Change in genetic properties of a group/population of organism over time

descent with modification

change in proportions of populations

only explanation of adaption

change in proportions of genetically diff populations

ex: shift in proportion of population white moths to dark moths population

morphological diversity

genetic diversity

species diversity

medicine

technology

evolution is not natural selection - natural selection is the process by which evolution uses; evolution is genetic 

individuals cannot have biological evolutions - its populations (change in individuals is considered development)

evolution is a substantial theory - fossils, DNA/genomic data, direct observations, antibiotic/pesticide resistence

evolution does not explain the origin of new species - evolutionary adaption to diff environments/diets promotes new species

fossil records - contain information of intermediate forms of species and missing links

Essentialism - variation is an accidental imperfection

eidos means idea/essence

Pre-Darwin: LaMark

Phenotypic Evolution - Inheritance of Acquired Traits

traits acquired during an individuals lifetime are passed on to its offspring

generation 1 develops trait

generation 2 inherits trait

Pre-Darwin: LaMark

Theory of Speciation

Darwin (1859)

Life/Background Info

Darwin

2 Main Points

1. Descent with modification (evolution)

2. Causal agent of evolutionary change (natural selection)

early generation 1 - genetics cause phenotype diff

later in generation 1 - natural selection

generation 2 - evolutionary change so that only the chosen survive

Dawin

Thought about Variation

Darwin

5 Theories

1. Evolution - traits change over time

2. Common descent - one big tree of life

3. Gradualism

4. Population change - change in proportions of individuals within a population

5. Natural Selection

Darwin

Alfred Wallace

Father of Biogeography

Wallace Line (separates ecozones of Asia and Australia region)

Wallace Effect for Speciation (changes occur due to geography

Post Darwin

Mutationalist Theories

Discretely diff organisms came about because of mutation so natural selection wasn't necessary for new species

considered the alternative to natural selection

Post Darwin

Mendelian Genetics

Post Darwin

Richard Goldschmidt

Evolutionary Synthesis (30's/40's)

Fisher, Wright, Haldane

Math theory

population genetics

mutation + natural selection --> adaptive evolution

mutation is not alternative - mutation is raw material

Evolutionary Synthesis (30's/40's)

Founder Effect

new population is founded by a small number of species from a larger population

loss of genetic variation

Evolutionary Synthesis (30's/40's)

Genetic Drift

Evolutionary Synthesis (30's/40's)

Ernst Mayr (3 theories)

1. Biological Species concept

2. theory of geographic (allopatric) speciation

3. theory of founder effect speciation

ernst mayr

groups of interbreeding species that are reproductively isolated

ernst mayr

new species form when populations are geographically isolated

can undergo genetic diversity

ernst mayr

drastic reductions in population size promote speciation (genetic revolutions)

evolutionary synthesis (30's/40's)

modern synthesis major points (9 points)

1. phenotype is not genotype

genotype + environment --> phenotype

2. heredity variation based on genes

3. evolutionary change = populational process (changes in proportions)

4. mutation occurs at a low rate - so genetic drift and natural selection take into account

5. natural selection occurs for both slight and dramatic change

6. mutations accumulate in populations so populations gain genetic change

7. difference between population and species - adaptive and based on genes

8. species are characterized by reproductive isolation and geographic isolation

9. tree of life - phylogeny - single common ancenstry

Motoo Kimura

Neutral Theory of Molecular Evolution

Wobble position

many genetic changes cause no phenotypic variation

importance: most evolution of DNA sequences came about by genetic drift, not natural selection - foundation for detecting natural selection

wobble: mutation at this spot of the nucleotide has no effect on phenotype - mutations not more frequent here but more observed because they survived

Hamilton, Trivers, and Social Theory

Kin Selection

cooperation vs conflict

cooperation: you help your kin (explains altruistic behavior like saving someone's life although they don't matter as they are a genetic copy)

conflict: struggle between gene centric ideas

NOW is the...

Age of Genomics - New Age of Induction

1. mutation - ultimate source/raw material

2. gene flow - movement of alleles btw populations

3. non-random mating - proportion of hetro/homo

4. genetic drift - effect of chance

5. selection - select the better fit

error (not adaption) in replication of a nucleotide - alter genome

alteration of DNA sequence, independent of phenotypic effect

evolutionary if passed on to offspring

mutation effects phenotype if occur in protein-coding regions

Types of Mutation

Synonymous (silent)

no effect on amino acid sequence of protein

no effect on phenotype

hidden from selection

Types of Mutations

Non-Synonymous Mutations

amino acid change

little/no effect on function of protein/phenotype OR

substantial functional/phenotypic effects

movement of alleles from one population to another

due to individuals/gametes physically moving

could change allele frequencies

hindered by mobility of organism/barriers/dispersal

without gene flow: populations so genetically diff, they would be considered diff species

Non-Random Mating

Sexual Selection

Sexual Selection

Assortative Mating

Assortative Mating

Positive vs Negative

positive - HOMO, more similar mates

negative - HETERO, dissimilar mates

sexual selection:

Inbreeding

CHANCE

alleles lost easily

new mutations raise/fall at high frequency

could negate natural selection

Genetic Drift

Founder Effect vs Bottleneck Effect

founder effect - small portion leaves large population to create new population - new population contains only original genes

bottleneck effect - drastic reduction in population allows only certain individuals to survive so only those genes get passed on - same population size but diff amount of genetic variation

Selection:

3 conditions

1. variation

2. genetically inherited variation

3. differing fitness due to variation

selection:

epistatic interaction

selection act on more than a single gene

act on interaction of a gene with other genes

some genes are selected only in presence of other genes

p2:2pq:q2

p2+2pq+q2=1 and p+q=1

null model - ratio remains constant then at equilibrium

1. random mating

2. large population

3. no gene flow

4. no gene mutation

5. no natural selection (equal probabilites of survival)

maintain variation

frequency dependent selection

negative vs positive

negative - rare is good

postive - rare is bad

Species

Reproductive Isolation

speicies

geographic isolation

species

subspecies

races/ecotypes

populations that aren't considered full on new species

species

hybridization

interbreeding btw diff species/population

can lead to introgression

species

introgression

movement/incorporation of genes from one species into another

fusion

species

monophyletic group

1. allows classification

2. includes discrete groups of organisms

3. how discrete groups arose

4. represents evolutionary history

5. applies to the max amount of organisms

species concepts

morphological species concept

species concepts

genotypic cluster species concept (GCSC)

species are distinct genetic clusters

no/few intermediates

genetic extension of morphological species concept

species concepts

phylogenetic species concept (PSC) - IMPORTANT

species = smallest monophyletic group of common ancestry

exclusive, closely related to those in group than any organism outside group

applied to sexual and asexual

species concept:

biological species concept (BSC) - IMPORTANT

1. only applies to sexual/outcrossing organisms

2. what about hybridization/incomplete reproductive isolation?

3. hard to experimentally test

1. diff concepts are related

2. concepts differ in what is considered a species

3. concepts differ in goals

4. all have multiple/arbitrary stages

speciation

process not an event!

initiation - no reproductive isolation

stage/completeness of speciation - starting to become reproductively isolated

completion - complete reproductive isolation

1. morphological - compare physical shit

2. genetics - phylogentic, consistent diff

3. reproductive isolating barriers - mechanism that prevents gene flow

4. combination of above

reproductive isolating mechanicsms

pre zygotic vs post zygotic

prezygotic - prevents zygotes from forming

postzygotic - prevents gene passing to offspring

1. ecological - habitat

2. temporal - seasons

3. behavioral

4. mechanical - not right fit parts

5. intrinsic genetic - gametes not viable (incorrect chromosome allignment, not right epistatic interactions) - most complete isolation & stage of speciation

1. intrinsic hybrid inviability - sterility/infertility

2. ecological selection against hybrids - gray moth dies in comparison to white/black

3. sexual selection against hybrids

post zygotic:

dobzhansky-muller model

specific type of intrinsic hybrid inviability

genetic incompatibility caused by negative interactions between loci (epistasis)

if alleles dont work well together, hybrids are unfit

reinforcement speciation:

reinforcement

process of strengthening premating isolation in response to selection against hybridization

evolution of divergent mating preferences in response to low fitness of hybrids

sympatric speciation:

polyploid speciation

sympatric speciation:

strong divergent ecological selection

adaption to diff habitats = populations diverge but gene flow make populations less diff

so selection must be so strong to combat effects of homogenization via inbreeding

species rapidly diversify to fill available ecological niches

caused by key innovation

1. adaptive radiation

2. diff rates of extinction

species evolve continuously

large changes in phenotype are due to many small changes over time

sporadic evolution

short periods of evolutionary time where major phenotypic changes occur

fossil records

genome evolution

structures: bacteria/viruses vs. eukaryotes

viruses/bacteria - efficiency (max speed of replication, min unnecessary genes)

eukaryotes - contains non-coding regions and unknown functions

part of gene

not translated into polypeptide

DNA sequence

copies inserted into various sites in genome

jumping genes

1. alternative splicing = greater variation in protein sequences

2. old dead parts of gene in the past

3. junk DNA

4. enhance expression of gene

5. evolved from transposable elements

copies of preexisting genes create new genes

caused by hiccup in transcription process

origin of key innovation

result in evolution of gene families

what causes spont origination of genes?

1. gene duplication

2. lateral/horizontal gene transfer

1. neofunctionalization - one copy remains original function, other copy gets new mutation (punctuated equilibrium)

A' mutation, A original

2. subfunctionalization - each duplicated copy still has its functions but can become more specialized because there are two separate genes to decouple

A' 1/2 original - open spot for mutation to occur

A other 1/2 original - open spot for mutation to occur

determining identity of embryonic regions in developing animals

info about formation of new body plans (specialization of functions)

activate or repress expression of gene at particular times/tissues

phenotypic change

non-coding DNA sequence in/near gene

contain binding sites for transcription factors

switch genes on/off

regulation of gene expression

is

rapid and flexible

rapid - no wait for mutations in coding regions/fixations

flexible - no one allele in coding region fits all the time/places - gene expression allows for rapid response to changing selective environments

1. 14 bill years ago

2.Precambrian

•  
  •  
    • origin of eukaryotes (2.5-2.0 bya)
    • evolution of multicellularity (1.2 bya)

3. Paleozoic Era - terrestrial life

4. Late Paleozoic Era - permian - most massive extinction event in history (volcano) - 96% all marines, 70% all land exinct

5. Mesozoic era - age of dinosaurs (first dinosarus, mammals, flowering plants)

6. Cenozoic Era - age of mammals

7. Late Cenozoic Era - Pleistocene (glacial advantage, continents shift like modern)

sea level lowered - mass migrations

diff habitat availibility

glacial refugia

species that were broadly separated became isolated in separate areas

favorable conditions throughout glacial periods

study of biological diversity and evolutionary relationship among organisms

test hypotheses about which group descended from common ancestor

extinct - no longer present

extanct - taxa doesnt exist

phylogeny 

sidenote: phylogentic trees, phylogenetics

organize groups of species into progressively smaller hierarchical groups

kingdom, phylum, class, order, family, genus, species

phylogenetic tree terms:

root

node

clade

common ancestor to all taxa

branchpoint in a tree

group of two or more taxa that includes both their common ancestor and all their descendants

1. character (trait)

2. character states (variant condition of character - color)

3. ancestral state (found in common ancestor)

4. derived state (state evolved from ancestor)

5. outgroup (taxon closely related to study group but not in study group)

type of character data

shared ancestral characters

no phylogentically informative

type of character state

unique derived characters

distinct for a taxon - used for id but dont tell about relationship with other groups

1. symplesiomorphies

2. autapomorphies

3. synapomorphies

shared derived characters

resolve relationships - phylogentically informative

simplest explanation is preferred with the fewest undocumented assumptions

most shared derived characters due to common ancestry not convergence are grouped

calculates likelihood of observing the data

given specific model of evolution and possible tree

max the probability of observing a particular tree

probability of a set of diff trees