Outline

Overview

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

Unit code	BIOL3944
Academic unit	Life and Environmental Sciences Academic Operations
Credit points	6
Prohibitions ?	BIOL3044 or BIOL3025 or BIOL3925 or PLNT3003 or PLNT3903
Prerequisites ?	An average mark of 75 or above in [12cp of BIOL2XXX] OR [6cp of BIOL2XXX and (MBLG2X72 or GEGE2X01 or GENE2002)]
Corequisites ?	None
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:
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: 28 Feb 2020 at 10:23	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
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 sydney.edu.au/students/guide-to-grades.

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.

You may only use artificial intelligence and writing assistance tools in assessment tasks if you are permitted to by your unit coordinator, and if you do use them, you must also acknowledge this in your work, either in a footnote or an acknowledgement section.

Studiosity is permitted for postgraduate units unless otherwise indicated by the unit coordinator. The use of this service must be acknowledged in your submission.

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	Practical (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

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

BIOL3944: Evolution and Biodiversity (Advanced)

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