BIOL4410 Environmental Genomics

Credit
6 points
Offering
(see Timetable)

If this unit does not have an online alternative, then students who are presently unable to enter Western Australia and whose studies would be delayed by an inability to complete this unit, should contact the unit coordinator (details given on this page) to ascertain, on an individual case-by-case basis, if alternate arrangements can be made to support their study in this unit.

AvailabilityLocationMode
Semester 1UWA (Perth)Face to face Predominantly face-to-face. On campus attendance required to complete this unit. May have accompanying resources online.
Details for undergraduate courses
  • Honours option in Conservation Biology; Zoology [Bachelor of Science (Honours)]
Content
This unit focuses on the ecological questions relevant to zoologists that can be addressed with DNA sequencing technologies. The unit will be divided into three components. The first part of the unit will be a block of lectures taught in one week that will describe DNA amplicon sequencing and the range of ecological and evolutionary questions that can be addressed by this group of technologies. The second part of the unit will be a short practical project also of a week, involving one day of experimental planning, one of fieldwork in groups of ~4 students for environmental DNA sampling from water, soil or other substrates on or near the UWA Crawley campus and three days of laboratory work to generate a DNA library for sequencing. The third part of the unit will take place 6-8 weeks later after DNA sequencing has been completed and will involve analysing the DNA sequence data with a standardised set of software tools, then analysis of the biological information that the environmental DNA provides. A group oral and visual presentation of the results of this work will required. An essay on an application of DNA sequencing to a different ecological question will be assigned to each student. This will be assigned at the end of the first week of lectures and will allow students to explore a specific application in depth and demonstrate the extent of their understanding of the area in detail
Outcomes
Students are able to (1) plan an effective ecological experiment that will involve DNA sequencing analysis; (2) conduct effective biological sampling leading to appropriate DNA samples for analysis; (3) generate amplicons by PCR appropriate for the ecological question; (4) process amplicons to create a DNA library for high throughput sequencing; (5) conduct bioinformatic analysis of a simple DNA library; and (6) analyse results from DNA sequencing.
Assessment
Indicative assessments in this unit are as follows: (1) essay on a specific topic; (2) online tests during the course (2); and (3) Final online exam. Further information is available in the unit outline.

Supplementary assessment is not available in this unit.
Unit Coordinator(s)
Simon Jarman
Unit rules
Prerequisites:
Second year UWA genetics or equivalent
Approved quota: 20—academic merit.
Contact hours
Block teaching of lectures and fieldwork over two weeks. Block teaching of bioinformatic analysis, biological data analysis and group presentation over 1 week, 8 weeks after initial block.
lectures x 15hrs, fieldwork x 8hrs, lab work x 24hrs, analysis x 40hrs, prep delivery & group presentation x 15hrs, essay prep x 48hrs
  • The availability of units in Semester 1, 2, etc. was correct at the time of publication but may be subject to change.
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  • Unit readings, including any essential textbooks, are listed in the unit outline for each unit, one week prior the commencement of study. The unit outline will be available via the LMS and the UWA Handbook one week prior the commencement of study. Reading lists and essential textbooks are subject to change each semester. Information on essential textbooks will also be made available on the Essential Textbooks. This website is updated regularly in the lead up to semester so content may change. It is recommended that students purchase essential textbooks for convenience due to the frequency with which they will be required during the unit. A limited number of textbooks will be made available from the Library in print and will also be made available online wherever possible. Essential textbooks can be purchased from the commercial vendors to secure the best deal. The Student Guild can provide assistance on where to purchase books if required. Books can be purchased second hand at the Guild Secondhand bookshop (second floor, Guild Village), which is located on campus.