Exam 1 Flashcards
Why do we study evolution?
To understand the great diversity of life.
To study how species, families, orders, classes, and phyla are interrelated.
To understand the evolutionary history contained in the fossil record.
To understand disease and develop effective treatments.
To manage endangered species.
What is Evolution?
- The process of species change over time.
- The way that new species arise.
- Changes in the genetics of populations from generation to generation.
- Change in gene frequency over time.
- Change in morphology of populations over time.
- Origin of new life forms from pre-existing forms of life.
What are the basic units of evolution?
Genes (regions of DNA) Organisms Populations Species Clades (related species with a common ancestor)
What is life’s history?
When did various species evolve?
Who: what groups can be distinguished; what are the criteria?
Where: what habitats and physical conditions were present?
How do we tell who’s related to whom and how close is that relationship?
What is Ecology?
The study of the abundance and distribution of plants and animals (of organism)
How these organisms relate to each other and to their environment
How do these disciplines (evolution and ecology) intersect?
Evolutionary forces shape the ecology of species
Species influence other species and their evolution
5 characteristics of life
- Growth and development
- Acquire nutrients and process energy
- Respond to stimuli/react to the environment
- Maintain homeostasis (regulation of organism)
- Reproduction
Where did ideas about evolution come from?
1700’s — Linnaeus: classification
1830 — Charles Lyell: Principles of Geology
1798-1826—Thomas Malthus—resource limitation
1859—Charles Darwin publishes the Origin of Species
Current evidence for the evolution of life:
Fossil record
Comparative morphology
Developmental patterns
Biogeographic patterns
Molecular systematic patterns
Mechanisms of evolution
Natural selection is one of the mechanisms by which evolution can occur
But there are others:
- Sexual selection
- Genetic drift
- Population bottlenecks
- Founder effects
Where did ideas about evolution come from?
1700’s — Linnaeus: classification
1830 — Charles Lyell: Principles of Geology
1798-1826—Thomas Malthus—resource limitation
1859—Charles Darwin publishes the Origin of Species
Fossils
Fossils: preserved remains of life on earth; “dug up from beneath the ground”
body fossils
trace fossils
body fossils
= direct evidence of prehistoric life
trace fossils
(footprints, burrows; chemical) = indirect evidence
Importance of Fossils
a record of ancient life
evidence that many species that used to exist are now extinct
evidence of change over time
Humans did not always recognize fossils as what they are–remains of plants and animals
Early Evolutionary Thought
Early Greeks-
~600 B.C.
-Hippolytus was an early describer
Early Evolutionary Thought
300 B.C.
-Theophrastus (Aristotelian); thought fossil bones grew due to a characteristic inherent in the rocks; did not believe the bones were from individual, once-live creatures
Early Evolutionary Thought
200-1400 A.D.
-The Great Interruption in Western thought (Dark/Middle Ages)
Early Evolutionary Thought
1500 A.D.
-Agricola (Georg Bauer); described fossils; thought some grew within rocks; others were alive and then petrified
Early Evolutionary Thought
~1600s
-once people started agreeing that fossils had once been alive, they were explained as remains of organisms killed during the Great Flood (Old Testament).
Early Evolutionary Thought
Bishop Ussher
-(1654) calculated the age of the earth based on Biblical geneologies (4004 B.C.)
This led to the conclusion that:
All fossils were the same age
All fossils were relatively recent
Biblical/Creationist Viewpoint
Life was created by a divine being
Life survives as it was originally created (unchanged over time)
No new life forms arise
Extinction did not occur except as a result of the Biblical Flood
Early Evolutionary Thought
1700’s—Age of Enlightenment:Advances in geology
Earth did not seem as young as Bishop Ussher thought.
Much time must be needed for thick layers of rock to form.
Much time must be needed for layers of rock to erode.
A single event (Biblical flood) seemed unlikely to produce thick sequences of rock layers.
Fossils were different in different layers, refuting idea that all the animals lived at the same time.
Early Evolutionary Thought
Carl Linneaus
Advances in biological studies
Carl Linneaus develops a rigid classification system for systematically describing organisms (Systema Naturae 10th edition 1758)
1700’s — Linnaeus: classification
Early Evolutionary Thought
Erasmus Darwin
Erasmus Darwin 1731-1802
Charles Darwin’s grandfather
Species evolve into each other
Linear progressive evolution–evolve toward increasing complexity
No extinction
Early Evolutionary Thought
Jean-Baptiste Lamark
Jean-Baptiste Lamark (1744-1829)
Organisms progress upward in response to environment
Spontaneous generation from inanimate ancestors
Trend towards increasing complexity
Change acquired during lifetime is passed on to offspring
No extinction, rather, transformation
Early Evolutionary Thought: 1800’s
George Cuvier (anatomist) compared bones of living animals to extinct ones and reconstructed their appearance
William Smith: fossils were distinctive in each different rock layer; could be used to identify rocks in different parts of the country (England)
Others demonstrated the phenomenon over Western Europe
Materialism
Everything is made of matter
Can be studied by science
A materialistic world view emphasizes matter, physical processes over spiritual causes
Simple, observable physical processes used to explain more complex events
Gods/spirits not used as explanations for phenomena
Catastrophism
Catostrophic events (geologic upheavals, Biblical Flood) could explain geological features (mountains, lakes)
Uniformitarianism
Gradualists
Change occurs slowly over long periods of time
Cumulative action of everyday processes (sedimentation, erosion) explains geology
A materialistic world view (emphasizes matter, physical processes over spiritual causes)
Early Evolutionary Thought
Thomas Malthus
1798-1826—Thomas Malthus—resource limitation
Thomas Malthus (1766-1834)
Noted the geometric rise in the human population (vs. the arithmetic rise in agricultural production)
Developed the idea of limitation of natural resources
Too many people and not enough food
–>famine, disease, conflict
Early Evolutionary Thought
Charles Darwin - 1809-1882
1859 - Darwin publishes the Origin of Species.
- Son of a doctor
- “Landed gentry”
- Abandoned medical training
- Began theological training at Cambridge
- An avid collector and naturalist
- Engaged as ship’s naturalist aboard the Beagle
- Captain Robert FitzRoy
- At sea 1831-1836
- Mission: study geology and biology of S. America
- Travels mainland and islands
- Collects huge numbers of specimens
- Back in England, studies mockingbirds, finches
- Island forms are similar to mainland forms due to colonization and change
- Develops idea of “transmutation”–species change from one to another
Early Evolutionary Thought Robert Chambers (1802-1871)
Publishes “Vestiges” in 1844
Argues in favor of evolutionary change
Initially popular; subsequently widely denounced
Darwin intimidated by public reception
Alfred Russel Wallace (1823-1913)
South Seas naturalist
Independently discovers evolution via natural selection
Writes to Darwin to ask for his comments
The Article
Darwin and Wallace co-publish an article on their findings in 1858
Journal of the Proceedings of the Linnean Society
“On the tendency of species to form varieties; and on the perpetuation of the varieties and species by natural selection”
“On the Origin of Species by Means of Natural Selection”
Charles Darwin, 1859
Elaborated, expanded ideas set forth in the paper
Used ideas from artificial selection (captive breeding) to support key arguments
An intellectual sensation
Darwin’s big idea #1:
“Descent with Modification”
New species are produced from existing species
Explains underlying similarities
Explains diversity of organisms
Explains pattern of the fossil record
Doesn’t explain the precise mechanism, though
Darwin’s big idea #2:
“Natural Selection”
More offspring are produced than can survive
Offspring vary in quality
More robust or better equipped survive better
Survivors pass on these traits to their offspring
Darwin 1859—3 important principles:
- Species are related by evolution, branching from common descent
- Species change through time, they aren’t static
- There is variation within species
Heredity
Charles Darwin did not understand heredity (used “variation”)
Gregor Mendel (1822-1884)—genetics of inheritance
Importance of Mendel’s work not understood until years after his death
Darwin: variability
-Did not understand how variability was generated (mutation)
-Did not know how variations are passed to offspring
-Thought that traits “blend”
(But phenotypes may blend; genotypes don’t)
The Modern Synthesis
Darwin’s ideas disputed for many years
Between 1932-1953, genetics were incorporated with Darwin’s ideas
Theory of Evolution is re-stated as the Modern Synthesis (Evolutionary Synthesis)
Gradual evolution
Origin of new species (macro-evolution) can be explained via natural selection on individuals (micro-evolution)
Some individuals are more successful than others
Individuals that survive and reproduce are those best adapted to environment
Over time, these adaptive alleles will become more frequent in the population
The Modern Synthesis
Gradual evolution =
result of small genetic changes acted on by natural selection
The Modern Synthesis
Restating Darwin’s original ideas:
Mutation creates new alleles; shuffling leads to variation within a population
Alleles are passed to offspring
How does evolution work?
Evolutionary processes tend to be invisible
We see the products of evolution, not the process
Natural Selection
Darwin
Darwin used natural selection to explain adaptation process
Lacked examples of natural selection
Used examples of artificial selection in plants and animals
Natural Selection
- Individuals in a population vary
- Variations are heritable
- Some variants survive and reproduce better than others
- Individuals with the best variations (adaptations) are selected
-Those “winners” become more common in the population over time - Darwinian evolution
- Natural selection is a testable theory
- Each postulate can be tested
- Natural selection exploits genetic variance to increase fitness
- It is an editor, not a writer
- Mutation is a writer, creating new forms
Natural Selection
Darwinian evolution:
gradual change in populations (gene frequencies) over time
Darwinian Fitness
The ability of an individual organism to survive and reproduce in its environment
Adaptation
A trait or characteristic of an individual that increases its fitness relative to individuals without the trait
Theory of Natural Selection is Testable!
Snapdragon experiment
-75% white with yellow dot, 25% all yellow
1. Population contained variation (white and all yellow individuals)
2. Variation in color was heritable (determined by different experiment)
SS; Ss = white, ss = yellow
Snapdragon Experiment
3. Do individuals vary in survival or reproduction (fitness)?
Counted bee visits (pollination = reproduction)
Counted seeds produced (# seeds = # offspring)
Answer: Yes!
Snapdragon Experiment
4. Is reproduction random? Or do some individuals reproduce better than others (fitness differences)?
Found some individuals received more bee visits
Some individuals had higher reproductive success
Answer: No! Some individuals are preferred!
Snapdragon Experiment
5. Did population evolve (did allele frequencies change over generations)?
Yes! Frequency of white flowers increased slightly in the population.
Natural Selection for Beak Size in Darwin’s Finches
1. Are finch beaks variable?
Yes! Ground finches vary in size. (All individuals were banded and measured).
Natural Selection for Beak Size in Darwin’s Finches
2. Is trait adaptive?
Yes! Birds with larger beaks can crack larger, tougher seeds than birds with smaller beaks, which have to eat smaller seeds
Natural Selection for Beak Size in Darwin’s Finches
3. Is variation in beak size heritable?
Yes! There are allele differences in beak size.
Natural Selection for Beak Size in Darwin’s Finches
Do individuals vary in survival and reproductive success (fitness)?
Yes!
Natural Selection for Beak Size in Darwin’s Finches
During drought, only large seeds are available
Birds with smaller beaks can’t eat them, so they starve
Significant change in beak size due to natural selection can be observed over just one generation
The Nature of Natural Selection
- Natural Selection acts on individual organisms (they are either selected or not)
- But change is seen in population characteristics over time
- Natural Selection acts on phenotypes
- But evolution consists of changes in allele frequencies
- Natural selection does not look to the future!
- Organisms do not plan for their evolutionary future!
- Evolution is always “behind the curve”
- Natural selection acts on existing traits
- However, new traits can evolve
- Selection acts on individuals
- NOT for the good of the species
The Nature of Natural Selection
new traits can evolve
- Mutations can produce new alleles
- Meiosis and fertilization shuffle the possible allele combinations to create new genotypes
The Nature of Natural Selection
Natural selection is not perfect:
Genes may affect multiple traits
Selecting for one trait may affect another in a different way
How does evolution work?
Ecological processes are visible
- Birth
- Death
- Feeding
- Competition
- Predation
Evolutionary processes tend to be invisible
We see the products of evolution, not the process
How does evolution work?
Evolutionary machinery =
= mechanism of evolution
- Genetics
- Natural selection
- Molecular evolution
- Speciation
- Extinction
How does evolution work?
What’s at the core?
Genetics is at the core of evolution
- Variation of genome
- Transmission of genetic info
Gregor Mendel (1822-1884)
First to describe how heredity works
Pea plants
Haploid
One copy of the whole genome
Diploid
Two copies of the whole genome
Polyploid
Multiple copies of the whole genome
Bacterial cell
There is no nucleus in bacteria, and the genome is a large, double-stranded, closed circle of DNA, without packaging.
Eukaryotic cell
In eukaryotic cells, the DNA is packaged in linear chromosomes, usually more than one chromosome for each cellular genome. Eukaryotic cells have their DNA wrapped around a backbone of proteins called histones.
Chromosome
= bundle of DNA
Genome
= an organism’s complete set of DNA (all chromosomes)
Locus/loci
= locations of particular genes
Gene
= region of DNA (that codes for a protein)
Alleles
= alternative forms of a gene at a given locus
How does genetic variation arise?
Chromosomes recombine during meiosis
- “Crossing over”
- Ends (“feet”) break off
- “Feet” recombine with other “legs”
- Foot/leg recombinations are random
How does genetic variation arise?
Law of Independent assortment
Genes on non-homologous chromosomes assort independently of each other
Different gametes can be produced from the same sets of chromosomes
How does genetic variation arise?
Fertilization occurs?
Randomly
- Many sperm are available, only one gets to pair with each egg
- Which sperm wins is random
How does genetic variation arise?
Mutations
- Point mutations
- Frameshift
- Inversions (Translocations)
- Duplications (and deletions)
- Genome Duplications
Mutations: Point mutations
One nucleotide is replaced (e.g. adenine replaces a thymine)
Description: Base pair substitutions in DNA sequences.
Mechanism: Chance errors during DNA synthesis or during repair of damaged DNA.
Significance: Creates new alleles
Mutations: Chromosome Inversions (Translocations)
“Flips” a piece of chromosome so gene order along chromosome changes
Description: Flipping of a chromosome segment, so order of the genes along the chromosome changes.
Mechanism: Breaks in DNA caused radiation or other insults.
Significance: Alleles inside the inversion are likely to be transmitted together, every unit.
Mutations: Duplications (and deletions):
Duplication of a short piece of DNA
Description: Duplication of the short stretch of DNA, creating an extra copy of the sequence.
Mechanism: Due to unequal crossing over during meiosis or retrotransposition.
Significance: Redundant new genes may acquire new functions by mutation.
Mutations: Genome Duplications
Duplication of entire genome
Description: Addition of a complete set of chromosomes.
Mechanism: Errors in meiosis or (in plants) mitosis.
Significance: May create new species; Massive gene duplication.
Effects of mutations in the real world…..
HIV infection process
(look at slide #75)
- HIV virion
- Binding
- Fusion
- DNA synthesis
- DNA splicing
- Transcription
- Translation
- New virion assembly
- Budding
- Muturation
How the Immune System Fights a Viral Infection
A
-Dendritic cells capture a virus and prevent bit of its proteins to naive helper T cells. Once activated, these naive cells divide to produce effector helper T cells. (76)
How the Immune System Fights a Viral Infection
B
- Effector helper T cells help stimulate B cells displaying the same bits of viral protein to mature into plasma cells, which make antibodies that bind and in some cases inactivate the virus.
- Effector helper T cells also help activate killer T cells, which destroy host cells infected with the virus. (77)
How the Immune System Fights a Viral Infection
C
-Most effector T cells are short lived, but a few become long-lived memory helper T cells. (78)
Immune system cells vulnerable to HIV:
Macrophages, effector helper T cells, and memory helper T cells all have CD4 and CCR5 proteins on their cell membranes. These proteins are HIV’s entry point into the host.
HIV infection timeline
- After initial infection, viral load increases rapidly, plummets, then gradually rises over time (years)
- In acute stage, CD4 T-cell numbers crash, rebound, then decline over the long term (years)
- Immune system is activated in acute stage, then plateaus at a high level over the long term (years)
How HIV Causes AIDS
HIV activates the immune system directly AND indirectly. Immune response and damage are ongoing. Eventually, the immune system is exhausted and can no longer function properly. This is the beginning of full-blown AIDS. (81)
AZT
- HIV’s reverse transcriptase uses nucleotides from the host cell to make a DNA strand complementary to the HIV virus’ strand.
- The anti-AIDS drug AZT mimics a normal nucleotide (T), but lacks an attachment site for the next nucleotide in the chain. AZT therefore blocks replication of the HIV virus.
AZT resistance
Individual HIV patients evolve resistance to AZT.
As therapy continues over time, higher percentages of virions have acquired partial resistance. Higher and higher doses of AZT are required to suppress HIV virions.
In most patients, AZT resistance evolves within six months.
What is the difference between AZT-sensitive and AZT-resistant reverse transcriptases?
Viral strains late in AZT treatment are genetically different from those found early in treatment. Reverse transcriptase is prone to errors, and HIV’s genome has no correction mechanism –> the highest mutation rate of any organism known so far.
Some of these mutations cause an amino acid substitution that makes AZT less likely to bind to HIV’s reverse transcriptase, leading to resistance. Resistance is adaptive, so virions that have it reproduce and pass on their resistance. Virions without this mutation fail to reproduce. Over time, the resistant virions dominate the population and the patient no longer responds to AZT.
Evolution of AZT resistance in AIDS patients
- Mutation
- Errors in reverse transcription generate a variable population. Some variants differ in resistance to AZT.
- Resistance (or susceptibility) is passed from parents to offspring.
- During treatment with AZT, many virions fail to reproduce.
- The variants that persist are the ones that can reproduce in the presence of AZT.
- Result: The composition of the population had changed over time.
HAART
Using a single anti-retroviral drug such as AZT will cause rapid selection for drug resistance. A solution has been to use a “cocktail” of multiple drugs (HAART).
As more AIDS patients use the multiple-drug “cocktail,” deaths from opportunistic infections decrease.
However, the virus remains, and side-effects of treatment are significant.
HAART uses a “cocktail” of multiple drugs. Treatment prolongs the lives of AIDS patients. However, resistance still arises in patients who miss doses.
Why are some people resistant to HIV?
Survivors tend to have a mutant CCR5 co-receptor (Δ32 allele; Δ32 is missing 32 base pairs that most people have) This CCR5 mutation prevents HIV from entering cells–>prevents infection
Un-infected Europeans tend to have one or two copies of Δ32; infected Europeans don’t
Humans have genetic variation for disease (HIV) resistance.
HIV-resistant people have a mutant CCR5 co-receptor (Δ32 allele)
HIV resistance can also be conferred by mutations in the CD4 receptor.
How common is the Δ32 mutation?
Allele frequency varies significantly in different countries. CCR5-Δ32 allele affects resistance to HIV infection. (91,92)
Where did HIV Come From?
Monkeys transmitted SIV virus to chimpanzees
Chimpanzees transmitted SIV to humans (HIV-1)
Pet monkeys and/or contact through hunting probably transmitted SIV to humans (HIV-2)
Two different sources of infection
Multiple transmissions of SIV strains to great apes (chimps, gorillas)
At least three separate infection events from great apes to humans (HIV-1 group M, N, O, P)
Where is HIV derived from?
Human HIV is derived from primate SIV
In monkeys, SIV generally causes little to no illness
Why is HIV fatal?
Why is chimp SIV and human HIV so harmful?
- HIV-1 has a mutation that fails to suppress the host’s immune system, allowing for indefinite reproduction of the virus (most viruses would try to shut down the immune system of the host)
- All hosts eventually die
- If a parasite (e.g. HIV) is to survive, it has to leave the host and find a new one
- Hosts vary in their resistance to HIV; viruses vary in their ability to move from one host to another (transmission)
- Strains good at getting transmitted will survive; strains that are bad at being transmitted will die with the host
Why is HIV fatal?
Evolution of HIV virons in a patient cause immune collapse in three ways:
Continuous evolution of new epitopes (short pieces of viral protein) keeps virus population ahead of immune system response and assures rapid replication
Viral population replication within a host becomes progressively more aggressive—later strains cause more damage than strains from earlier in infection
Evolution of strains that can infect naïve T-cells (CXCR4 co-receptor). This speeds up collapse of the immune system.
Short-sighted Selection in HIV:
HIV strains that use the CXCR4 co-receptor appear later in the life of the patient, when the patient is sicker
HIV strains that use the CXCR4 co-receptor cause the patient’s immune system to collapse, resulting in death of the host
HIV strains that use the CXCR4 co-receptor don’t get transmitted to new hosts, so they go extinct when the host (patient) dies
How do we look at genes and evolution?
Frequencies of alleles and gene combinations
- How often are certain combinations seen in a population?
- Rare? Common?
How do we look at genes and evolution?
Gene expression =
= how genes determine an organism’s characteristics
- Are all genes expressed at birth?
- How do genes interact with each other?
- How is gene expression related to environment?
How do we look at genes and evolution?
Genes’ effect on survival and fertility
- Survival and fertility are what natural selection acts upon
- Organisms with a survival advantage tend to survive and reproduce
- Trait becomes more common over time
How does evolution use genes?
Genotype =
= a part of the genome or a gene locus
How does evolution use genes?
Phenotype =
= what the organism’s physical traits are (e.g. what it looks like)
How does evolution use genes?
Population =
= members of a (sexually reproducing) species living within a given area
Selection Differential
= How much the selected population varies from the overall population
The selection differential = S
\_\_ \_\_ S = X whole pop — X selected pop
Response to Selection
The selected sub-group gets to breed
The change in the offspring relative to the original population = the Response to Selection = R
__ __
R = X offspring — X whole pop.
Response to Selection and Heritability are linked
The response (R) to selection = heritability (h2) times the selection differential (S)
R = h2 S
You can re-order this equation in terms of heritability:
Heritability equals the response to selection divided by the selection differential
h2 = R/S
Long-Term Selection on Corn: Results
- Able to select for extreme phenotypes (high oil or high protein)
- Selection effects are cumulative over time
- Many genes are involved
-Selection process can be reversed - Significant genetic variation is maintained over time
- All 4 strains evolved from a single ear of corn
Natural Selection
Populations are a mix of different phenotypes
Natural selection may affect different phenotypes in different ways
- Directional selection
- Stabilizing selection
- Disruptive selection
- Frequency-dependent
A normal population
- A typical population has a variety of phenotypes (look at slide 119)
- The traits follow a normal distribution (120)
Directional Selection
Favors one extreme phenotype in the population (look at slide 121)
Stabilizing Selection
Favors intermediate phenotypes (look at slide 122)
Disruptive Selection
Penalizes intermediates and favors both extreme phenotypes (look at slide 123)
Frequency-Dependent Selection
Perissodus microlepis
- Scale-eating fish displaying “handedness” for mouth shape
- Right-handed fish attack the left flank
- Left-handed fish attack the right flank
- “Mouth handedness” is genetically determined
- Prey fish guard against the prevalent phenotype; suffer more attacks from the un-guarded side
- In this way, the rare phenotype is favored for a time, then becomes common and loses out to the other phenotype, now rare
Uta stansburiana males have 3 different strategies:
- 3 different morphs: Orange, Blue, and Yellow.
- Orange: aggressive and territorial; large territories
- Blue: guard mates to prevent sneaking; lose to aggressive orange males
- Yellow: non-territorial sneakers (resemble females)
-Females appear to prefer to mate with the rare type - Type is genetically controlled
- Frequency of male types therefore fluctuates as the rare “preferred” type becomes more common and less desirable
Industrial Melanism in Moths
- A Visible Case of Natural Selection
- Two morphs, dark and light
- As industry and coal dust coated trees, light form was more visible, and eaten more often by birds
- Dark morph became more common in cities
Fitness
Fitness = ave. reproduction of an individual/genotype over its lifetime
Fitness reflects differences in net reproduction
Fitness = (total reproduction) x (survival probability)
Heterozygous superiority
Heterozygote is better than both homozygote
I.e sickle cell
Look up!
Sickle-Cell Anemia
-genetic disease
AA = normal Aa = carrier, partially affected aa = afflicted w/ sickle-cell
Normal red blood cells curve into a sickle shape
These cells form clots in the blood vessels
Victim suffers pain, bleeding, organ damage, death
Malaria Around the World
Heterozygote has an advantage over both other genotypes: malaria resistance
An example of heterozygote superiority
Population genetics
If there is no selection.... If there is no migration.... If the population is large.... If mating is random.... If there is no mutation….
Then meiosis and recombination do not alter allele frequencies
Population genetics
Hardy-Weinberg equilibrium
Hardy-Weinberg equilibrium occurs when there is no change in allele frequencies
Equilibrium is reached in 1 generation and remains stable unless acted on by some other force
Hardy-Weinberg equilibrium explains why dominant alleles don’t replace recessive alleles in a population
Hardy-Weinberg equilibrium is RARE in nature!
Population genetics
Do allele frequencies tend to change in a population?
Hardy-Weinberg says no
Hardy-Weinberg Equilibrium
Allele frequency
Consider a population with two alleles, A and a.
p = freq. of “A” allele
q = freq. of “a” allele
p + q = 1
Calculates allele frequencies in population
Hardy-Weinberg Equilibrium
Calculating genotypes
p^2 (AA) + 2pq (Aa) + q^2 (aa) = 1
p = freq. of “A” allele q = freq. of “a” allele pq = “Aa” alleles (2pq because “Aa” or “aA”)
Calculates genotypes in population
Population genetics
If allele frequencies deviate from Hardy-Weinberg equilibrium…..
…then evolutionary processes are occurring!
Population genetics
If allele frequencies deviate from Hardy-Weinberg equilibrium, then evolutionary processes are occurring!
- This is because in nature there is…
- Selection….
- Migration (gene flow)….
- Small populations (inbreeding)….
- Non-random reproduction….
- Mutation
- Random chance events (genetic drift)
Migration
- Increases gene flow
- Moves genes between populations
- Prevents alleles from disappearing from population
- Introduces mutations into larger population
Giant Pollen Cloud
May, 2006
Good weather causes mass birch tree flowering in Scandinavia
Pollen deposited throughout Britain
Non-random mating
Look up
Inbreeding
When related individuals mate
- Reduces heterozygosity (Aa)
- Increases homozygosity (AA, aa)
- Reduces genetic variance
- Can increase the chance of getting a recessive genetic disorder (CF, TS)
But inbreeding can vary by degree
Inbreeding Depression
Reduction of fitness
Reduction of functional characters
How do you measure the degree of inbreeding in a population?
F = inbreeding coefficient
- ~measures deviation from random mating
Ranges from 0.0 - 1.0
0 = not inbred
1 = highly inbred
Fixation
When an allele occurs 100% of the time, it has been “fixed” in the population
Inbred lines remain “true to their breed”: deviants are rare
Inbreeding Effects Can Be Subtle
A large population gets sub-divided
Several distinct, isolated populations result
Mutations occur, but not they are not the same in all the populations (diff. mutations, diff. frequencies)
So what happens to the overall population if you lose these small, distinctive sub-populations?
Loss of genetic diversity of the species
That’s why we care about small populations
Genetic Drift =
= a random fluctuation in allele frequencies due to sampling error
Leads to fixation of some alleles
Leads to loss of other alleles
Leads to an overall decline in genetic variation over time
Genetic drift
Who’s affected
Larger populations are less likely to be affected
Small populations more likely to lose alleles due to random fluctuations
Affects small populations more dramatically and more quickly
Can contribute to speciation by causing an isolated population to diverge
Qualitative Traits
Either/Or
One type or the other
- Brown fur vs. black fur
- Spots vs. no spots
- Pink flower vs. blue flower
Quantitative traits
Continuous; on a spectrum
- Height
- Weight
- Fertility
- Longevity
Quantitative Traits
How do we understand the genetics of continuous traits?
Phenotype = Genotype + Environment
Quantitative Traits
Variance in Phenotype =
Variance in Phenotype = Variance in Genotype + Variance in the Environment
VP = VG + VE
(See slide 47)
Variance
Shows the amount of dispersal around a mean (the amount of variation)
(See slide 48)
Epistasis
Different genes can interact with each other
How a gene is expressed (gene expression) is a result of additive and/or full dominance
Additive Genetic Variance
VA = genetic variation with no dominance or gene interaction (epistasis)
Heritability of Traits
h^2 = heritability
Heritability = the relative importance of heredity in character development
~The resemblance of offspring to parents
h^2 = VA / VP
VA = Additive genetic variance
VP = Phenotypic variance
-Value of h2 ranges from 0 to 1.0
0 = inheritance not important to trait (low h2)
1 = inheritance very important to trait (high h2)
- Size tends to be highly heritable
- Fertility tends to be less heritable
Founder Effect
Consider a colonization event where some individuals leave the population and form a new population
Allele frequencies in a new population are likely to be different than those in the original population
Founder Effect: Example
Amish
Amish
- High incidence of Ellis van Creveld syndrome (dwarfism + polydactyly; hole in the heart; nail and teeth deformity)
- One couple carried in 1744, passed to children
- Intermarriage spread trait
Founder Effect: Examples
Afrikaners in South Africa
Afrikaners in South Africa
- Originated from a few Dutch settlers
- High incidence of Huntington’s disease
- Founders carried Huntington’s disease allele at higher fq. than general population; over time it spread through S. African population
Founder Effect: Examples
Achromotopsia on Pingelap Island, Micronesia
Achromotopsia on Pingelap Island, Micronesia
- Typhoon killed most residents of island
- One survivor carried mutation
- Achromotopsia now affects ~6% of island residents
- Only 1 in 33,000 in general population
Population Bottleneck Example
-Cheetahs
-Florida panthers
-Northern elephant seals
–Heavily hunted in 1800’s
–Population crashed to ~20 individuals
–Now population ~30,000
–Reduced genetic variation compared to Southern elephant seals (a less hunted population)
(See slide 60)
Effective Population Size
Size of an ideal randomly mating population (no selection, mutation, or migration) that would lose genetic variation (via drift) at the same rate as is observed in the actual population
Factors affecting effective population size
Factors affecting effective population size (Ne):
Variations in mating success
Non-random mating
Unequal sex ratios
Correlations in repro success (inbreeding)
Fluctuations in population size
What is a Species?
There are several (3) definitions:
Biological Species Concept
Phylogenetic Species Concept
Morphospecies Species Concept
-Biologists usually use the Biological Species Concept
What is a Species? Phylogenetic Species Concept:
Examines phylogenetic trees and finds smallest groups (distinct branch tips)
Based on statistically significant differences in traits used to estimate phylogeny (family tree)—can be tested using DNA
(See slide 66)
What is a Species? Morphospecies Species Concept
Based on morphological differences between groups
But variation may not be indicative of different species; careful grouping necessary
Morphology may not reflect genetic diffs.
What is a Species?
Biological Species Concept
There is reproductive isolation between 2 populations
Members of the 2 populations do not reproduce successfully
Biological Species Concept
Reproductive isolation can arise from:
Failure to mate
Offspring are produced but are not fertile
Biological Species Concept
Barriers to Successful Reproduction
Pre-zygotic isolating mechanisms (prevent formation of an embryo)
Usually have relatively low fitness costs
POST-zygotic isolating mechanisms (act after fertilization occurs)
Usually have a high fitness cost
Biological Species Concept
Barriers to Successful Reproduction
PRE-zygotic isolating mechanisms:
- Different habitats
- Different mating seasons
- No sexual attraction
- Fertilization problems
- Coital problems (organs may not match up)
Biological Species Concept
Barriers to Successful Reproduction
POST-zygotic isolating mechanisms:
Successful mating occurs, but offspring is sterile
Mating occurs, but offspring does not survive
How Do New Species Arise?
- Populations become separated
- Each has an independent evolutionary fate (they evolve separately)
- Geographical separation of populations fosters speciation
- Dispersal barriers lead to independent evolutionary tracks for each population
- 2 separated populations may experience different environmental conditions
- This leads to adaptation to those different conditions
- Can lead to allopatric speciation (see slide 86)
How Do New Species Arise?
allopatric =
Geographically separated populations = allopatric
See slide 84
Dispersal vs. Vicariance
See slide 87
Genetic Mechanisms of Speciation
See slide 91
Transposable elements are different in different populations
When reunited, genomes may no longer be compatible (i)
Genomes may evolve duplications (ii)
One population has a larger genome that is incompatible with the other population due to size differences (e.g. muntjacs)
Chinese muntjac = 46 chromosomes
Indian muntjac = only 6 chromosomes
Sympatric Speciation
Sympatric populations occur in the same geographic area
Therefore, it is hard for complete population isolation to occur
(See slides 96,97)
How might sympatric speciation occur?
- Disruptive selection may occur
- Extreme phenotypes are favored
- Intermediate phenotypes are eliminated
-Hybrids of the extremes will be intermediate and will be selected against - Extremes will succeed better if they mate with similar phenotypes
- polyploidy
- Differences in insect/plant host associations may cause sympatric speciation
- Fruit flies can eat several types of fruit, but they tend to stay put on a single type
- Flies in different regions choose different plant hosts
- This leads to geographic isolation on a micro scale
How might sympatric speciation occur?
Polyploidy
Some organisms gain extra copies of chromosomes = polyploidy
Polyploid plants are no longer compatible with normal plants—> reproductive isolation
Normal plants = sexual reproduction
Polyploid plants = vegetative reproduction via clones/runners
(See slide 102)
5 ways …How might sympatric speciation occur?
- Disruptive selection may occur
- Polyploidization
- Differences in insect/plant host associations
- Assortative mating
- Sensory drive
Assortative mating/ sexual selection -
mating with someone that’s your type. There is variety but you pick the mate that most resembles you
Sensory drive
integration of environmental factors along with sexual Selection , mating preferences, acting together
Hybridization
When a species mates with another species and they produce offspring
Hybridization may cause:
- Alleles to spread across populations
- New hybrids = new types
- Inviable/infertile hybrids
Hybrid Zone
Area where local conditions permit hybridization to occur
Especially if 2 allopatric populations resume contact
Hybrids
Normally have reduced fitness relative to parents, but sometimes have better fitness
Plants especially have hybrids with higher fitness
(See slides 110, 112-116)
Hybrids
allopolyploidization
Can have extra chromosomes: allopolyploidization
1 parent contributes an extra set of chromosomes
Offspring is triploid
Hybrid Salamanders
See slide 120
A. jeffersonianum x A. laterale salamanders hybridize
1 parent contributes an extra set of chromosomes
Triploid offspring are produced
2 hybrid combos are possible: extra chromosomes can be contributed by either parent species
Parents reproduce sexually
Offspring reproduce parthenogenetically (asexually)!
Species Radiation
Also called adaptive radiation
When many new species arise in a relatively short period of evolutionary time
Often happens on islands
Many niches are empty
Little or no competition
Species can evolve to fill an ecological vacuum
Modern Examples of Adaptive Radiations
Darwin’s finches
Anolis lizards
Early Evolutionary Thought
Charles Lyell
1830 — Charles Lyell: Principles of Geology
Charles Lyell (1797-1875) Founder of modern geology
Recognized that rock layers represented depositions of different layers of fossils
Uniformitarianistic world view–change is gradual
1830: wrote Principles of Geology, an important book in its day; greatly influenced Charles Darwin.
Evolutionary (Phylogenetic) Trees
Phylogeny
Pattern of events that happen as a group diversifies
Sequence of lineages (what appeared when)
Generated by inference since most of our data is incomplete
Evolutionary (Phylogenetic) Trees
Phylogeny = a diagram depicting the evolutionary history of a group of organisms descending from a common ancestor
Pattern of events that happen as a group diversifies
Sequence of lineages (what appeared when)
Generated by inference since most of our data is incomplete
Phylogeny =
= a diagram depicting the evolutionary history of a group of organisms descending from a common ancestor
Phylogenetic Trees
A way to establish relationships between organisms
- What characters do they share?
- How closely related are they?
- When did major evolutionary events happen?
- Oldest organisms at the base
- Younger species at the tips
- Shape and orientation varies
Three different styles of trees that all express the equivalent relationships (see slide 11)
-Groups that are more closely related should share more traits
-Groups that are less related should share fewer traits
(See slide 15-17)
See slide 13
Phylogenetic Trees
Three trees that all express the equivalent relationships, regardless of branch length
See slide 14
Phylogenetic Trees
These trees depict equivalent relationships, despite the fact that certain internal branches have been rotated so that the order of the tip labels is different.
Creating Phylogenetic Trees
Traits used must be independent (change in one character cannot change another character)
Characters must be homologous (similarity in traits is due to a common ancestor)
Homology
Similarity in traits is due to a common ancestor
Synapomorphies = shared traits derived from a common ancestor
Evolutionary relationships are revealed by shared derived traits (synapomorphies)
A structure present in an ancestor species is retained in a descendent, but the structure may be highly modified (see slide 23)
Phylogenetic Trees
Synapomorphies =
= shared traits derived from a common ancestor
-Synapomorphies reveal relationships
(See slide 20, 21)
- Synapomorphies identify evolutionary branch points
- Synapomorphies are nested (each branching event adds more shared derived traits)
- Mutations can create synapomorphies, and you can map these changes onto a phylogenetic tree
- But…reversals may obscure the correct phylogeny.
- If a reversal has occurred, similar traits are NOT homologous (they are not synapomorphies)
- Reversals (“back-mutations”) can remove synapomorphies
- (See slide 26)
Phylogenetic Trees
Cladogram =
= phylogenetic tree created by clustering synapomorphies
See slide 25
Monophyly
A monophyletic group includes all of the descendants of the ancestor under investigation
(See slide 27)
Plesiomorphy
Ancestral character
Apomorphy
Derived character
Evolutionary Trees
- More than one tree may be possible
- How do you determine the best tree?
- Make a matrix of character states
- Draw all possible trees
- Mark evolutionary events on trees
- Count number of events needed for pattern
- Compare trees: which has the fewest transitions? Fewest transitions = most parsimonious
- Problems can arise in making a tree
- Homoplasy = similarity of characters NOT due to a shared common ancestor
Evolutionary Trees
Problems can arise in non-ideal situations:
We may not know anything about the common ancestor (no characters)
Similar evolutionary novelties sometimes evolve independently in different lineages (homoplasy)
Evolutionary novelties may evolve, then are lost (reversal), returning to ancestral condition
Homoplasy =
= similarity of characters NOT due to a shared common
Convergent Evolution
Convergent organisms may look very similar or have similar structures.
Convergent organisms may play similar roles in the environment, but they have:
- Different evolutionary histories
- Different ancestors
- Different DNA
- Organisms evolve solutions to environmental problems
- Natural selection favors similar traits in similar environments
See slides 58-60
Convergent organisms may play similar roles in the environment, but they have:
- Different evolutionary histories
- Different ancestors
- Different DNA
Convergent evolution
Thorny devil and Horned toad
Thorny devil (Agamidae; Moloch horridus) from Australia (left) and Horned toad (Phrynosomidae; Phrynosoma coronatum) from Texas ( See slide 59,60)
- Different families
- Both desert species
- Ant specialists
Analagous Structures
Perform similar functions
NOT derived from the same structure
Result of similar evolutionary pressures, not shared heritage
Shark claspers; squid hectocotylus (see slide 62)
Monophyly vs. Paraphyly
Monophyletic group = clade (related species with a common ancestor) – taking ancestor and all its descendants
Non-monophyletic group – looks at ancestor and SOME descendants
(See slide 64)
Polytomy
A polytomy occurs when there is not enough information to resolve evolutionary relationships into dichotomies
The result is “flat” trees or multiple branches emerging from the same point
(See slide 66)
Evolutionary History of the Whales
Two hypotheses about the origin of whales:
A. Whales are artiodactyls and belong inside that group
Alternatively,
B. Whales are relatives of artiodactyls and belong next to that group
(See slide 67-75, 77,78,80)
Maximum Likelihood
Branch lengths are proportional to number of nucleotide substitutions per site (per branch)
Optimize branch lengths
Compare alternative trees to predicted chance of certain sequences
Evaluating the best tree
Maximum likelihood/BMCMC:
- What is the chance that alternative trees are supported by the data?
- Given certain parameters, what is the likelihood that a certain tree will occur?
- Highest likelihood = better tree
Bootstrapping
You’ve used parsimony and/or maximum likelihood to make your tree; now just how sure are you about its accuracy?
You could collect more data and re-run your analysis, or you could bootstrap
Bootstrapping creates a new data set (bootstrap replicates) from existing data to compare trees with/without certain branches; see which is correct
- Make new data set: here, randomly select 6 nucleotides from the pool for each animal.
- Construct a new tree based on this random selection.
- Rinse. Repeat. 100-1,000+ times.
- Majority-rule consensus model = new tree that contains all the monophyletic groups that appear in at least 50% of the bootstrap replicates
- What percentage of replicates have this monophyletic grouping pattern? This number = bootstrap support = confidence in your clade
Evolutionary Trees:
How do you improve the chances of your tree being reliable?
Select characters carefully
Use more characters
Use more species
Use multiple techniques
Extinction
A species ceases to exist anywhere in the world
Species with larger geographic ranges survive longer
See slide 99,100
(Species) Over Time….
- New species arise
- Some go extinct
- Some evolve
- Some remain relatively unchanged over time
Existing species represent a balance between extinction and new species
(See slide 90)
Why do species go extinct?
Biotic factors:
- Disease
- Predation
- Competition with other species
- Pollinator loss
- Habitat loss
- Habitat fragmentation
Why do species go extinct?
Abiotic factors:
- Climate change
- Excessive heat
- Drought
- Salinity
- Ice Age
- Volcanic activity
Mass Extinction
When an unusually high number of extinctions occur
There have been several mass extinctions over Earth’s history
Permian/Triassic mass extinction
- 250 MYA
- A catastrophic species loss—the “great dying”
- Wiped out >50% of all families
- Wiped out >90% of all species
- Why?
Permian/Triassic Mass Extinction
What caused the P-T extinction?
- Not entirely clear
- Massive tectonic movement of continents
- Alteration of ocean currents
- Change in climate
- CO2 buildup to toxic levels
- Asteroid impact?
Cretaceous/Tertiary Mass Extinction
Also known as the K-T extinction
- 65 MYA
- Dinosaurs wiped out
- 50% of all genera
What caused the K-T extinction?
-The Alvarez hypothesis:
The Alvarez hypothesis:
Asteroid impact
Tosses up giant dust cloud
Affects climate and sunlight
Plant and animal die-off
Evidence for asteroid collision as cause of K-T (Cretaceous/Tertiary) extinction
- Iridium layer at K-T boundary
- Iridium is common in asteroids
- Shocked quartz, found with asteroid impacts
- Micro-tektites
- Chicxulub crater: impact site
(See slide 113-117)
Physical ecology
- The physical environment can affect abundance and distribution of species
- Organisms adapt to their environment
Physical limitations to life
- Temp
- Heat
- Cold
- Water
- Gas exchange
- Light
- Body size
- Metabolism
- Energy acquisition
- Energy use
- Nutrient acquisition (how do they get the food)
- Waste elimination
Temperature
- Enzymes work best in a narrow temperature range
- Freezing destroys cells
- Heating de-natures proteins
- Temp affects water balance
- Water balance affects Temp
- Light levels affect Temp
- Temp affects metabolism
- Organisms regulate their body Temp
- Have different strategies
Temperature
Cold blooded/warm blooded :
-animals are cool/warm to touch
Temperature
Poikilotherm :
-body Temp varies
Temperature
Homeotherms :
-body Temp stays constant
Temperature
Endotherms:
-generate heat internally via metabolism
Temperature
Ectotherms:
-need external heat source
