• Ecosystem ecology seeks to explain the transfer of energy and cycling of matter within ecosystems
• without energy transfer, there would be no heterotrophic organisms
• wothout the cycling of matter the soil would lose fertility, plant growth would cease and onece again we could not exist
• Ecosystem ecologists can address environmental issues that are caused or exacerbated by changes in nutrient cycles and energy flow

study the flow of energy and the cycling of matter in ecosystems

energy flows but matter cycles

• Energy is neither created or destroyed
• the amount of energy in the universe today is the same amount that was in the univers when it was formed
• Energy can be transferred from one body to another
• Energy can be transformed from one form to another
• Ecosystems are energy transformers

• energy transfer leads toward entropy
• At every transfer of energy, some energy is lost to heat to the abiotic environment
• the amount of useable energy declines with every energy transfer- energy lost as heat
• this sets a fundamental limit on energy flow through ecosystems

in contrast to energy matter can cycle from one body or compartment to another

for example: the element nitrogen can cycle from the atmosphere (N2 gas) into other inorganic forms (ammonia, nitrate) and into organic forms (proteins, nucleic acids) and then back into the atmosphere

Gross Primary Production - Respiration

GPP minus energy used by producers from cellular respiration- NPP is the amount available to consumers

between 5 and 20%

on average 10% is transferred to next higher trophic level

• A large fraction of energy is released as heat to the abiotic environment with each trophic transfer
• A large fraction of the energy present at each level is used to keep the organisms alive and functioning (cellular respiration, energy used to searc hfor food, catch prey or escape from preditors)
• not all organisms at lower trophic levels are consumed

Except for the world's deserts, terrestrial productivity declines from the equator toward the poles.

warm temperatures and high water availability generally increase rates of photosynthesis

• in terrestrial environments, productivity is limited by temp. and moisture on a global scale (remember biomes?)
• at smaller scales (within a single biome) terrestrial productivity is often limited by nutrients (especially useable forms of nitrogen)

• In most aquatic ecosystems, primary production is milted by nutrients and light
• light availability declines rapidly with depth in water, so most primary production occurs near the surface
• nutrients (particularly phosphorus) appear to limit primar production in the photic zone of most freshwater ecosystems; whereas iron is often limiting in open water marine ecosystems

food from above- whale carcasses

other deep sea communities supported by hydrothermal vents

significant pulses of organic material (phytodetritus) sink rapidly from surface waters to deepest bethic communities in aggregations called marine snow

phytodetritus- dead phytoplankton from the surface of the ocean

sinks rapidly to the deepest communities in the ocean to support their life

clean water

oxygen

food

decomposition, nutrient cycling, and fertile soils

protection of shores from erosion

pollination services

- we do not yet know enough to recreate functioning ecosystems

the path that an element takes as it moves from one compartment or pool to another

unlike energy, chemical elements remian in the biosphere where they cycle continually between organisms and the abiotic environment when one organism eats another- elements are also transferred - C,N,P, and others

play a critical role in ecosystems

• Bacteria, archaea, fungi and a few other eukaryotes
• make nutrients cycle from detrital pool back abiotic environment
• break down complex organic molecules (proteins, lipids, carbohydrates) from detritus (dead tissue) into inorganic molecules (CO2, NH4+, NO3-) that can be re-used by other organisms

• ground water replenishment- concrete/asphalt surface reduce the amount of precipitation that reaches deep soil layers
• conversion of forests/grasslands to agricultural fields increases runoff to streams and decreases groundwater replenishment
• irrigating agricultural fields removes water from groundwater storage
• in many parts of the world, people now have to mine water - populations in those parts of the world have already grown past carrying capacity for water

largest C reservior is in sedimentary rock; ocean has large active C resivoir, followed by terrestrial communities, followed by atmosphere; geological reservior is not active pool until humans access it such as by burning fossil fuels

photosynthesis takes CO2 out of atmosphere

Respiration releases CO2 into atmosphere

unavailable to producers because they can use nitrogen only in the form of ammonium NH4+ or nitrate NO3- ions

nitrogen is added to ecosystems in a usable form only when it is reduced or fixes- converted from N2 to NH4

Climate change

acid rain

hole in ozone layer

"dead zones" in the oceans

Mitosis

Meiosis

Binary Fission

produces 2 genetically identical daughter cells

only eukaryotes and only in somatic cells

produces 2 genetically identical cells

only in prokaryotes

produces 4 daughter cells

daughter cells are genetically different

only un eukaryotes; only in germ cells

development and growth

repair and tissue renewal

asexual reproduction

2 daughter cells that are genetically identical

same set of chromosomes barring any mistakes in DNA replication

occurs in all somatic cells (Eukaryotes

2 sister chromatids bound by a centromere

***look at pic in book***

Steps in Bacterial Cell Division

(Binary Fission)

1. Chromosomes attatch to plasma membrane

2. Chromosome replicates

3. Cell grows ringing of FtsZ protein forms

4. FtsZ ring contricts membrane and cell wall infold

5. fission complete

• dont need a mate
• dont need to expend time, energy, or resources to attract a mate
• fewer risks from predators
• fewer risks of sexually transmitted diseases (STDs)
• leads to faster population increases

• little genetic variaton for evolution to act upon
• no way to get rid of deterious mutations

• sex produces genetic variation and genetically diverse offspring may be more likely to survive diseases and parasites; therefore more likely to persist in changing environments (red queen hypothesis)
• sex allows purging of (bad) mutations (Deleterious mutation hypothesis)

tow consecutive cell divisions which reduce parental chromosone number by half and produce four haploid daughter cells

each daughter cell is genetically different from parental cells

only occurs in eukaryotes and is restricted to germ cells- located in the testes and ovaries

one set from mom, one set from dad

are similar in size, shape, pattern, and gene location

carry the same genes but alleles may differ

two consecutive cell divisions which reduce parental chromosome number by half and produce four haploid daughter cells

each daughter cell is genetically different from parental cell

how sperm and eggs get only one set of chromosomes

• longest phase of meiosis
• chromosomes condense
• centrosomes move toward poles
• spindle forms
• nuclear envelope breaks down
• homologous chromosomes pair up and synapsis occurs
• crossing over occurs between non-sister chromatids; 1 to 3 chiasmata per tetrad
• spindle microtubules attatch to kinetochores

• each pole now has a haploid set of replicated chromosomes
• furrow forms in animals
• cell plate forms in plants

Crossing over occurs during prophase 1 and produces recombinant chromosomes

 independent assortment of homologs

random fertilization of gamets

2^N- where N= haploid number of chromosomes

ex:

in humans 2^23 = 8 million different possibilities

• Genetics is the scientific study of inheritance (heredity) - how traits are passed from parents to offspring
• genetics influence morphology, physiology, behavior, even disease susceptibility
• understanding life on earth requires an understanding of genetics
• evolution could not occur if there was no genetic variation within a population

Sperm and eggs of parent organisms contain a sampling of parent's essence that is blended togehter in the offspring to give an intermediate resulting condition

Yellow + Red = Orange

• many true-breeding varieties available
• can easily control matings
• peas also self-pollinate
• short generation time
• many discrete traits (characters)
  • determined by action of 1 gene
  • phenotypes fall into only a few distinct categories

expressed observable characterisitics of organisms

Yy- shows dominant trait- dominant phenotype

genetic makeup of the individual (specific alleles it carries)

Yy- heretozygous genotype

the trait is expressed in the phenotype of the heterozygote

denoted by uppercase letter

the trait that is not expressed in the phenotype of a heterozygote

denoted by a lowercase letter

alternative molecular versions of the same gene all diploid individuals have 2 alleles for each gene

different alleles have different DNA sequences and were created by mutations

carries 2 of the same alleles

RR

or

rr

Carries 2 different alleles

Rr

Mendel's Conclusiong from Monohybrid crosses

Particulate theory of inheritance

• inheritance is determined by discrete factors- now we call them genes
• each individual has 2 alleles (alternate versions of a gene) for each character/trait
• 1 allele is inherited from each parent (alleles segregate into gametes) Law of segregation

now we know that this occurs when genes for 2 or more traits are located on seperate chromosomes or far apart on the same chromosome

genes that are in close proximity on the same chromoso me are often inherited together (phenomenon of genetic linkage)

1. Hereditary units are genes
2. Each individual has two alleles for each trait
3. Each gamete contains one allele of each gene (alleles segregate- law of segregation)
4. Alleles may be dominant or recessive
5. alleles for one trait assort independently of alleles for another trait (Law of independent assortment)
6. Used great system, quantitative approach, large samlpe sizes, and followed mulitiple generations
7. mendel know nothing about chromosomes yet he discovered rules of inheritance

Fly Labs:

Why we use fruit flies as a model system?

small size and easy to culture in the lab

short generation time

produces lost of offspring per mating

red eyes designated as w+ or +

+ always refers to wild type (common phenotype)

white eyes - mutant designated as w

in flies, genes named after mutants

heterozygous for eye color female and

hemizygous for eye color and genes located on X chromosome male

(SEX LINKED)

Female     x       Male

X^w+X^w               X^wY

X^w+         X^w

X^w          X^w+X^w         X^wX^w                  

Y          X^w+Y            X^wY          

50% of daughters have white eyes 50% of sons will have white eyes      

figured out this gene is located on the X chromosome after Nettie Stevens discovered how sex is determined in beetles: XX and XY system, just like humans-

no crossing over occurs between x and y chromosomes in males

genes located on the X or Y chromosome are said to be sex-linked

sex-linked traits are inherited differently in males and females

X and Y synapse in meiosis 1 but they are not homologous (X is much bigger- has many genes that Y lack)

color blindness

hemophilia

Duchenne's muscular dystophy

male pattern baldness

the law of independent assortment may be violated

the physical association of genes that are found on the same chromosome but that influence different traits

law of independent assortment may be violated if genes are located in close proximity on one chromosome (they may be inherited as a unit)

Remember: linkage is different than sex linkage

if two genes are right next to each other expect no recombinants

relative positions of genes on chromosome affect rate of recombination

very close- low RF; far apart- high RF

can use frequency of recombination to map relative positions of genes along the chromosomes

Genes 50 or more map units (cM) apart behave as if they were on seperate chromosomes

phenotype of heterozygotes is intermediate to the two homozygotes

red + white = Pink

both alleles are visible in the phenotype of heterozygotes

Mn blood groups in humans

NM homozygoted have only M molecules on surface of red blood cells

NN homozygotes have only N molecules on surface of red blood cells

MN heterozygotes have both M and N moecules on surface of red blood cells (both alleles are expressed simultaneously) - humans with AB blood type

the phenotype of a heterozygote can be observed at a variety of levels (scales): whole organisms, biochemical, or molecular. Conclusions about type of dominance vary with the level of analysis

Tay Sachs allele (t) and normal allele (T)

consider heterozygotes:

Individual organism level- Tt don't have disease- complete dominance

Biochemical Level: Tt has intermediate enzyme activity level - incomplete dominance

Molecular level: Tt produces equal amounts of functional and dysfunctional enzymes- codominance

polydactyly- extra fingers and toes- dominant trait

Achondroplasia- a form of dwarfism- dominant trait

Huntington's disease- dominant trait

most humans are homozygous recessive for these three genes- whether a triat is common or rare in a population will depend on the evolutionary processes at work

one gene alters the expression of another gene(or genes) - genes interact

ex: coat color in Labs

gene B codes for melanin production B= black coat bb=chocolate coat

gene E determines how much pigment is depositied in each individual hair

E= full deposition of pigment ee= blocked deposition of pigment= yellow coat

BE

Be

bE

be

          BE          Be            bE             be

BE        BBEE       BBEe       BbEE         BbEe  

     Be         BBEe      BBee        BbEe         Bbee       

bE        bBEE        bBEe        bbEE        bbEe  

be        bBeE        bBee        bbeE        bbee  

phenotypic rations- 9B:4Y:3CH

Epistasis occurs when one gene alters the expression of another gene

this happens often in gene regulation: one gene may code for a protein that prevent transcription of another gene

one gene affects several traits (2 or more)

period gene in fruit flies affects a fly's biological clock and it affects the male's courtship dance

defective fibrillin protein leads to Marfan syndrome

two or more genes affect one trait

no 3:1 phenotypic ratio in the F2 offspring

instead there is a continuum of colors- that is a clear indication of plygenic inheritance

you cross two shrimps with orange claws and you observe the following offspring phenotypes:

8 red clawed shrimp

15 orange clawed shring

6 yellow clawed shrimp

what is the simplest explanation for this pattern of inheritance?

incomplete dominance

1:2:1 ratio implies one gene is affecting it

more than 2 alleles for a gene exist in a population

but each individual has only two alleless for each geme gamete has only one allele for each gene

ABO blood groups in humans

3 alleles in population

1 gene codes for enzyme that attaches carbohydrates to surface of red blood cells

6 genotypes

4 phenotypes

Genotype- I^AI^A or I^AI phenotype- A

Genotype- I^BI^B or I^BI phenotype- B

Genotype- I^AI^B phenotype- AB

Genotype- ii phenotype O

Gene x Environment (G x E)

interactions

the effect of a gene depends upon the environment in which it is expressed

caot color in siamese cats and himalayan rabbits- enzymes can function in a certain temp

flower color in hydrangeas- pH changes the color

Errors in meiosis = non-disjunctions, may result in gametes that have missing or extra chromosomes

Down syndrome- extra copy of chromosome 21

• Mendel's laws and rules still provide the backbone for understanding the particulate nature of inheritace adn the segregation of alleles during meiosis
• we now recognize that pleiotropy, epistasis, and plygenic inheritance are common feaures of organisms
• moreover, the environment has a major impact on how genes are expressed. Phenotypes often represent the combined effects of genes and environment

heart disease

type II diabetes

cancer

alcoholism

Bipolar Disorder

Depression

poor undersanding of genetics

literal interpretation of the Bible

conservative political ideology

science is a formal process of generating new knowledge that uses evidence to construct testable explanantions and predictions of natural phenomena as well as the body of knowledge generated through this process

scientists used observations, experiments and reasoning to develop explanation for natural phenomena but science differs from other ways of knowing by its dependece on empirical evidence and testable explanations

all scientific knowledge is subject to revision in light of new discoveries; scientists never claim absolute knowledge

logically impossible- supernatural entities, by definition, cannot be measure, weighed, manipulated, added to or subtracted from controlled experiments

the supernatural is simply not tractable scientifically

science cannot address existential questions such as what is the meaning of life or how does one lead a moral life? in general scientific consensus is that religiously-themed topics such as intelligent design do not belong in science curriculum. A more appropriate venue for this topic vouw be courses on philosophy or theology

developed a nested classification of species by grouping species by morphological similarities

father of taxonomy

hierarchical classification

Scottish geologist- promoted gradualism- the idea that small changes occuring over long period of time can accumulate to cause large transformations of the earth

principles of Geol;ogy

a pioneer of paleontology- showed that extinctions were common however he believed in catastrophism rather than gradualism

father of paleontology

described many fossil species

showed that extinction had occured

species are immutable- they were created by a divine being and they don't change

the earth is young

populations have the potential to grow exponentially and will therefore compete for resources; many individuals will die

observed that in nature many species produce far more offspring than can survive. this promoted Darwin to focus on differential survival as a key mechanism in evolution

promoted the idea that species change over time

proposed that species evolve as environments change prior to Darwin..but his mechanism turned out to be wrong

Lamarck's ideas: species change, species are related, use and disuse, inheritance of acquired characterisitics

acquired traits cannot be inherited

(body building)

Darwin knew a great deal about artificial selection

humans had been selecting on specific traits in many different species for thousands of years

this process can change the genetic makeup of a population- it can cause evolution

ex: dog breeds

Darwin and Wallace's Big Ideas

Descent with Modification

life on earth had a single origin and all the diverse organisms around today are descendants, modified by evolutionary prcesses of this common ancestor

Darwin's and Wallace's Big Ideas

Mechanism to explain evolution: Natural Selection

1. must be variation in phenotypes of individuals in a population
2. variation must have a genetic basis
3. unequal survival and reproduction among individuals in the population; depends upon the heritable traits that individuals possess and environmental conditions

Field studies of evolution:

Galapagos Finches-

Variation in environment over a few years

in dry years few plants would reproduce, seeds were scarece and large seeds were predominante- birds with deep beeaks are favored (directional selection for deeper beaks)

in wet years, most plant reproduce, seeds are abundant especially small seeds and small beaked fincehs do better (directional selection for smaller beaks)

natural selection can change direction in short time spans

biotic and abiotic environment

traits that are favored in one generation may no longer be favored in the next generation as the environment changes

1. Genotype Frequencies- proportion of one particular genotype relative to total # of individuals in a population

2. Allele frequencies- proportion of one particular allele relative to total # of alleles (for gene under study) in a population

Population of 1000 butterflies in a field

490 dark blue wings = B¹B¹

420 medium blue wings = B¹B²

90 white wings = B²B²

what are the geotype frequencies?

what are the allele frequencies?

Genotype frequencies-

B¹B¹ = 490/1000 = .49

B¹B² = 420/1000 = .42

B²B² = 90/1000 = .09

Allele Frequencies

B¹ = .49 + 1/2(.42) = .49 +.21 = .7

B² = .09 + 1/2(.42) = .09 + .21 = .3

490 B¹B¹ = 490 x 2 = 980 B¹

420 B¹B² = 420 B¹ and 420 B²

90 B²B² = 90 x 2 = 180 B²

1400 B¹ alleles and 600 B² alleles

B¹ = 1400/2000 = .7

B² = 600/2000 = .3

the overall gene pool of a population

useful analogy: meiosis and random fertilixation are like shuffling a deck of cards- the proportion of hearts, spades, clubs, and diamonds in the deck does not change

a population's gene pool will remain constant unless evolutionary process (mutation, selection, gene flow or genetic drift) are acting on the population

p²: 2pq : q²

if the both the parents have heterozygous alleles

genotype and allele frequencies in the population will be stable (will not change over time) this is known as the Hardy Weinberg Principle

after one generation of random mating genotype frequencies for 2 alleles at one locys will be

p² + 2pq + q²

where p=freq dominant allele and q= freq recessive allele and p+q=1

genotype and allele frequencies will remain constant in successive generation as long as specific assumptions are met

p= freq B¹ and q = freq B²

p² = freq B¹B¹

q² = freq B²B²

2pq = freq B¹B² + freq B²B¹

Hardy Weinberg Equilibrium

p² + 2pq + q² = 1

1. population size is very large (no genetic drift affecting gene under study)
2. Population is closed (no gene flow)
3. No mutations are occuring at gene under study
4. Mating is random with respect to trait under study ( no sexual selection, no inbreeding at gene under study)
5. All genotypes in populations have equal chance of surviving and reproducing (no selection at the gene under study)

Natural Selection

Sexual Selection

Genetic Drift

Gene Flow

Mutation

biologists are especially interested in selection, other processes are also important - lead to change in genetic makeup of a population

Process by which alleles are transferred from one population to another

due to immigration or emigration of individuals/gametes

gene flow acts to homogenize populations

process by which new alleles arise in a population

due to errors in DNA replication or cell division

PKU in humans

genetic diease

autosomal recessive disorder

inability to break down phenylalanine due to defective enzyme

leads to severe cogniticve impairment

symptoms can be totally prevented is diagnosis is made at birth and a special diet prescribed

How can Biologists use HWE:

Sickle Cell Disease

Autosomal recessive disorder

defective hemoglobin molecule

leads to a variety of health problems

frequency is .02

frequency of carriers= 2pq - 2 x .098 x .02 = .0392

frequency of homozygous dominant genotypes = p² - .98 x .98 = .9604

the integration of discoveries and ideas from population genetics, paleontology, systematics, zoology, botany, ecologym and biogeography

according to the morden synthesis, genetic variation in populations arises from random mutations and is constantly reshuffled into new allelic combos by meiosos and fertilization

the gentic makeup of a population changes when evolutionary processes such as natural, sexual, or artifical selection, genetic drift, gene flow or mutation occur

• most biologists think that small evolutionary changes accumulate over long time periodsto generate large evolutionary changes like speciation
• even if its difficult to watch speciation taking place, natural selection works fast enough that we can often observe rapid phenotypic and genotypic change in populations in nature and lab
• focus on three examples- galapagos finches, Trinidadian guppies and HIV evolution within three patients

• Evolution by natural selection does not push organisms forward toward some ideal form; it is not progressive
• natural selection is more passive and reduces by killing or low reproduction the representation of those traits that are less advantageous in the current environment
• as environmental conditions change, the traitsthat lead to increases reproductiove success in the environment can also change as you saw in the natural experiments with finches during drought and flood years
• natural selection can move populations away from Hardy weinberg equilibrium
• of the prcesses that can cange the gene pool, selection is the only process that produces adaptations: heritable traits that increase survival and or reproductive success
• alleles increase or decrease in frequency based upon their influence in an individuals fitness

studied guppies in pools with two different predatory fish

guppies in pools with small predators were large and matured later in life

guppies in pools with large predators where smaller and matured earlier

transferred some guppies from each- over 11 years guppies became larger and matured later when exposed to killfish predators that selectively feel on smaller prey

this suggests that predators act as selective forces on the size of prey and over quite short periods of time

when humans target pathogens with drugs we impose very strong selection pressures

any rare pathogen individuals with drug resistance are at a tremendous advantage and will replicate rapidly

because pathogens reproduce so quickly, resistant strains can dominate the population extremely quickly

makes drug development and delivery a real challange in the fight against infectious diseases

changes the average value of a trait

one tail of phenotypic distribution is favored. if directional selection continues long enough, the favored allele(s) eventually reach a frequency of 1.0 or 100% and are siad to be fixed; those alleles that are no longer found in the population are lost freq = 0 and overtime genetic diversity is reduced

antibiotic resistence- evolved resistance to antibiotics

perticide resistance

herbicide resistance

= heterozygous advantage

a pattern of natural selection in which heterozygous individuals have higher fitness than homozygous individuals

occurs when intermediate phenotypes are selected against and extrene phenotypes are favored. Disruptive selection maintains genetic variation but does not change the mean value of a trait

opposite of stabalizing selection

loss of complex structures- if having a reduced complexity leads to higher reproductive success then the frequency of the alleles associate with that phenotype will increase in the population

- eye loss in darkness

-parasitic worms

males compete more intensely for mates than do females and females are choosier about their mates than are males

anisogamy- defined by the occurrence of gametes of different sizes

eggs are expensive whereas sperm are energetically cheap

difference in gametic investment between males and females leads to three predictions

Prediction 1- male fitness will be limited by the number of mates, whereas female fitness will not

Bateman's rule- only male fitness improves with # of mates

female fitness is limited by resources

Prediction 2- because females invest more into each gamete, they should invest more in parental care of an offspring

in nature females generally invest more in parental care

Prediction 3- given greater investment in gametes and in care of offspring, females should be choosier about who they mate with and males should compete more for mates than do females- we generally see both patterns

differences between sexes in traits related to attracting and obtaining mates

- males have exaggerated traits that they use in fighting or courtship

competition within a sex

competition between males selects for male reproductive traits

one sex select among variants of opposite sex

female mate choice selects for male reproductive traits

Intrasexual selection:

Male-male competition

male combat- males fight over access to mates

ritualized displays- males use displays to gauge strength of opponent- reduces risk of serious injury

sperm competition- males do not physically compete but their spern do. competition for fertilization

males have evolved- claspers to clutch female, a new penis with a scrub brush

female places her genitalia over the new penis. male then scrubs the old perm from the females sperm storage organ and deposits sperm

intersexual selection

cryptic hidden female choice

females not picky about mating

females are promiscuous = mate with many males

after mating females control which fertilize their eggs

females may remove or reject unwanted sperm

Direct benefits- males offer resources in addition to sperm: access to food and nest sites, gifts, parental care

Indirect benefits- males offer only sperm good genes and sexy sons

good genes model- females choose mates whose genes improve tiehr offsprings survival and reproduction

sexy sons- fisherian runaway model- females preference can initally be arbitrary but as females choose mates with certain traits both the male trait nad the female preference co-evolve