Author: Curtis A. Provencher and Andrew D. Nguyen

Affiliation: University of Vermont

Date initiated: 2016-03-29
Last Date modified: 2016-05-10

Funding source: National Science Foundation, Division of Environmental Biology (1136644)

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.

Table of contents

  1. Project Overview
  2. Objectives and Hypotheses
  3. Repository Layout
  4. Materials and Methods

Project Overview

This is an National Science Foundation supported project aiming to understand how climate change will impact critical species that perform key ecosystem services.

Objecives and Hypotheses

In this study, we assess the potential impacts of experimental warming in wild populations of the ant genus Aphaenogaster from a southern (Duke Forest, NC) and northern (Harvard Forest, MA) site near their range boundaries. Using Hsps as a proxy for sub lethal stress, we will determine the extent simulated warming between a northern and southern site imposes costs on foraging ant workers.

Repository Layout

  1. 2013_stress_in_nature_manuscript/ : folder for manuscript documents
  2. Data/ : All of the raw data generated and includes manipulated or manually parsed data.
    • qPCR_Plate_Layouts/ : organization of how samples were ran on each plate
    • qPCR_Raw_data_sheets/ : excel spreadsheets of the raw data generated from qpcr machine (SteponePlus)
    • Sequencing/ : sequenced amplicons from qpcr reactions
    • cdna_synthesis_template.xlsx : excel spreadsheet for caculating cDNA synthesis reactions (RNA-cDNA)
    • 20160211_prelim_normfinder.txt and normfinder_prelim.csv : preliminary normfinder data lay out (we opted for a different approch to find the most stable gene )
    • 2015_warming_prelim.csv : preliminary dataset
    • RNA_cDNA_Maps.xlsx : plate layout of how RNA was converted to cDNA
    • 20160222_anbe_sequencing_pog_aph_83_70_40.xls : sequencing layout for hsc70-4 h2, hsp83, and hsp40
  3. Results/ : Has preliminary results so far; pdf output of scripts
    • Figures/ : saved figures by date
    • 20150824_stressed_ants.pdf : analysis pdf from the Script_Analyses folder (most digestable view of data, metadata, and analyses)
  4. Scripts_Analyses/ : I use R and Rstudio for data analysis and data visualization and convert (knit) these analyses into pdfs(see results).

Materials and methods

Please click here for general lab protocols and reagents. For more details of the study details, data, metadata, and statistical analyses, please click here .