Unit 3 Evolution

photorespiration

photorespiration is when rubisco binds oxygen instead of carbon dioxide due to low levels. when rubisco bins O2 instead of Co2 it produces one molecule of 3-PGA and one molecule of 2-phosphogylcolate(toxic), overall it consumes ATP and NADPH without producing any sugar.

the adaptations of the C4 and CAM plants

C4 plants:

- spatially seperated the steps in photosynthesis:

in mesophyll cells CO2 is fixed into 4 carbon compound which does not react with O2. the 4- carbon compound is then transported into the bundle sheath cells where it realeases Co2 near rubisco, so calvin cycle can run with high CO2 concentration

- Reduces photorespiration even under high temperatures.

- Efficient in environments with high light and heat.

CAM plants:

- temporal seperation of steps

Night: stomata open and take in CO2 and fix it into organic acids like malate

Day: Stomata close to conserve water, CO2 is released from stored acids inside the leaf and used in the calvin cycle

photosynthesis and its connection to respiration

Photosynthesis:

Reactants: 6CO2, 6H2O, light

products: Glucose and oxygen

connection to respiration: G3p from calvin cycle used in cellular respiration. O2 used as final electron acceptor at the end of etc

population

a group of organisms of the same species who live in the same area at the same time.

natural selection

variation, heritability, consequences (some traits give individuals a better chance of surviving and reproducing)

Stabilizing selection

- favors individuals near the population average

- reduces diversity in the population but maintains trait that are already well-suited to the environment

ex) Human birth rate

Disruptive selection

- favors individuals with traits at both extremes

- increases diversity and can lead to speciation if the extremes become separate populations

ex) beak sizes in bird population: small beaks are good for eating soft seeds while large beaks are good for eating hard seeds. medium beaks are less effective at both

Directional selection

- favors one extreme trait

- against the other extreme trait and sometimes intermediate traits

- shifts the average trait in the population toward the favored extreme

Ex)

Peppered moths during the Industrial Revolution:

Light-colored moths were easily seen by predators on soot-darkened trees.

Dark-colored moths survived better → population shifted toward darker moths.

Antibiotic resistance in bacteria:

Bacteria with a gene for resistance survive antibiotics.

Over time, the population becomes mostly resistant.

How can evolution be measured by changes in allelic frequencies

allele frequency is the proportion of a specific allele in a population. A change in allele frequency from one generation to the next, indicates that evolution is occurring.

Factors that change allele frequencies:

- natural selection: favorable alleles increase in frequency

- Genetic drift: random changes in allele frequencies (important in small populations)]

- Mutations: introduce new alleles into the population

- Gene flow: Movement of alleles between populations

Define Bottleneck effect

A type of genetic drift that happens when a population is drastically reduced in size due to a sudden event (natural disaster, disease, human activity). This causes a loss of genetic variation and can change allele frequencies in surviving populations.

Effect:

- many alleles may be lost

- rare alleles might disappear completely

the surviving population may not represent the original population genetic diversity making the new population more vulnerable to disease and environmental changes

Define founder effect

The founder effect

A type of genetic drift when a small group of individual breaks off from a larger population to start a new population

Effect on Genetics:

Allele frequencies in the new population may differ from the original population.

Rare alleles in the original population may become common, or common alleles may be lost.

Long-term Impact: Can lead to rapid evolutionary changes and unique traits in the new population.

gene flow

movement of alleles from one population to another. it introduces new alleles to a population and can reduce differences between populations overtime.

- counteracts natural selection or genetic drift

- help populations adapt

Example:

- Pollen from one population of flowers is carried by bees to another population.

- The new alleles from the pollen mix with the local gene pool, changing allele frequencies.

genetic drift

random change in allele frequency due to chance events rather than natural selection. Most significant in small populations as it reduces genetic variation

impact on evolution:

- causes populations to evolve randomly

- can lead to fixation of certain alleles (allele frequency reaches 100%)

ex) bottleneck or founder effect

hardy-weinburg equilibrium

Allele frequency:

p= frequency of dominant allele

q= frequency of recessive allele

p+q=1

Genotype Frequency:

p^2= frequency of homozygous dominant (AA)

2pq = frequency of heterozygous (Aa)

q^2= frequency of homozygous recessive (aa)

When to Use Hardy-Weinberg Equations:

- To predict allele/genotype frequencies if a population is not evolving (no mutation, no migration, no selection, random mating, large population).

- To compare observed data with expected frequencies and see if evolution is occurring.

environmental change generating phenotypic change

An example is the peppered moths

. Original Environment (Before Industrial Revolution)

- Trees were mostly light-colored with lichen.

- Most moths were light-colored, which camouflaged them from predators.

- Dark-colored moths were rare because they were easily spotted and eaten.

- Phenotype frequencies: Mostly light-colored moths.

2. Environmental Change (Industrial Revolution)

- Pollution killed lichens and darkened tree bark with soot.

- Now dark-colored moths were camouflaged, and light-colored moths became highly visible to predators.

3. Phenotypic Change (Natural Selection in Response to Environment)

- Dark moths survived and reproduced more → their frequency increased.

- Light moths declined because they were eaten more often.

- Over generations, the population shifted to mostly dark-colored moths.

MC1R allele

- the MC1R gene controls skin pigmentation

- in equatorial Africa, the allele for darker skin is very common as it has intense UV radiation.

- Darker skin protects against UV damage

Connection to Darwin:

- dark-skinned individuals survived better under strong UV exposure and had more offspring and so the trait for MC1R was passed on

Result: Over generations, the MC1R allele became highly prevalent in populations living near the equator.

Convergent evolution

this is the process where unrelated or distantly related organisms evolve similar traits independently because they live in similar environments or face similar selection pressures.

Examples:

1. Wings in bats and birds:

- Both have wings for flying, but bats are mammals and birds are aves.

2. Streamlined bodies in sharks and dolphins:

- Sharks are fish, dolphins are mammals, but both evolved similar body shapes for efficient swimming.

define polyphyletic

polyphyletic is a group of organisms that are combined based n similar traits but do not share a recent common ancestor. Their similarities are usually due to convergent evolution

Example) grouping birds, bats, and insects together because they all have wings but their ability to fly evolved independently

define paraphyletic

A group of organisms that includes a common ancestor and some, but not all, of its decedents

- so it includes a shared common ancestor but excludes at least one descendent lineage

- considered incomplete

Ex) reptiles include lizards, snakes, turtles but excludes birds even though birds evolved from reptile ancestors

- so reptiles without birds is a paraphyletic group

define monophyletic

A group of organisms that includes a common ancestor and all of it's descendants. Also called a clade and accurately reflects evolutionary relationships

- include a shared common ancestor and all descendant species

phylogenetic tree

Root: base; represents common ancestor of all organisms and shows the starting point of evolution for that diagram

Branches: Lineages overtime and show how species diverge from ancestors

Nodes: The points where the branches split. Represent a common ancestor where a lineage diverged into 2 or more groups. Indicates a speciation event

Clade: a group consisting of a common ancestor and all its descendants

species

a species are a group of organisms that can interbreed naturally with one another, produce fertile offspring, and are reproductively isolated from other groups.

Explain the relationship between genetic divergence and reproductive isolation

- genetic divergence is the accumulation of genetic differences between populations overtime

- reproductive isolation occurs when 2 populations can no longer interbreed and produce fertile offspring. Can either be pre or post zygotic barriers

- when populations become separated they stop exchanging genes and over time, genetic divergence increases as each population evolves independently. As differences build reproductive barriers develop and eventually the populations become reproductively isolated, meaning they are now separate species

allopatric vs sympatric

Allopatric:

Formation of new species when a population is geographically separated into 2 or more isolated groups.

ex) physical barriers like mountains, rivers, islands prevent gene flow

Sympatric:

Formation of new species without geographic separation, usually through genetic, behavioral, or ecological differences

ex) factors like polyploidy, habitat preference, or sexual selection --> reproductive isolation arises within the same location

Describe examples of pre-zygotic and post-zygotic reproductive isolating mechanisms

pre-zygotic: prevents fertilization from happening in the first place

example)

- temporal: species reproduce at different times

- behavioral: mating rituals or behaviors don't match

- Mechanical: Physical differences prevent mating

- Gametic: sperm and egg cannot fuse

- habitat: species live in same area but different habitats

Post-zygotic: fertilization occurs but offspring is inviable or infertile

example)

- hybrid inviability: zygote fails to develop or dies early

- hybrid sterility: hybrid survives but is sterile (mule)

- Hybrid breakdown: hybrid can reproduce but offspring are weak or sterile

criteria of domestication

- flexible diet

- fast growth rate

- ability to breed in captivity

- manageable temperament

- tendency to follow a hierarchy

Explain the Neural Crest Hypothesis as a driver of domestication

The Neural Crest Hypothesis suggests that domestication works because selecting for reduced aggression alters neural crest cell development, which then produces the common physical and behavioral traits of domesticated animals.

phylogenetic analysis

phylogenetic analysis is the use of genetic, morphological, and evolutionary data to construct relationships among organism's and build phylogenetic trees. Shows common ancestry and tracking a trait evolution

In-vivo

- experimental medium is alive whole organisms

Drawbacks:

- need clear phenotypic expression in organisms response ot experimental treatment

- animals are hard to control

- ethical standards

In-cell

- experimental medium is cell cultures from organism of interest

In-vitro

- experimental medium is test-tubes of isolated and recombined biological molecules to ask questions about biological mechanisms of function

In-silico

- experimental medium is computer software analysis. Developing mathematical models to analyze data, make hypothesis, and draw conclusions

Multiple sequence alignment

- MSA's are software programs that "score" sequence similarities as 'conservation' or 'consensus'. Compares 3 or more DNA, RNA, or protein sequences to identify similarities and differences among them.

reveals: conserved regions, evolutionary relationships, mutation/variation

MSA

amino acid sequences, genomic sequences, mRNA seqences

Paralogs vs. Orthologs

Paralogs: genes within the same species that arose by gene duplication. Can evolve new or specialized functions overtime

Orthologs: genes in different species that evolved from a common ancestral gene due to speciation. Often retain similar funtions across species

MSAs and phylogenetic trees

in-silico

Paralogous genes

Gene duplication within a genome

Which data pairs would you expect to have the highest sequence similarity? Which would have the lowest?

lowest: unrelated genes from evolutionary distant organisms

Highest: Orthologous genes from evolutionary related organisms

Sexual selection

A form of natural selection in which individuals with certain inherited characteristics are more likely than other individuals to obtain mates.

Artificial selection

Breeding organisms with specific traits in order to produce offspring with identical traits.

Competition

the struggle between organisms to survive in a habitat with limited resources

reproductive success

refers to how well an individual passes on its genes to the next generation. How many viable, fertile offspring an organisms produces.

What is eumelanin and pheomelanin?

- 2 main types of melanin

Eumelanin:

- provides dark pigmentation and protects against UV radiation

Pheomelanin:

- provides lighter pigmentation and has less UV protection

relationship between UV exposure and spina bifida

- Folate is essential to develop brain and spinal chord

- UV radiation breaks down folate and can lead to a deficiency which can lead to spina bifida

- Populations in high-UV environments evolved darker skin pigmentation (more eumelanin) to protect folate from UV degradation.

relationship between eumelanin and vitamin D

- Body produces vitamin D when exposed to UVB radiation from sunlight

- High eumelanin protects against UV damage but reduces UVB, slowing vitamin D synthesis. However in equatorial regions sunlight is abundant so not an issue in vitamin D synthesis

In high-latitude regions (low UV):

Light skin evolved → allows sufficient vitamin D synthesis despite weaker sunlight.