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Unit outline_

BIOL3944: Evolution and Biodiversity (Advanced)

Semester 1, 2020 [Normal day] - Camperdown/Darlington, Sydney

The content will be based on the standard unit BIOL3044 but qualified students will participate in alternative components at a more advanced level. How did the diversity of life arise? Why are there so many species? Why do animals and plants seem so well designed for their environments? How do we explain patterns of distribution across continents? These are some of the key questions that we will examine in this Unit. The Unit begins with a survey of the history of evolutionary thought, and the so-called 'new synthesis'; the melding of Darwinian evolution, systematics and genetics. The Unit will provide training in the principles, methods, and applications of evolutionary biology including systems of classification, the genetics of speciation and hybrid zones, molecular evolution, reconstruction of phylogenies, population genetics, historical interpretation of geographic distributions, evolution of sex, adaptation, human evolution, and selfish gene theory. Examples from a broad range of organisms and data sources will be used throughout the Unit. This Unit is valuable for students who intend to seek employment in areas such as biodiversity research, bioinformatics, ecology, taxonomy, biological conservation and teaching.

Unit details and rules

Academic unit Life and Environmental Sciences Academic Operations
Credit points 6
Prerequisites
? 
An average mark of 75 or above in [12cp of BIOL2XXX] OR [6cp of BIOL2XXX and (MBLG2X72 or GEGE2X01 or GENE2002)]
Corequisites
? 
None
Prohibitions
? 
BIOL3044 or BIOL3025 or BIOL3925 or PLNT3003 or PLNT3903
Assumed knowledge
? 

None

Available to study abroad and exchange students

Yes

Teaching staff

Coordinator Benjamin Oldroyd, benjamin.oldroyd@sydney.edu.au
Type Description Weight Due Length
Final exam Theory examination
Written exam - short answer and mini essay questions
50% Formal exam period 2 hours
Outcomes assessed: LO1 LO2 LO3 LO8
Presentation Debate presentation & participation
‘Warrah’ field trip - attendance is compulsory
10% Week 04 24 hour period
Outcomes assessed: LO1 LO7 LO6 LO5 LO4 LO3 LO2
Assignment group assignment Task 1. Population genetics
Written report
2.5% Week 05
Due date: 26 Mar 2020 at 23:59
Short exercise
Outcomes assessed: LO1 LO2 LO3 LO4 LO5 LO6 LO8
Assignment Task 2. Draft Warrah introduction
Written report
10% Week 08
Due date: 20 Apr 2020 at 23:59
Short exercise
Outcomes assessed: LO1 LO2 LO3 LO4 LO5 LO6 LO8
Assignment group assignment Task 3. Using models in evolutionary biology
Written report
2.5% Week 10
Due date: 28 Feb 2020 at 10:23
Short exercise
Outcomes assessed: LO1 LO2 LO3 LO4 LO5 LO6 LO8
Assignment group assignment Task 4. Phylogenetics
Written report
5% Week 12
Due date: 21 May 2020 at 23:59
Short exercise
Outcomes assessed: LO1 LO2 LO3 LO4 LO5 LO6 LO8
Assignment Task 5. Final Warrah report
Final report
20% Week 13
Due date: 28 May 2020 at 23:59
See Canvas
Outcomes assessed: LO1 LO2 LO3 LO4 LO5 LO6 LO8
group assignment = group assignment ?

Assessment summary

  • Theory examination: The theory examination will comprise a range of short answer and mini essay questions from any area of the lecture or practical program. Options will be included so that it will not be necessary to answer all questions/parts of questions in the paper. Time allotted for each question is approximately proportional to the number of lectures presented.
  • Debate presentation & participation: There will be a field trip to the Crommelin research station (‘Warrah’) at Pearl Beach on the weekend of 22-25 March, 2019. Attendance is compulsory. You must attend one of three 24-hour periods (noon to noon) over the three days. Details will be discussed in the first practical.
  • Practical reports and assessments: Most of the assessment items will be short exercises, which are handed in or marked immediately. The population genetics project on the Warrah bees requires a complete analysis of your results written up as a scientific paper. Guidance on formatting and writing a scientific paper will be provided.

Detailed information for each assessment can be found on Canvas.

Assessment criteria

The University awards common result grades, set out in the Coursework Policy 2014 (Schedule 1).

As a general guide, a high distinction indicates work of an exceptional standard, a distinction a very high standard, a credit a good standard, and a pass an acceptable standard.

Result name

Mark range

Description

High distinction

85 - 100

 

Distinction

75 - 84

 

Credit

65 - 74

 

Pass

50 - 64

 

Fail

0 - 49

When you don’t meet the learning outcomes of the unit to a satisfactory standard.

For more information see guide to grades.

Late submission

In accordance with University policy, these penalties apply when written work is submitted after 11:59pm on the due date:

  • Deduction of 5% of the maximum mark for each calendar day after the due date.
  • After ten calendar days late, a mark of zero will be awarded.

Academic integrity

The Current Student website provides information on academic integrity and the resources available to all students. The University expects students and staff to act ethically and honestly and will treat all allegations of academic integrity breaches seriously.

We use similarity detection software to detect potential instances of plagiarism or other forms of academic integrity breach. If such matches indicate evidence of plagiarism or other forms of academic integrity breaches, your teacher is required to report your work for further investigation.

Use of generative artificial intelligence (AI) and automated writing tools

You may only use generative AI and automated writing tools in assessment tasks if you are permitted to by your unit coordinator. If you do use these tools, you must acknowledge this in your work, either in a footnote or an acknowledgement section. The assessment instructions or unit outline will give guidance of the types of tools that are permitted and how the tools should be used.

Your final submitted work must be your own, original work. You must acknowledge any use of generative AI tools that have been used in the assessment, and any material that forms part of your submission must be appropriately referenced. For guidance on how to acknowledge the use of AI, please refer to the AI in Education Canvas site.

The unapproved use of these tools or unacknowledged use will be considered a breach of the Academic Integrity Policy and penalties may apply.

Studiosity is permitted unless otherwise indicated by the unit coordinator. The use of this service must be acknowledged in your submission as detailed on the Learning Hub’s Canvas page.

Outside assessment tasks, generative AI tools may be used to support your learning. The AI in Education Canvas site contains a number of productive ways that students are using AI to improve their learning.

Simple extensions

If you encounter a problem submitting your work on time, you may be able to apply for an extension of five calendar days through a simple extension.  The application process will be different depending on the type of assessment and extensions cannot be granted for some assessment types like exams.

Special consideration

If exceptional circumstances mean you can’t complete an assessment, you need consideration for a longer period of time, or if you have essential commitments which impact your performance in an assessment, you may be eligible for special consideration or special arrangements.

Special consideration applications will not be affected by a simple extension application.

Using AI responsibly

Co-created with students, AI in Education includes lots of helpful examples of how students use generative AI tools to support their learning. It explains how generative AI works, the different tools available and how to use them responsibly and productively.

WK Topic Learning activity Learning outcomes
Week 01 1. Unit introduction and history of evolutionary theory; 2. Inbreeding, heterozygosity and population subdivision 1 Lecture (2 hr) LO1 LO2 LO4 LO6
1. Course intro; 2. Allocation of lab groups; 3. Organise Warrah excursion; 4. Population genetics simulation using Populus Practical (3 hr) LO1 LO2 LO4 LO7
Week 02 1. Inbreeding, heterozygosity and population subdivision 2; 2. Analysing population genetic data Lecture (2 hr) LO1 LO2 LO4 LO5 LO6 LO8
Tutorial on paper writing, and preparing PowerPoint presentations Practical (3 hr) LO1 LO3 LO5 LO7
Week 03 1. Conservation genetics 1; 2. Conservation genetics 2 Lecture (2 hr) LO1 LO2
1. Population genetics of mitochondrial DNA; 2. Analysis using GENALEX Practical (3 hr) LO1 LO2 LO4 LO8
Week 04 1. Conservation genetics 3; 2. Origins of life Lecture (2 hr) LO1 LO2 LO4 LO6 LO8
1. Field trip session 1; 2. Field trip session 2; 3. Field trip session 3 Practical (24 hr) LO1 LO2 LO3 LO4 LO5 LO6 LO7 LO8
1. Population Genetics of microsatellites; 2. Analysis using GENALEX Practical (3 hr) LO1 LO2 LO4 LO5 LO6 LO8
Week 05 Adaptation Lecture (1 hr) LO1 LO2
Analysis of Warrah samples day 1 – DNA isolation and PCR of mt-DNA Practical (3 hr) LO4
Week 06 1. Mechanisms of speciation; 2. What creates the variation necessary for adaptive evolution? Lecture (2 hr) LO1 LO2 LO3
Analysis of Warrah samples day 2 – Restriction digest Practical (3 hr) LO4
Week 07 1. The evolution of complex organisms; 2. Multilevel selection (genomes to ecosystems) Lecture (2 hr) LO1 LO2 LO3
Analysis of Warrah samples day 3 – Electrophoresis Practical (3 hr) LO4
Week 08 1. The evolution of sex; 2. The evolution of life histories Lecture (2 hr) LO1 LO2 LO3
Data analysis of Warrah samples using GENALEX Practical (3 hr) LO4
Week 09 1. Coevolution; 2. Evolutionary medicine Lecture (2 hr) LO1 LO2 LO5
Evolutionary origin of the two sexes: A game theoretical approach Practical (3 hr) LO1 LO2 LO4
Week 10 1. Tree thinking; 2. Phylogenetic methods Lecture (2 hr) LO1 LO2 LO4 LO5 LO8
The evolution of ratite birds: A phylogenetic investigation Practical (3 hr) LO1 LO2 LO8
Week 11 1. Bayesian phylogenetic analysis; 2. Molecular clocks Lecture (2 hr) LO1 LO2 LO5 LO8
A mysterious hominin from Siberia: Molecular-clock analysis using a Bayesian phylogenetic approach Practical (3 hr) LO1 LO2 LO8
Week 12 1. Molecular evolution; 2. Evolutionary psychology Lecture (2 hr) LO1 LO2
Week 13 1. Evolution of language; 2. Exam preparation Lecture (2 hr) LO1 LO2

Attendance and class requirements

Due to the exceptional circumstances caused by the COVID-19 pandemic, attendance requirements for this unit of study have been amended. Where online tutorials/workshops/virtual laboratories have been scheduled, students should make every effort to attend and participate at the scheduled time. Penalties will not be applied if technical issues, etc. prevent attendance at a specific online class. In that case, students should discuss the problem with the coordinator, and attend another session, if available.

Study commitment

Typically, there is a minimum expectation of 1.5-2 hours of student effort per week per credit point for units of study offered over a full semester. For a 6 credit point unit, this equates to roughly 120-150 hours of student effort in total.

Required readings

All readings for this unit can be accessed through the Library eReserve, available on Canvas.

  • Freeman, S., Herron, J.C. (2013) Evolutionary analysis (5th edition). Prentice Hall: New Jersey.

Learning outcomes are what students know, understand and are able to do on completion of a unit of study. They are aligned with the University's graduate qualities and are assessed as part of the curriculum.

At the completion of this unit, you should be able to:

  • LO1. Use biological language to discuss and explain the major themes in evolutionary biology, including population genetics, multilevel selection, the evolution of sex, mechanisms of speciation, adaptive evolution, and molecular evolution.
  • LO2. Interpret the application of evolutionary principles to real-world problems.
  • LO3. Independently source and critically interpret relevant evolutionary literature.
  • LO4. Select and use appropriate tools and concepts to analyse and critically interpret evolutionary and genetic data collected and collated in the field.
  • LO5. Describe and explain the meaning of evolutionary experimental results within the context of the current literature.
  • LO6. Generate objectives and hypotheses in experimental investigations and communicate these coherently in the form of a written scientific report.
  • LO7. Compare and debate the strengths and weaknesses of research in evolutionary biology and communicate these verbally in the form of an oral presentation.
  • LO8. Apply appropriate computational and statistical tools to analyse genetic and genomic data in order to address authentic problems in evolutionary biology.

Graduate qualities

The graduate qualities are the qualities and skills that all University of Sydney graduates must demonstrate on successful completion of an award course. As a future Sydney graduate, the set of qualities have been designed to equip you for the contemporary world.

GQ1 Depth of disciplinary expertise

Deep disciplinary expertise is the ability to integrate and rigorously apply knowledge, understanding and skills of a recognised discipline defined by scholarly activity, as well as familiarity with evolving practice of the discipline.

GQ2 Critical thinking and problem solving

Critical thinking and problem solving are the questioning of ideas, evidence and assumptions in order to propose and evaluate hypotheses or alternative arguments before formulating a conclusion or a solution to an identified problem.

GQ3 Oral and written communication

Effective communication, in both oral and written form, is the clear exchange of meaning in a manner that is appropriate to audience and context.

GQ4 Information and digital literacy

Information and digital literacy is the ability to locate, interpret, evaluate, manage, adapt, integrate, create and convey information using appropriate resources, tools and strategies.

GQ5 Inventiveness

Generating novel ideas and solutions.

GQ6 Cultural competence

Cultural Competence is the ability to actively, ethically, respectfully, and successfully engage across and between cultures. In the Australian context, this includes and celebrates Aboriginal and Torres Strait Islander cultures, knowledge systems, and a mature understanding of contemporary issues.

GQ7 Interdisciplinary effectiveness

Interdisciplinary effectiveness is the integration and synthesis of multiple viewpoints and practices, working effectively across disciplinary boundaries.

GQ8 Integrated professional, ethical, and personal identity

An integrated professional, ethical and personal identity is understanding the interaction between one’s personal and professional selves in an ethical context.

GQ9 Influence

Engaging others in a process, idea or vision.

Outcome map

Learning outcomes Graduate qualities
GQ1 GQ2 GQ3 GQ4 GQ5 GQ6 GQ7 GQ8 GQ9

This section outlines changes made to this unit following staff and student reviews.

In the last session students asked for ‘tutorials in population genetics’. In response we have replaced two lectures with tutorials.

Work, health and safety

We are governed by the Work Health and Safety Act 2011, Work Health and Safety Regulation 2011 and Codes of Practice. Penalties for non-compliance have increased. Everyone has a responsibility for health and safety at work. The University’s Work Health and Safety policy explains the responsibilities and expectations of workers and others, and the procedures for managing WHS risks associated with University activities.

General Laboratory Safety Rules

  • No eating or drinking is allowed in any laboratory under any circumstances
  • A laboratory coat and closed-toe shoes are mandatory
  • Follow safety instructions in your manual and posted in laboratories
  • In case of fire, follow instructions posted outside the laboratory door
  • First aid kits, eye wash and fire extinguishers are located in or immediately outside each laboratory
  • As a precautionary measure, it is recommended that you have a current tetanus immunisation. This can be obtained from University Health Service: unihealth.usyd.edu.au/

Disclaimer

The University reserves the right to amend units of study or no longer offer certain units, including where there are low enrolment numbers.

To help you understand common terms that we use at the University, we offer an online glossary.