BIS 2B

How do concepts from the field of geology influenced Darwin’s theory of evolution? Think about Lyell's gradualism and Darwin’s theory. How were the theories applied in biology compared to geology.

Influence from Lyell’s gradualism philosophy, which focused on impacts of changes that occur slowly over long periods of times. In geology, these processes were things like erosion and sedimentation(grand canyon), but in biology, Darwin applied these ideas to genetic and morphological changes in organisms over long periods of time.

What was Darwin’s theory of evolution?

Species change overtime with advantageous traits, genetic variations, and survival to fitness. It was a process of natural selection where those best adapted to the environment are more likely to survive and reproduce, passing on traits to the next generation.

Aristotle’s scala of naturae

Organized on a hierarchical level from least to most perfect organism. Every species had to be perfect, any difference was considered a mistake. Unchanging ladder.

Cuvier's Catastrophism

Earth history shaped and lineage disappearance caused by catastrophic events (floods, earthquakes, asteroid hits)

Lyell’s Gradualism

Gradual evolution from erosion and sedimentation(fossil and grand canyon)

Evolution: Genetic change over time. Both random and selected changes

Adaptation: type of evolution that occurs through natural selection

Describe the types of evolution, microevolution vs macroevolution.

Micro = changes in allele frequency across generations

Macro = changes in species, long period of time

Fitness: ability to survive and reproduce. More offsprings = more fitted

Describe absolute and relative fitness. The equations and what happens when RF is < or > to 1, how does it affect the average

Absolute fitness: # of offsprings/# of a species’ individuals

Relative fitness: # of offsprings/population mean fitness

RF>1 better than avg, RF<1 worse than avg

Breeder’s equation

R = h^2S

S: difference b/w initially selected breeder and the average of the whole population

R: how much the phenotype shifted(across generation)

Heritability is h^2, don’t take the square

Natural selection conditions

Genetic variation: phenotypic difference

Heritable traits: at least partially genetic/genes involved/can be pass on (0-1 scaled)

Differential success: more fitted survive and reproduce more

Drivers of Natural selection

Species Interaction

Environmental factors

Mate choice

Constrains(drive) of natural selection 

Recessive allele that aren’t expressed before reproductive age, deleterious trait beneficial in certain circumstances, changes in environment, law of physics, evolutionary history, tradeoffs, lack of variation (bottleneck effect, etc)

What are the patterns of natural selection?

Directional selection, stabilizing selection, and disruptive selection. There’s also balancing selection, which includes negative and positive frequency-dependent selection. Spatial/temporal variation and sexual selection

Describe positive and negative frequency dependent selection.

Primarily based on how common the trait is within the population. The rarer the trait, it’ll move towards it until it becomes common. Moves back and forth b/w traits.

• Positive, more common in population = higher fitness

• Negative, less common in population = higher fitness

Describe directional selection

Phenotype of one extreme has the highest fitness

Describe stabilizing selection? 

Phenotype near the mean has the highest fitness

Describe disruptive/diversifying selection?

Both extremes have the highest fitness

Balancing selection

Selection that maintains variation in a population

Disruptive selection maintains and balances selection

Directional/stabilizing decreases variation and doesn’t balance selection

Spatial/temporal variation

Creates diverse and changing environmental pressures that influence advantageous traits for survival and reproduction. Spatial variation across different regions favors local adaptations to unique conditions, potentially leading to speciation. Temporal variation depends on seasonal or climate shifts, changing selective pressures over time, favoring adaptable traits. 

Describe sexual selection. How does this affect natural selection?

A mechanism of evolution when one sex has a mate preference for specific traits.

Describe the factors that constrain the process of natural selection. Why does natural selection not always result in organisms that are perfectly adapted to their environment?

Physical constraints (Insect size↑, O2 lvl ↓, O2 lvl↑ in atmosphere, more -> into body), evolution history, trade offs(max one trait limites the other, energy trade offs), and lack of variation(natural disaster = less traits to select upon in the future. Traits that are beneficial now may not be in the future.)

Define a chromosome, loci, gene, alleles, and genome

Chromosome: A long sequence of DNA (everyone has 23 pairs of chromosomes, one from each parent, total of 46)

Locus: The position in the genome(where genes are located)

Gene: The section of DNA that codes for a particular protein (occupies position in genome)

Alleles: Variations, different forms of the same gene

Genome: All genetic material on individual carries (chart)

Define Nucleotide, main 4 nitrogenous bases, the pairings in DNA and RNA

Nucleotide: Organic molecules that make up DNA and RNA (building blocks)

Main 4: Adenine, Guanine, Thymine, Cytosine

Bonds: T/U(Uracil, used in RNA)-A, G-C

Describe the process of transcription and translation

Transcription (DNA->RNA):

Helix opens > enzymes enter and place RNA bases onto antisense strand

Translation (RNA->Protein):

mRNA leaves nucleus > enters cytoplasm > tRNA binds to mRNA strand with corresponding bonds > protein petite binds to the tRNA > helix closes

Describe substitution, insertion, and deletion mutation. How do mutations affect gene expression? What do they cause?

Synonymous and nonsynonymous

Substitution: A nucleotide is exchange

Frameshift

Insertion: Nucleotide added (3 base pair units shift down(frame shift), can change AA sequence, codon can stop early)

Deletion: Nucleotide removed (changes AA sequence, loses part of chromosome)

How can synonymous and nonsynonymous substitutions affect an organism’s phenotype?

Synonymous: Doesn’t affect AA sequence

Nonsynonymous: Can change, likely to have phenotypic consequence

Law of segregation

When an individual produces gametes, the two copies of a gene separate so each gamete receives only one copy. Homologous chromosomes > chromosomes replicates to sister chromatids > two chromosomes segregate and separate into daughter cells > separate into four haploid gametes, each contains one allele

Law of Independent assortment

Alleles of different genes assort independently during gamete formation.

Offspring probability

P(Y and R) = P(Y) x P(R)

P(BB) = P(B for one parent) x P(B for another parent)

Recombination

Genetic material exchange(crossover) to create for genetic diversity and to avoid both alleles from being on the same chromosome

Simple/Complete dominance

One dominant allele determines phenotype

Incomplete dominant

blending

Codominant

Heterozygous is both alleles fully expressed (splotches)

Understand how to read a pedigree analysis

Linkage

Alleles close together on the same chromosome are more likely to get inherited together

Far apart -> often/mostly inherited independently

Close together -> often/mostly inherited together

Sex linked inheritance

X-linked traits > male genotypes (x^BY, X^bY called hemizygous)

X chromosomes determine other genes, not Y

Y can’t inherit alleles

Describe the different inheritance patterns, pleiotropy, polygenic inheritance, environmental influence, and epistasis. Provide examples of each. 

Pleiotropy: Single gene that affects multiple traits

Ex. Marfan syndrome is a single allele, phenotype that affects multiple regions in the human body including vision problems, cardiac problems, and limb length

Polygenic Inheritance: A trait controlled by many genes

Epistasis: When multiple genes interact to determine the phenotype

Ex. Black/brown gene: Black complete dominance over brown. Extension gene: recessive trait (ee) lacks pigment in the fur (yellow)

Environmental Influences: environment affecting phenotypes

Define population

interbreeding group of organisms of the same species

How does natural selection act on individuals?

Determines who survives and who doesn’t. Determines who reproduces how much and who doesn’t.

How do populations evolve?

They evolve through genetically based changes in trait means across generations and through changes in allele frequencies across generations.

What are allele frequencies?

The proportion of allele across all individuals or gametes produced by those individuals.

Dominant and recessive alleles

What are genotype frequencies?

The proportion of individuals w/ a specific genotype in a population.

Homozygous dominant, homozygous recessive, heterozygous, hemizygous

Frequencies have to be between..

0 and 1

What is HWE and what are the 5 conditions it assumes?

In a non evolving population, genotype and allele frequencies reach equilibrium after one generation and remain constant in subsequent generations

Assuming: 

No mutations

no natural selection

no migration(genetic flow)

no genetic drift(have large population)

no random mating

If observed geno freq = expected geno freq, population in HWE

How do you calculate frequencies?

Freq of AA geno = # of AA individuals (NAA)# of total individuals (N)

Freq of A allele = # of A alleles# of total alleles=2NAA+NAa2N

Expected genotype frequencies. How to calculate for allele frequencies p and q

p+q=1

p^2+2pq+q^2=1

p = f(SS)+½ f(Ss) = #

q = 1 - p = #

How to check whether a population follows HWE?

1. Calculate genotype frequency based on observation

2. Based on genotype frequency, calculate allele frequency

3. Using observed allele frequency, calculate expected genotype frequency

4. Compare observed & expected genotype frequency

5. Different = not HWE, same = HWE

What changes the frequencies?

Mutation: 

Mistake during DNA replication

Violates HWE condition

Both beneficial/deleterious

Gene flow: 

Transfer alleles through movement of individuals/their gametes

Flow b/w two populations make them similar to each other

Can happen w/o individual moving (pollen carried by wind)

Genetic Drift: 

Chance event that cause allele frequency to fluctuate/unpredicted

RANDOM EVENT· No preference for any allele= nondirectional

May involve temporary increase in diversity, but eventually leads to loss of genetic diversity/ ↑ homozygosity of common allele

Smaller the population, greater its effect

Extreme cases

Rare alleles lost, deleterious rare allele becomes common

Make future generations susceptible for stressors

Non-Random Mating

Inbreeding and outbreeding

Natural selection

Directional, stabilizing, disruptive/diversifying

Calculating frequencies after selection

Initial frq x relative fitness = proportion surviving

Frequency after selection: proportion of surviving/sum of all proportion surviving

What is gene flow(refers to migration)?

The transfer of alleles through movement of individuals or their gamete. The population overtime will become more similar to each other. Makes populations more similar

Example:

Pop I is a large pop with birds of geno AA, Aa, and aa. A bird of geno aa migrates from pop I to pop II introducing the a allele. Pop II located far from pop I initially only had AA

How does genetic drift affect population size?

Small pop > lose allele > lost of allele in next gen

Large pop > lose allele > no effect bc there’s still many in next gen

What are extreme cases genetic drift can cause? Describe genetic bottleneck and founder effect.

Genetic bottlenecks: population size severely reduced

Founder effects: New populations created form a few founders

Describe what’s happening in this photo

How does inbreeding affect the allele frequencies compared to what we would expect in HWE?

Inbreeding reduces the # of heterozygous and increases the # of homozygous.

How does inbreeding expose deleterious recessive alleles? What are the consequences?

Genetic drift can cause high frequency of deleterious alleles in small populations. Consequences include human genetic diseases and conserving small populations of rare species.

Graph of Dominant vs. Recessive beneficial alleles

Describe a dominant and recessive beneficial allele. How does natural selection acts on these phenotypes?

Dom: Heterozygote gets dom pheno, allele frequency increases rapidly

Rec: Rare, mostly present in heterozygotes, allele frequency increases slowly

When the beneficial allele is recessive, have to wait for heterozygous individuals to make homozygous individuals > homo recessive individual > inc freq rapidly

Beneficial alleles, why?

Natural selection operates on phenotypes > beneficial allele is recessive > all alleles is masked in heterozygous > need both recessive alleles present

Define Biological concepts. Pros and Cons

Group of actually/potentially interbreeding natural populations that are reproductively isolated from other groups.

Pro: Easy to understand, linked to gene flow

Con: Doesn’t apply to some organisms, dont always have mating data

Define Lineage/phylogenetic species concept. Pros and Cons

Group of individuals that share an evolutionary genetic history on a phylogenetic tree.

Pros: Includes historical/evolutionary context, applies to all organisms for which genetic data are available

Cons: Requires modern genetic and computational tools

Define morphological species concept. Pros and Cons

Group of individuals that share morphological similarity

Pros: Good for groups with limiting data

Cons: Similarity and difference in appearance can be misleading

Reproductive barriers. Define prezygotic and postzygotic barriers

Prezygotic: Before zygote(fertilization), prevent mating or fertilization from occuring

Postzygotic: After zygote, prevents zygote from developing into a fertile and viable adult

What are some prezygotic barriers? Provide examples along with the isolations

Habitat isolation: Ecological and geographical, species occupy diff habitats > two species X contact

Temporal isolation: Different breeding time > two species X mate

Behavioral Isolation: Different behavior > X recognize potential mates

Mechanical Isolation: Physical differences b/w organisms > X successful mating

Gametic Isolation: Sperm can’t fertilize egg

What are some postzygotic barriers? Define

Reduced hybrid viability: incomplete development or low survivorship

Reduced hybrid fertility: viable offsprings, but incapable of reproducing

Hybrid breakdown: Hybrid offspring are viable and fertile, but the subsequent offsprings aren’t viable or are sterile

Reproductive Isolation and Speciation

Cont, pop w/ genetic diversity >new factor> divides into 2 pops that can’t breed w/ each other >time(mutation, natural selection, more fitted organism emerges)>speciation

Allopatric speciation: species arises in different places

Describe vicariance and founder effect in allopatric speciation

Vicariance: geographic separation of species due to physical barrier (ex. Flooding, buildings)

Founder effect: small portion of original population found bigger population

Sympatric speciation

Species arising in same region

Secondary contact

2 species diverge from a population, which creates a hybrid. 

3 different hybrids

Species fusion: Hybrid dominates, species merge together

Stable hybrid zone: Hybrid exists, but doesn’t collapse the species

Reinforcement: Hybrid isn’t selected. Increase reproductive isolation

Factors that affect speciation rate

Specialist vs Generalist: specialization leads to rapid speciation

Dispersal ability: lower dispersal ability leads to higher speciation

Adaptive Radiation: Rapid divergence of species form a single ancestor into an army of new species due to environmental pressure, sexual selection, vacant ecological niches, specialized diets, etc

Phylogenetic tree, describe the details

Graphic depiction of history of relationships among a group of organism

• One branch is typically called taxa

• Know how an interchangeable branch looks like

What is speciation and extinction on a phylogenetic tree?

Speciation: create branches, new lineage

Extinction: remove branches, loss of lineage

Monophyletic clade

Group that includes all of the taxa descended from a common ancestor

Cut clade horizontally not vertically

The calibrated phylogenies

Phylogenetic trees + radiation clating technology

Phylogenetic tree with time

Homologous trait: A trait that is present in different organisms because it is inherited from

common ancestor/produced by descent with modification

Analogous trait: A trait that is present in different organisms because of similar selective

pressure/produced, evolved independently