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Ecology Notes
Day 1
• Cells are the fundamental unit of life
• Cells define life by
o Metabolism
! Coordinated chemical reactions
! They are coordinated by genes
! Feature homeostasis
o Reproduction
! The ability to replicate
o Evolution
! Heritable change in populations over time
! Not directed-not always towards greater complexity
! No “progress” in evolution
! Phylogeny-evolutionary tree of animals
! Evolution builds on
! Not always necessary
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• Buffon, 18 century naturalist, saw mammals have similar bone structure so he
believed that they have a common ancestor
• Humans came from primates which had all fours so that our bodies are not
optimally designed
• History of Life
o Vast expanses of times
! Earth formed-4
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! Eukaryotic cell created-1
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6 bya)
! 1st prokaryotic cells

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! All of their organelles in one compartment
! Cell wall
Eukaryotic Cells-have a new design
! Nuclear envelope
! Flexible cell membrane
! Cytoskeleton
! Vesicles for digestion
! Organelles
Symbiosis-close relationship between two unrelated organisms
One prokaryote moved into another
Organelles have endosymbiosis origins
Organelles and prokaryotes
! DNA/RNA
Multicellularity
! Specialization of function
! Maintain homeostasis
! Big is better because “cells eat cells” world
Steps to multicelularity
! Form groups
! Groups increase size
! Cells special
! Special organs of cells
! Formation of an indivisible individual

DAY TWO
o Classification of phylogenies
o Aristotle 384-322 BC
! Believed beings are fixed identities
! Ranked on “scala naturae” or the great chain of being
! Progressive chain of being”
! March of progress-humans principal of evolution
o Carolus Linnaeus 1707-1778
! Father of taxonomy and practice
! Taxonomy-theory of classifying organisms
! Created binomial nomenclature
! Two names-Genus species
! Created hierarchical classification
! Similarities suggest forms share ancestors
! Domain-Kingdom-Phylum-Class-Order-Family-Genus-Species
! Human
• Eukarya, Mammalia, Primates, Hominidae, Homo, Sapien
o Phylogeny-the evolutionary history of organisms
o Phylogenetic Tree-describes that history, and shows evolutionary
relationships-near and distant relatives
o Lead to common ancestor-root
o Branch-lineage through time
o Node-common ancestor @ the time of split

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o Chimps and human-sister groups
o Gorillas-sister to chimps and humans
o Clade-common ancestor and all of it’s descendants
! Also called monophyletic
! If you can cut off everything to the right with one cut then it’s
monophyletic
o Evolution by Natural Selection was proposed by Charles Darwin-18091882
! 1831-1836-Naturalist aboard the HMS beagle
! In England-collectionist notes from voyage and breeding of new
varieties of pigeons and other species
! “Traits evolve through natural selection”-1859
! Evolution never appears in early edition of the book
Natural Selection
o West new Mexico-white gypsum sand and brown lizards near white sand
and desert
o Loggerhead shrikes-prey on lizards
o Matching body coloration (crypsis) to habitat evolved under Natural
Selection
o Variation in coloration is partly inherited which is important because it
can be passed to the offspring
o Genotypes-description of genetic basis of an individual-either entirely or
specific to a treat
o Phenotypes-coloration
o Live to reproduce
o Lizard coloration has adapted to the white sands environment
o Match of body coloration to substrate or crypsis
o Adaptations-inherited traits favored by Natural Selection
Evolution by Natural Selection:
o Variation that is genetically based (heritable)
o Certain genotypes produce more surviving offspring than others
o Differences in survival among genotypes are due to an agent of selection
Agent of Selection-loggerheaded shrift
o Can be-predator, weather, moisture, food quality, bacteria, pathogens
o Evolutionary process lead to color in the forms we see-NS
o Selections of colors
o Potential mates
o Prey attracted to bright colors
o Predators to avoid potential toxins
Humans are agents of artificial selection
o Dogs, leafy greens
Kinds of inherited traits on which selection can act
Discrete traits-controlled by one or two genes, and one form of that gene (allele)
is dominant
Many traits are continuous or quantitative, height, tail length, crop yield, animal
behavior

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Quantitative traits are often distributed as a bell curve
Also called “normal distribution”-height
Lizard color-discrete trait because no tan color
3 forms of Natural selection on normally distributed shape
Directional Selection-genotypes @ 1 end of distribution do worse than the other
(means it will shift to factor good trait) ex-maze running in performance rate done
to see if it is based on genetics
Stabilizing Selections average genotype does best ex-Human birth weight
Disruptive Selection-genotypes at both ends of distribution do best ex-bill size in
African seed cracker

Day 3
• Evolution-change in allele frequency over time in a population of organisms
• Populations-a group of potentially interbreeding individuals of the same species
ex-all catfish in a lake
• Allele-form a gene
• Allele frequency-proportion of that allele in a particular population ex-ABO blood
type
• Diploid-2 copies of gene
• What can happen with alleles over time-when an allele hit’s one it is fixed-only
that allele evolution occurs with allele frequency changes
• Natural Selection-variation, genetic, certain genotype has more survivor,
difference in reproduction to an agent of selection
• Pepper moth, biston betularia, rest on same collared tree bark, pollution put soot
on trees, dark morph appeared in 1848 watched sooty tree, dark and light have
different alleles at a single gene
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Agent
of selection-insectivorous bird in the 1950s pollution was reduced so that lichens
returned to the trees so dark morphs plummeted
• Human influenced-resistance to antibiotics
o Evolves-bacteria
o Agent of selection-antibiotics (toxins in them)
o Where are the bacteria and antibiotics? -In the body
o Result-antibiotic resistance
o Difficult-finish course of antibiotics
o Other bacteria to displace
• HIV resistance to drugs-public health concern
• 8 million people on antibiotics-retroviral drugs
• Bighorn sheep-big horns=hunted
• Gill nets catch fish of particular size, large size nets select for fish that grow more
slowly or small as adults
• Industrial melanin in pepper moths
• Resistant to antibiotics in bacteria
• Evolution of virulence in viruses
• Evolution can occur without NS
• Genetic Drift-random changes in allele frequency from 1 generations to the next

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Ex-go to old times when Vikings only have red hair, assume two alleles-A
(brown) and a (red) when frequency changes, evolution has occurred- this is
genetic drift
Small population-are more susceptible to loss and fixation of alleles=smaller
sample size
Real-tortoises on Galapagos
Population bottle neck is 1 way to get a genetic drift
Without genetic variation, popular adapt to environmental changes-can even go
extinct
Gene Flow-transfer of alleles from one population to another (usually involves
movements)
Its evolution because change in allele frequency in the population
Gene flow can counter local effects of natural selection
Ex-2nd lizard species has white morph in white sands but brown disperse in white
sand and scrub
Mutation-alteration of a gene that gives rise to a new allele
Usually involves change in DNA sequence
Point mutation-single nucleotide change
Eag-ether-a-go-go, kdn-knowndown per-period fru-fruitless qtc-quick to court
Spin-spinster sk-stuck
Genetic in lab using radiation or mutant pathogens
Rare per gene but common per genome
Fruit fly mutant rate-10^-5 per gene per genome
Mutations-rarely generate novel trait
Usually change pre-existing traits
Usually deleterious
In germ cells they are ultimately the source of almost all genetic variation in
populations
In each species white morph caused by loss of function in genetic coding for
melacortin
MCIR-3 different changes in 3 different positions in DNA coding sequence
Reduce genetic variation-NS-if allele gets fixed, gene flow (both), genetic drift
(decrease variation), mutation (increase variation)
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o Influenced by both genes and environment
• Try to find heritability-how much is genetic
• Most genes are both
• Population-group of potentially interbreeding individuals of the same species
(coexist at same place and time)

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Species-a group of individuals capable of interbreeding, and reproductively
isolated from other groups
Called biological species concept
Species may consist of several populations, all capable of interbreeding, but rarely
or never have the opportunity
Who really interbreeds?
o We rarely watch, we can use clues from morphology but it can be tricky
o Male and female can look different but are the same species
o Clues can be decisive
o Paleontologists-sequencing DNA look at time and place
o People can force some species to interbreed that in nature don’t,
! Liger
! Cama
o Some organisms never have sex to begin with ex-bacteria, protest, fungi
o The more we know (species ranges, morphology, genetic info, behavior)
the more confident we can be
How do new Species form?
o They diverge from existing species
Two critical processes
o Isolation/separation
o Genetic divergence and reproductive isolation
Species form in 3 steps
o 1 species is separated into two populations by a barrier
o Each population adapts to new habitat and diverges genetically
o When/if populations overlap again, they no longer interbreed
One interbreed group
o Become isolated in 2 subgroups
o Become more and more different
o If re-contact, cant interbreed
o 1 population is broken into two group
Allopatric speciation-physical barrier arises that prevents interbreeding
o Allopatric means different countries
o Thought to be the usual start to speciation
o Ex-antelope squirrels at Grand Canyon (different in North and South)
o VERY LONG TIME
Darwin’s finches-ancestor dispersed to Galapagos islands-island population then
lost contact with each other-changed beak
Sympatric speciation-no physical barrier arises-interbreed between groups stops
for another reason
o Sympatric-same country
Auto polyploidy-multiplication of chromosomes sets
Happens-spontaneous duplication of chromosomes
Combination of parents chromosomes number in offspring
Self fertilization-most common in plants before2n=6 diploid then 4n=12
tetraploid

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Can become new species if they breed with another polyploidy
Ex-triploid hybrids are often sterile because they give rise to gametes that are not
completely haploid nor completely diploid
Consequence-polyploidy offspring can mate with each other but not with
individuals like their diploid parents, they have become different species
Autopolypoidy-is very common in major plant group, angiosperms ex-coffee
(2,4,6 ect
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6bya
o Eukarya-1
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Peterin has anti-tumor activity gets it from
bacteria (from mom) gets it for defense
! Some anaerobic Archaea produce methane from carbon dioxide as
a key part of their energy metabolism
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In the process of meiosis
preserves the chromosome number is halved
• Mitosis preserves the chromosome number
o Sporophyte makes spores
o Gametophyte makes gametes
• In the nonvascular plants, the gametophyte (haploid) stage dominates
• In vascular plants, sporophyte dominates

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Nonvascular Plants (liverworts, hornwarts, mosses)
o Small plants
o Lack trancheids-specialized water and food conducting tubes of the
vascular plants
o Collect water on leaves, rely on direct absorb and fusion of water and
minerals

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