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BIO312: Evolutionary Biology

Unit 1: Review of Concepts   In this unit, we will review the important conceptual underpinnings of evolutionary biology. We will learn definitions of important terms such as evolution, selection, and species. We will also learn the mechanisms of evolutionary change and speciation. You learned the majority of this material in the introductory course BIO102: Evolutionary and Ecological Biology, so much of this unit will serve as a review. Upon completion of this unit, you should have a solid understanding of evolutionary theory.

Unit 1 Time Advisory
Completing this unit should take you approximately 12 hours.

☐    Subunit 1.1: 3 hours

☐    Subunit 1.2: 4 hours

☐    Subunit 1.3: 2 hours

☐    Subunit 1.4: 3 hours 

Unit1 Learning Outcomes
Upon successful completion of this unit, you will be able to: - define natural selection and provide specific examples; - compare and contrast natural selection and artificial selection; - define sexual selection as a special category of the natural selection; - define microevolution and list the five major factors that can lead to changes in genetic makeup of a population; - describe and compare microevolution and macroevolution; - compare and contrast allopatric and sympatric speciation; and - list the isolating mechanisms that can lead to speciation.

  • Lecture: Yale University: Professor Stephen Stearns’s “Adaptive Evolution: Natural Selection” Link: Yale University: Professor Stephen Stearns’s Adaptive Evolution: Natural Selection (YouTube)
     
    Also available in:

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    MP3

    Transcript
     
    Instructions: This video presentation will provide you with a basic understanding of the types of natural selection and the rates at which natural selection occurs.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

1.1 What is Evolution?   - Reading: Wikibooks: General Biology “Introduction to Evolution” Link: Wikibooks: General Biology Introduction to Evolution (HTML)
 
Instructions: In this article you will find a definition of evolution, evidence of evolution, and a discussion of the rates of speciation.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

1.1.1 Artificial Selection   - Reading: University of California Museum of Paleontology: Evolution 101’s “Artificial Selection” Link: University of California Museum of Paleontology: Evolution 101’s “Artificial Selection” (HTML)

 Instructions: The webpage defines artificial selection and presents
a brief historical perspective on the subject.  
    
 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

1.1.2 Natural Selection   - Reading: Estrella Mountain Community College: Michael Farabee’s Online Biology Text: “Natural Selection” Link: Estrella Mountain Community College: Michael Farabee’s Online Biology Text: Natural Selection (HTML)
 
Instructions: Read the section on natural selection up to the section on speciation.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

1.1.3 Sexual Selection   - Web Media: YouTube: Cambridge University’s “Flaunting It - Sexual Selection and the Art of Courtship” Link: YouTube: Cambridge University’s “Flaunting It - Sexual Selection and the Art of Courtship” (YouTube)

 Instructions: Watch this 15-minute video on courtship and sexual
selection.  

 Terms of Use: Please respect the copyright and terms of
use displayed on the webpage above. 
  • Web Media: iTunes: Illinois Springfield: Dr. James Bonacum’s “Week 12 Part 1: Sexual Selection or the Answer to Freud’s Eternal Question” Link: iTunes: Illinois Springfield: Dr. James Bonacum’s “Week 12 Part 1: Sexual Selection or the Answer to Freud’s Eternal Question” (iTunes)  

    Instructions: If you do not already have iTunes on your computer, you can go to Apple iTunes download. Click on “Download Now.”  Click on “View in iTunes” next to the name “Week 12 Part 1: Sexual Selection or the Answer to Freud’s Eternal Question.” Once in iTunes, click on the price column that says “Free” next to the name “Week 12 Part 1: Sexual Selection or the Answer to Freud’s Eternal Question.” 
     
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  • Web Media: iTunes: Illinois Springfield: Dr. James Bonacum’s “Week 3 Part 3: Advantages of Sex” Link: iTunes: Illinois Springfield: Dr. James Bonacum’s “Week 3 Part 3: Advantages of Sex” (iTunes)
     
    Instructions: If you do not already have iTunes on your computer, you can go to Apple iTunes download. Click on “Download Now.” Click on “View in iTunes” next to the name “Week 3 Part 3: Advantages of Sex.” Once in iTunes, click on the price column that says “Free” next to the name “Week 3 Part 3: Advantages of Sex.” 
     
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1.1.4 Maintenance of Sex by Sexual Selection   - Reading: Smithsonian Tropical Research Institute: West-Eberhard’s “The Maintenance of Sex as a Developmental Trap Due to Sexual Selection” Link: Smithsonian Tropical Research Institute: West-Eberhard’s The Maintenance of Sex as a Developmental Trap Due to Sexual Selection (PDF)

 Instructions: Download the PDF titled “Mary Jane
West-Eberhard. 2005. The maintenance of sex as a developmental trap
due to sexual selection. Quarterly Review of Biology
80(1):47–53.” Read the article and take notes.  
    
 Terms of Use: Please respect the copyright and terms of
use displayed on the webpage above.

1.1.5 Gradualism vs. Saltation   - Reading: Howard Hughes Medical Institute: Steve Mirsky’s “How Did We Get Here?” Link: Howard Hughes Medical Institute: Steve Mirsky’s How Did We Get Here?” (HTML)

 Instructions: Read this text.  

 Terms of Use: Please respect the copyright and terms of
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  • Interactive Lab: Howard Hughes Medical Institute: “The Virtual Stickelback Evolution Lab” Link: Howard Hughes Medical Institute: The Virtual Stickelback Evolution Lab (HTML)

    Instructions: At the end of this chapter on natural selection, you can learn more about the research in this field of science, by visiting the site below.

    This virtual laboratory teaches skills of data collection and analysis to study evolutionary processes. The lab includes a number of short videos explaining aspects of research methods or relating the evolutionary history of stickleback fish. We recommend that you view these videos, especially when going through the lab for the first time. Throughout the lab, bolded words in the text are defined in the glossary under the "Reference" tab.

    Click the Player Help link in the Flash video player for more information.

    The three-spine stickleback is a model organism for studying evolution, combining data from molecular genetics, field biology, and natural history, including fossils. The ancestral forms of stickleback fish are small ocean   dwellers that sport heavy armor in the form of bony plates and spines projecting from the back and pelvis. This armor protects ocean sticklebacks from predatory attacks. Some species of sticklebacks are anadromous and, like salmon, travel from the ocean via rivers to spawn in freshwater lakes. At the end of the last ice age, some stickleback populations became trapped in lakes that were cut off from the ocean in the wake of retreating ice fields. In the past 20,000 to 10,000 years, these stranded populations evolved dramatically over generations, as they adapted to living permanently in a freshwater environment.

    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

1.2 Evolution of Populations   - Reading: Oracle Education Foundation’s “Microevolution Introduction” Link: Oracle Education Foundation’s Microevolution Introduction (HTML)
 
Instructions: This material is an introduction to the different microevolutionary forces that influence a population.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

1.2.1 Mutations   - Reading: Massachusetts Institute of Techology’s Open CourseWare: “ Population Genetics: Mutation and Selection” Link: Massachusetts Institute of Technology’s OpenCourseWare: “Population Genetics: Mutation and Selection” (PDF)

 Instructions: In Lecture 26, you will learn more about the
mathematical modeling of mutations, as a factor of evolution.
Mutations are the source of variation in natural populations, yet
they would be a weak factor of evolution in the absence of selection
and genetic drift.  

 Terms of Use: This resource is licensed under a [Creative Commons
Attribution-NonCommercial-ShareAlike 3.0 United
States](http://creativecommons.org/licenses/by-nc-sa/3.0/us/). It is
attributed to Massachusetts Institute of Technology’s
OpenCourseWare.
  • Reading: Kimball’s Biology Pages’ “Mutation and Evolution” Link: Kimball’s Biology Pages’ “Mutation and Evolution” (HTML)
     
    Instructions: Read the material on the webpage for a good introduction to mutations.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

1.2.1.1 Genetic Mutations   - Reading: Biology Online’s “Types of Mutations” Link: Biology Online’s Types of Mutations (HTML)
      
Instructions: Read pages 7-8 about the different types of chromosomal and genetic mutations.

 Terms of Use: Please respect the copyright and terms of
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1.2.1.2 Epigenetic Influences   - Web Media: University of Utah: Learn Genetics: “Epigenetics” Link: University of Utah: Learn Genetics: Epigenetics (HTML and Flash)
 
Instructions: This website has several small articles, videos, and interactive tutorials that can further your understanding of the subject of epigenetics.

 Terms of Use: Please respect the copyright and terms of
use displayed on the webpage above.
  • Web Media: Nova’s “Epigenetics” Link: Nova’s Epigenetics (Flash)
     
    Instructions: This 13-minute video introduces you to what epigenetics is and how it influences genomic changes across generations.
     
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1.2.2 Migration   - Reading: Massachusetts Institute of Technology’s OpenCourseWare: “Lecture 25: Migration of individuals between different populations” Link: Massachusetts Institute of Technology’s OpenCourseWare: “Lecture 25: Migration of individuals between different populations” (PDF)
 
Instructions: Read this article.

 Notice that when individuals from populations with different
allele frequencies mix, the combined population will be
in **H-W **equilibrium after one generation of random mating. The
combined population will be out of equilibrium to the extent that
mating is assortatative.  
    
 If we are considering rare alleles we can make the
following approximations allowing us to avoid a lot of messy algebra
in our calculations.  
              
 For f(**a**) = **q**, and f(**A**) = **p**,  if  p+q=1
then **p**=1-q  
 From **H-W**: f(**A/A**) = **p**<sup>2 </sup>, f(**a/A**) = 2**pq
and**  f(**a/a**) = **q**<sup>2 </sup>  

 Terms of Use: This resource is licensed under a [Creative Commons
Attribution-NonCommercial-ShareAlike 3.0 United
States](http://creativecommons.org/licenses/by-nc-sa/3.0/us/). It is
attributed to Massachusetts Institute of Technology’s
OpenCourseWare.
  • Reading: Buffalo State University: Mendelian Genetics and Populations II “Migration” Link: Buffalo State University: Mendelian Genetics and Populations II Migration (HTML)
     
    Instructions: Read and study the section on migrations and how they influence allele frequencies in a population.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

1.2.3 Assortative Mating   - Reading: Mark Ridley’s Evolution: “Assortative Mating” Link: Mark Ridley’s Evolution: Assortative Mating (HTML)

 Instructions: This webpage provides a brief definition of both
positive and negative assortative mating and their influence on
genotypic frequencies.  
    
 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.
  • Reading: Massachusetts Institute of Technology’s OpenCourseWare: “Lecture 27: Effects of Inbreeding” Link: Massachusetts Institute of Technology’s OpenCourseWare: “Lecture 27: Effects of Inbreeding (PDF)

    Instructions: In this lecture (27) you will examine how inbreeding between close relatives (also known as consanguineous matings) influences the appearance of autosomal recessive traits. Note that inbreeding will not make a difference for dominant traits because they need only be inherited from one parent or for X-linked traits since they are inherited from the mother. In population genetics, inbreeding will lead to the decrease of the requency of heterozygotes and increase of the frequency of homozygotes.

    Terms of Use: This resource is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 United States. It is attributed to Massachusetts Institute of Technology’s OpenCourseWare.

  • Reading: University of California Museum of Paleontology: Evolution 101’s “Inbreeding Depression”and “Low Genetic Variation” Link: University of California Museum of Paleontology: Evolution 101’s “Inbreeding Depression” and “Low Genetic Variation” (HTML)

    Instructions: These readings illustrate the evolutionary consequences of assortative mating, focusing on inbreeding. Read the articles and compare possible evolutionary consequences of inbreeding with other factors of evolution.

    Terms of Use: Please respect the copyright and terms of use displayed on the webpages above.

1.2.4 Genetic Drift   Genetic drift is one of the common mechanisms of evolution, since the violation of the Hardy-Weinberg rule on the large population size is often found in nature. When population size decreases, the rate of evolution by the genetic drift is expected to be higher. Drift can lead to the loss or a fixation of an allele, regardless of the other factors of evolution. In nature, drift often happens if a population suffers a great loss of individuals (bottleneck effect) or when a new population is founded by a random small sample of individuals (founder effect). In the reading below we will examine both of these cases.

  • Reading: University of Arizona: The Biology Project’s “Genetic Drift” Link: University of Arizona: The Biology Project’s “Genetic Drift” (HTML)

    Instructions: Read this page on the role of genetic drift in populations. If you are really ambitious, go on to try the genetic drift simulator that follows!

    Terms of Use: The linked material above is from The Biology Project, developed at The University of Arizona. Please respect the copyright and terms of use displayed on their site.

1.2.5 Bottleneck Effect   - Reading: Wikipedia: “Population Bottleneck” Link: Wikipedia: “Population Bottleneck” (HTML)

 Instructions: Read the article on population bottleneck and its
<span class="Apple-tab-span" style="white-space:pre"> </span>effects
on the genetics of a population.  

 Terms of Use: This resource is licensed under a [Creative Commons
Attribution-ShareAlike
License](http://en.wikipedia.org/wiki/Wikipedia:Text_of_Creative_Commons_Attribution-ShareAlike_3.0_Unported_License).
  • Reading: University of California Museum of Paleontology: Evolution 101’s “Bottlenecks and Founder Effects” Link: University of California Museum of Paleontology: Evolution 101’s “Bottlenecks and Founder Effects” (HTML)

    Instructions: Read this page to learn about population bottlenecks and founder effects.

    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

1.2.6 Founder Effect   - Reading: Wikipedia: “Founder Effect” Link: Wikipedia: “Founder Effect” (HTML)

 Instructions: This short article introduces the founder effect
along with a couple of examples.  

 Terms of Use: This resource is licensed under a [Creative Commons
Attribution-ShareAlike
License](http://creativecommons.org/licenses/by-sa/3.0/).

1.3 Speciation   - Reading: University of California Museum of Paleontology: Evolution101’s “Evolution at Different Scales: Micro to Macro” Link: University of California Museum of Paleontology: Evolution101’s “Evolution at Different Scales: Micro to Macro” (HTML)

 Instructions: Read from “Evolution at Different Scales: Micro to
Macro” through “Patterns in Macroevolution,” using the “next” button
at the bottom right of the page, and take notes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.
  • Lecture: Yale University: Professor Stephen Stearns’s “Species and Speciation” Link: Yale University: Professor Stephen Stearns’s “Species and Speciation” (YouTube)

    Also available in:
    [Flash
    Quicktime
    MP3

    Transcript](http://oyc.yale.edu/ecology-and-evolutionary-biology/eeb-122/lecture-14)

    Instructions: This video presentation will provide a basic understanding of the species concepts and of the mechanisms of speciation. Be sure to take notes and pay particular attention to all the terms the presenter introduces.

    Terms of Use: This resource is licensed under a Creative Commons Attirbution-NonCommercial-ShareAlike 3.0 United States. It is attributed to Professor Stephen Stearns’s and the original version can be found here.

  • Interactive Lab: University of Wisconsin: Connecting Concepts: Interactive Lessons in Biology “Species and Speciation in Frogs” Link: University of Wisconsin: Connecting Concepts: Interactive Lessons in Biology “Species and Speciation in Frogs” (Flash)

    Instructions: This activity/tutorial demonstrates how speciation can occur in a species of frog over time. This will also test your understanding of three different species concepts.

    Note: The divergence of one species into two or more species will typically begin with some type of population isolation. Perhaps, a geographical barrier arises, cutting a portion of the population off from the rest. Or spatial differences in the availability of resources cause radical changes in foraging habits for a portion of the population, which in turn affects timing and availability for mating. Here, we will discuss population-isolating mechanisms, as well as how events of population isolation and reunification might affect the process of speciation.

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1.3.1 Isolating Mechanisms   *The isolating mechanisms are essential in speciation. To understand this we must start with the biological definition of species by E. Mayr (1942):

"Species are groups of actually or potentially interbreeding populations, which are reproductively isolated from other such groups."

Ernst Mayr's formulation of the biological species concept is one of the widely accepted concepts of species, yet it cannot be applied to all living organisms (e.g. asexual species). There are several types of isolating mechanisms and they are usually classified in two large categories: the prezygotic isolating mechanisms that prevent actual fertilization or the formation of a zygote, and the postzygotic isolating mechanisms (those that prevent prolonged existence of the hybrid zygotes, juveniles or adults).*

A) *Pre-zygotic isolating mechanisms*- prevent union of gametes -> zygote

*1. Mates do not meet (seasonal, temporal or habitat isolation)

  1. Mates meet but do not mate (ethological or behavioral isolation)

  2. Mates meet but no sperm transfer (mechanical isolation)

  3. Sperm dies before fertilization (chemical isolation) etc.*

B) Post-zygotic isolating mechanisms- varying degrees of hybrid mortality and/or sterility

*1. Zygote dies

  1. Zygote produces an F1 adult that has reduced viability (survival)

  2. Hybrid is viable, but partially or completely sterile (fecundity) or the F2 is deficient.

Species might simultaneously possess both types of isolating mechanisms.

As we will see below, the biological species concept begins to break down in some cases. For example at hybrid zones, the somewhat differentiated populations are in the process of speciation. An organism that mates with a different semi-species might produce low viability offspring (in any of the degrees listed above). This phenomenon is often called the hybrid breakdown and it occurs when F1 generation mating produces too many incompatible gene combinations.

Genetic similarity drops as we change from the different levels of differentiation, going up the hierarchy: Populations - Subspecies - Semispecies - Sibling species - non-sibling species - species.

As genetic similarity drops, the differences increase and the possibility of hybrid breakdown increases. A species is thought to have a coadapted genome in which many genes are finely tuned by the proper interactions with other genes. Genetic differentiation occurs during speciation but it is not always sufficient to define a new species.*

  • Reading: Estrella Mountain Community College: Michael Farabee’s Online Biology Text: “Speciation and Reproductive Isolating Mechanisms” Link: Estrella Mountain Community College: Michael Farabee’s Online Biology Text: Speciation and Reproductive Isolating Mechanisms (HTML)
     
    Instructions: Read the sections titled Speciation through the section labeled Punctuated Equilibrium.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Reading: University of California Museum of Paleontology: Understanding Evolution “Reproductive Isolation” Link: University of California Museum of Paleontology: Understanding Evolution Reproductive Isolation (HTML)
     
    Instructions: This website provides some ways that reproductive isolation can lead to speciation.
     
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1.3.2 Speciation Caused by the Changes in Chromosome Number   - Reading: Harvard University: Professor John Kimball’s Biology page “Polyploidy” Link: Harvard University: Professor John Kimball’s Biology page Polyploidy (HTML)
 
Instructions: This webpage defines polyploidy and how it can occur with an emphasis on plants.
 
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  • Reading: Douglas and Pamela Soltis’s “Polyploidy: Recurrent formation and genome evolution” Link: Douglas and Pamela Soltis’s Polyploidy: Recurrent Formation and Genome Evolution (PDF)
     
    Instructions: This article on polyploidy explains that the changes in chromosome numbers played a major role in the evolution of many eukaryotes. Although it is well known that polyploidy is very important in the plant evolution, some recent studies have demonstrated that there are many polyploid animal species, as well as other organisms.
               
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1.3.3 Hybridization   - Reading: Stanford University: Stanford Bird Group’s “Hybridization” Link: Stanford University: Stanford Bird Group’s Hybridization (HTML)
 
Instructions: The reading is a discussion of hybridization as it applies to several species of birds.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

1.3.4 Divergence and Convergence   - Reading: CK-12: “History of Life”

Link: CK-12:
[“](http://archive.ck12.org/flexbook/chapter/print/8550)[History of
Life](http://archive.ck12.org/flexbook/chapter/print/8550)[”](http://archive.ck12.org/flexbook/chapter/print/8550)
(HTML)


 Instructions: This is a reading on convergent and
divergent evolution along with coevolution.  
    
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use displayed on the webpage above.

1.4 Coevolution   - Lecture: Yale University: Professor Stephen Stearns’s “Coevolution” Link: Yale University: Professor Stephen Stearns’s Coevolution (YouTube)
 
Also available in:
[Flash
Quicktime
MP3

Transcript](http://oyc.yale.edu/ecology-and-evolutionary-biology/eeb-122/lecture-20)  
    
 Instructions: This video presentation will provide a basic
understanding of the coevolution including examples and terminology.
Be sure to take notes and pay particular attention to all the terms
the presenter introduces.  
    
 Note: Coevolution is concurrent change in two (or more) species, in
response to pressures exerted by the other species. It can occur
within the context of any close relationship between species. For
example, a prey species may evolve physically and behaviorally to
better blend in with the environment in order to avoid predation.
The predator species might then coevolve better eyesight, stalking
behavior, or methods of flushing the prey, in order to continue to
eat. Species that compete for the same resources also coevolve,
either through niche partitioning (where each species becomes more
specialized in resource use, so that the resources are basically
divided) or in other ways where one species takes better advantage
of the available resources than its competitor. Here, we will
discuss a few theories regarding how and why coevolution occurs.  

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1.4.1 Competition   - Reading: Brown University: “Coevolution” Link: Brown University: Coevolution (HTML)
 
Instructions: This is a general webpage about coevolution but includes an example of how competition relates to coevolution.
 
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1.4.2 Tangled Bank Theory   - Reading: Harvey Mudd College: Richard McKnight’s “The Tangled Bank” Link: Harvey Mudd College: Richard McKnight’s “The Tangled Bank” (HTML)
 
Instructions: Click on “The Tangled Bank” link on the left of the webpage. This reading is a description of the Tangled Bank Hypothesis.
 
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  • Web Media: YouTube: Talk Origins Archive’s “Charles Darwin’s ‘The Origin of Species’” Link: YouTube: Talk Origins Archive’s “Charles Darwin’s ‘The Origin of Species’” (YouTube)

    Instructions: Watch this video, a slideshow accompanying Darwin’s original “The Origin of Species,” and learn more about Darwin’s comparison of a “tangled bank” and his observations about the speciation. 

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1.4.3 Red Queen Hypothesis   - Reading: Indiana University, Department of Biology: C.M. Wiley “Red Queen” Link: Indiana University, Department of Biology: C.M. Wiley Red Queen (HTML)
 
Instructions: This reading presents the origin of the Red Queen hypothesis and a description of the theory.
 
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1.4.4 Evolutionary Game Theory   - Reading: National Academy of Sciences of the United States: C Bergstrom & M Lachmann (2003) “The Red King: When the Slowest Wins the Coevolutionary Arms Race” Link: National Academy of Sciences of the United States: C Bergstrom & M Lachmann (2003) The Red King: When the Slowest Wins the Coevolutionary Arms Race (HTML)
 
Also available in:
PDF

 Instructions: Read this paper as an example of how evolutionary
game theory can be applied to study coevolution.  
    
 Terms of Use: Please respect the copyright and terms of
use displayed on the webpage above.

Unit 1 Assessment   - Assessment: The Saylor Foundation’s “Unit 1 Assessment” Link: The Saylor Foundation’s “Unit 1 Assessment” (HTML)

 Instructions: Complete this assessment. The correct answers will be
displayed when you click Submit. You must be logged into your Saylor
account in order to access this exam. If you do not yet have an
account, you will be able to create one, free of charge, after
clicking the link.  
    
 You may retake the quiz as many times as you like to prepare for
the final exam. Good luck!