EEB Lab – 20 November 2014

1. Discussion of the fox phylogeography paper.

What were the goals of the study?

How did they test their hypotheses?

What did they find?

2. Lab Plan

Grapholita_molesta — Grapholita molesta life cycle. Click to enlarge

Today we will be testing hypotheses in an invasive pest called the Peach Moth (Grapholita molesta). Larvae of this moth attack the vegetative parts of a peach tree early in the season and then burrow into fruits as they develop. This species is a particularly bad problem for peach farmers because the larvae don’t cause any outward sign of infection on the fruit and therefore if you buy an infested peach you may get a nasty surprise.

As with many agricultural pests Grapholita molesta can now be found everywhere peaches are cultivated. Today we will use population structure analyses to ask a few questions:

1) Although unlikely, it is possible that this species has always had a worldwide distribution and then attacked peach trees as humans moved the fruit tree around the world. Alternatively the Peach Moth may have recently expanded its range by invading areas where peaches have been planted. We can test these alternatives by testing if Grapholita molesta shows a genetic pattern of population expansion.

2) If there was recent expansion, what is the likely source population of Grapholita molesta?

3) How large and how old are populations of Grapholita molesta?

3. Lab Exercise

3.1 Download and Install R

R is a open source statistical computing platform. You can download R here. There are many add-ons to R. One that you may find useful is RStudio an IDE (integrated development environment). Basically, RStudio helps you organize your scripts, data and results. Feel free to install RStudio but it is not needed for today’s lab.

3.2 Download Scripts and Data

I have made a zip archive that you can download by clicking here. After unzipping the zip archive, you should have the following files:

Aus.fasta
Canada.fasta
China.fasta
external_file.in
Fox_phylogeography.pdf
moth.fasta
Population_Structure_Lab.r
SKorea.fasta

The .fasta files are aligned COI sequences for Peach Moths that I collected from the Barcode of Life website. The .R file is a script that you will use to analyze these sequences.

3.3 Quick R crash course

Once everyone has the data downloaded, we will quickly go through how the basics of using R.

3.4 Analyze Data

The Rscript I provided gives you all of the tools you will need to answer our questions about Peach Moth population biology, but it will require some work on your part to put together results from the R script and information from the handout to answer our three questions.

Welcome

This is the academic webpage of Dr. Anthony J. Geneva. I am an Assistant Professor in the Department of Biology and the Center for Computational and Integrative Biology at Rutgers University. I received my PhD in Ecology and Evolutionary Biology from the University of Rochester and did my postdoctoral training in Organismic and Evolutionary Biology at Harvard University. I use computational evolutionary genetics to study the role of hybridization and introgression in speciation and adaptation. I also develop phylogenetic and population genomic methods when needed. I mostly study lizards but interesting questions and data have drawn me to other taxa including fruit flies and freshwater mussels. The title of this site loosely translates to “let knowledge grow”. In that spirit, my goal here is to present my work and to aggregate information on the topics that interest me.

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