Outline

Overview

Evolution is the biological process that has generated the biodiversity on this planet. It explains the common ancestry of all life on earth, why all organisms use the same genetic code, and why major life forms are constrained to a relatively small number of basic body plans such as four limbs in tetrapods. Thus, the principles of evolution and population genetics underpin all biology, including ecology, medicine and agriculture. For example, it is only because rats and humans share an evolutionary past that we can use rats as models for human medical research. In this unit, you will explore the mechanisms that generate evolutionary change at both contemporary and ancient scales. You will learn how to use DNA sequences to reconstruct the relationships among organisms and to estimate evolutionary timescales. Evolution is an ongoing process, so you will use genetic techniques to discover whether populations are divided into subpopulations. By completing this unit, you will develop skills in genomics, phylogenetic analysis, population genetics and conservation genetics. You will learn about fundamental aspects of evolution such as adaptation, sexual selection, and the origins of life. You will gain general skills in computer literacy, data management and statistical genetics.

Unit details and rules

Academic unit	Life and Environmental Sciences Academic Operations
Credit points	6
Prerequisites ?	(12cp of BIOL2XXX) or [6cp of BIOL2XXX and (MBLG2X72 or GEGE2X01 or GENE2002)]
Corequisites ?	None
Prohibitions ?	BIOL3044 or BIOL3025 or BIOL3925 or BIOL3944 or PLNT3003 or PLNT3903
Assumed knowledge ?	Students should be familiar with the structure of DNA molecules and the genetic code, understand the concept of a phylogenetic tree and have basic laboratory skills like pipetting and PCR. A knowledge of elementary statistics and algebra is assumed. Completion of intermediate units in genetics and genomics (i.e.GEGE2X01) and diversity (e.g. botany or zoology) is highly recommended.
Available to study abroad and exchange students	Yes

Teaching staff

Coordinator	Benjamin Oldroyd, benjamin.oldroyd@sydney.edu.au
Lecturer(s)	Simon Ho, simon.ho@sydney.edu.au
Lecturer(s)	Nathan Lo, nathan.lo@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:
Presentation	Debate presentation & participation ‘Warrah’ field trip - attendance is compulsory	10%	Week 04	24 hour period
Outcomes assessed:
Assignment	Task 1. Population genetics Written report	2.5%	Week 05 Due date: 26 Mar 2020 at 23:59	Short exercise
Outcomes assessed:
Assignment	Task 2. Draft Warrah introduction Written report	10%	Week 08 Due date: 20 Apr 2020 at 23:59	Short exercise
Outcomes assessed:
Assignment	Task 3. Using models in evolutionary biology Written report	2.5%	Week 10 Due date: 07 May 2020 at 23:59	Short exercise
Outcomes assessed:
Assignment	Task 4. Phylogenetics Written report	5%	Week 12 Due date: 21 May 2020 at 23:59	Short exercise
Outcomes assessed:
Assignment	Task 5. Final Warrah report Final report	20%	Week 13 Due date: 28 May 2020 at 23:59	See Canvas
Outcomes assessed:
= 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	At HD level, a student demonstrates a flair for the subject as well as a detailed and comprehensive understanding of the unit material. A ‘High Distinction’ reflects exceptional achievement and is awarded to a student who demonstrates the ability to apply their subject knowledge and understanding to produce original solutions for novel or highly complex problems and/or comprehensive critical discussions of theoretical concepts.
Distinction	75 - 84	At DI level, a student demonstrates an aptitude for the subject and a well-developed understanding of the unit material. A ‘Distinction’ reflects excellent achievement and is awarded to a student who demonstrates an ability to apply their subject knowledge and understanding of the subject to produce good solutions for challenging problems and/or a reasonably well-developed critical analysis of theoretical concepts.
Credit	65 - 74	At CR level, a student demonstrates a good command and knowledge of the unit material. A ‘Credit’ reflects solid achievement and is awarded to a student who has a broad general understanding of the unit material and can solve routine problems and/or identify and superficially discuss theoretical concepts.
Pass	50 - 64	At PS level, a student demonstrates proficiency in the unit material. A ‘Pass’ reflects satisfactory achievement and is awarded to a student who has threshold knowledge.
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.

Learning support

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.

Weekly schedule

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

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

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.

Outcomes
Graduate qualities

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
Learning outcomes

Responding to student feedback

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.

Additional information

Work, health and safety

Completion of the Canvas module “Zoonosis Awareness” is compulsory.

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.

Current students

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Weekly schedule

Weekly schedule

Attendance and class requirements

Study commitment

Required readings

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Work, health and safety

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect

Current students

BIOL3005: Evolutionary Biology

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

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Weekly schedule

Weekly schedule

Attendance and class requirements

Study commitment

Required readings

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Work, health and safety

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect