Contemporary VCE BiologySection 2: Phylogenetic trees ⟩ Module 1:
What evidence can we use to show relatedness between species?
The first module within Section 2 focuses on identifying the main evidence used to determine relatedness between species, listing some of the data collected by phylogenists and describing the DNA hybridisation technique. This module is expected to take 2 hours of class time.
Summary
VCE Biology (2017-2021)
Unit 4, Area of Study 1, Outcome 1, VCE Biology Study Design
Key knowledge
Determining relatedness between species
- Molecular homology as evidence of relatedness between species including DNA and amino acid sequences, mtDNA (the molecular clock) and the DNA hybridisation technique.
Duration
2 hours
Student learning outcomes
On completion of this module, students will:
- List the main forms of evidence used to determine relatedness between species
- Identify DNA and amino acid sequences as the most reliable evidence of relatedness
- Describe key words related to phylogeny
- Acknowledge the impact of DNA technologies on the study of relatedness between species
- Describe the DNA hybridisation technique
Teacher background information
Module description
Phylogenetics is the study of the evolutionary history and the relationships between groups of organisms. It involves the collection of morphological, behavioural and molecular (DNA, RNA, amino acid) data, to then compare the number of similarities or differences between them and use this information to construct phylogenetic trees.
Because behavioural data is analysed when discerning one species from another, there are species that are morphologically alike, but are considered different species because they live in different habitats and have different behavioural patterns, such as sexual selection choices or migratory preferences. Although this concept is often hard to grasp, it fits well into our most accepted understanding of what a species is: Organisms of the same group that can procreate and generate viable, fertile offspring. It is important to note, however, that there are cases where members of different species that were close enough could produce fertile hybrids, such as in orchids, salamanders (Fapesp, 2011) and even wallabies (Close & Bell, 1997).
Before the advent of DNA technologies, biologists used mainly morphological and behavioural traits to determine relatedness between species. One of the most revolutionary use of molecular data in phylogeny happened in 1977, when Carl Woese and George Fox published an article separating living organisms in three major groups (eubacteria, eukaryotes and archaebacteria) using small subunits of rRNA. Molecular data is often considered more reliable for constructing phylogenetic trees, being less prone to convergence evolution. This has recently been reiterated by an article published by Nature in 2016, when authors Zou and Zhang compared characters used in mammal phylogeny and proposed a way to increase validity of morphological data by ignoring convergence-prone traits. Despite the apparent advantage of molecular over morphological data, the latter is not, and should not, be disregarded. As Wiens (2004) argues, morphological data is relevant for a number of reasons, including the need to include fossil record on phylogenetic trees (p. 653).
In this module, students will consider the main forms of evidence used when determining relatedness between species and they will learn the key words in phylogeny.
Additional Information
Article
Morphological and molecular convergences in mammalian phylogenetics (Zou & Zhang, 2016)
An open article showing how authors Zou and Zhang concluded that morphological data is more prone to convergence evolution, but it can be improved by the addition of a new method in data analysis.
Article
When hybrids are fertile (Fapesp, 2011)
An article from one of the most important bodies of research in Brazil, Fapesp, about fertile hybrids. Examples of hybrids are described that were naturally bred and explanations are included on the frequency of this and how it can be possible.
Article
Evolutionary and molecular taxonomy (Harley, 2009) 310KB pdf
The PDF provided offers a section of the book “Biological science fundamentals and systematics, Vol. II”, in which it explains the DNA hybridisation technique and the difficulties related to the method.
Article
The Role of Morphological Data in Phylogeny Reconstruction (Wiens, 2004) 101KB pdf
In his work, Wiens argues against the sole use of molecular data to reconstruct phylogenetic trees, offering compelling reasons as to why phylogenists still benefit from including morphological data in their analyses.
Article
Molecular versus morphological approaches to systematics (Hillis, 1987) 1.9MB pdf
A document that compares the advantages of morphological and molecular approaches, addressing the cases of conflict between them.
Video
Comparing DNA Sequences (9:59)
A simple explanation of how morphological traits and DNA sequences are used to inform relatedness between organisms, and how these can be used to construct a phylogenetic tree. Watch until 4:14 min.
Video
Classification using DNA - AS Biology (2:05)
A brief description of the main methods to analyse molecular data for the classification of organisms, including DNA hybridisation and sequencing.
Website
Phylogenetic Data Types (The Conversation, 2012)
This website provides information on phylogeny, including the justification and importance of the topic and main data types used to construct phylogenetic trees. It also offers examples of applicability of phylogeny to address modern problems in conservation biology, epidemiology, pharmaceutical research, and others.
Website
DNA-DNA Hybridisation
A description of how DNA hybridisation can be used to determine relatedness between species.
Website
Reconstructing trees: Parsimony
A simple explanation of the law of parsimony and how it is applied in constructing phylogenetic trees.
Interactive
Biology | Molecular Homology as Evidence of Relatedness
Flashcards with key questions and answers about the use of molecular data in phylogeny.
Book chapter
Genomes, 2nd edition, chapter 16: Molecular Phylogenetics
This chapter is very useful to approach the topic of molecular phylogenetics, giving good perspectives on the origins and uses of molecular data in phylogeny.
Teaching sequence
Lesson 1 Identifying the main forms of evidence used in determining relatedness
1 hour
Student knowledge/ skills outcome
Students will be able to:
- list main forms of evidence used to determine relatedness between species
- describe key words related to phylogeny
- identify DNA and amino acid sequences as the most reliable evidence of relatedness
Prior Knowledge
- Understanding of the basic structure of DNA as well as the process of transcription is required.
Activities
Activity 1
Which information would you use to group organisms? (10-15 min)
In an attempt to assess student prior knowledge, choose five organisms and promote a whole-class discussion on which sources of data could be valuable when determining relatedness between species. For example, when comparing mammals, would the coat-colour be a relevant trait? Or perhaps the eating habits (herbivore, carnivore)? Which characteristics matter more when grouping organisms and why? How would you know if a black panther is more closely related to a black bear than to a tiger? Extending on this discussion, challenge students to represent the relatedness between the chosen organisms, with an explanation of their diagram. Alternatively to the whole-class discussion, separate students into small groups to develop their ideas and make sure everyone will participate. Students may also write an anonymous contribution to the topic in case they have difficulties sharing their opinions.
Video (10:25)
Matthew Symonds and Uday Sundara (Deakin University)
This interview serves as an introduction to phylogeny, describing the types of data used for reconstructing phylogenetic trees, how accurate these representations can be and some of the complexities involved in the process of reconstructing evolutionary history. The two researchers go on to give examples of phylogenetic trees they generated in their lab, and comment on the differences between morphological and molecular data as evidence of relatedness between species.
Activity 2
Phylogenetic trees (20 min)
https://www.nature.com/scitable/topicpage/reading-a-phylogenetic-tree-the-meaning-of-41956
Students read the text “Reading a Phylogenetic Tree: The Meaning of Monophyletic Groups” from Nature Education (Baum, 2008) to learn how phylogenetic trees are constructed and the key terms in phylogeny. They should then compare the trees with the diagram they had previously proposed for showing relatedness between organisms, pointing out the main advantages and disadvantages of each representation. This may be done individually or in small groups, with student analysis being guided by the teacher.
Activity 3
Key Terms – Whole Class Mind Map (10 min)
Along with the students, teacher compiles all key terms noted by students on the whiteboard. Student understanding of the terms can be assessed and further elucidated by the teacher.
Activity 4
Key Terms – Student Handout (10 min)
- Student handout: section2-module1-student-copy.pdf (35KB pdf)
- Teacher copy: section2-module1-teacher-copy.pdf (179KB pdf)
Upon distribution of the student handout, students are asked to link key terms to their definitions. The teacher copy provides corresponding answers.
Lesson 2 How DNA technologies revolutionised phylogenetic studies
1 hour
Student knowledge/ skills outcome
Students will be able to:
- acknowledge the impact of DNA technologies on the study of relatedness between species
- describe the DNA hybridisation technique
Activities
Background and resources
Book chapter
Molecular Phylogenetics : Sections 16.1 and 16.3
Genomes, 2nd edition, chapter 16: Molecular Phylogenetics
An outline of the origins and main advantages of molecular over morphological data, with examples of phylogenetic trees developed from the former that were used to solve important phylogenetic questions.
Activity 1
Debate: Morphological or Molecular traits? (20-30 min)
Students are given resources to study the contribution of molecular data to phylogenetic studies, which they can independently research on their computers or use handouts provided by teachers with main information to support the debate. The class is divided in two and students should know which side they are going to defend prior to their research. One side should support the sole use of molecular data to reconstruct trees, while the other side argues for the inclusion of morphological traits. Each member of both groups should be encouraged to participate, having 2-3 min to make their point and respond to their opponent’s arguments. The length of this activity will depend on how many students there are, and on how much time will be given to the study of supporting arguments for the debate.
Activity 2
Representational challenge: Create a resource explaining DNA hybridisation (20-30 min)
In this activity, students are challenged to create their own representation of the DNA hybridisation process. It is suggested that teachers attempt to create the representation prior to the class to both become familiar with the process and to offer their creation as an example of what can be done by students. Ideally the representational challenge would involve the use of ICT (Information and Communication Technologies).
Possible forms of representation include:
- Animation
- Slowmation (as specified in Section 1, Module 1, Activity 5)
- Use of materials such as sticks, paper and play dough
- Drawings
More information on how to scaffold students on representational challenges can be found at: http://dro.deakin.edu.au/eserv/DU:30069215/hubber-representation-post-2014.pdf (Hubber, 2014)
Note: Students can be offered the resources available in the teacher’s additional information section to inspire their debate.
Supporting resources
Video
DNA Probe DNA hybridization HD Animation (1:17 min)
This video may be used to inspire students to develop a resource that explains what DNA hybridisation is, giving one example of a possible – but not complete – explanation
Next module: How to represent relatedness between species?
