SBC322 Ecological and Evolutionary Genomics

y.wurm@qmul.ac.uk

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