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EEB 2208 WILL BE TAUGHT BY DR JOHN COOLEY IN SPRING 2018 AND HE WILL DEVELOP HIS OWN WEB SITE FOR THAT SEMESTER … SO DO NOT USE THE INFORMATION POSTED HERE. 

I EXPECT TO BE TEACHING THE CLASS AGAIN IN 2019.

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Spring 2017

This course will provide an introduction to the discipline of conservation biology. The first two-thirds of the course will focus on the biological aspects of the discipline. Topics covered will include patterns of biodiversity and extinction, causes of extinction and population declines, techniques used to restore populations, landscape level conservation planning, and the role of conservation in protecting ecosystem services. The final third will cover the practical aspects of implementing conservation actions and will include lectures on conservation economics and conservation law.

Basic course information

Credits: 3

Instructor: Chris Elphick (office: TLS 372/4, down the hall from the EEB office; office hours – at lecture hall 15 mins before or after class, and/or by appointment) Email: chris.elphick [AT] uconn.edu

Teaching assistant: Manette Sandor (office hours: 12:45-1:45 on Mondays in TLS 368, or by appointment; extra sessions from 3:30-4:30 on 13th and 27th Feb) Email: manette.sandor [AT] uconn.edu

Your emails to us must contain the phrase “EEB 2208” in the subject line; emails received without that phrase, and especially those with a blank subject line, may get treated as SPAM and be deleted without being read.

Lecture: M, W 2-3:15 PM

Location: BPB 131

Pre-requisites: There are currently no prerequisites for the course, but it is aimed at students who are at least sophomores.

Text book: Essentials of Conservation Biology (R.B. Primack, 6th Edition, Sinauer) is recommended reading. I lecture primarily from my own notes, but this textbook provides a good overview of the topics I will discuss.  On exams I will assume that you are familiar with the material that this book covers and may ask questions (though not many) about topics that are not covered in lectures. Reading beyond the lecture material will be helpful as I will expect you to know a range of examples for each phenomenon I describe. This New York Times article is a bit old now, but has suggestions for finding cheap text books that might be useful. Another book that might be helpful is available as a free download here. The free textbook covers many of the topics I’ll cover in class, but is not as comprehensive as Primack’s book. The 5th edition of Primack is also probably OK, but will not be as up-to-date as it could be (the author of this book treats revisions seriously).

Web site: This site will serve as the primary web site for information about the class. We will, however, also have a huskyct site where grades will be posted, where homework can be turned in, and where you can post questions for me, the TA, or your classmates.

Research paper readings: In some lectures, I will provide supplemental readings from the primary research literature to augment the text book readings. These readings will be the subject of class discussions and graded in-class questions; material from them may also appear on exams. See the syllabus below for more information on when these discussions will occur and what is expected of you.

Optional reading that might be helpful: If you are really interested in this topic, then you will be well served if you check out recent issues of the journal Conservation Biology (note that to read articles you will need to be connected to the UConn system).

Questions: Please ask lots of them! Class is much more interesting (for me and you) when people ask questions. If you send me questions over email, I will post them (anonymously) along with the answers on this web site (see below), so that everyone can read the responses.

Office hours: I do not have fixed office hours because they inevitably do not work for many students. But, I will generally be present in the lecture hall for at least 15 minutes before and after each lecture to answer questions. Please come up and introduce yourself – the class is big and it is hard for me to get to know people unless they come and talk to me. I am also happy to meet at other times by appointment. If you would like to meet, then email me, telling me (a) what you want to discuss, and (b) when would be good times to meet (Mon, Tues, or Wed will usually be best). The TA is also available to answer questions by email, during office hours, and/or by appointment (see above for details).

Course objectives and expectations: My goal is to provide you with a basic understanding of the scientific field of conservation biology and the application of science to solving conservation problems. My primary goal is for you to learn and understand basic concepts and general ideas, although to get an A or a high B, you will need to know plenty of details too. I will expect you to know examples relating to each major concept, so that you can relate theory to practical, real-world situations. I won’t expect you to memorize all of the minutia in my notes; for example, I wouldn’t ask you exactly how many species have gone extinct in the last 500 years. But, I will expect you to have a solid understanding of the core information that would be required of you in a job in this field; for example, I would expect you to know whether the number of extinctions this decade is likely to be closer to 6 or 20,000. The text book readings are intended to complement the lectures. My lectures will not repeat verbatim what is in those readings, and I will often use different examples or cover somewhat different topics. Both the lecture material and the readings, however, are important and could appear on exams.

Specific things that I hope you will learn are:

• to understand the basic issues that define the field of conservation biology;
• specific factual information about major issues in conservation biology;
• specific examples of all important concepts, problems, and solutions;
• to use general principles to think about ways to solve specific conservation problems;
• to extrapolate from examples I provide in class to other cases with similar characteristics (e.g., that I may ask about in exams!);
• to acknowledge scientific uncertainty when it exists, and to recognize when it hampers understanding and when it does not;
• to read scientific papers and understand the main points that they make;
• to interpret graphs, tables, and simple statistics presented in the scientific literature;
• to present scientific information to your peers in a format commonly used by scientists;
• to think about the work of others and provide constructive feedback.

If you are just taking this course out of general interest, then hopefully it will provide you with a sense of how the biological sciences can be applied to protection of the natural world, and will give you a better understanding of the main issues in conservation biology. For those of you wishing to pursue a career in conservation biology, I hope that this course will give you a solid foundation on which to build with future courses (e.g., EEB 5310, EEB 5370). If this is your goal, I’d also encourage you to check out EEB’s joint BS/MS program in Biodiversity and Conservation Biology. There are also links to good sites for finding internships and jobs (short-term and permanent) in conservation biology below.

General student help

Counseling and Mental Health Services: (860) 486-4705 (24 hours).

Alcohol and Other Drug Office: (860) 486-9431.

Dean of Students Office: (860) 486-3425.

UConn Police Department.

Important course documents

Grading policies

Plagiarism statement

Homework overview

Discussion papers

Exam format information

Poster project guidelines

Link to some poster design tips

Citation guidelines (for poster project)

Study guide

Academic rules and conduct

All students should be aware of the guidelines on academic integrity contained in the Student Code, which is available here.

Conservation biology in the news

Recent news articles that relate to the topics covered in this course will be posted on twitter and can be viewed here. You do not need a twitter account to view them. If you use twitter and want to contribute please do so using #eeb2208. If you want to get the class-related tweets that I post, follow @ssts.

Schedule of lectures and examinations (subject to change)

The schedule below describes the order in which we will cover material. Not every topic fits nicely into the time set aside for a lecture, so be prepared for us to start some topics a lecture early, and for others to take longer than the syllabus suggests. Snow days may also disrupt things,so don’t be surprised if the topic listing changes slightly.  (Note that assignments will not change unless something dramatic happens, in which case I will email everyone in the class at their UConn address.)

Each lecture has an outline summarizing the material (linked to the topic titles in the syllabus below). Reading these notes before each lecture should help you to follow the material, and some people like to print them out so that they can spend more time listening and less time writing. These outlines, however, ARE NOT a substitute for coming to class, making your own notes, or doing the assigned readings, and you should not expect them to include everything covered in class (e.g., none of the graphics will be in the web notes).  I will review and update each set of notes a day or two before each class, so minor changes may be introduced.

My advice is to look the notes over before class, make supplemental notes during the lecture, and then look over all the information again before the next class. Then, if there is anything that you do not understand, ask me about it at the start of the next lecture (I always try to be in class 10-15 mins early). In exams, you will be expected to know about all the things I talked about, not just the information in the web notes. If you choose to rely only on the web notes it will likely affect your grade.

The symbol ** in the “Reading” column means that there is important supplemental reading from the primary literature that we will discuss in class (if there is no ** then it is still important, but will not be the subject of graded in-class activities). Reading these papers is important as there will be graded writing assignments, conducted in class, for each one. I will also randomly pick people in class to answer questions about them. Links to the relevant papers can be accessed by clicking on the ** (note that links will not go live until a week or so into the semester). These links might not work if you are not using a computer that connects to the UConn network. It is possible to connect your home computers to the network by going to this site and signing in using your netID. We will also post the papers on the huskyct site.

Weekly homework will be assigned on Wednesdays, with each assignment posted on huskyct.  Your responses should be submitted via huskyct and are due by 11:59 pm on the Monday after the homework was assigned (see homework column in the table below). Answers will be posted on huskyct.

In the syllabus I have also noted special lectures or other events (in green) that will take place on campus this semester and that are at least loosely connected to this course. Attendance at these lectures is not required, but the presentations should be of interest to anyone interested in conservation biology.

Because conservation biology is a fast-moving field, with the latest research constantly changing, all of my course notes are updated annually. Links to the documents in the syllabus below will work as soon as each set of notes is updated – usually this will be a day or so before the relevant lecture.

Lecture	Date	Topic	Reading	Homework (due 8 pm, Sundays)	Supplemental information
1	18 Jan	What is conservation biology?	Chapters 1 & 6		A summary of what the course is about: Part 1 and Part 2
2	23 Jan	Interpreting statistics (when there’s an agenda)	Sutherland et al. 2013		Theory of the Stork
3	25 Jan	Forms of biological diversity	Chapter 2	Hwk #1 (due 29 Jan)	International Year of Biodiversity Ecosystem services
4	30 Jan	Patterns of biodiversity	Chapter 3		New species discoveries
5	1 Feb	Extinction rates	Chapter 7	Hwk #2 (due 5 Feb)	Thylacine video – all that’s left
	2 Feb	TEALE LECTURE: The Sixth Extinction (Elizabeth Kolbert)			4:00PM, Konover Auditorium, Dodd Center
6	6 Feb	Patterns of extinction	Chapter 8		A short extinction overview
7	8 Feb	Causes of population decline	Chapter 8 **Ceballos et al. 2015	Hwk #3 (due 12 Feb)	1ST DISCUSSION TODAY!!! The last passenger pigeon IUCN Red List
8	13 Feb	Habitat loss & degradation	Chapter 9: 175-196		Another victim of habitat loss
9	15 Feb	Over-exploitation	Chapter 10: 215-227 **Webb & Mindel 2015	Hwk #4 (due 19 Feb)	Bushmeat
10	20 Feb	Invasive species	Chapter 10: 227-238 Watch Cane Toads		IPANE Another invasive amphibian gets to Australia
11	22 Feb	Disease	Chapter 10: 238-245 **Rosa et al. 2016	Hwk #5 (due 26 Feb)	Salamander disease
	24 Feb	Poster info due via email before 4 pm today
12	27 Feb	Global change	Chapter 9: 197-216		National Academies video, part 1 USFS climate change atlases for trees and birds Climate Change Time Machine
13	1 Mar	Ecosystem services	pp. 1-24 MEA Summary for decision makers  **Bellard et al. 2016	Hwk #6 (due 5 Mar)	Millennium Ecosystem Assessment (MEA)
	6 Mar	Mid-term Exam	Study lectures 1-13		Key
14	8 Mar	Small population conservation	Chapter 11 **Stephens et al. 2016	Hwk #7 (due 12 Mar)
	13 Mar	No Class: SPRING BREAK	Reading for …
	15 Mar	No Class: SPRING BREAK	… poster projects
15	20 Mar	Population viability analysis	Chapter 12		Demos of PVA simulations in class today and/or Wednesday
16	22 Mar	Conservation genetics	Chapter 13 **Chen et al. 2015	Hwk #8 (due 26 Mar)	Frozen Ark Project POSTER PROSPECTUS DUE TODAY
17	27 Mar	Ex situ conservation, release programs	Chapter 14		Info on UConn’s endangered and extinct in the wild plants
18	29 Mar	Conservation reserves	Chapter 15 **Barnes et al. 2016	Hwk #9 (due 2 Apr)	US Protected Areas
	30 Mar	TEALE LECTURE: Building capacity for adapting to climate change (Maria Carmen Lemos)			4:00PM, Konover Auditorium, Dodd Center
19	3 Apr	Reserve networks	Chapter 16		Poster design tips
20	5 Apr	Conservation in the matrix	Chapter 18 **Butchart et al. 2015	Hwk #10 (due 9 Apr)	Flooding rice
21	10 Apr	Management	Chapter 17		Read about re-wilding
22	12 Apr	Habitat restoration	Chapters 19 **Runting et al. 2016	Hwk #11 (due 16 Apr)
	17 Apr	Poster presentations: session A	Start studying		Grading forms: Yours // mine
	19 Apr	Poster presentations: session B	Chapter 20	Hwk #12 (due 23 Apr)
	19/20 Apr	TEALE LECTURE: The Nile Project (Mina Girg1s)
23	24 Apr	Economics of conservation	Chapters 4 and 5		Instructor evaluations today
24	26 Apr	Conservation law and International legislation	Chapters 21 and 22 **Piaggio et al. 2017	Hwk #13 (due 30 Apr)	Short video on wildlife trade Valuing ecosystems
					Study Guide
	TBD	Final exam: confirm time and date here	Cumulative		Exam will cover material from entire course

* Questions about final exam rescheduling MUST be directed to the Office of Student Services and Advocacy: (860) 486-3426. I am not allowed to consider rescheduling requests unless you already have approval from that office. Except in emergencies, rescheduling of other graded activities will be considered only if a written request is made at least one week in advance. Rescheduling is not guaranteed.

Please note that these lecture notes are intended for students in EEB 2208 at The University of Connecticut, and may not make sense in other contexts. If, however, you are not a UConn student and they are useful to you, please use them – but kindly let me know first if you intend to use them for anything more than your own on-line reading. If you find errors, please let me know that too.

Poster topics

The following topics have been taken: If your poster number starts with an A then you will present on Monday. If it starts with a B then you will present on Wednesday. Please make note of your poster number. All posters must be turned in on Monday.

Honors conversion projects

Occasionally honors students conduct additional projects to get honors credit for this class.  Recently, those projects have involved developing web sites that provide information about conservation biology that relates to UConn or the state of Connecticut.  I will post examples of those projects here as the information may be of interest to other students:

• Wetland plants of Connecticut
• Diseases that threaten Connecticut wildlife

Other information

For information about EEB’s Joint B.S./M.S. degree program in Biodiversity and Conservation Biology click here

For information about the Society for Conservation Biology click here

For information on jobs in conservation biology click here

For information on jobs in wildlife biology click here

FAQs

If people send me questions about things that affect everyone I will post the questions (anonymously) and my answers here. Please check here before emailing me to make sure that I haven’t already posted an answer. Some items are rewritten to make them more general to the entire class (I have not corrected questions for poor spelling and grammar though – if you are appalled at how some of questions read, then your response is similar to the typical employer in this field). I will also set up a discussion forum on huskyct, where you can ask questions of me and/or fellow students.
QUESTIONS ABOUT THE WEB SITE

Q: I am having problems getting to the info about the class, I am a Mac user and it does not let me log in! I have been trying to get my Mac wired to the UConn system with no success. I did try from home and still not good.

A: You shouldn’t need to log in to anything to access the course web site. The EEBedia site, does have a log in button – but logging in is not necessary if you just need to view the content – which should be accessible from any machine connected to the web. The only parts of the web site’s content that would require a log-in are the papers that we will discuss in class (identified on the syllabus by ** in the “Readings” column). To get to these from an off-campus computer you would first need to log-in to the VPN (log-in shouldn’t be needed if you are on campus). Instructions on how to do this log-in are given just above the syllabus.

Q: I dont know if its just me but im a mac user and i cant open any of your notes but the first one. it says Not Found The requested URL /eebedia/images/d/dc/EEB2208_04_biodiversity.pdf was not found on this server. can you help me??

A: If you only looked at the web page after the first lecture, then the problem is just that I had not posted all of the notes at that time. As noted immediately above the syllabus (the red text), I usually post notes a few days before the lecture to enable me to ensure that they’re up to date, and account for any changes in the lectures. Links for future lectures will remain broken until I put up the notes. I don’t think that being a Mac user should make any difference, and I’ve never heard of any Mac-specific problems with any part of the web site in past years. <FOLLOW-UP: THIS PROBLEM WAS SOLVED SIMPLY BY REFRESHING THE BROWSER.>

Q: I wanted to let you know that i am having difficulties trying to access the pdf discussion file we are supposed to read before class. I did sign into VPN, and i still could not access the file you wanted us to read. I was wondering if you could attach the pdf file in an email.

A: One of my goals with this assignment is to ensure that you are able to access peer-reviewed literature on your own. You will need to do this for assignments throughout the course, and I won’t be able to always do it for you. Without more information on the problem you had I can’t easily determine how to help you.

That said, I’d suggest that you start by exiting your browser completely, then go to the vpn site and sign in. If the problem is that you can’t connect, call the UITS help center as I won’t be able to help you work this problem out. Once you’ve connected, return to my class page. Most papers should be accessible simply by clicking on the two red stars. In some cases you might go to a page with just the abstract – if this happens there should be a link to a pdf somewhere on the page (if you can’t see it, try searching for “pdf” with your browser’s “Find” function). If you want the paper’s full citation, go to the web notes for the lecture where it will be given (you can then just google the paper). Finally, we will post all of the papers in huskyct, so that is another place where you can look for them.

If none of this works, then you can simply look the paper up when you are on campus (e.g., in the library or a computer lab) as none of the stuff described above should be necessary on campus – the links should all work without need for the vpn. If all else fails, you can always look up the paper versions of the journals which should all be in the library.
QUESTIONS ABOUT GRADING

Q: I’m disappointed with my grade from the first half of the semester. Do you think it is possible for me to improve it to a [insert your target grade here]?

A: By spring break, when midterm grades are posted, only 35% of the total points for the class will have been allocated, so there is lots of scope for people to improve their grades. Using the information on huskyct (or on your returned papers), it is simple algebra to work out exactly how many points you will need to get for a given grade. I.e. for a B you need an overall average of 80%, so figure out how many points you have so far, then work out what % you need to get on the remaining assignments.

If you are trying to improve your grade, the first thing to do is to work out which type of assignments you’re having trouble with (i.e., surprise statements, poster project, or the mid-term exam). If it is the surprise statements, then talk to the TA to make sure that you really understand what we are looking for. One way to test your understanding of the task is to go back to previous papers and try to come up with new answers, then ask one of us whether they would have got you 2 points. If you are having trouble understanding material or did poorly on the exam, then please ask one of us to go over anything that you do not understand. And if you need advice on how to study for the class, please ask about that too.
QUESTIONS ABOUT THE POSTER ASSIGNMENT

Q: I can’t find any peer-reviewed articles related to the news article I’ve chosen for my poster project. Can you provide some guidance?

A: Most (but not all) topics will have relevant peer-reviewed literature, but it might be hard to find if you’ve not done literature searches before. First, you need to decide what your topic is. E.g., you might read an article that compares the threat of climate change to polar bears to the threat to species in the tropics. Based on this, you could do a project that focuses on how threatened polar bears are, or one that focuses on how climate change will affect tropical species, or on how the threat to different species around the world varies, etc. Any one of these would be fine (trying to do all three would likely be too much). Next, you need to identify some key words (e.g., “climate change” and “polar bear” or “global warming” and “tropical species”. Then do some searches in Scopus or one of the other databases available through the UConn libraries, or using Google Scholar. DO NOT use the regular Google search engine or you’ll get a lot of stuff that is not peer-reviewed. There are tips on how to identify peer-reviewed papers in my guidelines for the project.

Q: The problem is that most of the sites (Google Scholar, British Library Direct, etc.) are telling me to pay to access the articles. Could you please guide me where to go?

A: Sites will only tell you that you need to pay if you are off the UConn network. If you do your searches while on campus, or if you connect to the UConn system from off-campus using the VPN, you shouldn’t have any problems (if you do contact UITS). You can connect to the vpn here. If nothing else works, you can always go to the library.

Q: I am having a bit of trouble finding peer-reviewed articles about my topic. Do you have any recommendations? In addition, do all articles need to be peer-reviewed?

A: All of the information you base your poster on MUST be from the peer-reviewed literature. One reason for this is that there is no filter on most of the stuff just out on the web – which means that there’s lots of complete rubbish out there. Peer-review does not guarantee accuracy, but it provides at least some level of assessment. The goal is to help you to discern the difference. A second reason is that a goal of this course is to teach you to read and interpret the peer-reviewed literature – a critical skill for anyone wanting a career in science.

If you are finding little information, varying your search terms might help you find more – think about synonyms for your terms, and use “wildcard” terms like “declin*” to broaden the search (the * means that any word beginning with “declin” will be picked up – giving you “decline”, “declines”, “declining”, etc. all in one search). You can use regular Google to find web sites on the topic – although you can’t just use these sites, they might refer to peer-reviewed articles. Web sites might also give you ideas for more specialized search terms that you can try.

Q: Here’s several links to scholarly articles …. Are they OK to use?

A: The first and fourth articles are news articles, not pieces of scientific work, and certainly not peer-reviewed, the third is not a journal article (and so may not be peer-reviewed), the fifth url doesn’t seem to work. The second article (the one I talked about in class) is the only one that I can accept. On the posters themselves I will be taking points off anyone who uses inappropriate articles.

As fair warning, on exams, when people give me five pieces of information in response to a question that asks for one, and four of them are wrong, they generally get very few points even if the fifth was the answer I was looking for. This approach to answering exam questions sends the message that the respondent doesn’t really know the answer and is just putting down everything they can think of in the hope that something sticks.

Q: few questions about the poster-can we use pictures from non-journal articles?

A: Yes – but see the instructions

Q: also, if were presenting the info for the intro, background, etc., as bullet points, does each piece of info need a citation?

A: This depends – if a series of points all come from the same 1-2 papers, then you can cite them collectively at the end of the section. If every point comes from a different citation then you may need to cite them separately. But try to consolidate references as much as possible, as you don’t have a lot of space. The reference list is the one part of the poster that can be printed in small font so that it doesn’t take up much space.

Q. I was wondering if I could use this article (attached) in my poster project, even though it is not a primary source. While it is not peer-reviewed research, it is still from a scientific magazine, Science. I am using the article for the Recommendations section and am finding there is not much in the way of research that can be applied to the section. I feel as though this section is mostly about taking the research we’ve found, and using the methods we learned in class, to come up with reasonable solutions; it will not necessarily have experimental evidence to back it up. Is this assumption correct?

A: As noted in the guidelines ” …. your poster presentation must be based exclusively on information from the peer-reviewed scientific literature.” I’m not wavering on this as it gets too hard to decide what does and does not count.

As you imply, in the “Recommendations” section I am looking for YOUR recommendations. What do YOU think should be done, based on what you’ve learned in the class and read about the topic. You can/should certainly draw on information from other sources here, but this is the one section where you should not need to cite anything. Note that not every topic logically leads to recommendations, so this is not a required section.

Q: When doing our poster do you want each section (abstract, introcuction/background, current state of knowledge, and reccomendations) to be in a bulletpointed format? or in paragraph format?

A: You should use whatever form you think best communicates the information you want to convey. In general, lists using bullet points and “telegraphic” writing are more efficient and allow you to say more in less space – these are important goals in a poster presentation. Dense blocks of writing make it harder for the reader to extract key information quickly. But sometimes, complete sentences are useful (e.g., in poster introductions). Ultimately, you should decide what you think works best. One way to do this is to look at some of the posters that are on the walls outside research labs around the university (e.g., you can find many posters from EEB faculty and grad students on the walls on the 2nd/3rd/4th floors in the north wing of BPP).

Q: Also do you want us to do in text citations throughout the text of our poster or do all ciatations just go in the literature cited section?

A: You should cite your sources in the body of the poster, but try to consolidate citations as much as possible. You don’t want to have so many that you use up a huge amount of space (or that it gets hard to read). At the same time, it is your responsibility to make clear where your information comes from (both to give credit where it is due, and to let readers follow up on it). Using footnotes to connect text to citations is fine and can help save space. Using a reduced font size for the citation list is also OK.