This document outlines the schedule and content for an ecology and evolutionary genomics course. The course will introduce students to genomics methods and applications in these fields through lectures, student presentations, and workshops. It will cover major themes like social evolution, conservation, and speciation using a science-driven and interactive approach to help students improve their skills in critically analyzing literature, communicating science, and understanding the peer review process.

1. SBC322 Ecological and
Evolutionary Genomics
y.wurm@qmul.ac.uk

3. This changes
454
everything.
Illumina
Solid...
Any lab can
sequence
anything!

4. How does this change affect us
regarding ecology & evolution
research?

5. Novel approaches for
• relationships between species
• relationships within species
• species distributions
• life histories
• biodiversity assessments
• evolutionary histories
• identifying genes & mechanisms underlying
• phenotypes (behaviors, morphologies, physiologies…)
• constraints
• responses to changing environments
•…

6. Very exciting.

7. Aims (1/2)
To understand and critically evaluate:
• research questions
• methods
• experimental designs
• applications
in ecological and evolutionary genomics.

8. Aims (2/2)
Improving skills:
•critically reading scientific literature
•understanding interdisciplinary science
•oral scientific communication (formal & informal)
•written scientific communication (blog & exam)
Understanding:
•the peer review process for scientific publication

9. Science-driven.

10. Interactive
• Small groups - informal presentations
• Formal presentations in pairs
• Blog posts
• Peer review

11. ok?

12. Yannick Wurm
YW
Christophe Eizaguirre
CE

13. Main themes
1. Methods
2. Social evolution
3. Conservation
4. Genome dynamics
5. Speciation

15. SBC322 Ecological and Evolutionary Genomics Schedule 23/09/Date Time Room Teaching Title
1 2014-9-23 Tuesday 9:00 Eng. 3.24 YW Course overview + How to read a paper
13:00 Eng. 3.25 YW Genomics Methods in Ecology & Evolution
2 2014-9-30 Tuesday 9:00 Eng. 3.24 YW Genomics Methods explained (by you!)
13:00 Eng. 3.25 YW Research papers: Theme 1 introduction
3 2014-10-7 Tuesday 9:00 Eng. 3.24 YW Research papers Theme 1 explained (by you!)
13:00 Eng. 3.25 CE Research Talk: Conservation Genomics in Turtles + Theme 2 introduction
2014-10-9 Thursday 15:00 Scape 1.02 YW Methods recap (informal) & Organising blogging
16:00 Scape 1.02 YW (continued)
4 2014-10-14 Tuesday 9:00 Eng. 3.24 CE Informal Q&A session about the Theme 2 papers & presentations (only obligatory for presenters)
13:00 Fogg 3.15 Labjolly 3.15 Research Talk: Invited Seminar - Andre Moura – University of Lincoln
5 2014-10-21 Tuesday 9:00 Eng. 3.24 CE Research Papers Theme 2 - two student paper presentations (2 students per group)
13:00 Eng. 3.25 YW Research Talk: Genome dynamics underlying social evolution + Theme 3 introduction
6 2014-10-28 Tuesday 9:00 Eng. 3.24 YW Informal Q&A session about the Theme 2 papers & presentations (only obligatory for presenters)
13:00 Eng. 3.25 CE Theme 2 - student paper presentations
7 Reading week
8 2014-11-11 Tuesday 9:00 Eng. 3.24 YW Research Papers Theme 2 - four student paper presentations (2 students per group)
13:00 Eng. 3.25 YW (continued)
2014-11-13 Thursday 15:00 Scape 1.02 CE Workshop: R class MHC and parasites for instance
16:00 Scape 1.02 CE (continued)
17:00 Scape 1.02 CE (continued)
Week

17. Reading a paper
Sequence of events:
• Title
• Abstract
• Figures
• Main text
• (iterate)

18. Additional Guidelines
• Read critically
• authors aren’t always correct.
• Instead, be suspicious
• Read creatively
• what are the good ideas?
• what improvements could make important differences?
• Make notes
• underline/annotate/markup key points
• questions/ambiguities/criticisms
• After first read, summarise in 1-2 sentences
• then extend summary
• Compare to other works

19. Reading a paper / notes
• a one or two sentence summary of the paper.
• a deeper, more extensive outline of the main
points of the paper, including for example
assumptions
• made, arguments presented, data analyzed, and
conclusions drawn.
• any limitations or extensions you see for the
ideas in the paper.
• your opinion of the paper; primarily, the
quality of the ideas and its potential impact.

20. Methods papers