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CAL / Biology / BIOLOGY 1 / When did the community start producing more antibiotics?

When did the community start producing more antibiotics?

When did the community start producing more antibiotics?

Description

School: University of California Berkeley
Department: Biology
Course: General BIOLOGY Lecture and Laboratory
Professor: Bruce baldwin
Term: Fall 2016
Tags: Ecology, evolution, and plants
Cost: 50
Name: Bio 1B, Final Exam Study Guide
Description: The study guide covers all of the three sections that will be on the final
Uploaded: 12/09/2016
25 Pages 31 Views 4 Unlocks
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FINAL EXAM STUDY GUIDE 


When did the community start producing more antibiotics?



Evolution 

LECTURE 1

Relevance of Evolution

Evolution is important because everyone is affected by it

Antibiotic era

∙ Penicillin was discovered by Alexander Flemming in 1928

o He was in the process of reducing lethal infections due to wartime experiences

o Staphylococcus aureus: a benign bacteria that lives in our bodies, but harmful when gets into a wound and can cause blood  poisoning (aka septicemia)

o He advocated that physicians cut around the infected wound to prevent infection from spreading  

o Carbolic acids were used to treat wounds, but they destroy healthy tissue, which promotes more infection o He worked in London at St. Mary’s Hospital looking for an antibacterial agent that could hinder the growth of commonly  pathogenic bacteria


Who is nicolaus steno?



Don't forget about the age old question of What are the first signs of being a diabetic?

o After a month, he noticed that lots of his plates of Staph aureus were contaminated by a fungus that had inhibition of bacterial  growth around them

o In his series of experiments, he found that the fungal juice (penicillin) inhibited the growth of some of the bacteria and some of  the bacteria turned out to be positive controls, which was very exciting for Flemming to see; however, he found that the juice  was very unstable, and very hard to extract much of it so it wouldn’t be effective as a treatment

∙ Ernst Chain and Howard Florey set up a penicillin factory which produced enough extract to conduct research on mice in 1940 then  they moved onto humans

∙ Chain and Florey moved to the US to join Norman Heatly to develop a factory in Illinois

o They produced enough to save the lives of the soldiers from the WW2


What idea is presented by uniformitarianism?



o It was made available to the civilians when they found out about it

∙ Flemming, Chain, and Florey won the Nobel Prize in Physiology/Medicine in 1949, which resulted in the antibiotic era ∙ As early as 1940, there was a publication by Chain and Edward Penley Abraham regarding the bacteria that were not affected by  penicillin on the plate experiment  

o These bacteria produced an enzyme (penicillinase) that detoxified the penicillin fungus, which allowed them to grow in the  presence of the fungal juice Don't forget about the age old question of Does the disadvantage change when the context changes?

o By 1947, doctors had observed the first resistant pathogen in a patient  

o By 1967, penicillin resistant pneumococci had surfaced

o As antibiotic use spread, resistance to the antibiotic spread as well

∙ The medical community started to produce more antibiotics, but the bacteria evolved resistance, sometimes quickly and sometimes  it took a long time

∙ In 2013, federal officials discovered that antibiotic resistant bacteria are infecting at least 23000 Americans per year The emergence of antibiotic resistance is not unexpected, and this is an example of biological evolution Evolution:

1. It’s a fact, not just a theory

o Its not something that we can dismiss as it’s happening around us

o We cannot escape it; we can change the way we deploy antibiotics and slow down the evolution, but we cannot stop it 2. Evolution of traits, such as antibiotic resistance, has been caused by natural selection We also discuss several other topics like What is mill's principle of liberty?

o Natural selection is one of Darwin’s big ideas

o We can use experiments to measure natural selection in the wild If you want to learn more check out What are examples of diel alder's reactions?

LECTURE 2

Early Historical Development of Evolutionary Biology

Charles Darwin: 1809-1882

∙ Theory of Natural Selection and provided massive amounts of evidence to support his hypothesis

∙ He changed the ideas from the biblical view of a young earth to a modern view of the earth being old and being inhabited by species that are constantly evolving  led to modern view of Evolution

o Evolution: descent with modification  

∙ He was born in a highly educated and wealthy family; attended Cambridge University and trained to be a clergyman due to interest  in natural history

∙ He went on a voyage, HMS Beagle, with Captain FitzRoy for 5 years  

o He saw finches on the Galapagos islands that gave human insight about natural selection due to his observations  o He also saw mockingbirds on different parts of the island

∙ James Usher: believes the earth to be 4000 years old in 1658; Earth is very young

∙ Aristotle’s Scala Naturae (Natural Order): nature is like a ladder and it’s a hierarchy with God at the top and the rest follow; the  great chain of being (linear order of species)

∙ New Ideas:

o Nested Hierarchy and Classification

 Hieracrchical system of organization  systema naturae

 Linnaeaus: binomial classification Don't forget about the age old question of Which other genre shares a history with hip­hop?

o Common Ancestry, and Species change over time

 Idea of nested hierarchy led to the idea that species are more related to one another and they may share a common  ancestor

 Comte de Buffon: considered the possibility that animals of similar forms might share the same ancestor  Erasmus Darwin: made a radical argument that all life come from one common ancestor, and all species we see today  branched off from that ancestor at one point or another; didn’t suggest a mechanism to explain his argument o Paleontology and Deep time

 Nicolaus Steno: dissected a shark head and found that the tooth looked very similar to the stones found up on he hills;  proposed the stones were fossilized teeth

 3 principles in the field of Stratigraphy

 Law of Superposition: bottom layer is the oldest while the very top is the youngest; being able to see long periods of  time in rock recordDon't forget about the age old question of How infections can trigger cancers?

 Principle of Original Horizontality: when you have a cliff, you won’t have a lot of sediment build up on that cliff because  sediments settle down on horizontal spaces

 Principle of Lateral Continuity: idea where you have a large basin with multiple layers of sedimentary rocks and later  when you have a river cut through the basin, you will see that the layers on one side of the basin has the same layers  as on the other side of the basin

o Uniformitarian Principle (aka Uniformitarianism)

 Idea that past processes are happening in the same way as processes do today

 This was popularized by Charles Lyell

 This was important because it was a serious challenge to an older idea of Catastrophism

 Catastrophism: mainly from the idea of the great flood in the bible

 These processes were all gradual  Uniformitarianism had the idea od gradualism

 Sediments coming down into lake basins over many millennia; rocks forming and mountains building were gradual  Today’s geologists have rejected gradualism  learnt that over time, some natural events can be catastrophic o Old Earth

 Idea of uniformitarianism led geologists to predict that the earth is very old

 Lord Kelvin in the late 1890s used physical principles

 Heat loss model to estimate earths age 6000-20000 years old

 Earth = 4.54 + 0.05 billion years old  

o Homology and Comparative Anatomy

 George Cuvier defined homology as structural and positional similarities due to common ancestry

 Modern definition of homology: similarity in structure and position between different organisms, which indicates a common  ancestry or evolutionary origin

 Cuvier used homology to prove that fossil animals resembles the living ones

o Extinction

 He examined the jaw from megalosaurus and used comparative anatomy to demonstrate that this jaw was similar in  structure and maybe position to a lizard  proposed the concept of extinction

 Organisms that lived at one point in the past but they’re not there anymore  

 This idea was upsetting to those following the idea of great chain of being and the idea of single creation by a supernatural  being  challenged the religious dogma of the day

o Evolution

 Jean Baptiste Lamarck published a book in 1809 in which he stated that animals evolve from simpler forms, such as  amoeba, and that organism don’t go extinct, but they simply evolve to become more complex

 He believed evolutionary happened in two steps:

 Use of structures: giraffes that use their long necks make them longer

 Striving: the offspring acquire the form of the parent

 He did not provide evidence to support his ideas

LECTURES 3 & 4

On the Origin of Species

Darwin proposed the mechanism of adapted evolution to convince people that evolution really happens; then he also came up with the  mechanism of natural selection

Charles

∙ Darwin was influenced as he was sailing around the world and saw sea shells at the top of 11000ft, and he also experienced  earthquake while he was in Chile

∙ He saw the mockingbirds that lived in Peru and Ecuador and what looked like relatives out in the Galapagos islands ∙ “Mutability of species”: the fact that a species could change over time and diversify and diverge into multiple species; influenced by  Erasmus

∙ After the voyage, he no longer questioned whether or not species evolved, rather how they evolved ∙ After reading an essay by Thomas Malthus, his whole world view changed

o Malthus wrote that population was doubling every generation and that the population would outgrow its food supply, which  would lead to mass starvation, plague, taxation, etc.

o Darwin realized that not only human population produces more offspring that the world can support, but also all organisms do  that and the environment cannot support them so those offspring have to struggle for existence.

∙ “The pencil essay”: in this essay, Darwin outlined evolution by natural selection and the ideas that had been provoked by these  concepts

∙ Alfred Wallace sent Darwin a letter in 1858 containing an essay and he asked Darwin to review the essay and communicate it to Lyell for publication

o Darwin thought of the essay as a good abstract for his ideas on evolution by natural selection

o He went on an expedition for 4 years in 1848 with Henry Walter Bates; came back with lots of species but the ship caught fire;  18 months later in 1854, he sailed off again and came back with 125000 species and 1000 new to science o He was influenced by Lyell and Malthus, just like Darwin

o He independently conceived the idea of evolution by the mechanism of natural selection due to the struggle for existence ∙ In 1858, both Wallace’s essay and extracts from Darwin’s pencil essay were published for the journal of the Linnaean society; in late  1859, he got Origin of Species published

∙ Darwins’s points:

o Variation among individuals in a population

o Variation is passed from parents to offspring

o More individuals are born than can survive

o Some variants survive and reproduce at a higher rate than others

OUTCOME: the population changes from one generation to the next due to differential survival

∙ Darwin’s arguments in his book that people really understood and were not controversial followed by controversial ideas (thesis): o Variation within domestic species (variation is inherited)

o Artificial selection: favor of traits in consequent generations (consciously/purposeful); unconscious selection can also make  evolution happen

o Struggle for existence among individuals in the wild

o Those populations that bear some variant/trait that allows them to better survive/reproduce are the ones who are going to  contribute their traits to the next generation  reproductive advantage  natural selections

o Given the vast amount of time available, there wouldn’t be any limit to the amount of change that natural selection could cause ∙ Objections:

o People were concerned about the rarity of transitional varieties (missing link)

 Transitional forms that are fossils (existed in the past) – we don’t see much of this because fossils don’t get formed that  often

 Transitional forms that are extant species  

o Why don’t transitional forms exist as living organisms

o He pointed out that his theory explains a lot of unrelated observations in a very elegant way

 Biogeographic patters

 Similar organisms live in the same place because they diversify from a common ancestor

 Wallace’s line between Bali and Lombok => Common ancestry

 Descent with modification: can be explained by transmutation of species by evolution by the mechanism of natural  selection

 Hierarchical classification

 Nested hierarchy reflects more common relatedness, not just similarity

 He contrasted the religious dogma of special creation of species

 Homology

 Organisms have similar structures because they share a common ancestor that has that structure

 “Natural selection tends only to make each organic being as perfect as or slightly more perfect than the other  inhabitants of the same country with which it has to struggle for existence”

 Batesian mimicry: have the mimicked traits because their ancestors survived with those traits

 The reason that they are different from one another is because their common ancestors are much more further back  and they don’t have a recent common ancestor

 Rudimentary organs

 He pointed out that humans have a tail bone and we share a tail bone with monkeys; fact that humans and monkeys  have tail bones is evidence for common ancestry, precisely because tail bones are useless in humans

∙ Disagreements about two aspects of Darwin’s theory:

o Pattern of Evolutionary change

o Mechanism of evolutionary change

 Darwin asserted that evolution by natural selection is a gradual process and continuous

∙ Gaps in Darwin’s theory into the 20th century:

o Source of variation among individuals

 Wasn’t clear how variation could persist in the face of natural selection

o Mechanism by which individuals could persist in the face of natural selection

 Darwin did not manage to solve this problem, but Gregor Mendel did

LECTURE 5

Population Genetics I: Populations and Frequencies

∙ Gregor Mendel published his results from the crosses that he did with peas in 1865

o Mendel was counting the offspring and thinking about gambling and probability theory that was developing at that time ∙ Laws of inheritance were rediscovered around 1900 by: “plant breeders”

o E. Tschermak Von Seysenegg

o H. DeVries

o C. Correns

∙ Early geneticists projected Darwin’s idea of gradual evolution by natural selection, and DeVries and the others thought that  evolutionary change occurs discontinuously by jumps

∙ Geneticists argues that mutation is the thing that limits evolutionary change and not the rate or strength of natural selection ∙ Neo-Darwinism: modern biological/evolutionary synthesis; application of Mendelian inheritance to Darwin’s theory of natural  selection

o Descent with modification

o Changes in allele frequency across generations (new mechanistic approach)

∙ Biological population is a group of individuals of the same species who can freely interbreed with one another, and they are either  wholly or partly isolated from other individuals of that species

o Population is a basic unit of evolution, species is not

∙ Single gene polymorphism

o A trait is considered a single gene trait if by swapping out alleles at a particular gene/locus, that changes the phenotype of the  individual that those alleles are in

o Cross pollination: father and mother flowers were from different plants; aka intracross or hybrid crosses o Self pollination: flowers are hermaphroditic; they are self-compatible  

∙ Flower color polymorphism: this trait has no dominance  two alleles act equally on the heterozygote so it has a phenotype that’s  intermediate

∙ Phenotype: observable physical and physiological set of traits of an organism that are determined not only by the genes of an  organism but by the interaction of its genotype and the environment that it develops through

∙ Testcross: cross where you have a known individual that’s homozygous recessive and that can be crossed with an individual that has  the dominant phenotype so you don’t actually know what its genotype is and you want to find out its genotype ∙ Codominance: you can see phenotypically what the genotype is of the heterozygote; single locus with 2 alleles in the population  there would be three phenotypes, instead of two

Lectures 6 & 7: Population Genetics II: Hardy-Weinberg Principle

∙ There was thought to be no evolutionary change if there was only random mating  binomial equation  o If you know the allele frequencies of your parental generation at the time that they are reproducing, then you can predict the  allele frequencies and even the genotype frequencies of the progeny of those parents, assuming all those parents are mating at  random with one another with respect to the locus that you’re looking at

∙ HW assumptions: (assuming there is nothing affecting allele frequencies except the random mating) o Random mating

o Populations are infinitely large

o No selection

o No net mutation

o No net migration

∙ Stable equilibrium: allele frequencies in the population (as long as the HW assumptions are met) are going to stay the same from  one generation to the next

∙ HW equilibrium is stable because it is like a marble in a cone shaped container

∙ Most genes are at HW equilibrium  we can use the HW principle as the basis for things like genetic fingerprinting o CODIS uses 13 different single nucleotide polymorphisms to identify samples and suspects, and each of these loci rather than  being a single locus with two alleles, each of these loci in the human population has a large number of alleles o Controversies: sample found at the crime scene is often very degraded and are often not able to get all 13 loci genotype; only  able to get 2-3 loci

∙ For a lot of mutations that we see, they actually have no effect on the phenotype; they’re selectively neutral so they are mostly at  HW equilibrium

∙ HW deviations:

o Non-random mating

 Different from other deviations because non-random mating in its pure form actually doesn’t cause any changes in allele  frequencies, but it does change genotype frequencies

∙ Causes of deviations:

o Natural selection: “longitudinal studies”

∙ Mutation rates are pretty small  biologically, this HW assumption gets violated

o Point mutation

 Small/insignificant effect

 The genetic code is redundant

 Basis for SNPs

o Deletion (single mutation)

 Gene becomes dysfunctional due to the loss of a nucleotide

o Insertions (single mutation)

 Can cause it to be the stop codon and the gene can stop to be read (destructive)

∙ Type of duplications

o Tandem duplications

 Can be destructive by messing up regulation, or the duplicated region of the genome can be shut off and prevents it from  being expressed

o Full duplications of chromosomes

o Entire genome gets duplicated

 Duplication of genome is common in plants as it has an important impact on their evolution

 Hybridization  Tetrapodization  

∙ Gene flow

o Flow of genes from one population to another due to migration; multipopulation process

o Migrating individuals moving their alleles among populations across space and time

 When individuals migrate, they don’t necessarily deposit their alleles in that population

o Makes populations more similar to one another

∙ Genetic drift

o Something that happens within a single population over time; random process

o It’s basically the drifting of allelic frequency over time

o Larger population size = more likely to get the expected outcome

o It has two effects:

 Causes allele frequencies to change at random

 Can result in a loss of allele/loss of individuals at random

o Depending on what the starting frequency of an allele is, you can make some predictions about whether that allele will be lost or not

 If an allele doesn’t have any effect on the reproductive success/survival of individuals that carry that allele, then the  frequency of the allele can be used to predict whether that allele is more likely to be lost

 If an allele starts at a very low frequency, it’s much more likely to be lost that if it started at a high frequency o Genetic drift phenomenon

 Bottleneck

 Short term reduction (drastic) in the size of an existing population (living in the same geographic location)  Parent population  Bottleneck  Surviving individuals  Next generation

 Eg. Northern Elephant seals

 Founder effect

 A few individuals from a population start a new population on a different location (assuming the population is large  enough that a loss of few individuals will not change its allele frequency)

 Chance causes the founded population to have a different allele frequency than the original population  Eg. Huntington’s disease in San Luis, Venezuela

∙ Once an allele is lost, it’s frequency goes to zero and will not come back through mutation; it may come back through migration  (gene flow)

∙ Over time, isolated populations diverge due to genetic drift, mutation, and natural selection

LECTURES 8 & 9

Natural Selection

∙ Natural selection happens when individuals in a population vary in some traits  

∙ Requirements for natural selection to happen

o Variation causes individuals to have varying fitnesses

o Differential fitness among individuals

 The extent to which an individual contributes alleles to the gene pool of the next generation, relative to the contributions by other individuals

 Absolute fitness: probability that a particular individual will survive or the actual number of progeny  Relative fitness: standardized fitness

 Fitness is a phenotype just like any other phenotype that’s produced by a genotype

 Average fitness depends critically on the environment, thus the agent of natural selection

o Heritable variation so the traits these individuals vary in are genetically controlled

∙ Directional selection: occurs when one allele causes higher rates of survival/reproduction than the other allele ∙ Natural selection can happen not just because of differential fitness, but also due to differential mortality/reproductive success ∙ Purifying selection

o Essentially directional selection against a new/deleterious mutation

o This is a process of maintaining genetic variation because mutation is creating variation but selection is limiting it o Most evolutionary processes are eliminating genetic variation

∙ Balancing selection: another process that can maintain genetic variation

∙ Heterozygote advantage maintains genetic variation when an individual has a trait that’s controlled by a single gene ∙ Most traits we see in populations are “continuously distributed” (don’t have either/or categorical phenotype) ∙ “Qualitative Genetics” studies evolution of continuously distributed traits (aka polygenic traits)

o Polygenic traits: many genes affect each trait; each gene has a small effect; many small effects generate continuous variation  ∙ Evolution is defined as…

o Descent with modification

o Change in allele frequencies across generations  

o Changes in population trait distributions across generations

∙ Patterns of natural selection:

o Stabilizing selection

 Situation where the extreme phenotypes have low fitness and you end up with an evolved population that has changed in  the distribution of individuals

o Directional selection

 Situation where the next generation favors the other extreme phenotype

o Disruptive selection

 Intermediate phenotype is favored

LECTURE 10

Phylogenetics I

∙ Phylogenetic trees are very powerful because they link our ideas about classification of organisms, like Systema Naturae to the idea  of evolutionary change and descent with modification from common ancestors

∙ These also show the diversification of lineages through time; very much like a family tree

∙ The branches of the phylogenetic tree indicates our hypothesis about the origin of these taxa

∙ Clade means branch; includes the node at the base of that branch

∙ Basal taxon: group that’s most distantly related

∙ The root of the tree is defined by the basal node, which is the farthest back common ancestor of everybody who’s on the tree ∙ Shared derived trait: a trait that is more recent than others on the tree, and therefore, it’s derived because it happened since the  other taxa have branched off  

∙ Polytomy: a point where it branches into more than 2 different taxa; this indicates 2 things

o Not enough data yet

o Evolutionary/branching events all happened so close in time that there weren’t enough mutations between the first branching  event to the next branching event  

∙ Monophyletic clade: a group including the ancestor and all of its descendants

∙ Polyphyletic: a group that includes some descendants from different ancestors, but not their common ancestor ∙ Paraphyletic: a group that includes an ancestor and some but not sll of its descendants

∙ How to construct phylogenies

 Characters with which to construct phylogenies

 Dichotomous branching

 Shared derived character state

∙ In order to construct a tree with a bunch of taxa, we need to:

o Find homologous traits

o Make hypothesis about how those traits changed in state from ancestral state to derived state on some shared branch in the  past

∙ Analogous: characteristics that evolutionary converged because these organisms lived in similar environments or used similar kinds  of hunting/mobility strategy, and natural selection resulted in individuals having very similar characteristics, even though their  ancestors didn’t  

∙ Parsimony: the idea of opting for hypothesis that have the fewest possible assumptions  

o Occam’s razor

LECTURE 11

Species and Speciation I

∙ Morphological Species Concept

o We look at individuals and say that they look similar  they all must belong to the same species

o Useful when working with fossils

o Polymorphism: individuals look different from one another but they can still interbreed and produce viable offspring o Sexual dimorphism: male and female of the same species look different from one another but they can still interbreed ∙ Biological Species Concept  

o “Groups of actually or potentially interbreeding populations which are reproductively isolated from other such groups” o Doesn’t apply very well to fossil organisms or asexual organisms, or even individuals that don’t live in the same place

∙ Phylogenetic Species Concept

o Idea that you could do a phylogeny of individuals and in the phylogenetic tree, you see that they are completely distinct from  one another

∙ Speciation

o Large population interbreeding in cool climate

o Extirpation and isolation of the population in warm climate

o When the climate cools again, the isolated population meets again but cannot interbreed and produce offspring  The populations have become two different species!

Ecology 

LECTURE 1

Alexander van Humboldt (1769-1859)

∙ In 1802, he arrived in Ecuador at the Chimborazo volcano and climbed the 19000ft high mountain (probably the furthest any human  had gone)

∙ He looked down from the mountain and saw the extraordinary gradient that he had just climbed  

o Gradient: palm trees down at the bottom followed by tempered forests and then really low plants up until the snow line o He saw the incredible connectedness of nature

∙ He went back to Europe and published the diagram of the mountain (famous figures in the early history of ecology) o All the scribbled in the figure were the names of the plants that he found on each elevation as he climbed the mountain ∙ He never repeated his trip to South America; stayed in Paris and Berlin for most of his life writing books ∙ He died 6 months before “Origin of Species” was published (Humboldt era  Darwin era)

∙ In 2012: ecologists returned to the Chimborazo mountain and climbed again; they noticed the changes in the data that Humboldt  had collected

o Some kinds of grass had moved up several hundred meters on the mountain

o Glaciers have receded ~500m higher in elevation (due to it being warmer now than it was 200 years ago) o Human impact of grazing and agriculture at the low elevations

Key themes of Ecology  

∙ Latitude

o Latitude & Solar Energy

 Sunlight intensity varies with latitudes; when the sun hits the earth, it falls more directly on to the surface of the equator  where the intensity is spread out over a wide surface (more energy per area hitting at the equator)  that’s why it’s warmer  at the equator and colder near the poles  

 Sun overhead at equinoxes (equator)

 Low angle of incoming sunlight (north and south poles)

o Latitude & Rainfall

 Since it’s warmer at the equator, the warm air rises and pressure changes, and as the air rises, it cools so it descends   Warm air at the surface is due to the intensity of the sun

 Cool air does not hold much moisture, so all the moisture that’s taken up off the land surface and ocean surface then  falls as rain (tropical rainforest near the equator, 0 degrees)

 Large masses of air go in circles in the atmosphere because air doesn’t drift off in space

 The descending hot dry air absorbs moisture but doesn’t release it, so we get deserts (~25-30 degrees N/S)  Global pattern in rainfall: lots of rainfall near the equator (~250cm), at ~20-30 degrees, there isn’t much precipitation  (desert zone), and gets wet again further north/south (~40-60 degrees)

∙ Elevation (no pattern on seasonality)

o Elevation & Temperature

 As elevation increases, there is less atmosphere above you, which means there are less molecules pressing down on you, so there’s less energy and the temperature goes down  

o Elevation & Rainfall

 There’s a gradient from warm temperature to cold temperature on the mountains (similar from the equator to the poles)  due to:

 Mountain: air pressure

 Earth: geometry of the sun hitting the earth

 A lot of storm systems come off the ocean, pick up lots of water, so the atmosphere is full of moisture, and if the storm  system is moving from west to east, which they mostly do at mid-latitudes, and hit a mountain range, they physically get  pushed up, they cool, moisture condenses and it releases rain

 There’s high rain on the windward side of the mountain, and as the air moves over the mountains, it begins to drop and  absorbs more moisture and there’s very low rainfall on the leeward side of the mountain (resulting in rain shadow)  Windward: side of the mountain where the wind is blowing from

 Rain shadow: dry zone behind a mountain range relative to the direction of the winds movement

∙ Earth’s tilt and seasons

o We experience seasons because the earth’s axis is tilted

 For half the year, the northern hemisphere is tilted towards the sun, so the sun is more intense in the northern hemisphere  For the other half of the year, the sun is more intense in the southern hemisphere

o If we lived in a universe where the earth’s axis was perfectly vertical, then we would always get the same amount of solar  energy every month of the year as we rotated and revolved  more energy in the day than in the night

o Combination of the tilt and the orbit gives us seasons

∙ Maritime and Continental Climates

o Water has very high thermal inertia

 When the sun hits the water body, it warms up slowly, whereas land warms up quickly; water also cools off slowly, whereas  land cools off quickly

 Water is an insulator that buffers the seasons because it holds on to so much thermal energy

o Locations near the ocean don’t warm up as much in the summer and don’t cool off as much in the winter  maritime climate

World Biomes (ecological patterns)

∙ Temperature, rainfall, and seasonality have very strong influences on living organisms, and they set up the major global patterns of  different types of ecosystems

∙ Biomes: major terrestrial ecosystems at a global scale

∙ Biomes show parallel patterns on elevational and latitudinal gradients (Humboldt’s great observation) o Rainfall patterns aren’t the same as elevations and latitudes

∙ We interact with the environment, not the physical space (we know what the environment around us feels like, but don’t know what  latitude we’re on)

∙ When climate starts changing, the temperature and precipitation patterns are moving, and eventually, the biomes move as well  

California

∙ Some fairly unusual vegetation on the global scale: shrub lands in SoCal

∙ Mediterranean climate

o CA experiences similar climate to the Mediterranean basin

o Found in 5 regions in the world

 CA (driest summers)

 Mediterranean basin

 Central Chile

 South Africa (Cape Town)

 South-western and Southern Australia

o Factors that create this climate

 Mid-latitude

 ~30-40 degrees N

 Moderate rainfall and temperature in terms of global patters  

 Summer high pressure over Pacific

 Blocks summer storms from the west

 If a storm hits a high pressure system, it gets pushed around (pushed North)

 Cold ocean

 Maritime climate with wet, mild winters

o Distinctive problem of hot dry summer (not much water and lots of plants)

 Drought

 Fire

∙ Convergent evolution

o Process whereby organisms not closely related, independently evolve (via natural selection) similar traits as a result of having to adapt to similar environments or ecological niches

o Eg, Evergreen sclerophyll (‘leathery leaf’)

 Leaves are very drought tolerant; survive very negative water potential

 Photosynthesize in spring and fall and survive through hot, dry summer

LECTURE 2

Ecology

∙ Definitions of Ecology

1. The study of the relationships between organisms and their environment (Haeckel’s original definition) 2. The study of the distribution and abundance of organisms

3. The study of the transformation and flux of matter and energy in natural systems

∙ Ecological pattern in the Spring in Central Valley, CA

o Vernal pools: temporary pool of water that provide habitat to distinctive plants and animals

o In the spring, these depressions fill up with water and there’s native annual plants that pop out of the soil and have a really brief lifecycle and then it’d be like they were never there

∙ Zika Outbreak distribution pattern

o Public health crisis in North and South America

∙ Mountain lions

o Wander around the suburban bay area

o Now have collars to track their movement every ~4 hours

Species distribution

∙ Eg. Cacti (Carnegia gigantea) are found in some southern regions of Arizona; we may ask why these plants are found in that  particular region and not elsewhere?

∙ It’s much easier to think through a series of reasons why things do live in the places that they live so as to understand the series of  reasons as to why they might not live in a given place

o Does dispersal limit its distribution?

 Dispersal: the movement of individuals or gametes away from their parent location; this movement sometimes expands the geographic range of a population or species

 Eg. Cattle egrets are very common now, but aren’t originally native to the New World

 Introduced in the South America in the late 1800s from the Old World

 They weren’t found in North America before the 1960s because they’d simply not gotten here; they had the capacity  given enough time to disperse and offspring finding new habitats (dispersal limitation)

 Dispersal limitation: an organism has a limited ability to move and its offspring has a limiting ability to get to a new place in  one generation, but sometimes given enough time, they can burst these barriers, especially when people start moving  them around the world (global transportation)

 Dispersal limitation is an important part of evolutionary radiations and speciation

Continental drift + Dispersal limited clade = Evolutionary diversification

 If yes, that’s because area becomes inaccessible or there’s insufficient time

o Does behavior limit its distribution?

 Behavior limitations are more applicable to animals than plants because animals can actually perceive the world and  respond to it (active behavior)

 If yes, there’s habitat selection  

o Do biotic factors (other species) limit its distribution?

 Biotic: living components of the environment

 Environment: everything inside or outside of the organism

 If yes, there’s predation, parasitism, competition, or diseases

o Do abiotic factors limit its distribution?

 Abiotic: non-living components; basic factors that drive climate (latitude, elevation, etc)

 Abiotic factors can be measured, but the abiotic environment is altered by organisms that the other organisms encounter  Interactions between organisms happen by altering the environment and then the other organisms encounter the  environment that’s altered (no direct encounter)

∙ Environmental gradients

o Gradient: range of environmental conditions; eg. Low to high temp., low to high soil nutrients, low to high pH  Some gradients are physically continuous, such as the gradient in temperature moving from the bottom to top of a  mountain (warm to cold conditions are laid out next to each other physically)

 Other gradients are patchy in the natural world, and the patches span a range of environmental conditions; eg. Soil  nutrients

o Species vary in their distribution along environmental gradients

 Eg of cactus: found in regions of Arizona where the temperature never remains below freezing for more than 36 hours  One species in particular has an enormous effect on environment

High water quality vs. Low water quality

 High water quality: heterogeneous habitat with both slow and fast moving water (high oxygen), woody debris, substrate variety, and well-vegetated, stable banks

 Low water quality: low dissolved oxygen, high bacterial, nitrate or phosphorus concentrations, and low pH; result of run off fertilizer from farms  still, polluted environment

 Aquatic invertebrates and water quality

 Different groups (clades) often share ecological characteristics: intolerant of pollution, intermediate, and tolerant of  high polluted waters

Ephemeroptera (mayflies), Plecoptera (stoneflies), Trichoptera (caddisflies): intolerant or intermediate

Chironomids (dipterans): intermediate or tolerant

 Species can act as indicators of environmental conditions  

 Distributions are ‘unimodal’ (one peak); water quality (x-axis) vs. abundance (y-axis)

LECUTRE 3

Population Growth

∙ Malthusian insight: “… every organic being naturally increases at so high a rate, that if not destroyed, the earth would soon be  covered by the progeny of a single pair…” – Darwin, 1859

o Kruger National Park in South Africa (1903-2004): at the turn of the century, there were just a few elephants and then the  population slowly started increasing, and 70 years later, there were 9000 elephants

∙ Levels of organization in the biological hierarchy: global  landscape  ecosystem  community  population  organismal ecology ∙ Organism: a living thing

∙ Population: a group of individuals of the same species that live in the same area

∙ Species: a population or groups of populations whose members have the potential to interbreed in nature and produce viable, fertile  offspring (core biological concept)

∙ Demography: the study of the vital statistics of a population and how they change over time

Births/Immigrations  Population size  Deaths/Emigration

o B-D model: the size of a population in a given year is the size in a previous year plus the number of new individuals born minus  the number of individuals that died

Nt+1 = Nt + B – D

 Nt: number of individuals in a populations at time t

 B: number of births in the next time interval

 D: number of deaths in the next time interval

o When we assume birth and death rates per individual to be constant, this translates to a geometric or multiplicative model with  population size increasing at a constant rate (lambda) per year

 Lambda: λ = Nt+1

Nt Nt+1 = λ *Nt (population growth model)

 Geometric vs. Exponential population growth (log y-axis)

 Geometric: discrete time

 Exponential: continuous line; dN

dt=rN

dN

dt: slope of the curve 

 r : intrinsic rate of natural increase (constant as N increases); intrinsic capacity of a population grows with no  limitations

r>0: populations increases in size; λ>1

r=0: population size does not change; λ=1

r<0: population decreases in size; λ<1

 Population growth graphs: linear vs. logarithmic y-axes for population sizes

∙ Life tables: developed to track the fate of individuals or at least cohorts of individuals of the same age

o Cohort: a group of individuals born at the same time interval

o The proportion alive on life tables always starts at 100% (1000 or 1.000) and goes down  survivorship o Survivorship curves (log y-axis)

 Type I: large organisms, such as humans and elephants start with a low probability

 Type II: probability of death is constant in each year  

 Type III: juveniles mostly die (high mortality rate)

o Age-specific fecundity (reproductive output): reproduction is age-specific

 Most organisms have a phase where they aren’t reproductive as juveniles or older individuals; only reproductive upon  reaching maturity

 Some organisms, however, are reproductive until death

LECTURE 4

Logistic growth and life history

∙ No population grows forever because birth and death rates are not always constant

∙ When populations are placed in a finite space with finite amount of resources, they exhibit an S-shaped curve o Looks like a stable maximum population size

o Eg. Northern fur seals recovering from hunting

 Hunted for their fur but are now protected by the Marine Mammal Protection Act  

∙ Density-dependence  

o Density: number of individuals per unit area

o Exponential growth function: dN

dt=rN where r = b – d  

 Population grows when r is positive (b > d)

 Population declines when r is negative (b < d)

 No population growth and s-curve flattens out (b = d)

o Carrying capacity (K) is the property of a given population in a given place with a given food supply; the number of individuals  that can be sustained by the environment

o You can get a stable population as long as birth and death rates cross (b – d = 0)

o Oscillations in a graph often indicate that there is some kind of lag  

o Logistic population growth model: dN

dt=rN (K−N)

K

 This model generates an S-curve and captures the idea that there is some number around which the population fluctuates  (ocsillations)

∙ Density-independent populations

o Tied to external factors that are outside of the control; not related to the size of the population

o Exponential growth is density independent

o Density independent effect:

 Rate of growth of a population at any instant is limited by something unrelated to the size of the population  External environmental aspects, such as cold winters, droughts, storms, volcanic eruptions

 Populations display erratic growth patterns (due to the events mentioned above)

o Human population growth is not an s-shaped curve because it’s been an exponential growth in the past 100 years; past the  inflection point  

∙ Life history

o Term used to capture all of the different pieces of demography

o Definition: suite of traits related to species’ lifespan and the timing and the pattern of reproduction o Allocation and tradeoffs

 Allocation is the simple fact that there is limited energy and time and a whole bunch of things that have to get done in life  Natural selection is at its core and there’s tradeoff from limited energy

 Principle of allocation

 Individual organisms have a limited amount of resources to invest in different activities and functions  In life cycles, resources must be allocated among growth, survival and reproduction

 Animals primarily allocate time and energy to different activities; plants allocate biomass and nutrients to different  parts

 Cost of reproduction

 Producing offspring requires energy, which may leave adults drained of energy (tradeoff)

LECTURE 5  

Competition and Communities

∙ Competition

o It doesn’t require ant direct encounter between organisms

o There are different things that individuals compete for, such as food, space, opportunities to reproduce, and nest locations o Competition occurs when two or more individuals share a resource, and consumption by one reduces its availability for others,  causing reduced growth, survival or fecundity

 Intraspecific vs. Interspecific competition

 Intraspecific = competition between individuals of the same species; this is the mechanism behind density-dependent  population growth

 Interspecific = competition between individuals of different species

 Exploitation vs. Interference competition

 Exploitation = competition mediated by consumption of shared resource; individuals or species don’t actually  physically encounter each other

 Interference = competition involving direct, physical interaction

o Competitive Exclusion & Coexistence

 Principle of Competitive Exclusion (aka Gause’s Principle) = if two species are competing for a limited resource, the species  that uses the resource more efficiently will eventually eliminate the other locally

 Corollary: species can coexist indefinitely if they utilize different resources

 Eg. Paramecium caudatum and Paramecium bursaria

 Connell’s barnacles (Semibalanus vs. Chthalamus barnacles)

 Semibalanus = found below the low tide zone of the intertidal; not tolerant of being exposed to the air  Chthalamus = found between the low tide line and the high tide line of the intertidal; can tolerant being exposed  to air for up to 4-6 hours a day every time the tide drops

 When Semibalanus is removed, Chthalamus expands its range (ecological niche)

∙ Community: interacting populations

o Ecological niche

 Fundamental niche

 The full range of environmental conditions (biotic or abiotic) in which a species is able to maintain a stable population  in the absence of competitors

 Fundamental niche limits are based on physiological tolerance limits and resource needs

 Realized niche

 The actual set of environmental conditions (biotic or abiotic) in which the species establishes a stable population in the  presence of particular competitors

o Resource (niche) partitioning  

LECTURE 6

Predator-Prey

∙ Predation = an interaction in which the predator kills and eats the prey

o In predator-prey interaction, one species is the resource for the other species  + effect on one, and – effect on the other o Herbivores and other grazers may not kill prey, but will remove parts or consume biomass with negative effects on growth,  survival and reproduction

 Herbivory = an interaction in which an organism eats parts of a plant or alga, but (often) does not kill it  Grazers on plants have big impact on distribution

o According to ecological definition, animals eating seeds are in fact predators

o Parasitism = an interaction in which one organism – the parasite – derives nourishment from another – the host, which is  harmed in the process; parasites are smaller than the host and live in or in the host’s body

o Gause worked on predator-prey interaction with Paramecium (unicellular protozoan) and Didinium (predator of Paramecium)  Intraspecific competition would limit population growth, but different results are obtained when Paramecium are given  refuge in sediment  

o Natural experiment to see how species survive in nature without going to extinction soon  lynx-hare interaction (9 oscillations  without extinction)

 Illustrates common phenomenon that predators and prey undergo natural oscillations; no stabilizations, rather it’s  fluctuating up and down

 In most cycles, hare population peaks a little before the lynx population, but never after

o Lotka-Volterra predator-prey model simple theory predicts predator-prey populations will cycle

 When a predator peaks, we see a decline in the prey population

 Prey is most abundant at the steepest growth of the predator curve

o Carl Huffaker’s mites

 Tested the theory of oscillations in lab with 2 species of mice and trays of oranges (one species feeds on the oranges and  the other species feeds on the first species)

 In a simple arena, the same result was obtained as Gauses’  

 A more complex environment was made and three oscillations were obtained before they went extinct ∙ Avoid, escape, and defend

o Competition and predator-prey drive natural selection

o Camouflage, fight (direct defense), flight

 Physical defense = the way they look, eg. porcupines

 Chemical defense = the prey poisons the predator if it eats it

o Mimicry

 Batesian mimicry vs. Mullerian mimcry

LECTURE 7

Mutualism and Disease

∙ Types of species interaction

o Competition

o Predator/prey

o Grazing

o Parasitism

o Mutualism

o Commensalism/facilitation

∙ Symbiosis: a tight and persistent relationship  

∙ Parasites and pathogens

o Parasites: an organism that feeds on cell contents/tissue/fluids of a host while in or on the host organism; they harm but usually  do not kill their host

o Pathogen: an organism or virus that causes diseases

o Why study them?

 Influence distribution and abundance

 Disease organisms can evolve quickly  

 Parasites often exhibit complex life cycles with multiple hosts

∙ Disease as a metapopulation

o Metapopulation: population of populations; group of all the populations where individuals are going back and forth between  them

o Each host is a population of the disease

o Population of hosts is metapopulation of disease organisms because each host has an entire population inside that’s multiplying  and dividing and evolving and jumping and transmitting

o What happens to the pathogen when host dies?  Disease goes extinct, unless they jump and get transmitted to another host ∙ S-I-R model

o Plays a pivotal role in disease theory

o S = Susceptibles (healthy); I = Infected; R = Recovered

 The R population may have antibodies and immune to the disease, but they may lose immunity over time o What affects the spread of the disease?

 Transmission coefficient (beta): susceptible individuals become infected

 Higher values mean that when an infected individual comes into contact with a susceptible, the disease is more likely  to be transmitted and the susceptible gets sick

 Recovery rate (r): possibly immune

 Higher values mean infected individuals recover more quickly and may have temporary of lifetime immunity  Death (d): whether healthy or sick, but in some conditions, infected individuals will have a higher death rate  causing  mortality

 m=r+d

odIdt=βSI−mI (rate of change of infected individuals over time)

 βSI−mI > 0

 If S = 0, number of infected cannot go up

 If I = 0, there is no disease to be transmitted

 S>r+d

β disease will spread when susceptible population exceeds critical threshold population size, ST 

 < ST  disease will crash  

 > ST  epidemic

∙ Disease spreads when susceptible population exceeds critical threshold, ST  disease spread can be prevented if S is lower or ST is  higher

LECTURE 8

Disturbance and Succession

∙ Disturbance: a natural or human event that changes a biological community and usually removes organisms (or biomass) from it o Event is discrete; happens suddenly

∙ Succession: a slow, orderly progression of changes in community composition (i.e. which species are present) through time, usually  following disturbance

o Very temporal process; unfolds over time

o Usually as a concept linked to what happens after a disturbance

o Primary succession

 Following creation or appearance of bare substrate, devoid of life

 Not witnessed very often

 Stages of succession in Glacier Bay, Alaska

 Pioneer stage

 Dryas stage

 Alder stage

 Spruce stage

o Secondary succession

 Following disturbance to an existing community, and some organisms survive

 Fertility of an ecosystem isn’t necessarily disrupted; sometimes it’s enhanced actually

 Succession takes up very quickly

o Early successional plants

 Small seeds and extended dormancy, disturbance triggered germination, rapid growth and short lifespan, early  reproduction and high fecundity

 Dormancy is due to unpredictable gaps

 Environmental doesn’t last for very long so they grow really quickly, reproduce, and die and are replaced by other trees o Late successional plants

 Large seeds, no dormancy, shade tolerant seedlings, slow growth and long lifespan, later onset of reproduction and lower  fecundity

 Very important in place with lots of rain

o Ecological mechanisms involved in replacement of early successional by late successional species

 Facilitation

 Early species modify the environment in ways that favor later-arriving species

 Promoting later-arriving species

 Tolerance

 Early species have little influence on later arriving species

 Each species sort of does their own thing

 Some grow fast and some slow, some disperse quickly and some slowly; they don’t directly impact each other very  much

 Inhibition

 Early species inhibit the establishment of later species, but early species are short-lived

LECTURE 9

Diversity in Space and Time

∙ Ecological community: all organisms that inhabit a particular area; an assemblage of populations living close enough for potential  interaction (influencing each other)

o There is no fixed definition of how large a locality or what period of time defines a community

∙ Species diversity and composition

o Richness: total number of species

o Evenness: relative abundance of species

 Contributes to diversity

 How many individuals are there for each species

o Composition: which species are present

o Fundamental diversity concept: if you bumped into an individual in the community, what’s the chance that it’s a different  species from the last individual you bumped into

∙ Species-area relationship

o Area and the number of species on the graph are both log

o Species-area on islands

 Whenever given a scatter plot with more than one line, there are 3 things that you can immediately read from the graph  Average slope (general relationship)

 Are the slopes the same?

 At a given x value, are some of the lines higher than the others

 MacArthur and Wilson Island Biogeography

 Process of adding species to the island

 Species that colonize the island come from a nearby mainland (relatively nearby) species pool

 Island diversity = 0, and colonization rate = maximum

 Process of removing species from the island

 Extinction  species disappear; they don’t have to fly away as they simply disappear

 Extinction rate will go up with diversity  

 Prediction that the colonization line and extinction line will cross

 The model tells us that a level of diversity does exist at which the rate that new species arrive is the same rate  that species are going extinct  diversity is stable

 Curves on the graph are sensitive to island area (size) and island distance  

∙ Latitudinal diversity gradient

o Diversity changes with latitude  more species in the tropics

o ‘Stressful’ climates, eg. the arctic, limit diversity

∙ Energy, water and diversity

o As the amount of energy and amount of water go up in the system, the diversity tends to go up as well

LECTURE 10

Energy and Primary Productivity  

∙ Photosynthesis: solar energy captured in C bonds

∙ Respiration: stored energy released for use in metabolism

∙ Net Primary Productivity (at ecosystem level)

o NPP = GPP – R or GPP = NPP + R

 GPP = gross primary production; NPP = net primary production; R = respiration

o GPP is all of the glucose produced; total amount of carbohydrate captured during photosynthesis o Some of the glucose captured is lost to respiration  

o NPP is the amount that stays in actual structural biomass  

o World is green because there is high NPP  lots of plants are being produced

o World is NOT always green because of low evapotranspiration and because the green layer sits at the bottom of the trophic  cascade with an even number of trophic levels

∙ Energy flow through ecosystem

o Primary producers  Herbivores  Primary consumers  Secondary consumers  Detrivores

∙ Trophic cascade with ODD number of levels have more plants, and EVEN number of levels mean there’s fewer plants

LECTURE 11

Nutrient and Water Cycles

∙ Earth is an open system with respect to energy, and a closed system for chemical elements

∙ Stock = amount of a compound (C, N, P, and H2O) in one compartment of an ecosystem

∙ Flux = amount of a compound moving between one compartment and another per unit time (rate of movement) ∙ 4 compartments: atmosphere, biosphere, hydrosphere, and geosphere

∙ Water cycle

o Precipitation

o Ocean evaporation

o Evapotranspiration

o Sea to land transport of water vapor

∙ Carbon cycle

o Photosynthesis

o Food webs

o Decomposition

o Respiration

o Fossil fuel burning

∙ Nitrogen cycle

o N-fixation: bacterial, lightening, and industrial (Haber-Bosch process)

o Decomposition and soil N cycling

o Plant uptake and assimilation

∙ Phosphorus cycle

o Weathering from rock

o Plant uptake from soil

o Food webs

o Decomposition

o Wind-borne dust

LECTURE 12

Conservation Biology

∙ The values of biodiversity

o Uses of wild plants and animals beyond the crop plants

 Non-market consumption by indigenous groups around the world

 Large scale commercial harvesting

 Scientific and educational value

 Amenity value

o Values that we cannot put a number on:

 Existence value: the value we derive from knowing that a species exist

 The concept is that one’s knowledge of a species existence even if we haven’t really seen them

 Intrinsic value: it’s not for us to say that species have value

 We conveniently forget the species that we don’t like because we don’t value all species equally in all context  ∙ Two dominant hypotheses

o Sampling hypothesis

o Complementarity hypothesis

∙ Causes of biodiversity decline

o Habitat loss

o Overexploitation

o Pollution

o Invasive species

o Climate change

∙ Conservation genetics  population size and in-breeding

∙ Minimum Viable Populations (MVPs) = a heuristic guide for conservation

∙ Corridors: connecting existing protected areas and not letting that cut off by further development in between; aka connectivity;  allows gene flow

LECTURE 13

Global Change

∙ Greenhouse effect: some of the infrared radiation passes through the atmosphere but most is absorbed and re-emitted in all  directions by greenhouse gas molecules and clouds  effect is to warm the Earth’s surface and the lower atmosphere ∙ Temp. and GHG

o GHG concentrations are tightly coupled with temperature in the past

o CO2 added to the atmosphere increases temperature, which also increases CO2 release to atmosphere o Over geologic time, CO2 and CH4 concentrations in the atmosphere go up and down and seem to track with global temperature ∙ Human impacts on climate

o Energy generation

o Land use change

∙ Albedo is the percent of solar radiation that’s reflected back to the space by surface

o High albedo = more white  reflecting radiation

o Low albedo = more dark  absorbing radiation

∙ Feedbacks in the climate system

o Amplifying (positive) feedback loop is a loop where one thing causes another which causes another and comes back around and  the first thing that started the loop is reinforced further

o Stabilizing (negative) feedback loop might start with one factor that may increase the greenhouse effect but it could have some  feedbacks that come back and dampen and stabilize the component

∙ Temperature and rainfall changes will differ around the world

o Warming is more intense at high latitudes than at the tropics

o Wet places get wetter and dry places get dryer

∙ Biotic responses to climate changes

o Ecophysiology

o Demographic responses

o Community dynamics

o Biogeochemical cycles

o Distributions, diversity, biome boundaries

∙ Phenology: seasonal timing of biological events

∙ Species distribution shifts

o If climate conditions are changing, the fundamental niche conditions are moving on the landscape

o Study on mammals

∙ Adapting to a changing climate is not an evolutionary adaptation

Plants 

∙ Life on earth is more than plants and animals, but this thought went on until late 1960s

o Animals: organisms that are animated, literally have “soul” that can move about freely and have sensory/perceptive  capabilities; study focused on animals is called “zoology”

o Plants: everything else other than animals; not a monophyletic group; these organisms can more about freely as young ones,  but not in their adult stage; they have nutritive and reproductive capabilities but cannot perceive the environment in any  obvious ways; study focused on plants and fungi is called “botany”

∙ Old view was simplified and it was recognized that there were 5 kingdoms: animals, plants, fungi, Protista, and monera [the first 4  are eukaryotes, while the fifth one is a prokaryote]

o Eukaryotes: these organisms have membrane bound nucleus and organelles in their cells (mitochondria and plastids)  Plastids are a group of organelles that includes chloroplast where photosynthesis occurs; not all eukaryotes have plastids  Within the cell, some of the membrane bound organelles are actually incorporated bacteria that have become part of the  cell

 Eukaryotes diverged only about 2 bya (billion years ago)

o Prokaryotes: organisms that lack a nucleus and organelles; only ~10,000 recognized species; now represent 2 of the 3 major  domains of life (bacteria and archaea)

 Prokaryotes ruled the world between 3.5-2 bya  

 Archaea are more closely related to the eukaryotes than they are to the bacteria

 Extremophiles: literally means “lovers of extreme conditions”; these extreme conditions are toxic and deadly for many  organisms; these organisms are mostly archaea and some bacteria

 Halophiles: lovers of salty/saline conditions

 A lot of halophiles (archaea) will die if the salinity goes below ~9% as their membranes do best at high salinities  Specialization of proteins allow them to survive in these conditions

 There are halophiles that are bacteria as well but don’t survive in conditions as extreme as archaea  Thermophiles: lovers of very hot environments

 There are also bacterial thermophiles, but the archaeal are the only ones that can live in boiling conditions (>100  degrees Celsius)

 Methanogens: group of archaea that live in anaerobic conditions such as the gut

 Anaerobic conditions = oxygen-free conditions

 Methane is a waste product for them

 Also found under the Greenland ice sheet

∙ Bacteria

o Represent all modes of nutrition and metabolism that are found as a separate group

o Cyanobacteria (aka blue-green algae) is capable of O2-producing photosynthesis and are responsible for the development of our O2-rich atmosphere; they’re also critical for nitrogen fixation

o These also include critical decomposers  recycle organic compounds that other organisms can use o They have mutualistic associations with other organisms

∙ Diversity of modes of living

o Autotroph: organisms that basically can fix C in organic forms; generate food from inorganic C

 Photo-autotrophs: use light as their energy source to fix C; include all the photosynthetic organisms  Chemo-autotrophs: include organisms like archaea that can use inorganic compounds as energy source to fix C o Heterotroph: organisms that use other sources (at least one organic C source) generated by another living organism ∙ Viruses

o Left out of the 3-domain system and are often treated as non-living; are pathogens which are disease causing agents o They are highly reduced on their morphology where they have very little hereditary material for phylogenetics/reconstructing  relationships; they evolve very rapidly so their DNA/RNA sequences are changing very quickly

∙ Fungi

o Monophyletic group if slime molds are excluded, whereas algae are extremely polyphyletic and land plants are monophyletic  group

o Distantly related to land plants, even though they’ve been traditionally classified together; they are pretty closely related to  animals

o Independently evolved multicellularity from different unicellular ancestors

o Very few fungi have cells with flagella at the posterior end; most of them are non-motile

o Characteristics of fungi

 Very diverse group of ~10000 species called macro-fungi (fungi with large fruiting bodies/reproductive structures)  The large structures are usually only a fraction of the overall body of that individual fungus because the main body of  the fungus is growing embedded within a substrate that isn’t apparent to us

 Microscopic fungi are hard to study as they don’t have as much morphology to understand relationships o Characteristics of fungi as a natural group

 Eukaryotes (have nuclei and mitochondria)

 Non-motile bodies (sessile adult bodies)

 Filamentous: bodies made up of interconnected filaments

 Absorptive mode of nutrition (heterotrophic)

 Filaments are excreting hydrolytic enzymes into the environment that digest complex organic molecules into simpler  molecules that they can absorb

 Digestion is done outside their bodies and then the simpler molecules are absorbed along with osmosis  Cell walls outside their membrane provide rigidity and if this rigidity wasn’t present, they would explode due to the  turgor pressure from the water entering the cell

 Cells walls are present made up on chitin, not cellulose

 Store carbon as glycogen, not starch

 Life cycle includes spores

 Unicellular and multicellular

 Quick transport system through the mycelium (individual fungus)

 Can quickly marshal resources to a new food source that they have discovered by growing into it

 They find food mostly under moist conditions and can quickly produce the reproductive structures

 As a mushroom forms, the cap expands, stipe elongates and then releases up to about a billion spores from the  underside of the cap, which is extensively lined with gills, in the case of a lined mushroom

 Some fungi, like the shelf fungi or large bracket fungi grow off of dead longs and can produce up to about a trillion  spores from their fruiting bodies  important that their fruiting bodies are above ground to allow wind dispersal

 Have large openings within their hyphae which allow with quick transportation; in some cases there is no cellular  partition

 Septate hyphae: compartmentalized by partially open partitions which allows free movement of cytoplasm to allow the fungus to move resources from one place to another quickly; it’s a condition seen in fungi with large fruiting  bodies, such as Ascomycota and Basidiomycota

 Coenocytic hyphae: ancestral condition in multicellular fungi where there are no partitions at all and the cytoplasm is very free to move around; nuclei are not compartmentalized

 Most important decomposers

 Some are pathogenic that cause major diseases, especially in plants

 Some are mutualistic where they have critical symbiotic associations with other organisms

 Mycorrhizal associations: mutualism between fungi and plant roots

 Typical situation is where the fungus is getting benefit from the plant by getting organic compounds and the plant  is getting benefit of better absorption of water and inorganic nutrients from the soil

 2 basic types:  

∙ ectomycorrhizal fungi

◊ less common but very important in the survival of a lot of woody plant species (hard woods and conifers) ◊ external relationship  fungal hyphae develop around the outside of the root

◊ mantle penetrates through the root to go in between the cells, which provides a more intimate  

relationship

∙ arbuscular mycorrhizal fungi

◊ very common as found in ~85% of vascular plants

◊ they don’t form the dense mantle on the outside as they penetrate to an extensive degree; they digest  through the cell wall of individual root cells

◊ more intimately in contact with the root cells

 Some are carnivorous that are predatory on nematodes

o Haplontic life cycle with a diploid zygote

 The zygote does not undergo mitotic divisions as it immediately undergoes meiosis to produce unicellular spores  The spores germinate to produce mycelium

 For sexual reproduction, mycelium undergoes plasmogamy (fusion of cytoplasm) to produce a dikaryotic stage (n+n; two  nuclei of two parents occurring side by side within each cellular compartment of the dikaryotic hyphae that grow out from  plasmogamy)

 This is then followed by the process of karyogamy (fusion of nuclei) which is the second and final stage of fertilization to  produce a zygote, wbcih immediately undergoes meiosis to produce sexual spores

o 5 major groups

1. Chytridiomycota

 They share some features that are ancestral to all fungi

 Commonly found in aquatic environment, and sometimes in moist soils  important decomposers  Mostly unicellular and some are filamentous, but they’re generally microscopic with coenocytic hyphae  used to be  classified as protists rather than as fungi

 Some are in association with the guts of ruminants like sheep and cattle  anaerobic respiration   These include disease-causing organisms, which affect animals, eg. Caused ‘chytridiomycosis’ which led to mass extinction  of amphibians worldwide

2. Zygomycota

 ~1000 species out of ~100000 described fungi species  not very diverse

 very important ecologically

 responsible for bread mold and other molds of produce

 mold is an ecological term, not taxonomical term

 can grow rapidly and produce large numbers of spores, mostly by asexual reproduction  effective dispersers  also reproduce sexually

 typical haplontic life cycle where zygote is the only diploid stage

 when two swollen hyphae come together, they produce a zygosporangium, which is high resistant to desiccation;  fertilization occurs within the zygosporangium where large numbers of haploid nuclei are contributed by the sexual hyphae  of the two individuals that come together

 the two haploid nuclei fuse together to form zygote, which is immediately followed by meiosis to produce stalked  sporangium and release haploid spores  

 have coenocytic hyphae, but they have a partition that develops upon fusion of the sexual hyphae and these structures can then reside for quite a while in dry conditions that are not favorable for growth

 they have multiple mating types; no male and female

 Pilobolus is a genus that is capable of aerial feeds because it can explosively eject its sporangia upto a distance of ~2m 3. Glomeromycota

 Responsible for arbuscular mycorrhizal associations; have Coenocytic hyphae

 Only ~250 species recognized taxonomically

 Reproduce asexually only  lack sexual reproductive structures

 Some of the oldest fungal fossils are from this group

 They have been thought to have been possibly critical for the success of land plants to become established in terrestrial  habitats

 Have large fruiting bodies  sister to ascomycetes and basidiomycetes

 Their associations with plants involve ~85% of plant family

4. Ascomycota

 Most diverse group, ~65000 out of ~100000 known species

 Called “sac fungi” because of their distinctive structure called “ascus” that looks sac-like, that’s out at the tips of the  hyphae and the reproductive structures

 Zygote forms inside the ascus which is immediately followd by meiosis

 Have 8 spores instead of 4 due to an additional single meiosis that takes place

 Not all of them have large reproductive structures but they all have ascus, even if they’re microscopic  Not all produce sexually; have the potential to reproduce asexually, eg. yeast

 Invaginations are observed on the outside of the ascocarp (large reproductive structure) producing the ascus  more  surface area for the production of spores

 Have septate hyphae

5. Basidiomycota  

 Pretty diverse as well, ~30000 species

 Have really conspicuous fruiting bodies

 Have septate hyphae

 They include some plant parasites called rusts and smuts

 Basidiocarps (fruiting bodies) are often produced at leading edge of radiating mycelium where resources are richest,  creating “fairy rings”

 The dikaryotic mycelium is the vast majority of the mycelium; haploid mycelial stage doesn’t last very long o Groups that fall out of the 5 phyla of fungi

1. Deuteromycota (aka fungi imperfecti)

 Artificial fungi; group of convenience because it included the ascomycetes and the basidiomycetes that don’t produce any  fungal fruiting bodies

 Asexual fungi

2. Oomycota

 Used to be called fungi because of the ending in their name (“-mycota”)

 Water mold is a better term for them

 They do produce hyphae due to convergent evolution  

 The hyphae are actually diploid

 They’re not closely related to fungi, instead they are closely related to some photosynthetic groups   They include a lot of destructive disease-causing organisms with plants, eg. Phytophthora

 This genus is known to have caused massive die-backs of various species

 Responsible for Irish potato famine in 1890 which led to widespread starvation

 Caused “sudden oak death” in CA ~20 years ago

 Have differentiated gametes (sperm and egg)

 The eggs are huge, thus the name “egg fungi”

3. Slime molds

 They are o more closely related to fungi than they are to animals, but pretty closely related to both together  Part of the amoebazoan group that includes the amoebas and relatives that have the plasmodial life cycle where they sort  of creep around and engulf other organisms by phagocytosis

 Plasmodial slime molds are one of the strangest ones; they have diploid nuclei throughout their plasmodium  Plasmodium refers to the big multinuclei blob that grows out in all directions in search for food sources   Grow in moist environments

 Undergo a lot of free nuclei divisions without the formation of cell membranes around those nuclei  As conditions dry out, they start to produce sporangia and will get the production of meiotic spores from those  sporangia

 Spores are the desiccation resistant stage

 Serve the function of reproduction

 Have no cellular compartments

o Importance of fungi in ecosystems

 Fungi as symbionts: lichens

 Lichen is the name for the association between fungus (typically ascomycetes) and photosynthetic organism  (cyanobacterium or unicellular green alga)

 They can reproduce sexually as well as asexually

 Mutualistic relationship

 Alga is getting home and protection from UV light and desiccation

 Fungus is getting carbohydrates from the alga

 They come in a diversity of forms and ecological roles, but are generally categorized into 3 major types: 1. “leafy” lichen – small/little leaf-like bodies on soil; aka Foliose lichen

2. “shrubby” lichen – pretty common form observed in dead trees; aka Fruticose lichen

3. “encrusting” lichen – observed on barren rock surfaces, especially in more extreme habitat; aka crustose lichens  Characteristics that are true for all lichens, including the three major types above:

 Capable of withstanding really extreme conditions

 Important pioneers for breaking down substrates that are otherwise unavailable surfaces for growth of other  organisms

 They capture a lot of wind-blown material that helps also in the creation of soil surface

 Fungi that are associated with cyanobacteria are capable of nitrogen fixation

 Lichens are very vulnerable to air pollution, so they really cant handle H2S and a lot of other atmospheric  pollutants  good bioindicators of air quality

 Fungi as symbionts: mycorrhizae

 This is a relationship between fungi and land plants

 This happens in the roots, but if they don’t have roots, this happens in some cells of the plant body  This is critical to the fitness of the plant; they don’t survive past seedling stage without fungal association  Endophytic fungi are fungi that live inside the plant leaves; they enter the leaf through stomata  Fungi as decomposers

 They’re really good at digesting wood as they can break down cell walls made of cellulose

 One substance in wood that is especially resistant to decay is called lignin

 Presence of fungi in the ecosystems got to be really critical for breaking down plant materials, especially woody plant  materials

 Fungi as pathogens

 Almost 1/3 of all known fungal species are disease-causing organisms

 Eg. Dutch Elm disease, Chestnut blight

 Fungi can also attack animals and be important disease-causing agents in animals

 Genus Cordyceps caused a disease that attacked insects and basically invades the insect body and replaces the  entire insects biomass with mycelium  

o Direct importance of fungi to humans

 Fungi as food

 Importance of fungi to humans is more positive than negative  without fungi, we would be in big trouble in terms of  our ecosystem function

 They’re critical in alcohol fermentation, raising bread, and cheese making

 Basidiomycetes and Ascomycetes provide us with some edible fungi that have substantial biomass, but some of them  can be deadly

 Disease causing fungi

 Common fungal disease of human skin

 Aren’t deadly, unless the individual has some kind of immune-compromised situation

 Disease preventing fungi

 They’ve saved a lot of human lives  antibiotics

 They impede the growth of bacteria by interfering

∙ Algae

o Photosynthetic organisms that occur mostly in aquatic/moist environments

o They are land plants that have gone back to aquatic situations

o Represent a huge range of morphology, chemistry and ecology

o They are found in the 4 of the 5 supergroups of eukaryotes

o Endosymbiosis: one organism living inside another  

 Believed to have happened in the early eukaryotic history

 Eukaryotes have a cytoskeleton that’s made up of microfibers and microtubules that imparts some flexibility to the cell that  allows it to engulf other organisms

 Endosymbiotic theory leads to a conclusion that cooperation between distantly related organisms was key to evolution on  earth

 Primary endosymbiosis: ability to conduct O2-producing photosynthesis came to occur in all diverse lineages of  eukaryotes was due to the capture of cyanobacterium by heterotropic unicellular eukaryote that pre-dates the common ancestor of all photosynthetic eukaryotes

 Evidence for this theory

 Size

 Replication

 Ribosomes

 Antibiotics

 Genomes

 Secondary endosymbiosis: second capture of an organism that descended from earlier capture event  Evidence for this is that when you look at the number of membranes surrounding the chloroplast in some lineages  of eukaryotes, they have more than the expected 2 membranes (3-4 membranes)

 Two groups of planktonic algae that derived from the secondary endosymbiosis involving unicellular green algae ∙ Chlorarachniophytes

◊ Group of tropical marine species that provide some of the best evidence for secondary endosymbiosis  because they still possess inside their chloroplast a tiny vestigial nucleus of the unicellular green algae  that was originally captured

∙ Euglenids

◊ More widespread group in freshwater rather than salt water that represents another independent example of secondary endosymbiosis from capture of unicellular green alga

o Main groups of algae (1-5 include phytoplankton, and 6-8 include seaweeds)

1. Blue-green bacteria

 Original group that evolved O2-producing photosynthesis

 Very diverse group

 Unicellular/filamentous colonial organisms

 Some occur in terrestrial environments (important in soil development  fix N to provide nutrients), while others in aquatic  environments

2. Dinoflagellates

 These are representative of secondary endosymbiosis, but involving the capture of eukaryotic red alga instead of green alga  They spin through the water with two flagellae, one that propels them forward and one that wraps around a grove right  around their mid-part of their bodies that causes them to swim through the water when it whips  distinctive spinning  motion through the water

 Planktonic  account for a lot of primary productivity in water systems

 Unicellular or colonial organisms

 Have cell walls made of cellulose, but it’s presented as an armor around them and they look like medieval contraption  Spines and projections probably to protect them against predation

 Have the ability to produce toxins, which protect them from predation; also use this to stun/paralyze prey items and engulf  them  mixture of autotrophic and heterotrophic

 Can create “red tides”, which are known to be really destructive as they can be toxic to a lot of marine organisms as well as  humans

 The coloration comes from carotenoid pigments inside their cells and is evident when they’re highly concentrated in  number

 Coral reefs have a symbiotic relationship with dinoflagellates

 Dinoflagellates live inside their tissues, not inside their cells, and they’re important for the health of coral as they  provide carbohydrates through photosynthesis to the corals and the loss of that delicate association creates trouble for  the coral

 Dinoflagellates are sister group to the Apicomplexans

3. Euglenids

 Common in pond water that swim freely

 They have a really distinctive flagellum that’s different from that of all other eukaryotes

 Even though they have the ability to photosynthesize, they also have the ability to engulf other organisms through  phagocytosis (heterotrophic)

 They can lose their chloroplast and still survive because they’re heterotrophic in addition to being autotrophic  They have identical pigments inside their chloroplast to those of green algae

4. Diatoms

 Responsible for ~25% of the earth’s primary productivity of all photosynthetic organisms

 Hugely diverse (>100000 described species)

 Great fossil record because they preserve well because their cell walls are made of glass (hydrated silica)  They can reverse global warming when they die

 Planktonic organisms

 Unicellular or colonial, not multicellular or microscopic

 Have a life cycle like that of animals where the only haploid stage is the gamete

5. Golden algae

 Unicellular or colonial organisms

 Closely related to diatoms and brown algae

 Have golden coloration because of the carotenoid pigment

 Both freshwater and marine organisms

6. Brown algae

 Marine organisms

 Mostly seaweeds, and some get to be huge

 Keystone ecological taxa

 Kelp have evolved multicellularity independently of other algae groups

 Have forms that look very similar to that of a land plant  convergent evolution

 Cells are bathed in gel-like polysaccharide which provides them with flexibility that keeps them from getting damaged with  the waves

 Polysaccharide also keeps them from drying out in case of exposure to the atmosphere, so it slows the rate of  desiccation

 Occur in intertidal zones and in deep waters up to ~200 feet deep  

7. Red algae

 Another main group of seaweeds, which can be pretty conspicuous, but not as big as brown algae

 Have the reddish coloration, thus the name

 Red color from the pigment masks the green color of chlorophyll

 Red pigment (phycoerythins) are really important for capturing energy from sunlight in the blue end of the visible  spectrum, where the rate of photosynthesis is the highest

 Don’t commonly occur in shallow water

 Mostly found in marine systems, and can live up to ~850 feet deep

8. Green algae

 Includes the ancestor of the land plants

 Come in wide diversity of species = unicellular, colonial, and some multicellular organisms

 Various habitats, including sea water, fresh water, and even high-elevation snowfields

∙ Alternations of generations life cycle

o Presence of both, haploid and diploid stages

o Spores germinate and undergo mitosis to form haploid multicellular gametophyte

o Gametophyte produces gametes by mitosis

o Gametes fuse and produce a zygote

o Zygote undergoes mitosis to produce a diploid multicellular sporophyte

o Spores are produced by the sporophyte via meiosis

∙ Land plants

o Why colonize land (advantages)

 Resource availability benefits of photosynthetic organisms going to have much more light if its not being filtered by the  water

 Abundant CO2, which photosynthetic organisms need to fix C

 Abundance of inorganic minerals in terrestrial habitats  

o Problems with colonizing land

 Potential to desiccate/dry out

 Need for structural support as they don’t need that support when floating in water currents

o Early land plants

 Charophytes

 Closest relative to land plants

 Have branching growth in many cases

 Only multicellular phase is haploid  no alternation of generations

 Life cycle is similar to that of fungus

 Only true diploid stage is the zygote

 Even though they grow in fresh water, if the pond that they grow in dries out, they can resist the drought period in the  zygote stage, and once water becomes available, meiosis occurs immediately to produce spores followed by  germination to produce new haploid organism

 Bryophytes

 Most conspicuous and dominant phase is the gametophyte (n)

 Sporophytes (2n) are very reduced compared to the gametophyte

 Relatively short-lived and independent on the haploid stage

 Include the liverworts, hornworts, and the mosses

 Liverworts

∙ The first to branch off of all land plants

∙ Don’t have stomata for gas exchange

∙ Sporophytes are tiny and very inconspicuous compared to those of mosses and hornworts

∙ ~9000 described species

∙ Most have a thalloid plant body, which kind of looks like a lichen plant bodies – flattened, lobed, little green,  prostrate body that doesn’t have elongated stem with leaves

∙ Sometimes have an elevated structure on which the sporophytes are born

 Hornworts

∙ Least diverse group  ~100 described species

∙ Possibly the closest relatives of the vascular plants

∙ Have indeterminate growth of the sporophyte generation, even though sporophyte is still hooked to the  gametophyte and it’s nutritionally dependent on it

∙ Have a well-developed stomata on their sporophytes and a well-developed cuticle

 Mosses

∙ Represent the bulk of diversity of the bryophytes, which include ~15000 described species and many more  that aren’t described

 Paraphyletic because their most common ancestor is the same as that of the vascular plants, so they don’t constitute a clade

 Don’t have vascular tissue which would allow transport of water and nutrients into a large plant body; most have a  body of about single cell in thickness and they absorb water directly from the environment

 Don’t have large bodies; largest ones are mostly only about 15cm in height

 Release spores directly into the environment to reproduce

 Require free-standing water for fertilization  free swimming sperm to reach the egg

 Not well adapted to function under dry conditions

 They don’t have a root system; they have rhizoids

 Rhizoids are filaments that are a cell in thickness that anchor the plant to the substrate

 They don’t serve in the absorption of water and nutrients to a great extent  

 Don’t have features that are in tune with living in harsh terrestrial environments, but they do share some of the  ancestral features with vascular plants that allowed in the colonization of land

 Dominant phase is desiccation tolerant  

 Have the ability to completely dry out and then resume active metabolism once water becomes available  Drying out doesn’t damage them due to the presence of heat shock proteins and other adaptations   Life cycle involves the alternation of generations (Haplodiplontic life cycle)

 Haploid spores undergo germination by mitotic divisions to produce a multicellular haploid organism  (gametophyte), which produces gametes inside the gametangia by mitosis

∙ The gametophytes of mosses are of two types, one that produces sperm and the other egg

 Haploid gametes fuse together to form a zygote, which undergoes mitosis to form an embryo (retained inside the  female gametangium, aka archegonium)

 Diploid embryo starts to develop into a mature sporophyte, and sporangia are produced on the sporophyte in  which meiosis occurs to produce haploid spores

 Economic use

 Peat mosses  inhibit decay

o Early plant adaptations to land

 Desiccation resistant spores

 Spores are surrounded by sporopollenin, which makes them resistant to drying out

 This is also shared with the zygotes of the charophytes (fresh water green algae)

 As spores are developing in land plants, they’re enclosed within multicellular sporangium

 Sporangium is a specialized structure in which sexual reproduction is going on where meiosis takes place to  produce haploid spores

 Multicellular sporangium is thought to be an important adaptation to land environment  

 Cuticles (waxy outer covering)

 On the outside of the plant body, the epidermis is covered by a waxy protective coating called the cuticle  It’s really well developed in the sporophytes of vascular plants

 The presence of the cuticle makes it a little difficult for CO2 to enter the leaves making it hard for photosynthesis to  take place

 Stomata on sporophytes

 These are pores on the underside of the leaf that allow for CO2 to enter during photosynthesis

 Pores are regulated so the plant can control when those pores open and close

 Stomata are localized to the sporophyte of all vascular plants, mosses and hornworts

 Presence of these pores allow for gas exchange, which is an early adaptation

 Gametangia

 In terms of gamete production by mitosis, it occurs within a jacketed structure called the gametangium  2 types of gametangium: megagametangium (produces egg) and microgametangium (produces sperm)  Embryo  

 Within the female gametangium after fertilization occurs and the zygote has been produced, initial development of the  diploid sporophyte happens within the megagametangium and is protected by the female parent  embryo period  Protection of young, vulnerable sporophyte is a novel feature of all land plants

 Fungal association

 Fungal association is critical in terms of absorbing water and inorganic nutrients on terrestrial environments  This association goes back to before the origin of roots

 Rich secondary chemistry

 Light is abundant in the atmosphere, but that means UV light is also abundant  can damage tissues and cause  mutations

 Land plants are noted for rich chemistry of compounds that are not involved in primary metabolism o Vascular plants  

 Innovations

 Haploid gametophyte generation is highly reduced, and the dominant generation is the diploid sporophyte generation  Well-developed cuticle  additional protection against desiccation

 Presence of vascular tissue (xylem and phloem) which allow to conduct water throughout the body of the large plant  that can develop

 Tracheids

 These are specialized cells inside the xylem that have their secondary walls strengthened by lignin, which makes  them hard and resistant to collapse under weight of gravity and negative pressures that build up during water  conduction

 Branched sporophyte

 Roots

 Extensive roots are developed that anchor the sporophyte and allow it to tap water and inorganic nutrients at great depth

 Heterospory vs. Homospory

 Heterospory: different spores

 This is a bridge between free-sporing vascular plants and seed plants

 This is a condition in some vascular plants where there are 2 different types of spores produced by 2 different  sporangia of a particular species

 Spores are differentiated

∙ Megaspores/large spores give rise to female gametophytes, which produce eggs

∙ Microspores/small spores give rise to male gametophytes, which produce sperm

 The gametophytes develop completely within the confines of the spore wall, so the gametophytes are usually tiny  Derived evolutionarily; happened 3 times:

∙ Lycophytes in the selaginella, the whisk ferns and relatives

∙ Aquatic ferns

∙ Ancestral to all seed plants

 Homospory: same spores

 Ancestral condition in vascular plants

 Include lycophytes, pterophytes, gymnosperms, and angiosperms

 Lycophytes

 Need free-standing water for fertilization

 Lack seeds as they disperse by spores

 May have evolved their roots and leaves independently

 Gametophytes are highly reduced

 Occur in wide range of environment  wet tropics, sub-polar conditions, and deserts

 ~1200 species recognized today, but much more diverse in the past  suffered extinction

 Can undergo extreme desiccation but still recover  unusual in vascular plants

 Pterophytes

 Include ferns, horsetails, and whisk ferns

 More closely related to the seed plants

 ~12000 species worldwide

 Readily dispersible as found in all sorts of environment  

 Main plant body of a fern is mostly leaves above the ground with rhizome (underground horizontal stems) from  which roots are produced

 Horsetails have ~15 species in the entire lineage where they’re found worldwide  

 Fern life cycle

∙ Undergoes alternation of generations

∙ Sporophyte is dominant generation where it is long-lived, large, dominant, and free-living

∙ Sporangia are born under the surface of the leaf in these units called sori  

◊ Indusium protects the sporangia during early growth/development

∙ In sporangium is where meiosis occurs to produce spores

∙ Gametophytes in most ferns are hermaphroditic and produce both, archegonia as well as antheridia on the  same plant

 Gymnosperms

 Seed plants are monophyletic as all living seed plants descend from a common ancestor that bore seeds  Represent only ~1000 species worldwide

 Representatives are all woody plants and have their seeds in cones

 Can be ecologically dominant, especially at high latitudes/elevations; not very diverse at the tropics  Coniferophyta are the most diverse group within the gymnosperms (~>600 species)

∙ Massive because they live for long times and they are decay resistant

∙ Can be dominant in higher elevations, and are not particularly well represented in the low tropics ∙ Most living conifers have needle-shaped leaved with really thick waxy cuticle

 Second most diverse group of gymnosperms after conifers are cycades (aka cycodophyta)

~300 species

Look palm-like with unbranched trunk

Bear the largest cones with pretty massive seeds that are animal dispersed and brightly colored Found in sub-tropical and tropical environments

Not common plants in nature as they’ve been heavily overharvested for cultural purposes

 Next most diverse group of gymnosperms after the cycades are the Gnetophytes

∙ ~75 species

∙ Grow in wide range of environment from wet tropics to deserts

∙ Bear seeds in distinctive cones

∙ Eg. Ephedra

 Gikgophyta includes only 1 species, Ginkgo biloba, which is widely grown as ornamental

∙ Unclear of what it must have been like in its native environment  

∙ Highly diverse in the Mesozoic era

∙ Have very distinctive deciduous leaves

∙ Seeds are not born in cones, rather have flesh outer covering

 We get an increase in the size of the sporophyte generation in general (Bryophytes < Pteridophytes <  Gymnosperms); we get a reduction in the size of the gametophyte generation (Bryophytes > Pteridophytes >  Gymnosperms)

 Pine life cycle

∙ The 2 different types of sporangia are born in separate seeds

◊ Seed cones represent the megasporangia cone

◊ Pollen cones represent the microsporangia cone

∙ Alternation of generations where sporophyte is dominant

∙ Meiosis occurs in the microsporangium within the pollen cones to produce haploid microspores, which then  germinate by mitotic divisions without leaving the confines of the cone, to form pollen grains; the pollen grains are released and ultimately wind dispersed

∙ On the upper surface of the seed cone scale, there are two ovules (megasporangia) with protective outer  coating called the integument

∙ Only one cell inside the megasporangium undergoes meiosis, which gives rise to 4 megaspores, but only 1  survives and the other 3 wither; the single megaspore germinates to become a female gametophyte ∙ NO gametangia within the gymnosperms in the male

∙ The pollen grain gets delivered directly to the ovule, and if lucky, it ends up inside the pollination chamber and the pollen tube grows down to the archegonia and delivers the sperm directly to the egg without the need for  free-standing water

∙ Fertilization occurs and a zygote is produced in each archegonia

∙ The embryo eventually gets to a point where it ceases growth and the seed becomes dormant and can be  dispersed

∙ When conditions are right, germination will take place

 Angiosperms

 Have their seeds in the ovary

 Angiosperms literally means vessel seeds as their ovules are contained within an enclosed structure called the  carpel

∙ Ovule is enclosed throughout development and I’s never exposed to the atmosphere

∙ Carpel provides protection to the developing ovule; it’s the most distinctive feature of angiosperms  Floral variation exceeds that of all other land vascular plants (~250000-300000+ species)  The flower

∙ Simple, bisexual cone that’s made up of generally 4 sets of appendages, which are homologous to leaves ◊ Carpels

♦ Fertile appendages

♦ Enclosed structures that contain the ovule

♦ Found at the center of the flower

♦ It’s a single pistil

♦ Carpel is the leaf that’s sealed around the ovules, whereas pistil is the structure that has stigma,  style, and ovary, regardless of whether it’s made up of one carpel or multiple carpels fused together ◊ Stamens

♦ Fertile appendages  

♦ Bear the microsporangia

♦ Doesn’t look like a leaf, whereas petals and sepals do

♦ Most have very narrow stalk called the filament and there is an anther at the tip of the stalk which  contain the microsporangia

◊ Petals

♦ Sterile appendages

♦ Brightly colored appendages

◊ Sepals

♦ Sterile appendages

♦ Outermost part of the sterile floral appendages

♦ Main function in a perfect flower is the protection of the rest of the flower parts while the flower is in  bud

∙ Once the appendages are formed with the carpels at the tip, there is no further growth of the shoot ∙ Imperfect flower is when one or more of the sets of appendages are lost evolutionarily, whereas a perfect  flower has all 4 sets of appendages lined right on top of each other

∙ When looking at fossil records, we see some plants with extended internodes between the appendages ◊ Eg. Archaefructus sinensis: oldest flowering plant from the cretaceous; most closely related to water lilies  The inflorescence

∙ Arrays of flowering stalks

∙ There are multiple flowers that are born on a flowering stalk in a diversity of ways

∙ Arrangement is taxonomically distinctive, as well as important in how pollination and dispersal occurs  Mechanisms against selfing

∙ Self-incompatibility (SI)

◊ Genetic mechanism that allows the sporophyte parent of the female gametophyte in the ovules to  recognize whether it’s self pollen or not

∙ Imperfect flower

◊ Imperfect flower that produce either functional stamens or functional pistils, but not both ∙ Spatial separation within an individual bisexual flower

 Pollination (biotic/abiotic)

∙ Pollen is delivered to a receptive stigma, and not directly to the ovules

∙ 80% of all flowering plants is animal pollinated

∙ Common features found in these systems

◊ Attractant on part of the plant

◊ Reward for pollinator for their service  nectar

∙ Pollen grains are typically clumped together by oil

∙ Flowering activity has to be synchronized with the activity of the pollinator

∙ Types of animal pollination

1. Bee pollination

◊ Effective pollinators as they’re intelligent insects

◊ Flowers that they associate with are often in the yellow to blue range of the visual spectrum (shorter  wavelength)

◊ Scents can be variable

◊ Bees collect nectar as well as pollen at the same time

◊ “Deceit pollination”  no reward

2. Moth pollination

◊ Involves hovering moths that have activity under low light conditions

◊ Moth flowers have long tubes that are delicate

◊ Flower color is bright, usually white, to be easily seen under light conditions

◊ Flowers have strong fragrance

◊ No landing platform as moths hover over the flowers

3. Butterfly pollination

◊ Butterflies operate during the daylight

◊ Flowers tend to be brightly colored

◊ Butterflies land when they feed  landing platform is present

◊ Butterflies are nectar feeders

◊ Butterflies have good sense of smell

◊ Flowers don’t tend to be complicated as butterflies aren’t intelligent

4. Bird pollination

◊ Birds are intelligent

◊ They hover when they feed  

◊ They have excellent vision in the red end of the visual spectrum

◊ They have really bad sense of smell

◊ Flowers tend to produce large amount of nectar  

◊ Flower tubes have to be able to withstand pretty harsh probing by the birds’ beak, so the tubes tend to be pretty strongly reinforced in bird-pollinated flowers

5. Bat pollination

◊ There are nectar-feeding bats, especially in the tropics and south-western deserts where there are  evening flowering cacti

◊ Bats have high nutritional demand so the flowers typically produce large amounts of nectar and pollen ◊ Flowers have to be really tough to withstand pretty rough handling by bats

◊ Activity of bats is in low light conditions

◊ Flowers are brightly colored and put out a strong odor that can carry over long distances 6. Fly pollination

◊ Strong scents is typical

◊ Flies that pollinate plants that have specialized fly pollination generally have odors that are attractive to  fecal feeding flies

◊ Flowers have a reddish-brown coloration

∙ Wind-pollinated angiosperms

◊ Ancestral within seed plants

◊ Changes include loss of showy attractant, no need for reward, flowers become unisexual to debilitate  selfing, petals are small or absent, and flowering before leaves expand

∙ Water-pollinated angiosperms

◊ Only ~2% of angiosperms are water pollinated

◊ Plants are aquatic

◊ Problem is that pollen gets damaged by getting wet

 Evolutionary changes in floral structure

∙ Loss of parts

◊ Either the reduction in # of parts or a complete loss of one of the sets of appendages ∙ Fusion of parts

◊ Ancestral state is to have the parts free, but fusion is a derived trait

◊ Fusion can improve accuracy and precision of pollination resulting in more floral integration ∙ Change in floral symmetry

◊ Some flowers are radially symmetrical whole others are bilaterally symmetrical

◊ Greater accuracy and precision in pollination appears to stimulate diversification

∙ Fusion of floral parts around the ovary or sinking of the ovary into the base of the flower  Life cycle of angiosperms

∙ Development of the male gametophyte

◊ There are 4 microsporangia in the 2 pollen sacs found in the anther

◊ Inside the microsporangia, there are large numbers of diploid microsporocyte cells that undergo meiosis  to produce 4 haploid microspores

◊ Each of the microspores germinate by mitosis to produce male gametophyte inside the walls of the  microspore

∙ Development of the female gametophyte

◊ Megasporangium is found inside the ovule and there are 2 layers of integument around the  megasporangium

◊ Meiosis takes place and 4 cells are produced from one cell and only one megaspore survives ◊ Mitotic divisions take place to produce a mature female gametophyte with 7-8 nuclei

◊ At maturity, there is an egg at the open end of the ovule where the pollen tube enters, and on either side  of the egg, there is a cell (synergids)

◊ At the other end of the gametophyte, there are 3 antipodal cells with unclear function, and there are 2  nuclei known as polar nuclei at the center

∙ Double fertilization

◊ Pollen tube grows down from the stigma toward the ovule in the ovary and goes around the ovule and  enters through the micropyle

◊ One of the sperm fuses with the egg to form a zygote, and the other sperm fuses with the 2 polar nuclei  to form a triploid endosperm nucleus which is followed by a large number of mitotic divisions to produce  an endosperm

 Fruit

∙ Fruit in its most simple form is just the ripened ovary of a pistil

∙ Walls of the ovary can be modified during development that aid in seed dispersal in various ways ∙ Fruits at maturity can be either fleshy or dry, and they can be either dehiscent or indehiscent ∙ 3 types of fruits

◊ Simple fruit

♦ Ancestral and most widespread type

♦ Fruit derived from a single ovary of a single flower

♦ Eg. Cherries, pea pod

◊ Aggregate fruit

♦ Fruit that’s derived from more than 1 separate carpels of a single flower

♦ Each fleshy unit on the outside is an individual ovary from distinct carpels

♦ Eg. Raspberry or blackberry

◊ Multiple fruit  

♦ Fruit that involves multiple flowers taken together and condensed into a single protective/dispersal  unit

♦ Eg. Pineapples

∙ Accessory fruits

◊ Term used for fleshy fruits and cuts across all 3 types of fruits

◊ A fruit with fleshy parts derived from tissues other than the ovary

◊ Eg. Apple, strawberry, fig

 Monocots vs. Eudicots  embryo, leaf venation, stems, roots, pollen, and flowers

 Why diversity is so high? Because coevolution between animals and flowering plants has led to specialization  Seed morphology

∙ Diversity in seed morphology in plant reflects that the establishment of seedlings is the most challenging part  of the plants life  

∙ Investment in nutrition for the embryo is delayed until reproduction is assured

∙ Monocot: eg. Corn kernel; eudicot: eg. Bean

 Germination

∙ High mortality during this period, so natural selection has operated to ensure that germination happens at a  time that’s favorable for the survival of seedlings

 Plant anatomy

∙ Vascular plants have a nice integration of their various tissues and cell types that allow them to acquire,  distribute, and store resources throughout the plant body, from the roots through the shoot ∙ Tissue systems are functional units that connect all the plant organs (leaves, stems and roots) ∙ Tissue systems:

1. Dermal tissue

◊ Outer protective tissue of a plant

◊ In non-woody parts of the plant that have just initiated growth, the dermal tissue is epidermis, which is  found through out the shoot and root

◊ In secondary growth, the epidermis gets replaced by a secondary type of dermal tissue called periderm 2. Ground tissue

◊ Found in the anterior to the epidermis, and it’s everything except for the vascular tissue ◊ They serve a variety of functions

♦ Most metabolically active tissue

♦ The cells that undergo photosynthesis are ground tissue as are the cells involved most actively in  storage of starch

♦ Some of the structural support is provided by the ground tissue

◊ Cell types

♦ Parenchyma

♦ Collenchyma

♦ Sclerenchyma

3. Vascular tissue

◊ There are 2 major types that are found adjacent to one another in the organs

♦ Xylem

♦ Phloem

◊ They are very discrete developmentally and functionally  

∙ The plant organs are organized into 2 main systems that are morphologically, anatomically, and  developmentally distinct, but are completely interconnected

1. Shoot system

◊ Part of the plant (stems and leaves) that’s above the ground

◊ Sugars that are manufactured here get transported down to the roots

◊ Phyllotaxis: arrangement of leaves on a stem

♦ Alternate leaves = one leaf per node

♦ Opposite leaves = 2 leaves per node

♦ Whorled leaves = 3 or more leaves per node

◊ Leaf morphology and anatomy

♦ Blade is the expanded part of the leaf within which photosynthesis typically occurs

♦ Petiole is the stalk of the leaf

♦ When it comes to leaf morphology in grasses, it’s a bit unusual as the grass leaf blade where the  stem diverges from the stem is not where it attaches to the stem

♦ In the lower epidermis is where stomata is typically found as these areas are typically shaded ♦ Inside the leaf, there are two types of ground tissue: palisade mesophyll and spongy mesophyll ♦ Vascular tissues are tightly enveloped by the bundle sheath

♦ Leaves don’t undergo indeterminate growth

◊ Modified leaves

♦ Include tendrils, spines, water-storage organs, and trap leaves

◊ Modified stems

♦ Include rhizomes, bulbs, stolon, and tuber

◊ Secondary growth

♦ Thickening growth

♦ There are 2 lateral meristems in woody plants: vascular cambium and cork cambium

♦ Consequences include bark always getting sloughed off and girdling can kill the tree

2. Root system

◊ Found below the ground which comprises the roots

◊ Function is the absorption of water and inorganic nutrients and moving them up to the stems and leaves ◊ Roots have a root cap that’s distal to the apical meristem

◊ Formation of lateral roots

♦ Pericycle starts to produce lateral roots that force their way out through the cortex and epidermis,  disrupting them as they emerge

◊ Mode of absorption: apoplast vs. symplast

◊ Water transport

♦ 3 mechanisms: passive transport, active transport, and bulk flow

♦ Movement between cells includes osmosis

♦ What determines the direction of water movement: concentration of solutes and physical pressure ♦ How does water get transported? Pull from the leaves

∙ Phloem transport

◊ Movement of sugars in the phloem is an example of bulk flow where differences in pressure are important  in the transport

◊ Phloem sap moves from area of higher sugar concentration (source) to area of lower sugar concentration  (sink) via semi-permeable membrane

◊ Loading of sieve tube by source cell and osmotic movement of water from xylem into sieve tube creates  pressure at source

 Determinate vs. Indeterminate growth

∙ Indeterminate growth: there are parts of the plant that always remain embryonic and those embryonic cells  are in the apical and axillary buds and in some other parts of the plant as well in woody plants ∙ Places with these embryonic cells are called meristems

 Light

∙ Plants have an amazing ability to detect and respond to light, not just the presence of light, but its quality,  intensity and directionality

∙ Eg. Photoperiodism  short-day plants vs. long-day plants  

 Plant chemistry

∙ They face pretty significant challenge compared to animals in terms of coping with environmental changes  and stimuli

∙ Plant hormones are organic compounds that modify or control over one or more physiological processes within a plant

◊ They are generally transported from a site of stimulus reception to a site of growth response, which is  initiated by the hormone

◊ They are often effective in regulating growth at very low concentrations

◊ Eg. Auxin, cytokinin, gibberellins, brassinosteroids, abscisic acid (ABA), and ethylene

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