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Bios 230 > Exam 1 > Flashcards

Exam 1 Flashcards

0
Q

Why do we study evolution?

A

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.

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1
Q

What is Evolution?

A
  • 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.
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2
Q

What are the basic units of evolution?

A 
Genes (regions of DNA)
Organisms
Populations
Species
Clades (related species with a common ancestor)
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3
Q

What is life’s history?

A

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?

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4
Q

What is Ecology?

A

The study of the abundance and distribution of plants and animals (of organism)

How these organisms relate to each other and to their environment

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5
Q

How do these disciplines (evolution and ecology) intersect?

A

Evolutionary forces shape the ecology of species

Species influence other species and their evolution

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6
Q

5 characteristics of life

A
  1. Growth and development
  2. Acquire nutrients and process energy
  3. Respond to stimuli/react to the environment
  4. Maintain homeostasis (regulation of organism)
  5. Reproduction
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7
Q

Where did ideas about evolution come from?

A

1700’s — Linnaeus: classification

1830 — Charles Lyell: Principles of Geology

1798-1826—Thomas Malthus—resource limitation

1859—Charles Darwin publishes the Origin of Species

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8
Q

Current evidence for the evolution of life:

A

Fossil record

Comparative morphology

Developmental patterns

Biogeographic patterns

Molecular systematic patterns

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9
Q

Mechanisms of evolution

A

Natural selection is one of the mechanisms by which evolution can occur

But there are others:

  • Sexual selection
  • Genetic drift
  • Population bottlenecks
  • Founder effects
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10
Q

Where did ideas about evolution come from?

A

1700’s — Linnaeus: classification

1830 — Charles Lyell: Principles of Geology

1798-1826—Thomas Malthus—resource limitation

1859—Charles Darwin publishes the Origin of Species

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11
Q

Fossils

A

Fossils: preserved remains of life on earth; “dug up from beneath the ground”

body fossils

trace fossils

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12
Q

body fossils

A

= direct evidence of prehistoric life

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13
Q

trace fossils

A

(footprints, burrows; chemical) = indirect evidence

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14
Q

Importance of Fossils

A

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

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15
Q

Early Evolutionary Thought
Early Greeks-
~600 B.C.

A

-Hippolytus was an early describer

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16
Q

Early Evolutionary Thought

300 B.C.

A

-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

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17
Q

Early Evolutionary Thought

200-1400 A.D.

A

-The Great Interruption in Western thought (Dark/Middle Ages)

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18
Q

Early Evolutionary Thought

1500 A.D.

A

-Agricola (Georg Bauer); described fossils; thought some grew within rocks; others were alive and then petrified

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19
Q

Early Evolutionary Thought

~1600s

A

-once people started agreeing that fossils had once been alive, they were explained as remains of organisms killed during the Great Flood (Old Testament).

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20
Q

Early Evolutionary Thought

Bishop Ussher

A

-(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

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21
Q

Biblical/Creationist Viewpoint

A

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

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22
Q

Early Evolutionary Thought

1700’s—Age of Enlightenment:Advances in geology

A

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.

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23
Q

Early Evolutionary Thought

Carl Linneaus

A

Advances in biological studies

Carl Linneaus develops a rigid classification system for systematically describing organisms (Systema Naturae 10th edition 1758)

1700’s — Linnaeus: classification

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24
Q

Early Evolutionary Thought

Erasmus Darwin

A

Erasmus Darwin 1731-1802

Charles Darwin’s grandfather

Species evolve into each other

Linear progressive evolution–evolve toward increasing complexity

No extinction

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25
Q

Early Evolutionary Thought

Jean-Baptiste Lamark

A

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

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26
Q

Early Evolutionary Thought: 1800’s

A

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

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27
Q

Materialism

A

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

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28
Q

Catastrophism

A

Catostrophic events (geologic upheavals, Biblical Flood) could explain geological features (mountains, lakes)

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29
Q

Uniformitarianism

A

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)

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30
Q

Early Evolutionary Thought

Thomas Malthus

A

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

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31
Q

Early Evolutionary Thought

Charles Darwin - 1809-1882

A

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
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32
Q 
Early Evolutionary Thought
Robert Chambers (1802-1871)
A

Publishes “Vestiges” in 1844

Argues in favor of evolutionary change

Initially popular; subsequently widely denounced

Darwin intimidated by public reception

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33
Q

Alfred Russel Wallace (1823-1913)

A

South Seas naturalist

Independently discovers evolution via natural selection

Writes to Darwin to ask for his comments

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34
Q

The Article

A

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”

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35
Q

“On the Origin of Species by Means of Natural Selection”

A

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

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36
Q

Darwin’s big idea #1:

A

“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

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37
Q

Darwin’s big idea #2:

A

“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

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38
Q

Darwin 1859—3 important principles:

A
  1. Species are related by evolution, branching from common descent
  2. Species change through time, they aren’t static
  3. There is variation within species
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39
Q

Heredity

A

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

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40
Q

Darwin: variability

A

-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)

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41
Q

The Modern Synthesis

A

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

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42
Q

The Modern Synthesis

Gradual evolution =

A

result of small genetic changes acted on by natural selection

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43
Q

The Modern Synthesis

Restating Darwin’s original ideas:

A

Mutation creates new alleles; shuffling leads to variation within a population

Alleles are passed to offspring

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44
Q

How does evolution work?

A

Evolutionary processes tend to be invisible

We see the products of evolution, not the process

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45
Q

Natural Selection

Darwin

A

Darwin used natural selection to explain adaptation process

Lacked examples of natural selection

Used examples of artificial selection in plants and animals

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46
Q

Natural Selection

A
  • 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
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47
Q

Natural Selection

Darwinian evolution:

A

gradual change in populations (gene frequencies) over time

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48
Q

Darwinian Fitness

A

The ability of an individual organism to survive and reproduce in its environment

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49
Q

Adaptation

A

A trait or characteristic of an individual that increases its fitness relative to individuals without the trait

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50
Q

Theory of Natural Selection is Testable!

Snapdragon experiment

A

-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

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51
Q

Snapdragon Experiment

3. Do individuals vary in survival or reproduction (fitness)?

A

Counted bee visits (pollination = reproduction)
Counted seeds produced (# seeds = # offspring)

Answer: Yes!

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52
Q

Snapdragon Experiment

4. Is reproduction random? Or do some individuals reproduce better than others (fitness differences)?

A

Found some individuals received more bee visits

Some individuals had higher reproductive success

Answer: No! Some individuals are preferred!

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53
Q

Snapdragon Experiment

5. Did population evolve (did allele frequencies change over generations)?

A

Yes! Frequency of white flowers increased slightly in the population.

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54
Q

Natural Selection for Beak Size in Darwin’s Finches

1. Are finch beaks variable?

A

Yes! Ground finches vary in size. (All individuals were banded and measured).

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55
Q

Natural Selection for Beak Size in Darwin’s Finches

2. Is trait adaptive?

A

Yes! Birds with larger beaks can crack larger, tougher seeds than birds with smaller beaks, which have to eat smaller seeds

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56
Q

Natural Selection for Beak Size in Darwin’s Finches

3. Is variation in beak size heritable?

A

Yes! There are allele differences in beak size.

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57
Q

Natural Selection for Beak Size in Darwin’s Finches

Do individuals vary in survival and reproductive success (fitness)?

A

Yes!

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58
Q

Natural Selection for Beak Size in Darwin’s Finches

A

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

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59
Q

The Nature of Natural Selection

A
  • 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
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60
Q

The Nature of Natural Selection

new traits can evolve

A
  • Mutations can produce new alleles

- Meiosis and fertilization shuffle the possible allele combinations to create new genotypes

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61
Q

The Nature of Natural Selection

Natural selection is not perfect:

A

Genes may affect multiple traits

Selecting for one trait may affect another in a different way

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62
Q

How does evolution work?

A

Ecological processes are visible

  • Birth
  • Death
  • Feeding
  • Competition
  • Predation

Evolutionary processes tend to be invisible

We see the products of evolution, not the process

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63
Q

How does evolution work?

Evolutionary machinery =

A

= mechanism of evolution

  • Genetics
  • Natural selection
  • Molecular evolution
  • Speciation
  • Extinction
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64
Q

How does evolution work?

What’s at the core?

A

Genetics is at the core of evolution

  • Variation of genome
  • Transmission of genetic info
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65
Q

Gregor Mendel (1822-1884)

A

First to describe how heredity works

Pea plants

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66
Q

Haploid

A

One copy of the whole genome

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67
Q

Diploid

A

Two copies of the whole genome

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68
Q

Polyploid

A

Multiple copies of the whole genome

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69
Q

Bacterial cell

A

There is no nucleus in bacteria, and the genome is a large, double-stranded, closed circle of DNA, without packaging.

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70
Q

Eukaryotic cell

A

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.

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71
Q

Chromosome

A

= bundle of DNA

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72
Q

Genome

A

= an organism’s complete set of DNA (all chromosomes)

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73
Q

Locus/loci

A

= locations of particular genes

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74
Q

Gene

A

= region of DNA (that codes for a protein)

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75
Q

Alleles

A

= alternative forms of a gene at a given locus

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76
Q

How does genetic variation arise?

A

Chromosomes recombine during meiosis

  • “Crossing over”
  • Ends (“feet”) break off
  • “Feet” recombine with other “legs”
  • Foot/leg recombinations are random
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77
Q

How does genetic variation arise?

Law of Independent assortment

A

Genes on non-homologous chromosomes assort independently of each other

Different gametes can be produced from the same sets of chromosomes

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78
Q

How does genetic variation arise?

Fertilization occurs?

A

Randomly

  • Many sperm are available, only one gets to pair with each egg
  • Which sperm wins is random
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79
Q

How does genetic variation arise?

Mutations

A
  • Point mutations
  • Frameshift
  • Inversions (Translocations)
  • Duplications (and deletions)
  • Genome Duplications
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80
Q

Mutations: Point mutations

A

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

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81
Q

Mutations: Chromosome Inversions (Translocations)

A

“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.

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82
Q

Mutations: Duplications (and deletions):

A

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.

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83
Q

Mutations: Genome Duplications

A

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.

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84
Q

Effects of mutations in the real world…..

HIV infection process

A

(look at slide #75)

  1. HIV virion
  2. Binding
  3. Fusion
  4. DNA synthesis
  5. DNA splicing
  6. Transcription
  7. Translation
  8. New virion assembly
  9. Budding
  10. Muturation
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85
Q

How the Immune System Fights a Viral Infection

A

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)

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86
Q

How the Immune System Fights a Viral Infection

B

A
  • 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)
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87
Q

How the Immune System Fights a Viral Infection

C

A

-Most effector T cells are short lived, but a few become long-lived memory helper T cells. (78)

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88
Q

Immune system cells vulnerable to HIV:

A

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.

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89
Q

HIV infection timeline

A
  • 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)
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90
Q

How HIV Causes AIDS

A

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)

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91
Q

AZT

A
  • 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.
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92
Q

AZT resistance

A

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.

93
Q

What is the difference between AZT-sensitive and AZT-resistant reverse transcriptases?

A

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.

94
Q

Evolution of AZT resistance in AIDS patients

A
  • 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.
95
Q

HAART

A

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.

96
Q

Why are some people resistant to HIV?

A

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.

97
Q

How common is the Δ32 mutation?

A

Allele frequency varies significantly in different countries. CCR5-Δ32 allele affects resistance to HIV infection. (91,92)

98
Q

Where did HIV Come From?

A

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)

99
Q

Where is HIV derived from?

A

Human HIV is derived from primate SIV

In monkeys, SIV generally causes little to no illness

100
Q

Why is HIV fatal?

Why is chimp SIV and human HIV so harmful?

A
  • 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
101
Q

Why is HIV fatal?

Evolution of HIV virons in a patient cause immune collapse in three ways:

A

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.

102
Q

Short-sighted Selection in HIV:

A

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

103
Q

How do we look at genes and evolution?

A

Frequencies of alleles and gene combinations

  • How often are certain combinations seen in a population?
  • Rare? Common?
104
Q

How do we look at genes and evolution?

Gene expression =

A

= 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?
105
Q

How do we look at genes and evolution?

Genes’ effect on survival and fertility

A
  • 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
106
Q

How does evolution use genes?

Genotype =

A

= a part of the genome or a gene locus

107
Q

How does evolution use genes?

Phenotype =

A

= what the organism’s physical traits are (e.g. what it looks like)

108
Q

How does evolution use genes?

Population =

A

= members of a (sexually reproducing) species living within a given area

109
Q

Selection Differential

A

= How much the selected population varies from the overall population

The selection differential = S

    \_\_		                 \_\_                S  =  X whole pop — X selected pop
110
Q

Response to Selection

A

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.

111
Q

Response to Selection and Heritability are linked

A

The response (R) to selection = heritability (h2) times the selection differential (S)

R = h2 S

112
Q

You can re-order this equation in terms of heritability:

A

Heritability equals the response to selection divided by the selection differential

h2 = R/S

113
Q

Long-Term Selection on Corn: Results

A
  • 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
114
Q

Natural Selection

A

Populations are a mix of different phenotypes

Natural selection may affect different phenotypes in different ways

  • Directional selection
  • Stabilizing selection
  • Disruptive selection
  • Frequency-dependent
115
Q

A normal population

A
  • A typical population has a variety of phenotypes (look at slide 119)
  • The traits follow a normal distribution (120)
116
Q

Directional Selection

A

Favors one extreme phenotype in the population (look at slide 121)

117
Q

Stabilizing Selection

A

Favors intermediate phenotypes (look at slide 122)

118
Q

Disruptive Selection

A

Penalizes intermediates and favors both extreme phenotypes (look at slide 123)

119
Q

Frequency-Dependent Selection

A

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
120
Q

Uta stansburiana males have 3 different strategies:

A
  • 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
121
Q

Industrial Melanism in Moths

A
  • 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
122
Q

Fitness

A

Fitness = ave. reproduction of an individual/genotype over its lifetime

Fitness reflects differences in net reproduction

Fitness = (total reproduction) x (survival probability)

123
Q

Heterozygous superiority

A

Heterozygote is better than both homozygote
I.e sickle cell

Look up!

125
Q

Sickle-Cell Anemia

A

-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

126
Q

Malaria Around the World

A

Heterozygote has an advantage over both other genotypes: malaria resistance

An example of heterozygote superiority

127
Q

Population genetics

A 
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

128
Q

Population genetics

Hardy-Weinberg equilibrium

A

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!

129
Q

Population genetics

Do allele frequencies tend to change in a population?

A

Hardy-Weinberg says no

130
Q

Hardy-Weinberg Equilibrium

Allele frequency

A

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

131
Q

Hardy-Weinberg Equilibrium

Calculating genotypes

A

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

132
Q

Population genetics

If allele frequencies deviate from Hardy-Weinberg equilibrium…..

A

…then evolutionary processes are occurring!

133
Q

Population genetics
If allele frequencies deviate from Hardy-Weinberg equilibrium, then evolutionary processes are occurring!
- This is because in nature there is…

A
  • Selection….
  • Migration (gene flow)….
  • Small populations (inbreeding)….
  • Non-random reproduction….
  • Mutation
  • Random chance events (genetic drift)
134
Q

Migration

A
  • Increases gene flow
  • Moves genes between populations
  • Prevents alleles from disappearing from population
  • Introduces mutations into larger population
135
Q

Giant Pollen Cloud

A

May, 2006

Good weather causes mass birch tree flowering in Scandinavia

Pollen deposited throughout Britain

136
Q

Non-random mating

A

Look up

137
Q

Inbreeding

A

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

138
Q

Inbreeding Depression

A

Reduction of fitness

Reduction of functional characters

139
Q

How do you measure the degree of inbreeding in a population?

A

F = inbreeding coefficient
- ~measures deviation from random mating

Ranges from 0.0 - 1.0
0 = not inbred
1 = highly inbred

140
Q

Fixation

A

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

141
Q

Inbreeding Effects Can Be Subtle

A

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)

142
Q

So what happens to the overall population if you lose these small, distinctive sub-populations?

A

Loss of genetic diversity of the species

That’s why we care about small populations

143
Q

Genetic Drift =

A

= 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

144
Q

Genetic drift

Who’s affected

A

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

145
Q

Qualitative Traits

A

Either/Or

One type or the other

  • Brown fur vs. black fur
  • Spots vs. no spots
  • Pink flower vs. blue flower
145
Q

Quantitative traits

A

Continuous; on a spectrum

  • Height
  • Weight
  • Fertility
  • Longevity
146
Q

Quantitative Traits

How do we understand the genetics of continuous traits?

A

Phenotype = Genotype + Environment

147
Q

Quantitative Traits

Variance in Phenotype =

A

Variance in Phenotype = Variance in Genotype + Variance in the Environment

VP = VG + VE
(See slide 47)

148
Q

Variance

A

Shows the amount of dispersal around a mean (the amount of variation)
(See slide 48)

149
Q

Epistasis

A

Different genes can interact with each other

How a gene is expressed (gene expression) is a result of additive and/or full dominance

150
Q

Additive Genetic Variance

A

VA = genetic variation with no dominance or gene interaction (epistasis)

151
Q

Heritability of Traits

A

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
152
Q

Founder Effect

A

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

153
Q

Founder Effect: Example

Amish

A

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
154
Q

Founder Effect: Examples

Afrikaners in South Africa

A

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
155
Q

Founder Effect: Examples

Achromotopsia on Pingelap Island, Micronesia

A

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
156
Q

Population Bottleneck Example

A

-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)

157
Q

Effective Population Size

A

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

158
Q

Factors affecting effective population size

A

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

159
Q

What is a Species?

There are several (3) definitions:

A

Biological Species Concept
Phylogenetic Species Concept
Morphospecies Species Concept

-Biologists usually use the Biological Species Concept

160
Q

What is a Species? Phylogenetic Species Concept:

A

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)

161
Q

What is a Species? Morphospecies Species Concept

A

Based on morphological differences between groups

But variation may not be indicative of different species; careful grouping necessary

Morphology may not reflect genetic diffs.

162
Q

What is a Species?

Biological Species Concept

A

There is reproductive isolation between 2 populations

Members of the 2 populations do not reproduce successfully

163
Q

Biological Species Concept

Reproductive isolation can arise from:

A

Failure to mate

Offspring are produced but are not fertile

164
Q

Biological Species Concept

Barriers to Successful Reproduction

A

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

165
Q

Biological Species Concept
Barriers to Successful Reproduction
PRE-zygotic isolating mechanisms:

A
  • Different habitats
  • Different mating seasons
  • No sexual attraction
  • Fertilization problems
  • Coital problems (organs may not match up)
166
Q

Biological Species Concept
Barriers to Successful Reproduction
POST-zygotic isolating mechanisms:

A

Successful mating occurs, but offspring is sterile

Mating occurs, but offspring does not survive

167
Q

How Do New Species Arise?

A
  • 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)
168
Q

How Do New Species Arise?

allopatric =

A

Geographically separated populations = allopatric

See slide 84

169
Q

Dispersal vs. Vicariance

A

See slide 87

170
Q

Genetic Mechanisms of Speciation

See slide 91

A

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

171
Q

Sympatric Speciation

A

Sympatric populations occur in the same geographic area

Therefore, it is hard for complete population isolation to occur

(See slides 96,97)

172
Q

How might sympatric speciation occur?

A
  • 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
173
Q

How might sympatric speciation occur?

Polyploidy

A

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)

174
Q

5 ways …How might sympatric speciation occur?

A
  1. Disruptive selection may occur
  2. Polyploidization
  3. Differences in insect/plant host associations
  4. Assortative mating
  5. Sensory drive
175
Q

Assortative mating/ sexual selection -

A

mating with someone that’s your type. There is variety but you pick the mate that most resembles you

176
Q

Sensory drive

A

integration of environmental factors along with sexual Selection , mating preferences, acting together

177
Q

Hybridization

A

When a species mates with another species and they produce offspring

178
Q

Hybridization may cause:

A
  • Alleles to spread across populations
  • New hybrids = new types
  • Inviable/infertile hybrids
179
Q

Hybrid Zone

A

Area where local conditions permit hybridization to occur

Especially if 2 allopatric populations resume contact

180
Q

Hybrids

A

Normally have reduced fitness relative to parents, but sometimes have better fitness

Plants especially have hybrids with higher fitness

(See slides 110, 112-116)

181
Q

Hybrids

allopolyploidization

A

Can have extra chromosomes: allopolyploidization

1 parent contributes an extra set of chromosomes

Offspring is triploid

182
Q

Hybrid Salamanders

See slide 120

A

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)!

183
Q

Species Radiation

A

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

184
Q

Modern Examples of Adaptive Radiations

A

Darwin’s finches

Anolis lizards

185
Q

Early Evolutionary Thought

Charles Lyell

A

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.

186
Q

Evolutionary (Phylogenetic) Trees

A

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

187
Q

Evolutionary (Phylogenetic) Trees

A

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

188
Q

Phylogeny =

A

= a diagram depicting the evolutionary history of a group of organisms descending from a common ancestor

189
Q

Phylogenetic Trees

A

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)

190
Q

See slide 13

Phylogenetic Trees

A

Three trees that all express the equivalent relationships, regardless of branch length

191
Q

See slide 14

Phylogenetic Trees

A

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.

192
Q

Creating Phylogenetic Trees

A

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)

193
Q

Homology

A

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)

194
Q

Phylogenetic Trees

Synapomorphies =

A

= 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)
195
Q

Phylogenetic Trees

Cladogram =

A

= phylogenetic tree created by clustering synapomorphies

See slide 25

196
Q

Monophyly

A

A monophyletic group includes all of the descendants of the ancestor under investigation
(See slide 27)

197
Q

Plesiomorphy

A

Ancestral character

198
Q

Apomorphy

A

Derived character

199
Q

Evolutionary Trees

A
  • More than one tree may be possible
  • How do you determine the best tree?
  1. Make a matrix of character states
  2. Draw all possible trees
  3. Mark evolutionary events on trees
  4. Count number of events needed for pattern
  5. 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
200
Q

Evolutionary Trees

Problems can arise in non-ideal situations:

A

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

201
Q

Homoplasy =

A

= similarity of characters NOT due to a shared common

202
Q

Convergent Evolution

A

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

203
Q

Convergent organisms may play similar roles in the environment, but they have:

A
  • Different evolutionary histories
  • Different ancestors
  • Different DNA
204
Q

Convergent evolution

Thorny devil and Horned toad

A 
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
205
Q

Analagous Structures

A

Perform similar functions

NOT derived from the same structure

Result of similar evolutionary pressures, not shared heritage

Shark claspers; squid hectocotylus (see slide 62)

206
Q

Monophyly vs. Paraphyly

A

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)

207
Q

Polytomy

A

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)

208
Q

Evolutionary History of the Whales

A

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)

209
Q

Maximum Likelihood

A

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

210
Q

Evaluating the best tree

A

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
211
Q

Bootstrapping

A

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

  1. Make new data set: here, randomly select 6 nucleotides from the pool for each animal.
  2. Construct a new tree based on this random selection.
  3. Rinse. Repeat. 100-1,000+ times.
  4. Majority-rule consensus model = new tree that contains all the monophyletic groups that appear in at least 50% of the bootstrap replicates
  5. What percentage of replicates have this monophyletic grouping pattern? This number = bootstrap support = confidence in your clade
212
Q

Evolutionary Trees:

How do you improve the chances of your tree being reliable?

A

Select characters carefully

Use more characters

Use more species

Use multiple techniques

213
Q

Extinction

A

A species ceases to exist anywhere in the world

Species with larger geographic ranges survive longer
See slide 99,100

214
Q

(Species) Over Time….

A
  • 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)

215
Q

Why do species go extinct?

Biotic factors:

A
  • Disease
  • Predation
  • Competition with other species
  • Pollinator loss
  • Habitat loss
  • Habitat fragmentation
216
Q

Why do species go extinct?

Abiotic factors:

A
  • Climate change
  • Excessive heat
  • Drought
  • Salinity
  • Ice Age
  • Volcanic activity
217
Q

Mass Extinction

A

When an unusually high number of extinctions occur

218
Q

There have been several mass extinctions over Earth’s history

A

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?
219
Q

Permian/Triassic Mass Extinction

A

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?
220
Q

Cretaceous/Tertiary Mass Extinction

A

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:

221
Q

The Alvarez hypothesis:

A

Asteroid impact

Tosses up giant dust cloud

Affects climate and sunlight

Plant and animal die-off

222
Q

Evidence for asteroid collision as cause of K-T (Cretaceous/Tertiary) extinction

A
  • 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)

223
Q

Physical ecology

A
  • The physical environment can affect abundance and distribution of species
  • Organisms adapt to their environment
224
Q

Physical limitations to life

A
  • Temp
    • Heat
    • Cold
  • Water
  • Gas exchange
  • Light
  • Body size
  • Metabolism
    • Energy acquisition
    • Energy use
  • Nutrient acquisition (how do they get the food)
  • Waste elimination
225
Q

Temperature

A
  • 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
226
Q

Temperature

Cold blooded/warm blooded :

A

-animals are cool/warm to touch

227
Q

Temperature

Poikilotherm :

A

-body Temp varies

228
Q

Temperature

Homeotherms :

A

-body Temp stays constant

229
Q

Temperature

Endotherms:

A

-generate heat internally via metabolism

230
Q

Temperature

Ectotherms:

A

-need external heat source

Bios 230 (2 decks)

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