Exercise Manual for
BIOL 471
Methods in Systematics
Spring 2007
by Christopher R. Hardy,
James C. Parks Herbarium, Dept. of Biology, Millersville University
Millersville, Pennsylvania
USA
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Exercise Manual for Methods in Systematics | BIOL 471, Study notes of Plant Taxonomy and Evolution
Material Type: Notes; Professor: Hardy; Class: Topics:Plant Developmental Bio; Subject: Biology; University: Millersville University of Pennsylvania; Term: Spring 2007;
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Exercise Manual for
BIOL 471
Methods in Systematics
Spring 2007
by Christopher R. Hardy, James C. Parks Herbarium, Dept. of Biology, Millersville University Millersville, Pennsylvania USA
BIOL 471 – Methods in Systematics
Exercise Manual Table of Contents Exercise page
Biotic Inventory & Related Activities Exercise 01: Traditional Dichotomous Keys and Biotic Inventory ................................................ 4 Exercise 02: Interactive Key Construction ..................................................................................... 8
Biogeographic Mapping, Analysis, and Modeling Exercise 01: DIVA-GIS Tutorial .................................................................................................. 14 Exercise 02: DIVA-GIS: Distribution and Diversity of Wild Potatoes........................................ 28 Exercise 03: Distribution and Diversity of Parks Herbarium Specimens..................................... 34 Exercise 04: Georeferencing and Generating Distribution Maps ................................................. 39 Exercise 05: DIVA-GIS: Biogeographic (Distribution) Modeling using Herbarium Specimens and Climate Data........................................................................................................................... 41
Phylogenetic Inference Exercise 01: Simple, Manual Cladogram Construction................................................................ 48 Exercise 02: Character State Optimization for Choosing Most Parsimonious Cladograms and Reconstructing Ancestral States. .................................................................................................. 51 Exercise 03: Morphological Datamatrix Construction and Basic Cladistic Analysis .................. 53 Exercise 04: DNA Sequences for Phylogenetic Inference ........................................................... 55
Species Delimitation, Diagnostics, and Conservation Forensics Exercise 01: Species Delimitation using Population Aggregation Analysis ................................ 58 Exercise 02: DNA in Species Delimitation, Diagnostics, and Conservation Forensics ............... 61
Exercise 01. Traditional Dichotomous Keys and Biotic Inventory One of the most important activities systematists do is conduct biotic inventories. We will conduct a biotic inventory of the genera of conifers on campus. Since we are not yet experts in identification, we will use a traditional dichotomous key to identify the genera of conifers that we have on campus (next page). Once we have this inventory, we will prepare an interactive key that will be posted online (at the Herbarium website) and will be used by future classes and other botanical enthusiasts of the MU Community.
Procedure for today and as homework:
- Collect conifers around campus.
- Key them out to genus.
- Construct a working checklist of the genera on MU campus.
- Enter these alphabetically into the rows of datamatrix or spreadsheet.
- Make a master list of the structural characteristics by which they differ.
- Sort and name these characteristics (and their states) logically.
- Enter these “characters” and “character states” logically as column headers in your datamatrix or spreadsheet.
- Score these species for the appropriate character states. Use your specimens and literature to complete this.
A. Plants not evergreen B. Branchlets short and stubby, persistent, alternate....................................... Larix , Larch BB. Branchlets elongate, deciduous, opposite..................... Metasequoia, Dawn Redwood AA. Plants evergreen C. Leaves needle-shaped or otherwise elongate and well-diverging from the stem D. Leaves in fascicles of 2, 3, or 5......................................................... Pinus , Pine DD. Leaves borne singly or tufted on stubby side-branches (but not fascicled) E. Leaves tufted on stubby side-branches........................... Cedrus , Cedar EE. Leaves borne singly F. Leaf ending at stem so that stem is woody in texture & color. G. Leaves sharp-pointed and square in cross-section, with small woody peg-like leaf-stalk.................... Picea , Spruce GG. Leaves round-pointed and flattened, woody peg-like leaf-stalk absent or if present not very prominent H. Leaves usually <1.5 cm long, with distinct leaf- stalk; cones 1-2 cm long ............... Tsuga , Hemlock HH. Leaves >1.5 cm long, with no distinct leaf- stalk (although perhaps with a gradually narrowed leaf-base); cones >2.5 cm long I. Cones erect with scales deciduous at maturity; needle-base swollen and round, leaving a round leaf-scar............... Abies , Fir II. Cones pendulous, scales persistent, with very long 3-lobed bractsthat look like the rear-end of a mouse; needle-base not swollen, leaf-scar either not round or not very big............... Pseudotsuga , Douglas Fir FF. Leaf-base decurrent along (i.e., the base runs along) the stem for some distance, such that twig stem to which leaves are attached appears green. J. Leaves flattened and round pointed; cones with just a single seed which is partially enclosed in fleshy red aril; often bushes or shrubs....................................... Taxus , Yew JJ. Leaves angular (not flattened) in cross-section and pointy; cones without fleshy red aril, more than one seed K. Cones round and >1 cm diameter, dry and brown at maturity; leaves silvery green; trees ......... Cryptomeria , Japanese Cedar K. Cones soft and berry-like; both needle leaves (juvenile) and scale leaves (adult) usu. present; trees or shrubs... Juniperus , Juniper CC. Leaves scale-like (or at least not especially elongate) K. Branchlets forming flattened fan-like sprays L. Twiglets much flattened, aromatic; cones elongate; cone-scales flattened, 8-12 .............................................................. Thuja , Arbor Vitae
Illustrated glossary for help with conifer key.
Exercise 02. Interactive Key Construction.
Today we build the interactive, Web-accessible key to conifer genera of MU’s campus. I have compiled everyone’s scorings of their genera into one master Excel sheet. Excel provided us with a convenient way to manage our scoring process and will also allow us to save some time as we format a .txt data file that the program SLIKS can use.
SLIKS stands for “Stinger’s Lightweight Interactive Key Software” and is available for free at http://www.stingersplace.com/SLIKS/. “Stinger” is a plant systematist who works at the USDA and one of his jobs is managing and programming for the USDA PLANTS Database. Although there are many interactive key programs available, SLIKS is novel in that it runs (via JavaScripts) on any computer operating system and through most Web browsers.
Procedure:
- Conifer-data.xls contains our datamatrix and character plus character state definitions. Open it.
- On the first sheet labeled “Datamatrix”, execute FILE > SAVE AS > .CSV FILE”. Name it “Conifer-data01.csv. A CSV (comma separated variable) file is simple a text version of your spreadsheet where the columns divisions are denoted by commas.
Thus, the hypothetical spreadsheet entry: Pinus (pine) 2 1 LEAF CLUSTERING borne singly on short, stubby side shoots
Becomes: Pinus (pine), 2, 1 LEAF CLUSTERING, borne singly, “on short, stubby side shoots”
Note that in the second row, “on short, stubby side shoots” is enclosed by quotes because it contains a comma. In order for this comma NOT to be recognized as a column delimiter, the entire phrase is automatically enclosed by quotes by Excel when you save as a CSV file.
- Now save the second sheet in Conifer-data.xls labeled “characters_in_rows” as a CSV file with the name Conifer-data02.csv.
- Working within your BIOL 471\SLIKS\ directory on the computer, rename these CSV files to have a .TXT extension, rather than a .CSV extension.
- Next, open Conifer-data01.txt in NOTEPAD. It should look like Fig. 2.
Fig. 2. Conifer-data01.txt as seen in a simple text editor.
- Then do a EDIT > REPLACE to replace all commas by commas in quotes (Fig. 3).
Fig. 3.
- Delete everything above and below the highlighted datamatrix portion. These character and character state titles were used only during the Excel phase to facilitate our scoring the genera for their numerical character states.
Doing so makes your datamatrix look like this (Fig. 4).
Fig. 4. The transformed data matrix file.
- Now, copy this datamatrix text block into your existing Conifer-key-file.txt, and paste it below the existing characters block, just as in the maple.js sample file.
Add formatting (brackets, quotes, commas) to this matrix block in the same manner as before with the characters block.
- Add at the end of each matrix block line a script that will transform the genus’ name when viewed on the Web into a link to a GOOGLE IMAGE search for that genus.
Using our maple example, the line for maple would read (all in one line):
["Acer","2","2","2","2","2","2","?","2","2","?","1","?","?","2","2","?","1","2","http://image s.google.com/images?hl=en&q=Acer&btnG=Search+Images"],
For your conifer genera, you would simple substitute “Acer” for “Pinus” or “Abies”, etc., as appropriate.
- Finish the formatting with a title and block headers as exemplified in maple.js.
SAVE and then change the extension from .TXT to .JS
- Now open maple.html in NOTEPAD. This is the command file that will spawn Conifer-key- file.js. Change the phrase near the beginning of maple.html that reads “maple.js” to “Conifer- key-file.js”. Save the html file as Conifer-key.html. Now, loading this HTML file into MS Internet Explorer should run your key!
Biotic Inventory
& Related Activities:
The Use of GIS for
Biogeographic Mapping,
Analysis, & Biogeographic
Modeling
Exercise 01. DIVA-GIS v5nTutorial
(Feb 2005 version; from www.diva-gis.org).
This tutorial guides you through some commands in DIVA-GIS, in order to become familiar with the some of the most basic aspects of the program.
More details can be found in the manual and in the exercises.
The data used in this tutorial can be downloaded from the Internet at http://www.diva- gis.org. You can place these in any folder, but here we assume they are in the “C:\DIVA\tutor\” folder, and we will refer to this folder as the "data folder".
1. Layers Start DIVA-GIS and Click on Layer – Add Layer
The “ Open” window appears. In this window, go to the data folder and select the file bo_mroad and press the Open button.
Notice how you can also pan through your map by clicking on the overview map (when the map is zoomed in).
To change the way this layer is displayed, click once on the bo_department layer in the table of contents (not on the checkbox, but next to it). This makes that layer the “active Layer”.
Now click on Layer/Properties and the Properties window appears. (This window also appears after double clicking on the layer in the table of contents). Now you can change display properties such as the color and border size.
Change the Style to "SolidFill", and the Fill Color to green (double click on the rectangle in the Preview to show the color palette). Change the label to "Departments". Click on Apply and Close. The departments layer should now be green.
Now go to the Properties of the departments layer again. Go to the “Unique” tab, select the field "Departments", press Reset Legend and Apply. Each department should now have a different color.
Change the color back to green.
Double click on bo_mroad (in the table of contents) and change the Style of the lines to "Dash line", the Color to red, the Size to 3. Change the label to "Main roads".
To be able to see the roads layer, drag (click on it and move it while keeping the mouse button down) it to the top in the TOC.
Save your work using the Save or Save As commands in the Project menu and save the “Project” in a folder of your choice. Then use Project - Close to close the project and Project - Open to open it again. (note that you can also pick this file from the "recently used files" list in the Project menu).
The project file only stores the names of layers and some information about them, not the data. If you want to save the project with the data in a single file, you can use File- Export. This can be handy for sending a project to somebody else.
Make the bo_department layer active by clicking on it in the TOC.
Choose the option Layer – Identify Feature from the Layer menu or from the toolbar:
After that, click on any part of the map of Bolivia. The Identify window will appear and show the data that are associated with the part of the map you clicked on (e.g., the name of the department).
You can save a map as a graphics file using Project/Map to Image and copy the map to the clipboard. Try pasting it again into Powerpoint.
You can also make a more elaborate map by clicking on the "image" tab at the lower right of the DIVA window. There you can add a legend, scale, and more (e.g. text).
Start with adding the main map. Then you can set where other objects are displayed by selecting them in the toolbar, setting some options on the left hand panel, and then by clicking on the map.
It may take a couple of rounds of trial and error to get the placement and properties right. You can repeat the placement of an object (e.g. scale bar) until you have found the place you like. The settings are stored in the text boxes and the objects can be placed on the exact spot on the map again by pressing OK (instead of clicking on the map). Thus, you can go through all the objects, and then start all over again with a fresh map, and only press the OK buttons.
In some cases it can be easier to add additional pieces to the map in Powerpoint or comparable program.
Open the file bolivia_wp.txt with Excel (or other spreadsheet program). Each record (row) in this file describes localities where wild potatoes have been collected.
First complete the LATITUDE and LONGITUDE columns by filling them with coordinate data in decimal degrees. Use the columns LATD, LATM, LATH, LOND, LONM, LONGH. LATD y LOND have degrees data, LATM y LONGM have decimal minutes (not minutes and seconds)), LATH and LONGH indicate the hemisphere (N/S and E/W). To calculate Latitude use a formula like “=-1*(LATD+LATM/60)” (but replace the variable names by the cell references in excel). The values in the first data row have already been calculated.
It is important that in Excel you set the format of the cells to a certain number of decimals (e.g. 5). Otherwise, all the decimal numbers may be cut off when exporting the file.
When you are done save the file under a different name. After that, save it as a TAB delimited text file again (.TXT).