General Bio 2

Evolution

exploring the mechanisms that allow for change

Charles Darwin Education

went to the University of Edinburgh to study medicine

-wanted to go into surgery (didn’t have the stomach)

switched to study natural sciences at University of Cambridge

-led to divinity school (priesthood)

Charles Darwin journey

went on the HMS Beagle (ship)

-early 1830’s (was young)

-went to South America

\*England--→ South America

-went along the coast of the Galapagos’ Island

Charles Darwin’s Inspiration

used Charles Lyell and Thomas Mathus’ findings in his journey

Charles Lyell

studied geology and geography

-noted geology changed gradually

-noted for cliff and rock formations

\*Newest materials surfaced over old ones

Thomas Malthus

studied population science

-resources are linear (stressor/adaptive forces)

-populations are exponential

at the point that resources and populations meet there is a Malthusian catastrophe

Malthusian catastrophe

the point where resources and populations meet and population either crashes or platues

Adaptive forces and stressors due to resources

\-different species thrived better based on what was available

\-animals will change to be able to survive; drives change

Darwin’s discoveries

animals in South America are much different than in England

-the animals in South America throughout the coast were similar but different

Selective selection

parent--→offspring

* (crossing over and genetic variability)
* select traits in a population to create ideal conditions

Alfred Wallace was

Darwin’s problem

-was on the verge of publishing before Darwin (similar finding)

\*Darwin sat on his knowledge for 30 years

Alfred Wallace journey

went to the Malay Arch (Malasia) in 1858

Darwin’s Origin of Species was published in

1859

Gregor Mendel (1865)

inheritable traits; have dominant and recessive genes

Throughout 1900-1918

tied genetics into evolution

around the end of World War 1

-survival of the fittest (Darwinism)

-science was used in politics to pit countries against one another (fitness competition)

Fitness

having offspring that are viable

-alive

-survive

-successful genetic makeup

-offspring reproduce viable offspring

Fitness drives

natural selection

Adaptations allow for

better fitness

Natural selection

traits within a population and how they evolve

-what are the adaptations made?

Traits will

evolve in offspring

-crossing over/genetic variability

-it is generational

Traits have a

1. Phenotype
2. Genotype (AA, Aa, aa; in diploid organisms)

Population definition

1 species with a common local

ex. one cell makes up a tissue

ex. giraffes living in a desert

Population will have

genetic variation (frequency)

-what is the pattern (balanced, fixed)

Genetic variability (allele frequency)

(A= p) (a= q)

all loci= gene pool

p+q=1

* 2N (measuring genetic variability in genotype)
* 2NA+NA/2N (total)
* 2Na+Na/2N (total)

Wild Mustard Plant

terminal bud= cabbage

lateral bud= brussel sprouts

flowers= cauliflower

bud+ stem= broccoli

* different alleles
* selective variation

Hardy Weinburg Equilibrium

Null hypothesis


1. mating is random
2. large population
3. no gene flow
4. no mutations
5. natural selection does not affect survival (does not favor a particular genotype)
* p= AA
* q= aa
* pq=Aa
* p^2+2pq=q^2 (change in the formula is evolution)

Polymorphic

population with homozygosity and heterogosity

Monomorphic

population with one form of either homozygosity or heterogosity

1 million cell cycles

at least one mutation

Mutations

change in DNA --→ change in RNA --→ change in codons

* could change the amino acid that the codon codes for
* amino acid could change the protein that is formed

3 situations if codons are changed during mutations

1. no change (same amino acid is coded for)
2. missense mutation (different amino acid than original)
3. stop codon (nonsense)
* don’t get a full protein

Most mutations are

spontaneous

Gene flow

migration

* similar species
* different population of the same species

Genetic drift

1. Population bottleneck
* decreases genetic frequency
2. Founder effect
* introducing new alleles to a scene
* new region
* new population

Non-random mating

Sexual selection

* males will make themselves more attractive to mate with
* compete for accessibility and fitness
* how healthy is the male (fit)
* good color? parasites?
* choose best fit
* females favor homozygote traits

Natural selection

* represented by a bell curve

Natural selection adaptive forces

1. Stabilizing
2. Directional
3. Disruptive

Stabilizing adaptive forces

both tails (adaptive forces)

* stabilizes along the average
* makes the beel curve skinnier in

Directional adaptive forces

on one side/tail

* moves either left or right away from the mean’s original spot
* moves the mean over and changes the overall mean

Disruptive adaptive forces

* adaptive forces work against the mean
* select tail traits
* creates a wavy graph

Genetic variation is maintained by

1. neutral alleles
2. sexual recombination
3. frequency-dependent selection
4. environmental variation
5. geographic area (large)→ sub populations

Neutral alleles

fitness is neither better nor worse

Sexual recombination

* individual level= cross over (happens in meiosis)- gamete variability
* fertilization=combining gametes

Frequency-dependent selection

ex. left sided and right-sided jawed fish

* the fitness of a phenotype or genotype depends on the phenotype or genotype composition of a given population
* the fitness of a phenotype or genotype increases as it becomes more common

Environmental variation

no genotype is good for environmental variation

* different genotypes thrive in different areas

Geographic area (large)-→ sub populations

different selective forces in each geographic area

* migration affects species by different selective forces

Selective forces

This selective pressure (or selective force) causes certain alleles to become more common in the population

Constraints on evolution

1. small population
2. developmental process
3. trade-offs
4. short term vs. long term

Small population (constraints on evolution)

\-limits genetic variation in sexual reproduction (randomizing doesn’t help)

Developmental process (constraints on evolution)

original structure→ changes overtime by adaptive forces

Trade-Offs (constraints on evolution)

\-fitness causes trade-offs

* consequences (cost vs. fitness)

Short-term vs. long-term (constraints on evolution)

\-is it going to thrive for a while?

\-long term success

Speciation (Darwin)

\-causes a population to split

* isolate
* cannot successfully reproduce

Carl Linnaeus

\-Morphological species concept (Greek/Latin)

* Kingdom: general
* Phyla
* Classes
* Order
* Genus
* Species: specific

The genus and the species

give the thing a name

* Homo (genus) Sapiens (species)

Reproductive Isolation

no mating with opposite population; reduces overall fitness- will not work

Allopatric speciation (dominant form)

physical barrier separating a population

* mountains, water, continental drift, highway, climatic change

Sympatric speciation

have genetic diversity arise without a physical barrier


1. genotypes (AA, Aa, aa)
* population→ location (alters nature)
2. poly ploidy (more than 2 copies)
* N+ 2N= 3N
* amphibians can have 3N (polyploidy)

Reproductive barriers

1. Prezygotic barriers: before fertilization
2. Postzygotic barriers

Prezygotic barriers

\*natural selection favors them

\-anything that prevents sperm and egg from forming zygote


1. Habitat isolation
2. Temporal isolation
3. Behavioral isolation
4. Mechanical isolation
5. Gametic isolation

Habitat isolation (Prezygotic barriers)

* never come in contact
* locations are not close enough for interaction

Temporal isolation (Prezygotic barriers)

* no overlapping mating time

Behavioral isolation

* act to impress/ behaviors need to match

Mechanical isolation

* lock and key (skeleton key)
* genitals don’t fit

Gametic Isolation

* receptors are different on different species (not all are different, some match)
* egg and sperm receptors

Zygote

\-most undifferentiated cell

\-Sperm + Egg → Zygote → Embryo → Adult

* affected by prezygotic and postzygotic barriers

Postzygotic barriers (viability)

\-viability: may not pass viability to live to an adult

* Zygote doesn’t make it to an embryo
* Embryo, does not make it to an adult

Postzygotic barriers (besides viability)

1. viable but decreased fitness
2. viable but infertile
* ex. horse + donkey = mule (infertile)
* physically fit but infertile

Hybrids

\-come from 2 different species

* ex. mule/tiger

Hybrid outcomes

1. merge/mingle with either population
2. hybrids don’t exist due to barriers
* 2 different populations
3. occasional hybrids
* more narrow reach on both populations

Speciation rates vary

\-likelihood of speculation


1. large population
* lots of individuals with genetic variation
* large population is going to cover a large area
* likelihood of having physical barriers
* allopatric speciation
2. Specific diet
* more likelihood for speciation
* need a specific diet; will need to change diets
* vs generalist: no specific diet

Increased mechanisms of sexual selection

cause increased speciation rates

Disperalness

\-ability to disperse

* ex. pollination

Genome

an organisms full set of genes as well as any non-coding regions of DNA (for some viruses it is RNA)

* Genes of eukaryotes mostly found on chromosomes in nucleus
* Must be replicated to be transmitted to offspring
* Mistakes in DNA replication (mutations) provide material for evolutionary change

Genes of an organism can be looked at

as interacting members of a group (differing dependencies, expressions, locations)

The positions of genes and their sequences are

subject to evolutionary change

Codons represent

amino acids

Genes will code for

protein chains (shape)

Mutations

a different protein is formed

* good/bad/no affect

Steps of translation and transcription

DNA → pre-mRNA → mRNA → protein

Exons

* code→ protein
* need to exit nucleus in order for the protein to get to the ribosome
* the non-code get spliced out (introns)
* broken down A, G, C, T

Messenger RNA (mRNA)

exons

* 5’ (P) end 3’ (OH poly-a-tail)

The study of molecular evolution

investigates the mechanisms and consequences if the evolution of macromolecules

* study the relationships between the structures of genes and proteins and the functions of the organisms
* reconstruct the genetic histories of genes, proteins, organisms to understand biological diversity

Ways in which genes evolve

* nucleotide substitutions which can result in amino acid replacements in proteins
* changes in amino acids can result in changes in secondary and tertiary structures of proteins

Homologous

a feature shared by two or more species that has been inherited by a common ancestor

Genes and proteins are compared through

sequence alignment

Sequence alignment

move the amino acid sequences to align them

* align the like nucleotides/amino acids

Similarity matrix

counting the number of nucleotides or amino acids that differ between two sequences

* gives a measure of the minimum number of changes that have occurred during divergence of a pair of organisms

Mutations

change of a letter

* most are spontaneous

Multiple substitutions

more than one change at a given position

* T→C→G
* was a T, then became a C and shows as a G

Coincident substitutions

at a given position different substitutions occur between ancestor and each descendants

* G

Parallel substitutions

the same substitution occurs independently between the ancestors and both descendants

* G

Back substitutions

after a change at a position subsequent substitution may return position back to ancestral state

* A → G → A

Silent substitution

* does not change the amino acid that is specified
* do not affect the functioning of a protein
* unlikely to be influenced by natural selection
* occur 5x more often in protein encoding regions than non-synonymous mutations

Non-synonymous substitution

* does change the amino acid sequence encoded by a gene
* likely to be deleterious to organism
* does not always alter protein shape and size \`

Missense mutation

codes for a different amino acid

Nonsense mutation

stop codon

Phylogenic Tree

diagram of evolutionary relationships

* create common ancestor to find speciation events

Larger genome does not always indicate

greater complexity

Non-coding sequences have become

coding sequences overtime

* changes appearance
* substitutions can enact it