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BIO312: Evolutionary Biology

Unit 4: Speciation, Classification, and Phylogeny   At this point, you should have an understanding of how evolutionary changes and speciation occur, but how do scientists learn about the past evolutionary history of a species or another taxonomic group? In this unit, we will look at the methods that biologists use to create and reconstruct phylogenies (family trees of species). We will then look at some example phylogenies and practice creating our own. A main student activity in this unit will involve an assignment/ simulation, in which you will be required to estimate the distance between the species and create a phylogeny.

Unit 4 Time Advisory
Completing this unit should take you approximately 15 hours.

☐    Subunit 4.1: 4 hours

☐    Subunit 4.2: 2 hours

☐    Subunit 4.3: 9 hours

Unit4 Learning Outcomes
Upon successful completion of this unit, you will be able to: - construct a phylogeny using molecular data; and - define adaptive radiation and give an example of this type of phylogeny.

  • Lecture: Yale University: Professor Stephen Stearns’s Lecture “Phylogeny and Systematics” Link: Yale University: Professor Stephen Stearns’s Lecture Phylogeny and Systematics (YouTube)
     
    Also available in:
    [Flash
    Quicktime
    Transcript

    MP3](http://oyc.yale.edu/ecology-and-evolutionary-biology/eeb-122/lecture-15)
     
    Instructions: This video presentation will cover the idea of creating phylogenies along with important terminology associated with classifying organisms. Be sure to take notes and pay particular attention to all the terms the presenter introduces: also covers section 4.3.1.2.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Reading: NCBI: A Science Prime “Phylogenetics: Classifying Evolutionary Relationships” Link: NCBI: A Science Prime Phylogenetics: Classifying Evolutionary Relationships (HTML)
     
    Instructions: The reading begins at the section labeled “Phylogenetic Trees: Presenting Evolutionary Relationships.” The reading covers basic terminology, methods of phylogenetic analysis, and assumptions behind building phylogenetic trees.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

4.1 How Is a Phylogeny Created?   Note: A phylogeny is created by comparing characteristics among species and calculating the number of differences in order to determine likely evolutionary relationships. The process of creating phylogenies often relies on parsimony, or the assumption that the least number of evolutionary changes (both divergence and convergence in characters) is a most likely scenario in the history of the lineages. But among all the possible measurable characteristics of a species, which are compared? Morphological phylogenies compare the physical or developmental characteristics of species, while molecular phylogenies compare the DNA sequences such as microsatellites (known areas of repeating sections within the genome, subject to relatively rapid change due to mutations) or other molecular data. In this subunit, we will discuss and show examples of both.

4.1.1 Morphological   Note: Phylogenies based on morphological traits identify the synapomorhies, or the shared derived traits that are found in the most recent common ancestor and all of the taxons in a group.Such traits define a monophyletic group in the phylogenetic tree. This topic is covered in the reading in section 4.2.

4.1.2 Molecular   Note: Phylogenies based on molecular data (such as nucleotide sequences) compare molecular homologiesamong species.

  • Reading: Peripatus’ “Molecular Phylogeny” Link: Peripatus’ Molecular Phylogeny (HTML)
     
    Instructions: Read this page to learn about key terms used in molecular phylogeny, neutral theory, caveats to molecular phylogeny, the Universal Tree of Life, and molecular clocks.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

4.2 Phylogeny and Systematics   Note: This subunit also covers the topic in subunit 4.1.1.

  • Reading: evoled.org’s “Pathways of Evolution” Link: evoled.org’s Pathways of Evolution”  (HTML)
     
    Instructions: Click on the printable format link and read pages 1–9. The reading will give you a look at systematics and phylogeny including uses and creating phylogenetic trees.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

4.2.1 Classification of Species   - Reading: BMC Biology: Koepfli et al. “Multigene phylogeny of the Mustelidae: Resolving Relationships, Tempo and Biogeographic History of Mammalian Adaptive Radiation” Link: BMC Biology: Koepfli et al. Multigene Phylogeny of the Mustelidae: Resolving Relationships, Tempo and Biogeographic History of Mammalian Adaptive Radiation (PDF)
 
Instructions: Read this article on the phylogeny of weasels (Musteliade). This will give you a good example of how molecular data is used to create a phylogeny and to make inferences about evolutionary relationships.

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

4.2.2 The Timeline of Evolutionary History   - Reading: New Scientist: Michael Marshall’s “Timeline: The Evolution of Life” Link: New Scientist: Michael Marshall’s “Timeline: The Evolution of Life” (HTML)
 
Instructions: Read the article and take notes on the evolution of life.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

4.3 Examples   4.3.1 Comparative   - Lecture: Yale University: Professor Stephen Stearns’s “Comparative Methods: Trees, Maps, and Trait Lecture” Link: Yale University: Professor Stephen Stearns’s Comparative Methods: Trees, Maps, and Trait Lecture (YouTube)
 
Also available in:
[Flash
Quicktime
MP3

Transcript](http://oyc.yale.edu/ecology-and-evolutionary-biology/eeb-122/lecture-16)  
    
 Instructions: This lecture introduces you to the use of data
from biogeography and the fossil records, in reconstructing
phylogenies. Professor Stearns also discusses how trees are combined
with maps and traits.  
    
 Terms of Use: Please respect the copyright and terms of
use displayed on the webpage above.

4.3.1.1 Data Collection   - Activity: Indiana University’s Evolution & the Nature of Science Institutes: “Making Cladograms” Link: Indiana University’s Evolution & the Nature of Science Institutes: Making Cladograms (HTML)
 
Instructions: Follow the instructions on this lesson plan to begin constructing your own phylogeny or a cladogram, based on morphological traits. Pick a group of animals you would like to compare: you can identify a group of species to compare (using the web or an encyclopedia), and select a few traits you will focus on in your comparison. For example, you could compare species based on the skull shape, femur length, and/or number of phalanges (fingers and toes). Use the handouts provided on this page, which will walk you through creating your own cladogram based on the selected traits.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

4.3.1.2 Construction of Phylogeny   - Reading: The Science Creative Quarterly: Faride Unda’s “Introduction to Phylogenetics” Link: The Science Creative Quarterly: Faride Unda’s Introduction to Phylogenetics (HTML)
 
Instructions: The article describes many basic aspects of phylogenetics and common methods for constructing trees. This reading also covers section 4.3.2.2
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

4.3.1.3 Choosing Between Alternative Phylogenies   - Reading: International Microbiology: D Moreira & H Philippe (2000) “Molecular Phylogeny: Pitfalls and Progress” Link: International Microbiology: D Moreira & H Philippe (2000) Molecular Phylogeny: Pitfalls and Progress (PDF)
 
Instructions: Under the “Archive Online Issues,” click on March under the year 2000. Click on the PDF file to open the corresponding document under “Review Articles.” This paper emphasizes the data from a microbial phylogenetic study. The data is used as a basis for discussing complications that arise during the construction and comparison of phylogenies.

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

4.3.2 Molecular Evolution   Molecular evolution is based on using biomolecules to reconstruct evolutionary history and understand the relations between different taxa. Based on the both molecular and morphological data, evolutionary biologists can construct phylogenetic trees. Molecular traits such as DNA, RNA or protein sequences are often used in the modern taxonomy. Phylogeny is very important because many biological phenomena of interest can be modeled as bifurcating processes. Phylogenetic analysis has many other applications, beyond Biology. For instance, it could be used to solve criminal cases, such as the one described in the reading below.

  • Reading: PNAS: Metzker, M. et al’s “Molecular Evidence of HIV-1 Transmission in a Criminal Case” Link: PNAS: Metzker, M. et al’s Molecular Evidence of HIV-1 Transmission in a Criminal Case (HTML)

    Instructions: Click on link "Full Text", available as a PDF and in HTML, on the left hand side of the page. Read this article, which describes how understanding of the phylogeny of HIV viruses helped catch a doctor criminal.

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

  • Assignment: Indiana University’s Evolution & the Nature of Science Institutes: “Molecular Biology and Phylogeny” Link: Indiana University’s Evolution & the Nature of Science Institutes: Molecular Biology and Phylogeny (HTML)
     
    Instructions: Follow the instructions on this lesson plan to construct your own phylogeny or a cladogram based on amino acid (protein) sequences characteristic to a species. The amino acid sequence data is provided in a PDF that is accessible via the link under the “Materials” heading. Use the same method that you used in comparing physical traits among species, to compare the protein sequence, and estimate evolutionary relationships among the species you are comparing.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

4.3.2.1 Construction of Phylogeny   - Reading: NCBI’s “Systematics and Molecular Phylogenetics” Link: NCBI’s Systematics and Molecular Phylogenetics (HTML)
      
Instructions: Read from “Phylogenetic Trees: Presenting Evolutionary Relationships” through “The Importance of Molecular Phylogenetics” and take notes on each section. 
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

4.3.2.2 Choosing Between Alternative Phylogenies   - Assessment: The Saylor Foundation’s “Assessment 2: Phylogeny” Link: The Saylor Foundation’s “Assessment 2: Phylogeny” (PDF)

 Instructions: Here, you will work with a popular software program
for creating and interpreting phylogenies. You will work with one of
the data sets provided in the program MEGA to answer specific
questions. This should give you further insight into the actual
process of evolutionary classification in research.  

 When you are done, please check your work against the answers
provided [here](http://www.saylor.org/site/wp-content/uploads/2012/06/bio312-assessment-2-answers-final.pdf) (PDF).

Unit 4 Assessment   - Assessment: The Saylor Foundation’s “Unit 4 Assessment” Link: The Saylor Foundation’s “Unit 4 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!