Wednesday, January 18

Unity of underlying mechanisms

Central dogma
Central metabolism
Mitosis & Meiosis
Diversity of outcomes
Tissue types
Individuals within species
Species
Interactions
Ecological communication
Biology
Broadest disciplines
Rapidly growing
Time scale ranges 10^-9 sec to hundreds of years
Published papers everyday>textbook
Organization of biological sciences
o Biosphere
o Ecosystem
o Community
o Population

01/29/2012

o Multicellular individuals
o Cells
o Molecules
o Atoms
o Subatomic particles
Emergent Properties
o System that cant be predicted or explained from antecedent
conditions
Goal of science
o Understand how nature works
Correlation of Patterns
o Identify the
Processes
o Proximate causes
How, mechanistic questions
What is genetic variation
o Ultimate causes
why questions
Why did mutation, natural selection develop?
Science
Experimentsobservationshypothesisexperiment or new
observation
Widow birds

 Elongated tails had more nests on average

Controlcut and used a pin to vary tail length
Cactus
?
1:9-14
1.4 Evolution Explains Both Unity & Diversity of Life
Evolution
Change in the genetic makeup of biological populations through
time
Themes
o Unity
o Diversity
Natural Selection
Differential survival & reproduction among individuals in a
population
Adaptations
Structural, physiological, or behavioral traits that enhance an
organisms chance of survival and reproduction in its environment
Sexual selection
Selection due to mate choice
Genetic drift
random fluctuation of gene frequencies in a population due to
chance events
Theory
A body of scientific work in which rigorously tested & wellestablished facts & principles are used to make predictions about
the natural world

Evolutionary theory
(1) a body of knowledge supported by facts
(2) resulting & understanding of various mechanisms by which
biological populations have changed & diversified over time & by
which Earths population continue to evolve
1.5 Science is based on Quantifiable Observations and Experiments
Natural history of organisms in a group
how the organisms get their food, reproduce, behave, regulate their
internal environment (cell. Tissues, & organs) and their interactions
with other organisms
Inductive logic
Taking observation or facts and creating a new proposition that is
compatible with those observations or faacts
Hypothesis
Tentative proposition
Deductive logic
Make predictions based on a hypothesis
Dr. Hayes
Frogs and Atrazine (herbicide)
o Affects development of frogs
o Males have female organs
Null hypothesis
Any observations are the result of random differences
Ch15: Mechanisms of Evolution
15.1 Evolution is Both Factual & the Basis for Broader Theory
Evolutionary theory

The resulting understanding and application of the mechanisms of

evolutionary change to biological problems
Darwin
Species not immutable, they change over time
Divergent species share a common ancestor
Natural selection produces change
Science
Hard Scienceahistorical
o Physics
o Chemistry
o Molecular Bio
Soft ScienceHistorical
o Climatology
o Paleontology
o Anthropology
o Geology
o Evolutionary Bio
Widow birds
Two controls
o #1 cut tail
o 2 cut tail & glued back extension

o ones with the longest tail had more nests than the birds with
shorter tails
Pocket Mice and Fence lizards
Vary in color depending on their surrounding
Sand duneswhite color
Grasslandsbrown color
Lava fieldsblack color
Cactus?
Genus:?
Species:?
Diamond
Mates bring gifts (resources)
o Usually take from spider webs
o The bigger the better
Human gifts
o Diamond rings
Spiders
o Female spider usually eats the male spider before he
Some races have a higher genetic intelligence
Colonization of the Pacific
Islands that have social stratification
Islands that have more resources will support social stratification

 Control: all of the islands came from the same source

More resources
Social stratification
o Divisions in society
Science
The accumulation of knowledge to be obtained by whatever
methods are most appropriate to the particular field
History of Evolutionary thought (to Darwin)
Linnaeus
o Wanted to classify
o Proposed taxonomy used today
Genus
Homo
Species: ?
European colonization
Bring back fossils
Rich upper class that didn't have to work
o Naturalists
Trying to figure things out
Honey Bee
Genus: Apis
Species: ?

Lemurs
Genus: Lemur (Eulemur)
Species: Macaco
Named in 1766 by Linnaeus
Butterfly
Genus: Papilio (Parnassius)
Species: Apollo
Named in 1758 by Linnaeus
Charles Lyell & Uniformitarianism
Basaseachic Falls (Mexico)
Ocampo Municipality, near Creel, Chihuahua
Formed by processes that happen everyday
o Over time change happens
Earth is really old
Evidence for Evolution
Fossils from strata
o Extant= existing today
o Processes happening very slowly
Earth is very old
Bones
o Looked at structures

o Comparative anatomy
Development
o Beginning of development of different species similar
Finding similar processes
Charles Darwin
From a rich family
Didn't want to become a surgeon
Botanist mentor (name?) of his told him to go on the expedition of
the H.S. Beagle
Voyage of the Beagle (1831-6)
o Barnicles
?
o Vicidious notetaker
o Vicidioius
?
o Galapagos Islands
Models of evolutionary change
o Descent with modification
Natural selection
Genetic drift
o Speciation
o Extinction

Darwins finches
o Different beak sizes
o Common ancestor from South American mainland
Birds
o Dinosaurs that can fly
Origin of Species
o Sold out immediately
o Domestic breeding
Artificial selection
Natural selection
o Variation in population that is inheritable
Alfred Wallace
Independently came up with the same ideas
Dogs
All modern domestic dogs are from the gray wolf
Decent with modification
Geological data supports old Earth
Common ancestor
Evidence for Evolution
Paleontology
o Extinct species & groups

o Giant oysters in Andres (Peru) 2 miles above sea level

o Fossils that show transitional between part and present
o Vestigial organs
Fish lives in cave
Astyanax fish
Doesnt ?
Homology
o Shared similarity due to common ancestor
Modified in different ways
o Due to decent with modification
o Antannae
Modified foot
Bee
Developmental error
Poorly designed structions
o Evolution is not directed
Human eyes
Recurrent Nerve
Embryonic development
Linnaean classification
o Consistent with evolution

Concordant phylogenies
o ?
Biogeography
o Related species on isolated islands
o South America, Antartica, Austrlia
Last to break apart
o Anolis lizards of Carribean
Rapid Evolution in nature
Artifical Selection
Resistant species
o Grow & reproduce
Process of Evolution
Requires time (lots of it)
15.2 Mutation, Selection, Gene Flow, Genetic Drift, & Random Mating
Result in Evolution
Evolution
Changes in the genetic makeup of population over time
Population
A group of individuals of a single species that live and interbreed in
a particular geographic area at the same time
Individuals do not evolve; populations do!
Natural Selection acts with 3 other processes
Genetic Flow

 Genetic drift
Nonrandom mating
Genetic variation
Due to mutation
Deleterious mutations
Harmful to their bearers
Neutral mutations
Have no effect
Beneficial mutations
Advantageous in a particular environment
Alleles
Genes at a particular locus
Allele frequency
The proportion of each allele in the gen pool
Genotype frequency
The proportion of each genotype among individuals in population
Artificial selection
Choosing species for specific characteristics & breeding
Brassica oleracea
Drosophila melanogaster
Fruit fly

 Number of Abdominal bristles varies in population

Adaptation
Favored trait that evolves through natural selection
Gene flow
Migration of individuals & movements of gametes between
populations
Can change allele frequencies in population
15.2 Selection can be Stabilizing, Directional, or Disruptive
Qualitative traits
Discrete qualities
Quantitative traits
Quantitative variation
Stabilizing selection
Preserves the average characteristics of a population by favoring
average individuals
o Reduces variation in population but does not change mean
o Purifying selection because selection against deleterious
mutation to usual gene
Directional Selection
Changes characteristics of a population by favoring individuals that
vary in one direction from the mean of the population
o Favors one extreme
o May result in positive selection
Favoring a particular genetic variant
Disruptive selection

Changes the characteristics of a population by favoring individuals

that vary in both direction from the mean of the population
o Favors extremes over mean
o Bimodal (two peaked distribution
o Extremely rare
Scleria verrucosa
Finches with small & long beaks
Evolutionary trend
Directional selection over many generations
Texas Longhorn cattle
Longhorns favored
o Protect against predators
o
(1)Evolution
On going
Lineages change through time
(2)Gradualism
evolve by innumerable small steps through intermediatary forms
(3)Common descent
?
Bird species
Some bird species are indistinguishable by appearance

(4)Population speciation
differential representation in next generation
evolution occurs by changes in the proportions of individuals within
a population that differ in one or more inherited traits
Fitness of individuals
Number of offspring that live to reproduce
(5)Natural Selection
changes among individuals in a population (NOT species
Human
69 babies
Cat
420 kittens
Conditions
(1)variation among individuals
(2)variation inheritable
(3)more offspring every generation than survive
(4) non-random survival &fertility
Finches
Different beaks
o Different food
Larger bills were able to
Geospiza fortis

El nino
walker current
unusually cold on top
zuric
dry
midparent
average between mom and dad
flat line means there was not a correlation
Cross fostering
Exchange the extremes of
Takes out environmental component
Resistance
Insecticides
o Made by
Heritable
Proportion of variation in a trait which is attributable to genotype
within a specific environment
Monozygote twins
From same egg
o Same genotype
Dizygote
From two eggs

o genetic similarity
Types of selection
Stabilizing selection
o Human birth weight
Directional selection
o Drought
Mean changes
Disruptive selection
o H. minikly
Fish
Teeth
o Mouth
Left jawed or right jawed fish
Genetic drift
Random changes in allele frequencies from 1 generation to the next
Population bottleneck
Environmental events that only a small number of individuals
survive
Founder effect
Change in genetic variation
Sexual selection
Specific type of nonrandom mating in which an organisms
phenotype influences its ability to attract mates

o Peacocks
Male tail feathers
Intrasexual selection
Features improved the ability of their bearers to compete for access
to mates
Intersexual selection
Made their bearer more attractive to meembers of opposite sex
Indeterminate growth
Continue to grow throughout their lives
o Frogs
African longtailed widowbird
Genus: Euplectes
Species: progni
Allele frequencies
# of copies of allele in population
total # of copies in all alleles in population
Polymorphic
A population with more than one allele at a locus
Let N(AA) be the number of individuals that are homozygous for A
allele (AA)
Let(Aa) be # of heterozygous (Aa)
Let N(aa) be the number of individuals that are homozygous for a
allele (aa)
N(AA)+ N(Aa) +N(aa)= N, total # of individuals in population

2N = both copies of alleles in population

Frequency of allele A
2N(AA)+2N(Aa) = p
2N
Frequency of allele a
2N(aa)+2N(Aa) = q
2N
Frequency of genotype AA = N(AA)/N
Frequency of genotype Aa = N(Aa)/N
Frequency of genotype aa = N(aa)/N
p+q=1
q=1-p
Monomorphic
One allele
Allele is fixed
Genetic structure
Frequencies of different alleles at each locus & frequencies of
different genotypes in a population
Polygynous
Male has more than 1 mate

Variation
Must be heritable
Where does variation come from?
Phenotype
External expression of the genotype
o Developmental factors
Developmental history
Current patterns of use or disuse
Environmental circumstance
Change phenotype
Use muscle (current patters of use or disuse)
Can depend on past or present
Genes & information
Sesame Street
Kids in __?
Hawks teaching their children
?

Spousal abuse?
Phenotypes vary
Neanderthals
Sight
Nearsightedness
Lack of sunlight
Obesity
Biggester killer in next generation
300 genes linked to obesity
o 70 specific genes
o
Genes make an outcome possible
R gene ?
o Breast cancer
Where variation occurs
Germ cells
o Heritable (offspring)
Green cells are germ lines
Somatic cells
o Mutations in somatic cells are not heritable
Thus Natural selection cannot act upon these mutations

Genetic Variation
Mutations
o Copying errors
o DNA polymerase makes some errors
E. coli
o 4.6 million base pairs
o 1 hour to replicate entire genome
o 920 errors/genome replication
Homo sapiens
o 6 billion base pairs
o 2-3hours to replicate
o 1,200,000
Primer Sequence
o Increase confidence
o Reduce error rate
o 1/10 million errors after proofreading
0,92 errors E. coli
1,200 errors Homo sapiens
Point mutations
Substitution at position 3 in codon usually do not change
o Silent substitution does not affect phenotype

 Thus Natural selection cannot act on it

So silent substitutions can accumulate
Change in amino acid(s)
Missense
o Amino acid changed
Nonsense
o Stop codon
Shift reading frame
Missense
Nonsense
Mutation rates
Drosophila
o 10^-5
RNA viruses
o Phage: 1.5 x 10^-3
o ___?: 1.8-2.5 x 10^-8
Humans
o 60 mutations per gamete
o 120 mutations per individual
Mutations
may or may not have an effect on phenotype

o Subject to Natural selection only when expressed in

phenotype
o Usually deleterious when in coding region
DNA
Exons
o Make proteins
Introns
o (1.5% of genome)?
Transposable elements
Unique noncoding DNA
o 15%
27,000 genes
noncoding
o regulatory regions
o etc.?
o
Kinds of traits
Quantitative
o Continuous variation, many genes
Traits very complex
Simple genotype-phenotype relationship
o Qualitative traits

Ex. Red and White flowers

o 1 gene 2 alleles
o heterozygous
zygote think diploid
F1= filio?
Adaptation
Changes
Mendelian genetics
Population genetics
Frequencies produced in entire population include consideration
mating systems, Natural Selection, and random mutation.
Allele
o Something considered in gamete
Allele frequency
o Number of allele copies in population
Genotype
o Diploid
Phenotype
o External expression of genotype
Gene pool
o ?
Population

o ?
Allelic variation and populations
1 blood group locus
Individual gene with 1 or 2 alleles
Dominant-recessive
Dominant over
Hetero or Homozygote
Ex. Purple to white flowers
o Phenotypic ratio
3:1
Purple: White
o Genotypic ratio
1:2:1
PP:Pp:pp
o Allele frequency
P(A)= 206/316=0.64
P(a)= 110/316=0.36
o Genotypic frequency?
P(AA)=0.385= 62/58
P(Aa)=0.509=82/158
P(aa)=0.106=14/158

 Short cut use Hardy Weinburg!

Hardy-Weinburg equilibrium
Allele A is dominant
Cross AA (tall) x aa (short)
F1= Aa (tall)
Cross F1 x F1
0.25 Homozygous recessive
p^2+2pq+q^2=1
p^2= dominant homozygous
q^2= recessive homozygous
2pq= heterozygous
Conditions
o Random mating
o Extremely large population size
o No
gene flow
selection
mutation
conditions that are rarely met in nature
Takes 1 generation to achieve Hardy-Weignburg for Autosomal
genes except in special cases

Traits
Need hertitability
o Otherwise NS cannot act onit
Galapagos
o Drought
Finches
Variation in trait
Changes in DNA
o Mutations
o Noncoding region
Silent substitutions?
o Coding region
Often deleterious
o High number of mutations
Most are in introns
Noncoding region
Frequencies
Always add to 1
Gametes?
o P=p(A)

o Q=q(a)
P + q=1
Hardy-Weinburg
o Diploid Genotype frequencies
P^2 + 2pq+ q^2=1
Hardy-Weingurg
Unrealistic
Important null model
o Why is it important?
Ex.
o Alleles in opposiums
Green hair
dominant
Pink hair
Recessive
1000 sample
16 pink haired
16/1000=?
Conditions __?
o Take 1 generation to achieve HW in autosomal genes
Independent Assortment

o Genotpyes vary
1:2:1
o assumption?
Alleles remain unchanged over time
o No Evolution
Homozygous are extremely rare
o Q=0.01
o Frequency aa=q^2=0.001 (1 in 10,000)
o Far more individuals are carries of rare deleterious recessives
than expreses the phenottpe and most ?
o Albinism
1/20, 000 = q^2
q= (1/20,000)^(1/2) = 0.0071
99.3% of albinos come from 2 normal parents
same general conclusion?
20% pediatric visits of children with rare genetic
diseases
Hardy-Weinburg
null model
Flower color
Codominance
Violations of HW
1 Non-random mating

2 inbreeding
o Florida panthers
crick in tail from severe inbreeding
on their way out.. into extinction
o cheetah
all homozygous
o Albinoism
1% inbreeding increases albinoism by 2.4 times?
3 Genetic drift
o 2 drosophila population
small populations
lost genetic variation
o Names passed down on male side
Eventually a female generation will occur
Name will be lost
20 families?
o General populations
Small N (population)
Good change of large change in 1 population
Large N (population)
Smaller the random change in population?

Very large N (population)

Random genetic drift occurs over a long period of
time
4 Balancing selection
o Heterozygote advantage
Ex. Sickle Cell Anemia
Red blood cells
Hemoglobin
o Carries less ozygen
o Lower oxygen efficiency
Malaria
Parasite lives in mosquitos
Sickle cell Anemia
o Advantagous where malaria
transmission is high
Tsunami in 2004? killed same amount of
people Malaia kills in 2 weeks
Ex. Thalassemia
Defective hemoglobin and severe anemia
Minor carriers have mild anemia but are less likely
to be ?
Compromised hemoglobin carry less O2
?
5 Selection
o Frequency of dependent selection

Perissodus
Right jawed or left jawed fish
Sex Chromosomes
Inherited differently than autosomal chromosomes
o Hemizygosity
?
Sex-linked inheritance
o Humans
Red-green color blindness
More common in men than females
o Drosophila melanogaster
Eye color
Red vs. white
Red color dominant
Alleles in Mendelian traits
Complete dominance
o Phenotypic ratio
3:1
Codominance
o Phenotypic ratio
1:2:1

White flowers (25%)

Sex-linked traits
Mitosis
Parent cell
o ?
Meiosis
A mechanism for diversity
Crossing over
Generator for variation
Toal genetic diversity
Tremendous amount of variation
Genetic variation
Structural genomes
o Chromosomes broken
(1) Deletion
(2) Insertion
(3) Inversion
(4) Copy-number variant
?
(5) segment duplication
Transopoable elements

Genomes bigger than needed

o Flowering plants have really large genomes
Genetic parasites
o CFTR gene (chloride channel)
o ?
Selfish DNA
o Transposable elements
Can change relative position within genome of a single
cell
Bacteria transformation & plasmids
Plasmids really small circular pieces of DNA which can be moved
rapidly
Structural changes
Gene duplication
o 1 can become a pseudo gene
o how genomes grow
Gene
Direct descendant
Ortholog
o Straight descendant
Diverge with duplication
o Paralogs
Evidence of duplication

HOX genes?
Developmental genes
Ex. Tetrapods
o Duplications of HOX genes
Whole genome duplication
Happens a lot in plants
Animals as well
o Zebrafish
o Mdaka?
Anciently conserved
o Genes conserved from ancestors
o