Difference between revisions of "Introduction to Conservation Biology"
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*A Oil spills and marine life (Kelsey, Evan, Heather)
*A Oil spills and marine life (Kelsey, Evan, Heather)
*B Koalas in trouble (Hae, Jongho, Mattheus)
*B Koalas in trouble (Hae, Jongho, Mattheus)
Revision as of 14:29, 27 February 2012
EEB 2208: Spring 2012
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
Instructor: Chris Elphick (office: BioPharm 300A , behind the elevator at the north end of the building) Email: chris.elphick [ AT ] uconn.edu
Teaching assistant: Brian Klingbeil (office: BioPharm 310, office hours: Tues 3pm, by appointment) Email: brian.klingbeil @ uconn.edu [ 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 2:00-3:15 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, 5th Edition, Sinauer) is strongly recommended reading. On exams I will assume that you have this material and may ask questions (though not many) about topics that are not covered in lectures. Reading beyond the lecture material is especially important as I will expect you to know a range of examples for each phenomenon I describe. This New York Times article has suggestions for finding cheap text books that might be useful. Another book that might be helpful is available as a free download here.
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 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; they 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 benefit from the answers.
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's 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 their 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 the 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 could ask you whether the number of extinctions is 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;
- to use general principles to think about ways to solve specific conservation problems;
- specific factual information about major issues in conservation biology;
- specific examples of all important concepts, problems, and solutions;
- to extrapolate from examples I provide in class to other cases with similar characteristics (e.g., that I ask about in exams!);
- 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 acknowledge scientific uncertainty when it exists, and to recognize when it hampers understanding and when it does not;
- to present scientific information to your peers in a format commonly used by scientists.
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.
Important course documents
Citation guidelines (to come)
Schedule of lectures and examinations (subject to change)
For a printable version of the syllabus click here (print double-sided to save paper!)
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.
For each lecture I will aim to post an outline ahead of time (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).
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. In exams, you will be expected to know about all the things I talked about, not just the information in the web notes. Based on past experience, you can expect to drop at least a grade if you choose to rely only on the web notes.
The symbol ** in the "Reading" column means that there is important supplemental reading from the primary literature that we will discuss in class. Reading these papers is important as there will be graded writing assignments, conducted in class, for each one. I will randomly pick people in class to answer questions about them. Links to the relevant papers can be accessed by clicking on the **. 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.
In the syllabus I have also noted special lectures (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 seriously 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.
|1||18 Jan||What is conservation biology?||Chapter 1||A summary of what the course is about|
|2||23 Jan||Interpreting statistics (when there’s an agenda)||Chapter 6; Wiki||Theory of the Stork|
|3||25 Jan||Forms of biological diversity||Chapter 2||International Year of Biodiversity video|
|4||30 Jan||Patterns of biodiversity||Chapter 3; Hahs et al. 2009**||New species discoveries 1ST DISCUSSION TODAY!!!|
|5||1 Feb||Extinction rates||Chapter 7||Thylacine video - all that's left|
|6||6 Feb||Patterns of extinction||Chapter 8; Short et al. 2011**||The last passenger pigeon|
|7||8 Feb||Causes of population decline||Chapter 8||Check out the IUCN Red List|
|8||13 Feb||Habitat loss & degradation||Chapter 9; Fonseca 2009**||Another victim of habitat loss|
|9||15 Feb||Over-exploitation||Chapter 10||Bushmeat|
|10||20 Feb||Invasive species & Disease||"Cane Toads" (5 parts); Myers et al. 2007**|
|11||22 Feb||Global change||pp. 204-212; Thomas et al.||USFS climate change atlases for trees and birds Climate Change Time Machine|
|23 Feb||TEALE LECTURE: The Future of Plants (Sir Peter Crane)||4:00PM, Konover Auditorium, Dodd Center|
|12||27 Feb||Ecosystem services||MEA Trends Synthesis Kross et al. 2011**||Millennium Ecosystem Assessment|
|13||29 Feb||Small population conservation||Chapter 11||POSTER INFO DUE TOMORROW|
|1 Mar||TEALE LECTURE: In Pursuit of a New Environmentalism" (Dr. David Gessner)||4:00PM, Konover Auditorium, Dodd Center|
|5 Mar||Mid-term Exam||Study lectures 1-13|
|14||7 Mar||Population viability analysis||Chapter 13||Demos of PVA simulations in class today|
|12 Mar||No Class: SPRING BREAK||Reading for ...|
|14 Mar||No Class: SPRING BREAK||... poster projects|
|15||19 Mar||Conservation genetics||Chapter 12; Garrick et al. 2012**|
|16||21 Mar||Ex situ conservation, release programs||Chapter 14||Info on UConn's captive bred plants.|
|17||26 Mar||Conservation reserves||Chapter 15|
|18||28 Mar||Reserve networks||Chapter 16; Fuller et al. 2010**|
|29 Mar||TEALE LECTURE: The Hockey Stick: On the Front Lines in the Climate Wars (Dr. Michael Mann)||4:00PM, Konover Auditorium, Dodd Center|
|19||2 Apr||Conservation in the matrix||Chapter 18|
|20||4 Apr||Management||Chapter 17; Fleishman et al. 2011**|
|21||9 Apr||Habitat restoration||Chapters 19, 4||Read about re-wilding|
|22||11 Apr||Economics of conservation||Chapter 5; Gutiérrez et al. 2011**||Valuing ecosystems|
|23||16 Apr||Poster presentations: session A||Start studying||Class will be in Wilbur Cross Building (North Reading Room) Grading forms: Yours // mine|
|24||18 Apr||Poster presentations: session B||Chapter 20||Class will be in Wilbur Cross Building (North Reading Room)|
|25||23 Apr||Conservation law||Chapters 21||Instructor evaluations today; Study Guide|
|26||25 Apr||International legislation||Chapter 22; Economist 2008/2010**||A debate; to view the TWO articles go to HuskyCT and look under "Discussion Papers"|
|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: 486-3426. I am not allowed to consider rescheduling requests unless you already have approval from that office. Except in emergency circumstances, 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.
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.
- A African wild-dogs (Axel, Emily, Dina)
- B Noise pollution & whales (Alexandra, Alexis, Andrew)
- A Honeybee declines/CCD (Purbita, Amanda, Jessica)
- B Wild bee declines (Katherine, Brian, Nicole)
- A Genetics of species (re)discovery (Zoe, Jordan, Alec)
- B Kakapo conservation (Kali, Nicole, Eric)
- A Burmese pythons in the Everglades (Dante, Kyle, Aurora)
- B Polar bear declines (Thomas, Emily)
- A Salmon (Michael, Jan, Ryan)
- B White-nose syndrome in bats (Samantha, Laura, Colleen)
- A Marine mammal strandings (Grace, Angela, Nemil)
- B Lion conservation (Stephen, Sean, Rohaan)
- A Wolverines and climate change (Alexander, David, Manuel)
- B Sea turtles (Jarrod, Michael)
- A Wildlife trade and tigers (Cody, Ashley, John)
- B Tuna conservation (Kaitlin, Natalie, William)
- A Tasmanian devil facial tumor disease (Rachel, Eric, Stephanie)
- B Barn owl declines (Stephanie, Tony, Erika)
- A Coral reefs (Cecily, Jaunetta, Katie)
- B African penguin declines (Dister, Leslie, James)
- A Shark conservation (Anthony, Jade, Kimiya)
- B Sixth mass extinction (Pete, Lisa, Alexandra)
- A Sea-lion declines (MaryGrace, Melisa, Mary-Kate)
- B Effects of mercury (Ryan, Justin, Joe)
- A Coastal pollution/habitat degradation (Hillary, Patrick, Luis)
- B Gorilla conservation (Kayla, Michaela, Heng)
- A Louisiana black bears (Allison, John, Jonathan)
- B Chytrid disease (Abikela, Kristyn, Matthew)
- A Eutrophication (Nicole, Andrew, Amy)
- B Rhino conservation (Dana, Stephanie, Jacques)
- A Tapir conservation (Annie, Sammy, Warrier)
- B Effects of ocean plastic on animals (Christine, Jeanette, Katelyn)
- A Oil spills and marine life (Kelsey, Evan, Heather)
- B Koalas in trouble (Hae, Jongho, Mattheus)
- A Lionfish invasion (Dillion, Dan, Philip)
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 are posted on a separate page, here.
For a great web site providing information on recent conservation-related research, check out the Conservation Maven web site.
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 you should be). 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 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 (you need to do the sign in, then click the "start" button on the right, then wait while the computer connects). 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 THE LECTURES
None posted yet.
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 Web of Science (available through the UConn libraries) or 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: 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. It's enough for the 5 points for this assignment, but you should make sure that you know the difference between peer-reviewed journal articles and other types of articles. On the posters themselves I will be taking points off anyone who uses inappropriate articles.
And, 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 (#8 on last page)
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 site for the citation list is also OK.
General student help
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