2014 09-23-sbc322-intro
DESCRIPTION
course introTRANSCRIPT
This changes everything.454
Illumina Solid...
Any lab can sequence anything!
How does this change affect us regarding ecology & evolution
research?
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
• …
Very exciting.
Aims (1/2)
To understand and critically evaluate:
• research questions
• methods
• experimental designs
• applications
in ecological and evolutionary genomics.
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
Science-driven.
Interactive
• Small groups - informal presentations
• Formal presentations in pairs
• Blog posts
• Peer review
ok?
Yannick Wurm
YW
Christophe Eizaguirre
CE
Main themes
1. Methods
2. Social evolution
3. Conservation
4. Genome dynamics
5. Speciation
Schedule 23/09/2014 08:28SBC322 Ecological and Evolutionary Genomics
Page 1 of 1https://docs.google.com/spreadsheets/d/1hbVaFxIp8LOvm23-qND4gbLpcf8ealhzMbjaH9cfMHM/pubhtml/sheet?headers=false&gid=1070083897
Date Time Room Teaching Title
1 2014-9-23 Tuesday 9:00 Eng. 3.24 YW Course overview + How to read a paper13:00 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 blogging16:00 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 instance16:00 Scape 1.02 CE (continued)17:00 Scape 1.02 CE (continued)
9 2014-11-18 Tuesday 9:00 Eng. 3.24 CE Theme 4 Ecological speciation13:00 Eng. 3.25 CE Theme 4 Genomics of speciation
10 2014-11-25 Tuesday 9:00 Eng. 3.24 YW Designing an experiment/project: choose topics & discuss in groups13:00 Eng. 3.25 YW (continued)
2014-11-27 Thursday 15:00 Scape 1.02 YW Practice exam (handwritten)16:00 Scape 1.02 YW (continued)
11 2014-12-2 Tuesday 9:00 Eng. 3.24 YW Present experimental designs/project proposal; 8 groups of 2; each for 8+4 minutes13:00 Eng. 3.25 YW
12 2014-12-9 Tuesday 9:00 Eng. 3.24 CE Practice exam feedback13:00 Eng. 3.25 CE Revision session
Week
Reading a paper
Sequence of events:
• Title
• Abstract
• Figures
• Main text
• (iterate)
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
• 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.
Reading a paper / notes
Methods papers