Doing Science: The Biology of Variation (Biol 2005)


SYLLABUS (August 20, 2017)

USU Aspen Bibliography site

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2013 GROUP PROJECT REPORTS AND GENERAL TREE/LEAF DATA

The final Group Project reports (addressing variation in ...)
Group 1 (gnarly rough bark on the lower trunk)
Group 2 (central leaf vein scaling in relation to leaf size)
Group 3 (secondary vein numbers and scaling in relation to leaf size)
Group 4 (bark color)
Group 5 ("Leaf me alone" you nasty folivorous insects!)
Group 6 (trunk height/diameter scaling)
Group 7 (wood density)
Group 8 (leaf size in relation to tree size)

The 2013 Leaf Sheets
Group 1, Trees 1-8
Group 2, Trees 1-4, 7
Group 3, Trees 1, 2, 5, 6, 9
Group 4, Trees 1-9
Group 5, Trees 1-2, 5-12
Group 6, Trees 3-6, 9
Group 7, Trees 1-10
Group 8, Trees 1-6, 8-10

The Genotypes spreadsheet (allele calls at eight microsatellite loci)
genotype_calls_8a.xlsx December 2, 2013

The Trees Spreadsheets (locations, clone memberships, circumferences, etc.)
trees_long_lat_size_5.xlsx September 22, 2014
re_sample_list_2.xlsx trees from 3rd field trip

Google-Earth Maps with trees color-coded by clone memberships
tree_map_clones_2013.pdf 2013 trees, WNW is up.
tree_map_N_up_paths_2014_group_targets.pdf 2014 plan for sampling, N is up.
tree_map_14_sept_14_full.pdf With trees from 3 September, some misplaced!

The leaf spreadsheets from 2013 -- suitable for analysis in R!
allgroups_culled.csv no stunting, minor damage only: December 2, 2013
allgroups_raw.csv stunting and all damage codes: December 2, 2013
R_exercises_2.R skeleton script for class exercise November 5, 2014
R_exercises_3.R skeleton script for class exercise November 17, 2014

2014 GROUP PROJECT REPORTS AND GENERAL TREE/LEAF DATA

The final Group Project reports (addressing variation in ...)
Group 9 (leaf edge serration)
Group 10 (leaf color)
Group 11 (leaf petiole length)
Group 12 (leaf symmetry and damage by herbivores)
Group 13 (curvy trunks)
Group 14 (effects of altitude on leaf size and shape)

The JPEG leaf-sheet scans from 2014
leaves_2014 folder with 2014 leaf-sheet scans

The JPEG leaf-sheet scans from 2015
leaves_2015_new folder with 2015 leaf-sheet scans for new trees
leaves_2015_resampled folder with 2015 leaf sheets for resampled trees
leaves_2015_resampled_fixed folder with 2015 leaf sheets for resampled trees, after repairs

The simplifed leaf-spreadsheet template for 2014
leaves.xlsx download and fill in with your data!
a guide to completing your leaf spreadsheets

Leaf-sheet images for practice with ImageJ
Group_2_tree_2_sheet_1.jpg
Group_8_tree_7_sheet_5.jpg

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Resources for R exercise on human height ANOVAs, October 20th
heights_3.R skeleton script, to be modified
family samples folder with 8-family spreadsheets

Resources for R exercises on longitude and leaf shape, November 24th ...
locations.R skeleton script, to be filled in
clone_4-6_leaves.csv
clone_8_leaves.csv
leaf_areas_67_3.csv

NEWER DATA SHEETS! (UPDATED December 14)
leaves_2014_c.csv your measurements, all of this year's leaves
leaves_2014_c_culled.csv your measurements, no stunted or seriously damaged leaves
leaves_asymm_serr_ALL.csv from images, with asymmetries and serration statistics
trees_asymm_serr_ALL.csv averages for the image-analyzed trees
trees_long_lat_size_8.xlsx the tree locations and identities sheet

GOOGLE-EARTH MAPS OF THE SITE WITH ~ALL TREES AND ALL MAJOR CLONES
tree_maps folder with .jpeg images of the maps

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SOME RESOURCES FOR WRITING, R AND DNA EXTRACTION

chapters from Writing Science, by Joshua Schimel
Writing Science Chs. 1 & 2 intro & storytelling
Writing Science Chs. 3 & 4 sticky stories & structures
Writing Science Chs. 5 & 6 opening & funnel
Writing Science Chs. 7 & 8 challenge & action
Writing Science Chs. 9 & 10 resolution & internal structure
Writing Science Chs. 11 & 12 paragraphs & sentences

The Golden Book On Writing, by David Lambuth and colleagues
The Golden Book On Writing

Getting Started with R, by Andrew Beckerman and Owen Petchey
Getting_Started_With_R_1

Laura Suttle's brilliant video introductions to R
Playlist for the Entire Series
Part 1: Introduction and the Console 
Part 2: Functions and Variables 
Part 3: Working Directory 
Part 3.5: Default Working Directory in Windows 
Part 4: Importing Data into R 
Part 5: Functions 
Part 6: Libraries (Pulled due to terminology errors)
Part 7: Creating and Saving Scripts 
Part 8: Getting Help with R 
Part 9: Interpreting a Script 
Part 10: Running a Script 
Part 11: Tips for Debugging a Script 

Qiagen's Plant DNA purification protocol, with theory, etc.
DNeasy Plant Handbook
Meggan's notes on procedures and techniques for DNA extraction lab
DNA extraction: preparation

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PAPERS, LECTURE SLIDES, YOUR PROPOSALS AND REPORTS, ETC.

Papers for Karen Mock's guest lecture
Clonal dynamics of aspen, including Pando
Widespread triploidy in aspen
Diversity and population structure of aspen
Folder full of other papers recommended by Karen

Paper for John Sperry's guest lecture
Water and carbon as causes of aspen die-off

Some papers on leaf fluctuating asymmetry, and evolution of leaf shape generally
Wilsey 1998 FA in hybrid and tree-line birches
Review of CO2 effects on leaf FA
Review of Kaligaric 2008
Kaligaric 2008 CO2 effects at a natural CO2 vent in Italy
Nicotra 2011 review of work on leaf-shape evolution and function

Lecture slides
Jon 24 September leaf shape and longitude at Silver Lake
Jon 6 October introduction to quantitative traits
Jon 20 and 22 October Proposals and more about ANOVA (for first R exercise)

Your proposals, papers, presentations, etc.
The preproposals, and review guidelines October 29th, 2014

Proposal review exercise
Peer review rubric & form November 17th, 2014

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