.

• If genotypic frequencies of the next offspring do not match the predictions of genetic equilibrium than evolution may be occurring.

• Determining which condition is not met is the first step in understanding why gene pool is changing.

Conditions that must be met for genetic equilibrium to occur

1. No mutations are occurring

2. The population is closed to migration from another population

3. Population is infinite in size (no genetic drift)

4. All genotypes in the population survive and reproduce well (no selection)

5. Individuals mate randomly with respect to traits being considered

• Allele frequencies don’t change if they meet these conditions. Evolution occurs if they do change.

How the dominance status of alleles affects their frequency, in the absence of selection

• Even if dominant over another in the absence of selection, allele frequency does not change

• Dominance and excessiveness of alleles do not cause evolution. Every individual and phenotype has an equal likelihood of surviving and reproducing.

• As long as there is no selection, the allele frequencies in population remain relatively the same.

How the dominance status of alleles affects the response to selection

• Selection against dominant alleles would cause the allele to disappear

  • If there is a harmful dominant allele, population can remove that allele

  • Selection removes genetic variation from the population

• Selection against recessive allele will not cause the allele to disappear.

  • Will just decrease in frequency

  • Heterozygous fitness is fine so recessive allele can hide from selection

• There can be selection that does not result in evolution.

Difference between positive and negative frequency – dependent selection, and how each affects genetic variation

• Negative Frequency – Dependent Selection:

  • Rare phenotypes have advantage (increases in frequency)

  • Common has disadvantage (decrease in frequency)

  • Maintains genetic variation in population

    • Increases frequency of rare alleles and decreases frequency, of common, until common become rare and it switches

• Positive Frequency – Dependent Selection:

  • Rare alleles phenotypes have a disadvantage (decrease in frequency)

  • Common have an advantage (increase in frequency)

  • Eliminates genetic variation in population

    • Removes rare phenotype completely

Effect of heterozygote advantage on genetic variation
- Heterozygote have higher fitness (W_RR= W_SS < W_RS)

• Sometimes heterozygotes can have different phenotypes from either homozygote (incomplete dominance/ codominance).

• With pigs s allele is a lot of spots, no s is no spots but if heterozygote its an intermediate of a little and lot of pigs.

• Both alleles get maintained. Genetic variation is maintained as both allele frequencies reach 0.5.

• More common alleles will decrease and less common will increase reaching 50/50.

• Evolution is not occurring when population reaches genetic equilibrium of 50/50 even though there is selection.

Similarities between negative frequency dependent selection and heterozygous advantage

• This will cause the most common phenotype to decrease in frequency as the allele for the rare alleles are most common and the more rare one to increase

  • Will cause 50/50 split (relatively close)

Effect of heterozygote disadvantage on genetic variation

• Advantage maintains diversity and allows alleles to reach a genetic equilibrium

• W_RR = W_SS > W_RS

• Whichever allele has a higher frequency will increase in and reach one and lower frequency to start will reach 0 in heterozygote disadvantage.

• Has opposite effect as heterozygous advantage: has to do with the fact that the frequency of an allele whether common or rare influences how likely the allele will be found in homo or heterozygotes.

• Rare alleles are mostly found in heterozygotes so they decrease in frequency thereby approaching zero in HD.

Similarities between positive frequency- dependent selection and heterozygous disadvantage

• In both cases the rare phenotype frequency decreases until it hits zero

  • The most common phenotype will have an advantage

Whether selection always results in evolution

• Evolution only occurs when allele frequencies change. Once at equilibrium due to selection, the frequencies do not change.

• Therefore, it is possible to have selection without evolution. Even though it is not in Hardy-Weinberg it is not evolving.

Processes that reduce, remove, or maintain heritable variation in populations

Reduces Variation:

• Genetic Drift: (bottleneck, founders effect)

• Non-Random Mating: inbreeding decreases variation as homozygous traits are common.

Increases Variation:

• Gene Flow: introduces new genes to population

• Mutations: introduces new genetic variation, crossing over in meiosis

Effect of non-random mating (e.g., inbreeding) on allele frequencies and on genotype frequencies

Inbreeding: special form of nonrandom mating where genetically related individuals mate.

• Self-fertilization occurs in plants (pollen of plant fertilizes egg of the same plant) and occurs in some animals

• Organism in small, relatively closed populations carry the same alleles

• Inbreeding increases frequency of homozygous genotypes and decreases heterozygous.

• Amish as discussed also are affected by inbreeding increasing expression of disease.

• Does not generally change allele frequencies but prevents genetic equilibrium.

• Being out of HWE does not mean evolution is occurring. Even though it violates an assumption that allele frequencies stay the same.

• Assertive mating: mating with people that look like you

• There is no selection (same number of offspring) and the only violation of HW is nonrandom mating. Allele frequencies are the same but no longer in HW equilibrium.

• Disassortive Mating: mating with different phenotypic

Effects of genetic drift and gene flow on variation within a population

Gene Flow (Immigrants)

• Gene flow is the transfer of genes from one population to another through the movement of individuals or gametes.

• Immigrants who reproduce may introduce novel alleles shifting its allele and genotype frequencies. It is not just movement alone that fosters gene flow.

• Dispersal Agents: responsible for gene flow in plant populations. E.g. pollen carrying wind or seed carrying animals.

Contribution to a gene pool by immigrants must occur to foster gene flow and variation.

• Gene flow is dependent on the genetic variation between populations and the rate of gene flow between them.

Genetic Drift (By Chance)

• Chance events that cause allele frequencies in a population to change unpredictably

• Has more of an effect on smaller populations violating the Hardy Weinberg assumption of an infinitely large population.

  • Easier for allele frequencies to be drastically changed.

• Generally, leads to loss of alleles and reduced genetic variability

Bottleneck Effect

• When a stressful factor like disease, starvation or drought reduced a population greatly and eliminates alleles reducing genetic variation.

• Analogy: when environmental event occurs, only a certain number of alleles will pass through a bottle neck and increases likelihood of rare alleles being eliminated.

Founders Effect

• A population that was established by a few individuals has only a fraction of genetic diversity.

• Some alleles may be missing or rare alleles back home might be high in frequency

• 13% of Amish of Pennsylvania carry a rare recessive allele for dwarfism, shortened limbs and extra fingers. All individuals with these syndromes are descended from a couple who helped founded the community in mid 1700’s.

Relative fitness for each genotype, given a set of absolute fitnesses

• Selection is when different genotypes have different finesses

• Absolute Fitness(W): average number of surviving offspring for each genotype.

• Eg WAA=20 Waa= 15 Waa= 12 Selection is happening

• Relative fitness(w): divide absolute fitness by absolute fitness of most successful genotype(w = W/W_max).

  • Therefore, most successful will have a relative fitness of 1 and all others will have 1 or less.

**What type of selection is operating, given a set of relative fitnesses

How genetic drift can affect allele frequencies even in the absence of bottlenecks or founder events

• Random changes in frequencies due to sampling errors. Random changes in allele frequencies are always happening.

• Reduces genetic variation over a long period of time… happens by chance.

It is not a self-correcting process the fact that an allele decreases in one generation does mean it will increase in the next. It is random regardless of what happens in a previous generation.

*Which assumptions of Hardy-Weinberg equilibrium have likely been violated, given an observed set of genotype or phenotype frequencies

• No mutations are occurring

• The population is closed to migration from another population

• Population is infinite in size (no genetic drift)

• All genotypes in the population survive and reproduce well (no selection)

• Individuals mate randomly with respect to traits being considered

If observed genotype does not match expected, then HWE is violated and external factors caused discrepancies such as selection pressures or small population.

Cycle 7

Examples of genetic exchange/ recombination without reproduction, and of reproduction without genetic exchange/ recombination

• Reproduction without sex: binary fission

• Sex without reproduction: bacteria exchanging genetic info

How recombination contributes to population genetic variation

• Generates new multilocus combinations of alleles

• Offspring are genetically different from parents

Meanings of monoecious, dioecious

• Dioecious: separate sexes mating

• Monoecious: individual is male and female (hermaphroditic)

Difference between sequential and simultaneous monoecy

• Simultaneous: can be both sexes at once

• Sequential: can change from male to female or female to male

Examples and predictions of size-advantage model of sex change

• M to F: Protandry - F to M: Protogyny

Examples and predictions of adaptive sex ratio manipulation

• Which offspring sex has more to gain from being in good condition?

• Which offspring sex has less to lose from being in poor condition?

• Ex: male blue birds with bright feathers will mate more and produce brighter males, male blue birds with dull feathers won’t mate a lot and produce more daughters

Reason why most populations have 1:1 sex ratios

• When ratio is 1:1, there is no sexual advantage to being male or female

• When lots of males, there are not as many females to mate with and male advantage goes down, vice versa

Prevalence of sexual vs asexual reproduction in animals, plants and other forms of life

• First living things reproduced asexually

• Most organisms reproduce asexually

Costs of reproducing sexually as opposed to asexually

• Asexual populations grow 2x as fast since they don’t rely on males to fertilize females

Benefits of reproducing sexually as opposed to asexually

• Increases rate at which disadvantageous mutations can be discarded

• Increases rate at which advantageous mutations can be brought together

• Decreases likelihood of extinction

• Recombination speeds up evolution

How environmental stability influences whether sexual or asexual reproduction is

favoured

• Sexual reproduction is favoured when there is an immediate advantage that increases fitness of individuals due to their diversity

Lottery principle and Red Queen principle as environmental (short-term) benefits of sex

• Sexual reproduction is favoured if environment is likely to change

• Lottery Principle: buying many copies of the same ticket (asexual) VS buying many different tickets (sexual)

• Red Queen Principle: “it takes all the running you can do just to stay in the same place” 🡪 the world around us is constantly evolving rapidly and we must evolve to keep up

How sexual reproduction places different selective forces on males vs. females

• An attractive trait might not increase survivability

• Males have many traits that might not benefit them

• Males must compete for access to females

Distinction between intrasexual selection and intersexual selection

• Intrasexual Selection: direct competition between males for access to females

• Intersexual Selection: traits that females prefer in one male over another

Why males usually compete for access to females (rather than vice versa), and why in some species this pattern is reversed

• It’s easier for females because they invest more in reproduction whereas males have to be given the right to be the father

• It’s a lot easier for females to find willing partners

• Males can always increase their mating success

Which sex has higher potential fitness

• Males, since they can produce many offspring

Which sex has higher average fitness

• They have the same

Relationship between sexual selection and parental investment

• Females invest more (usually), thus females are choosy and males compete

• If parental investment is equal between both sexes (ex: humans, penguins), both sexes are choosy

Advantages and disadvantages of living in a group

• Advantages: helps capture prey, improves defense,

• Disadvantages: increased competition for food, dominant individuals get priority

Meaning of dominance hierarchy, kin selection, altruism, reciprocal altruism, eusocial, haplodiploidy

• Dominance Hierarchy: social system in which behavior of each individual is constrained by that individual’s status in a highly structured social ranking

• Kin Selection: allowing close relatives to produce proportionately more surviving copies of altruist’s genes than the altruists themselves could

• Altruism: individuals sacrifice their own reproductive success to help others

• Reciprocal Altruism: individuals help nonrelatives if they are likely to return the favour in the future

• Eusocial: a form of social organization in which numerous related individuals live and work together in a colony for the reproductive benefit of a single queen and her mate

• Haplodiploidy: sex determination in insects in which females are diploid and males are haploid

Calculate degree of relatedness between two individuals, given the type of relationship (parent-offspring, cousins, etc)

• Likelihood 2 siblings will receive same allele from mother at the same time is (0.5)(0.5) = 0.25

• Each link drawn in family tree represents 0.5

Identify why haplodiploidy can favour high levels of cooperation in social insects

• They are all related, therefore they wish to care for their siblings because they are all 75% related

• One of their siblings may become the future queen

Whether a particular social behaviour represents cooperation, competition, spite or altruism

Why "altruistic" and "spiteful" behaviours are both difficult to reconcile with natural selection

• Spiteful individuals have low fitness

How kin selection theory explains the persistence of helpful behavior

• If benefit to the actor’s indirect fitness outweighs the cost to the actor’s direct fitness, behavior is favored by kin selection

• Helpful behavior is favoured if rb > c (b = benefit, r = degree of relatedness, c = cost to actor’s direct fitness)

Situations in which kin selection does, or does not, favour helping non-descendant relatives

• Decreases individual fitness but increases overall fitness of population

• However, anything that reduces an individual’s fitness is vulnerable to being selected against

Meaning of direct fitness, indirect fitness, inclusive fitness

• Direct Fitness: producing your own descendant offspring

• Indirect Fitness: offspring produced with the help of the actor (increases the # of related alleles in the population)

Why interests of parents may conflict with interests of their offspring

• Helping create more offspring for your parents can have a better benefit than producing your own offspring

• “Do I help my parents or do I help me?”

Meaning of cultural intelligence, ultimatum game, rational maximizer

• Cultural Intelligence: the capability to relate and work effectively across cultures

• Ultimatum Game: proposer is offered money and can decide whether or not to share it. If responder rejects offer, neither of them get anything. Economic model predicts the proposer will offer the responder the minimum reward.

• Rational Maximizer: will accept an offer regardless of how low. Even 20% of the original is better than nothing.

Similarities and differences between humans and closely related species (eg chimpanzees) in cognitive ability, "cultural intelligence", response to the "ultimatum game", and the value of fairness

• Chimps are rational maximizers, whereas humans value fairness.

Relative risk of child abuse in families in which not all the adults are genetically related to all of the children

• Chance that a young child would be subject to criminal abuse was 40x higher when children lived with one stepparent and one genetic parent.

• Might be more difficult for people to invest in children that share no genetic info with them.

How asymmetries in relatedness can generate conflict between relatives

• Asymmetry in relatedness 🡪 disagree over when helpful behavior is appropriate

• If helping your brother benefits him (b) but costs (c) you, it depends on how big the benefit is

• Your brother is half as valuable to you as you are to yourself, therefore to help your brother b > 2c

• To your mom, you and your brother are equally valuable so your mom wants you to help your brother as long as b > c

• To your brother, he is twice as valuable as you so your brother asks you to help whenever b >

Conditions that favour or disfavour cooperation between non-relatives

• Mutual cooperation gives a better outcome is better than mutual betrayal

• Mutual betrayal is the rational outcome

Most recent common ancestor (MRCA) for a given group(s), given a phylogenetic tree.

• Homologies: similarities due to similar ancestors

• Common ancestor for all living things is called LUCA (Last Universal Common Ancestor)

• Only one LUCA, many MRCAs, one for each grouping

Why the idea that “humans are descended from chimps” is inaccurate.

• Chimps and humans have a MRCA that is not exactly like chimps or humans

Why some traditional groupings of organisms (“reptiles”, “fish”) do not reflect evolutionary relationships

• There are things we call monkeys that are more closely related to humans than of other monkeys which is alarming.  (Old world monkey vs New world monkey)

• Names we give organism ought to reflect their evolutionary relationships

• For reptiles it is not a sensible name to give a group of organism

• Evolutionary relationships between groups of reptiles are more closely related to birds than with turtles. Although turtles are reptiles, some reptiles are more closely related to birds than turtles.

• Fish does not reflect evolutionary relationships: they have multiple rendezvous points,

• Lung fish are closer related to us (humans) or birds than they are to other fish.

• Term prokaryote is not a good term to describe evolutionary relationships as archaea are more closely related to eukarya than bacteria.

How the relative position of fossils in sedimentary rock strata (higher vs lower) reveals their relative age

• Lower = older

• Higher = newer

Ways in which fossils can form

• Dissolved minerals can enter the spaces within bones and solidify (fossil skeletons)

• Can be preserved in amber (tree resin) to show fine details

• Moulds or impressions

• Footprints on mud

Reasons why the fossil record is incomplete

• Very few organisms fossilize completely

• Some organisms are more likely to fossilize than others

• Natural processes destroy many fossils

Importance of animal skeletons to the fossil record

• Hard tissues lend themselves to mineral fossilization

• Soft tissues are usually fossilized as moulds

Approximate age of the first living things, the first eukaryotes, and the first multicellular eukaryotes, based on fossil evidence

• First living thing: 3.5 billion years ago

• First eukaryote: 2 billion years ago

• First multicellular eukaryote: 1.2 billion years ago

What types of traits are useful in determining evolutionary relationships

• Characters that are independent markers of underlying genetic similarity and differentiation

• Traits in which phenotypic variation reflects genetic differences, while trying to exclude differences caused by environmental conditions

• Ex: tropical lizards can climb trees with sticky pads under their toes. They use the # of pads on the 4^th toe of the left hind foot. They wouldn’t consider the right foot’s 4^th toe as a separate character.

• They don’t care about fine details, its more about the bigger picture

Meanings of mosaic evolution, ancestral character, derived character

• Mosaic Evolution: some characters evolve slowly, while some evolve rapidly. Every species shows a mixture of ancestral and derived characters

• Ancestral Characters: old forms of traits present in distant common ancestors

• Derived Characters: new forms of traits

Whether ancestral or derived characters are more useful in determining evolutionary relationships

• Derived characters are more useful because they provide the most useful knowledge about evolutionary relationships. Unless derived characters are lost or replaced, they can serve as markers for entire evolutionary lineages.

Ways in which cladistic systematics differs from traditional evolutionary systematics

• Cladistics ignores morphological divergence, producing phylogenetic hypotheses and classifications that reflect only the branching pattern of evolution

• Species that share derived characters are put in one group

Recognize monophyletic and non-monophyletic groupings (taxa), given a phylogenetic tree

Difference between homologous and homoplasious traits

• Homologous: same shape but different function

• Homoplasious: characteristics shared by a set of species, but not present in their common ancestor. Ex: flattened tails of beavers and platypuses are homoplasious

Relatively close and relatively distant relatives, given a phylogenetic tree

• Look at how far apart the branches are from each other

• Look for how far the MRCA is

Whether or not two phylogenetic trees convey the same information

• Phylogenies can be moved around in orientation and still mean the same thing

• Branching pattern MUST stay the same, but nodes can be rotated

Monophyletic and non-monophyletic groupings, given a phylogenetic tree

• Monophyletic groups must include ALL of the descendants of the group’s MRCA (clades)

• Non-monophyletic groups don’t show all of the descendants of the MRCA

Meaning of synapomorphy, symplesiomorphy, autapomorphy; and know which of these is considered informative in cladistic analysis

• Synapomorphy: shared, derived traits (ex: birds and turtles share a trait, but lizards do not) USEFUL!!

• Autapomorphy: unique to a single taxon, derived trait (ex: birds have feathers, but lizards and turtles don’t) NOT helpful for cladistics analysis

• Symplesiomorphy: shared by 2 or more taxa, ancestral trait (ex: birds turtles and lizards all have the same trait from their MRCA) NOT helpful

Traits that are probably derived vs probably ancestral, given a phylogenetic tree and a suitable outgroup

• Probably Ancestral:

  • present in the outgroup AND the ingroup

  • present in outgroup and SOME of ingroup

• Probably Derived:

  • absent in outgroup, present in SOME of the ingroup

• Unknown:

  • present in outgroup, but NONE of the ingroup

  • absent in outgroup, present in ALL of ingroup

Distinction between parallelism and convergence, and how both of these differ from homologous similarities

• Both used to describe the tendency of organisms living under the same conditions to develop similar bodies

• Convergent Evolution: refers to distant phylogenically related organisms

• Parallel Evolution: closely related organisms

Whether carnivorous plants have likely evolved once or multiple times, and thus whether this trait is homologous or homoplasious

• They likely evolved many times

• Thus they are homoplasious

How the principle of parsimony informs outgroup analysis and helps identify the most likely phylogeny

• Whichever tree requires the fewest evolutionary changes (gains/losses), is probably correct

• Example:

  • Ingroup:

    • Chicken - No milk, No fur, Wings, Beak

    • Bat - Milk, Fur, Wings, No beak

    • Chipmunk – Milk, Fur, No wings, No beak

  • Outgroup (use something distantly related but not too distant):

    • Shark – No milk, No fur, No wings, No beak

Traits that are, and are not, synapomorphies (given a suitable outgroup and a distribution of traits)

• Is “having a beak” a synapomorphy?

• No It’s not shared, only one species has the beak

Which phylogeny is more parsimonious, given a suitable outgroup and a distribution of traits

Distinction between homology and homoplasy

• Homology: similarity that reflects recent common ancestry

  • Not all similarities are homologies

• Homoplasy: misleading similarity or dissimilarity (convergence and divergence)

  • Ex: placement of eyes in crocodiles and hippopotamuses, placed at the top because they need to see above water, not because they are closely related (convergence)

  • Ex: Darwin’s finches are very related but have very different beaks (divergence)

• Homoplasious traits have a superficial similarity (shape, colour) but deep structure are very different 🡪 ex: bats and flies both have wings, but made up of very different structures

Most likely phylogenetic tree of a group of organisms, given a suitable outgroup and a matrix of traits

• Think about which trait the common ancestor probably had (if outgroup and SOME of ingroup has trait)

• Look for autapomorphies (only ONE of ingroup has the trait)

• Which traits are synapomorphies?

Criteria used by the morphological, biological and phylogenetic species concepts to define species

• Species: a population of organisms capable of interbreeding and producing fertile offspring

• Morphological Species Concept:

  • Idea that all individuals of a species share measurable traits that distinguish them from individuals of other species

  • Applications – Identifying species of fossilized organisms

  • Weakness – Consider the variation in shells of snails. How can a variety of shells represent only one species of snail? Morphological species definitions tell very little about the evolutionary processes that produce new species

• Biological Species Concept:

  • Idea that all individuals of a species can interbreed and produce fertile offspring

  • If members of 2 populations can interbreed and produce fertile offspring, they belong to the same species

  • Genetic Cohesiveness – Populations of the same species experience gene flow, mixing their genetic material. Thus, a species is like one large gene pool

  • Genetic Distinctness – Populations of different species are reproductively isolated; thus they cannot exchange genetic info. The evolution of reproductive isolation between populations.

  • Weakness – Does not apply to organisms that reproduce asexually (bacteria, protists, fungi, plants)

• Phylogenetic Species Concept:

  • A concept where a species is the smallest population that can be united by shared derived characters.

  • They construct a tree of life for organisms of interest, tiniest twigs are species.

  • Advantage – Can be used on any group of organisms

  • Weakness – Detailed evolutionary histories have not been described for many species so biologists cannot apply the phylogenetic species concept to all forms of life.

Distinguish between pre-zygotic and post-zygotic isolating mechanisms and recognize examples of each

• Reproductive Isolating Mechanism: Any biological characteristic that prevents gene pools of 2 species from mixing.

• Pre-Zygotic Isolating Mechanisms

  • Exerts their effects before production of a zygote

  • 5 Types: ecological, temporal, behavioural, mechanical, and gametic

  • Ecological – species living in the same geographical region experience isolation if they live in different habitats. (ex: lions live in open grasslands and tigers live in dense forests, the 2 species do not encounter eachother)

  • Temporal – species living in the same habitat, if they mate at different times of the day/year. (ex: different fruit flies mate in the morning and some at night, different flowers release pollen in different months)

  • Behavioural – when signals used by one species are not recognized by another. (ex: a specific female bird song is not recognizable to other species of birds)

  • Mechanical – differences in the structure of reproductive organs or other body parts. (ex: plants have certain structures that allow only certain pollinators)

  • Gametic – an incompatibility between the sperm of one species and the eggs of another. (ex: surface proteins on gametes of each species recognize eachother and different species won’t match)

• Post-Zygotic Mechanisms

  • Exerts their effects after production of a zygote (when pre-zygotic mechanisms between 2 closely related species are ineffective, they will be isolated if the hybrids have lower fitness)

  • 3 Types: hybrid inviability, hybrid sterility, hybrid breakdown

  • Hybrid Inviability – hybrid organisms frequently die as embryos or at an early age because the developmental instructions from each parent do not interact properly. (ex: domestic sheep and goats can mate but the embryos always die before coming to term)

  • Hybrid Sterility – when the hybrids do survive, but cannot produce functional gametes. These hybrids have 0 fitness since they produce no offspring. (ex: Mules, the product of a female horse (2n = 64) and a male donkey (2n = 62) are always sterile)

  • Hybrid Breakdown – hybrids are capable of reproducing but their offspring either have reduced fertility or reduced viability. (ex: crosses between fruit fly species can produce functional hybrids, but offspring experience a high rate of chromosomal abnormalities)

Whether coming into secondary contact is required for speciation to occur

• Secondary contact is not necessary

• All that needs to happen is to separate a single population and have it diverge due to selection

Ways in which secondary contact can affect speciation

• Depends on how long the populations have had to diverge

• Populations may resume interbreeding if secondary contact happens soon after isolation

• Populations might have become partly or completely reproductively isolated 🡪 secondary contact has no effect

Whether prezygotic or postzygotic isolating mechanisms tend to be more costly

• Postzygotic isolating mechanisms waste a lot of reproductive effort

• You are investing lots of time into an offspring that ends up dying or reaches a reproductive dead end

Mutualistic, competitive and antagonistic relationships between species, given 'real world' examples

• Mutualistic: both species benefit (ex: ants live on a tree, protecting it from predators but using it as a source of food and shelter)

• Competitive: both species may experience a cost (ex: lions and cheetahs fighting for food, species all sharing at the same water resource)

• Antagonistic: one may use the other as a resource (ex: a caterpillar eats a plant, hosts and parasite)

Factors that advantage one side or the other in an evolutionary arms race

• Keeps escalating until costs of continuing to escalate outweigh the benefits

• Follows life-dinner principle

Meaning of 'life-dinner principle'

• What’s on the line if they don’t win the arms race?

• There’s stronger selection pressure on the prey

• If the prey loses, it dies, but if the predator loses, it simply has to find another meal

Difference between prudent-parasite hypothesis and trade-off hypothesis, in terms of the evolution of virulence

• Prudent-Parasite Hypothesis: virulence (strength of damage the parasite causes) decreases over evolutionary time

• Trade-Off Hypothesis: parasites balance costs/benefits of virulence

Factors that influence the optimal virulence of a given host/parasite relationship

• Transmission mode, host ecology

Costs and benefits of being highly virulent (from the point of view of the parasite)

• Benefits: increases competition between the host, helps transmit it to new host individual

• Costs: kills the host quickly, so lifespan is short

Why improving equipment for survival does not always translate into 'winning' an evolutionary arms race

• If a predator adapts overtime to run faster, their prey also adapts to run faster, thus, there is no higher success

Competing theories about where modern humans (Homo sapiens) evolved, and which is best supported by available evidence

• African Emergence Hypothesis:

  • Early hominin descendants left Africa and established populations in the middle east, Asia, and Europe. Later, Homo sapiens arose in Africa and also migrated.

  • Homo sapiens drove hominins to extinction

  • Genetic data supports this hypothesis

  • It was later confirmed from work on the Y chromosomes that people from all over the world were all descendants of a single migration out of Africa

• Multiregional Hypothesis:

  • Populations of H. erectus and archaic humans spread through Europe and Asia and modern humans evolved from their descendants.

How different species concepts resolve (or do not resolve) the question of whether Homo sapiens, neandertals and Denisovans were all members of the same species

• Vital components of our immunes system were acquired through the HLA-B*73 allele inherited from Denisovans in west Asia 🡪 some HLA haplotypes entered modern European and Oceanian populations from both neandertals and Denisovans

• Genomic analysis shows that ancestors of modern humans interbred with both neandertals and Denisovans 🡪 therefore all one species under biological species concept

• Morphological evidence from fossils is incomplete thus the phylogenetic species concept cannot be used

Arguments for and against the idea that human are no longer evolving

• For:

  • Humans now are very similar to humans hundreds of years ago

• Against:

  • Genetic Drift is occurring

  • Population size is continually growing (increasing helpful mutations)

Evidence for recent evolution in humans

• Selective Sweep: when a favourable new mutation increases in frequency, adjacent stretches of DNA come along for the ride (hitch-hiking)

• Recently selected alleles have little variation in surrounding

• Eventually, recombination introduces variation around the favourable allele

• Detecting selective sweeps allows you to estimate the age of the selection event by analyzing the sequence variation around polymorphisms

• Adaptations have been found for new food sources, and higher altitudes

Costs of large brains

• Brain is only 2% of body weight but takes up 20% of your energy

• Logistics of childbirth (large head is hard for females to give birth)

Possible advantages of large brains as proposed by the "utility hypothesis" vs. the "mating mind hypothesis"

• Utility Hypothesis: language, tool use, and planning are needed in order for survival

• Mating Mind Hypothesis: art, wordplay, humour, and music are needed in order for mating success.