Bio 2B - Final Exam Review

Adaptation

permanent change in any trait over time due to changes in environment

How bacterial cells exchange genes

Transformation - living cells take in DNA from dead bacteria cell

Transduction - bacteriophage packages host genome instead of viral genome, inject bacterial DNA into another bacterium (transferred DNA)

Antibiotics

produced as a means to compete with other microorganisms

heavy antibiotic use can select for rapid evolution of antibiotic resistance in bacteria

Major ecosystem services: Provisioning

things we harvest from ecosystems

ex: food, water, genetic resources(all dec), biofuel (inc), wood (stable), coal

Probiotics

aid in re-colonization of the patient’s body by beneficial bacteria

Bacteriophages

infects and replicates within bacteria, but doesn’t infect invertebrates. Targets other bacteria

Pierce’s Disease

plants along creeks are affected by sharpshooters, causing this disease

ecosystem disservice for native vegetation growing along creeks

Short-term threats to ecosystem

degradation of water supply

climate change

invasive species

species extinction

Biodiversity

full diversity of life on earth, diversity of all organisms in all habitats across all levels of organization

Relationship between Biodiversity & Ecosystem function

Pathogens

virus, bacterium that can cause disease

Abiotic environmental conditions

non-living part of an ecosystem that shapes its environment

Organism’s niche

Environmental conditions and the availability of key resources that must be satisfied simultaneously to allow an organism to grow, reproduce, and survive

Endotherm vs Ectotherm

Endotherm relies on metabolically-generated heat as predominant source of warmth

Enzymes

need to maintain proper shape and to work they need the right amount of flexibility

Cooler environment = fewer bonds needed = more flexible

Warmer environment = kinetic energy is greater = stronger chemical bonds = more rigid

Too high temperature (exceeds optimal range) —> becomes denatured

Photoinhibition

too much light intensity for the plant; prevented by holding leaves at an angle to “dilute” radiation and keep it at optimum level for photosynthesis

CO2

• increase in CO2 concentrations induced by industrial revolution (burning fossil fuels; can’t be recaptured by plants)

• increasing more rapidly than we’ve known in history of earth

• stomata - CO2 diffuses in; open stomata=loss of H2O

• CO2 lets energy and not out, energy is trapped in the form of heat

Photosynthesis

visible light 400-700nm

Macronutrients vs micronutrients

macronutrients - uptake in large amounts

micronutrients - uptake in small amounts

roots branch to take in valuable nutrients; amino acids are NOT essential resource for plants

R0

R0 - basic reproductive rate

r

r - intrinsic rate of increase

(b-d+i-e)

senescence

• “deterioration” with age

• somatic cell lineages (sex cells, eggs, seeds, spores, etc.)

• age-independent mortality factors favor senescence because benefit outweighs cost of repairing/avoiding senescence

  • freezes, fires, predation

• NO SENESCENCE - fission, budding (any cell could be passed onto future generations, thus maintained w/out senescence)

Trade offs

• between current and future reproduction

• between reproduction and somatic maintenance

Exploitative competition

• indirect

• scramble competition: more or less evenly

• overcompensating density-dependence

  • very strong influence on population growth rates

Interference competition

• interaction between competing individuals (one prevents other)

• contest competition: unequal division of resources (winners/losers)

• exactly compensating density-dependence

  • occurs when # of individuals surviving competition is constant across a range of high values of initial # of competitors

resource-weighted density vs consumer-weighted density

Essentialism - Plato

in natural world, # of unchanging essences that are discrete

• constancy (opp of change)

• discontinuity

• variation

Great chain of being (Scala Naturae) - Plato

all things on earth can be arranged in linear sequence (topology)

Jean Baptiste de Lamarck

theory:

• spontaneous generation

• intrinsic tendency to strive towards perfection

• inheritance of acquired characteristics

Darwin and Wallace

• common descent (common ancestor)

• causation of adaptive evolution - natural selection

  • inheritance, variation in traits, variation in fitness

• evolution could occur as automatic process that produces adaptation

DONE WITH MIDTERM 1 CONTENT BIO

Lec 1-11

Mendel’s first law

segregation; genes are particulate or discrete

• every individual has 2 alleles, and only one allele is passed onto offspring

  • genes, chromosome, gametes

common garden experiment: keep environmental conditions stable/constant, then diff in traits shows that genes is the reason

Mendel’s second law

independent assortment

• genes located on different pairs of homologous chromosomes assort independently during meiosis

  • autosomal linkage and crossing over

Autosomal linkage

any chromosome other than sex chromosome 2 genes located on same chromosome (and close)

• 2 or more genes being carried on same autosome

Crossing over

chromosomes of same type are lined up

Genetic recombination

when two molecules of DNA exchange pieces of their genetic material with each other

• occurs within chromosomes, through crossing over

• occurs across chromosomes, through meiosis and fertilization (normal sexual reproduction)

Darwin’s lack of understanding mechanism of inheritance

NO BLENDING MECHANISM

• natural selection would be ineffective in producing evolutionary change

Genetic variation

1. mutation

2. immigration - gene flow

3. genetic recombination - new combination of genetic variations

   1. withing (crossing over) and across chromosomes (normal sexual diploid gamete)

Mutation

• often occurs during DNA replication

• most important source of genetic variance

  • point mutations

  • chromosomal mutations

  • insertions/deletions

Hardy - Weinberg equilibrium

if:

1. very large population (infinite)

2. random mating

3. no gene flow (immigration)

4. no mutation

5. no selection

then: NOT EVOLVING

• allele frequencies will stay same across generations

genotype frequencies

p² + q² + 2pq

if expected frequency = actual frequency —> NO EVOLUTION

Selection

Tay-Sachis

an enzyme that doesn’t metabolize lipids (lethal if defective) ←recessive alleles expressed

Genetic drift

process by which allele frequency change due to chance events (survival) in finite populations

• smaller population = more changes in allele frequencies

• drift is more important than selection

  • 1/N > S

Traits with continuous variation

1. control by many genes

   1. polygenic

2. environmental effects

P = G + E

phenotype = genotype + environment

Stabilizing selection

• mean doesn’t change

• variance DECREASES

Disruptive selection

• mean doesn’t change

• variance INCREASES

Directional selection

• mean continues to rise

• variance doesn’t change

Bacillus thuringiensis

part-time pathogen

• kills host by producing protein toxin in gut

• receptor-cadherin (kills cell)

highly selective

• toxic to insects but not to mammals

mechanisms of resistance

1. detoxication - dominant alleles

   1. toxin is broken down before lethal dose reaches host

2. target site insensitivity

4 things to know about resistance evolution + management

1. resistance proceeds through discriminating with individuals with different genotypes

   1. mortality does not equal effective selection

2. functional dominance - environment determines if trait looks dominant/recessive

3. fitness costs of resistance (R)

4. dilution of resistance by immigration

resistance management

low dose strategy

high-dose, refuge strategy

Lotka-Volterra Model of Interspecific Competition

Zero-growth isocline

Predation + prey tactics

• effects all: birth, death, immigration, emigration

Prey tactics:

refuge in time - not around when predator is around

refuge in space - not being in same place as predator

refuge in body size - being too big/small for predator

SIR model for an epidemic

Susceptible

Infectives

Removed

• 1/y is the mean time that an infected individual has the disease and can infect other individuals within the host population

• S is # of susceptible hosts present

Herd immunity + mandatory immunization

big enough proportion of population vaccinated, protect all population (even unvaccinated)

ex: pertussis (whooping cough)

• mandatory immunization is important where 100% immunization of the host population isn’t possible

Virulence

severity or harmfulness of a disease/poison

avirulence theory - pathogens have no effect on host

Mutualism

interaction between 2 species that’s beneficial to both

• exchange of service/resources

Major classes of mutualism:

1. protective services

   1. ants + plant (nectar for ants, ants protect)

2. dispersal services

   1. plant + human/animal (produces fruit/nectar, seed spreads)

3. digestive services

   1. build population by eating

4. biosynthesis services

   1. allow insects to survive via eating microbes

5. resource exchanges

   1. trade sugar for another resource (ex: corals, lichens)

Food Web - trophic cascade

• direct and indirect effects

Density-mediated indirect effect

Trait-mediated indirect effect

occurs because of predator effects on prey traits rather than prey density

predator effects behavior

ex: aquatic system

prey refuge strategies

Biological species concept

species are groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups

• measured reproductive components

Morphological/Phenetic species concept

individuals are grouped into species based on their similar physical appearance

• appearance/grouping

Reproductive isolating mechanisms

post-zygotic

• hybrid sterility - hybrid can’t make gametes (no mating)

• hybrid inviability - hybrid zygote dies early on

allopatry

a population or species that is physically isolated from other similar groups by an extrinsic barrier to dispersal

Anagenesis

microevolution

• evolutionary change within an evolutionary lineage

Cladogenesis

speciation

• splitting events

Anastomosis

fusion of two lineages

Ring species

set of populations whose distribution is shaped like a doughnut

• one location around the ring, there’s a clear absence of gene flow between two classes of individuals

shows the idea that what makes two species different is often the amount of genetic divergence, rather than some fundamental difference in the type of genetic differences that exist

Modes of Speciation

Allopatric - geographic isolating at the initiation of the divergence event

Sympatric - splitting of an ancestral species into two or more reproductively isolated groups without geographical isolation of those groups

Polyploidy

• genome duplicated (diploid gamete)

initial mutation occurs when cells that have replicated their DNA in prep for cell division have failed to divide properly

Symbiosis (and anastomosis)

• basis for evolution of plants and eukaryotic cell

• explains why mitochondria and chloroplast has own DNA

• can cause two independently evolving lineages to fuse into a single lineage (anastomosis)

• key evolutionary innovation

• favored by ability of two organisms to exchange needed nutrients

• may lead to eventual fusion

• NO it is NOT ultimate source of all genetic variation because it’s different from mutational event

Mutualistic symbiosis

• two species with different metabolic needs (waste product from one is a key resource for other)

• reduction in overall genome size of symbiont

• trend towards increasingly strict dependence of symbiont and host on each other

• increased number of genes within the symbiont’s genome

ex: mitochondrion has own DNA because it descended from proteobacterium that formed mutualistic symbiosis with a host cell

Macroevolutionary history

How to generate new genes

1. gene duplication

   1. meiosos: alignment of homologous chromosomes

   2. misalignment: mistake, can lead to mutation

2. differentiation of the multiple B genes

major changes in gene copy number occurs rapidly - little as 10yrs

Gene death

1. Deletion - unequal crossing over, or DNA replication error (lose part of gene)

2. Mutational damage (pseudogene - dead gene)

   1. damage to promoter

   2. insertion/deletion

   3. nonsense mutation

   4. other

2-fold cost of sexual reproduction

cost of securing the mate

and

risk of not finding a mate

Muller’s ratchet

accumulation of harmful mutations in a generation

evolutionary consequences of the absence of recombination

• can lead to long-term cost of asexual reproduction

HIV-AIDS

• relies on host to replicate, intracellular

  • is in the immune system, incapasitates immune system (susceptible to other infections that harm human)

• mutation rate is HIGH

  • low dose, and high dose refuge won’t work

Disease

1. human population is EXTREMELY LARGE

2. become much more mobile

serious new disease epidemics in the future

Gene-centric

purpose of offspring is to project copies of genes into future generations

• reproduce yourself

• help relative to reproduce

Hamilton’s Rule

altruistic allele (donor/recipient) will be favored

• not always right because it doesn’t take into account genes

male sex

produces smaller gametes

broadcast spawning

large # of gametes released in ocean and have to find each other to fertilize

• HARD

Isogamy

• sexual reproduction involving haploid gametes that are all the same size

• found in diverse organisms (algae, yeasts, fungi, etc)

Anisogamy

idea of how it evolved:

• small male gametes are parasites of the larger female gametes

Intersexual selection

females are picky when choosing male

Intrasexual selection

competition among males