Lab 9 prelab.
In today's lab, you will learn how we can best use the type of data we collected next week. Biodiversity can evaluated in many ways and each measure, metric, and index tells us something slightly different about the biodiversity in a given community. Statistics play an important role in biodiversity measurement and ecological work in general. This lab will also introduce you to another simple statistical test, called a ttest. It relies on some of the same principles as the chisquare test with which you are already familiar. You will use this new knowledge to finishing our exploration of watershed health and bioindicators and you will put it all together in a scientific manuscript.

Introduction

Do you know enough?

What we will do in lab?

LABridge
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how is biodiversity measured?
DO you know enough about Analyzing biodiversity?
Because biodiversity can be measured in multiple ways, an index is often use so that one number can provide a good metric for biodiversity across a community. These indices often include measures of both richness and abundance, and therefore take evenness into account. Simpson's Biodiversity Index (SDI) is a common such measure. It ranges from 0 to 1, where high scores (close to 1) indicate high diversity and low scores (close to 0) indicate low diversity. One of the more the useful aspects of the index is to compare two sets of data to see which is more diverse. For example, if one region has an SDI of 0.5 and another has an SDI of 0.35, then the region with the SDI of 0.5 is more diverse. Let's work through the example below.
The example data were collected from a water sample and show the abundance of five species (A thru E). This community would have a richness = 5. With low evenness as it appears to be dominated by taxa A and B. We can use the SDI as a general calculation to solve for diversity (D). The formula is provided and some of the initial calculations are shown in the table.
According to the table:

It is also possible compare the biodiversity of two locations with statistics. In this lab, you will be using a paired ttest to assess the biodiversity of two different water samples, based on the richness and abundance of protists. You will be provided with an excel sheet, a demonstration video on you tube, and a ttest calculator to use online. But, read on to see why we need statistics in the first place...
Different is different. Why do we need to run a ttest? We look for patterns to help us understand the natural world. As we do so, we are fighting our own human tendency to see patterns where none truly exist, and to take what we see in a specific context and try to apply it more broadly. Let’s say you notice that within your friend circle, those who regularly eat breakfast did much better on their first BIOL 122 exam than those who skipped your morning meals together. You might then assume that somehow, eating breakfast is causing the better grades. But! Consider the following: 
 How much of a difference in test averages should there be between breakfasteaters and breakfastskippers for that to be true? 90 vs. 60? 80 vs. 70? Reasonable people could disagree.
 How often do you need to see this relationship for that to be true? On exam 1 and 2? On all the BIOL 120 exams? Reasonable people could disagree.
What will we do in lab & how will we do iT?
Lab 9 contains three exercises and an introduction to your next assignment.
Last week, you collected diversity data on water samples from two streams (stream A and stream B). This week we will use those data to draw conclusions about the health of each watershed. 
If you feel confident with this material, click the bridge icon below and navigate to Blackboard to take the LABridge for this week. Be ready to be tested on this material before you go to the quiz, and make sure you have your Lab Notebook Guide ready to submit as well.
Lab 9 Protocol
Following this lab you should be able to...
 Use the scientific method including hypothesis creation, data collection, and analysis with a ttest
 Calculate common diversity indices including: richness, abundance, and Simpson's Diversity Index
 Create tables and graphs for inclusion in a manuscript
 Produce a scientific manuscript
 Exercise I. You will calculate species richness and abundance in your samples, as well as the Simpson's Diversity Index (SDI).
 Exercise II. You will explore your data further using a ttests.
 Exercise III. You will review your hypothesis and determine which metrics use and how they should be visually represented.
 Exercise IV. Begin work on your manuscript.

Exercise I

Exercise II

Exercise III

Exercise IV. Manuscript
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Exercsie i. Calculate metrics of biodiversity
Procedure. Calculate biodiversity metrics (richness, abundance, and SDI)

Exercise II. Conduct a Ttest
Procedure.

Exercise III. Further Analysis
You now have several different measures of "biodiversity" in our two streams. You can use all your data and calculations, or strategically match them up to your predictions.
Procedure.


Exercise IV. Scientific Manuscript
You will be producing a scientific manuscript to communicate your results for this research project. Remember, communicating your results is a vital part of the scientific method; without this step, the field could not grow.

Faculty Spotlight: Dr. Scott Grubs
Scott Grubbs specializes in food web and nutrient dynamics of karst riverine watersheds and the taxonomy, systematics, and biogeography of stoneflies (order Plecoptera). Stoneflies are widely recognized as valuable bioindicators of stream health. The are used, along with Ephemeroptera (mayflies) and Trichoptera (caddisflies) to calculate the EPT index. Streams with higher numbers of these species, and higher EPT index values, are considered healthier and lessimpaired. A few of Dr. Grubb's recent publications are available below.
Students who are interested in this work, please email @ [email protected]. Assorted Publications: A surprising rediscovery and description of a new species of Soyedina Ricker, 1952 (Plecoptera: Nemouridae) from Great Smoky Mountains National Park... An update on the stonefly fauna (Insecta, Plecoptera) of Maryland, including new and emended state records and an updated state checklist... 